diff --git a/configs/016_rmp_sam_test/editable.txt b/configs/016_rmp_sam_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/016_rmp_sam_test/env.yml b/configs/016_rmp_sam_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..8080717befc76278fa389f680c45cac12ec49dba --- /dev/null +++ b/configs/016_rmp_sam_test/env.yml @@ -0,0 +1,68 @@ +name: 016_rmp_sam_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.3 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - addict==2.4.0 + - charset-normalizer==3.4.3 + - contourpy==1.1.1 + - cycler==0.12.1 + - fonttools==4.57.0 + - idna==3.10 + - importlib-resources==6.4.5 + - kiwisolver==1.4.7 + - markdown-it-py==3.0.0 + - matplotlib==3.7.5 + - mdurl==0.1.2 + - mmcv==2.1.0 + - mmdet==3.3.0 + - mmengine==0.10.7 + - numpy==1.24.4 + - opencv-python==4.13.0.92 + - packaging==25.0 + - pillow==10.4.0 + - platformdirs==4.3.6 + - pygments==2.19.2 + - pyparsing==3.1.4 + - python-dateutil==2.9.0.post0 + - pyyaml==6.0.3 + - requests==2.32.4 + - rich==14.3.4 + - scipy==1.10.1 + - six==1.17.0 + - termcolor==2.4.0 + - terminaltables==3.1.10 + - tomli==2.4.1 + - torch==2.4.1+cpu + - urllib3==2.2.3 + - yapf==0.43.0 + - zipp==3.20.2 +prefix: /home/lily/yz979/anaconda3/envs/016_rmp_sam_test diff --git a/configs/016_rmp_sam_test/explicit.txt b/configs/016_rmp_sam_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/016_rmp_sam_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/016_rmp_sam_test/meta.json b/configs/016_rmp_sam_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..b8c92530c07115e0ffd2a0b5c5723350cb8fcbdb --- /dev/null +++ b/configs/016_rmp_sam_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "016_rmp_sam_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/016_rmp_sam_test", + "exported_at": "2026-05-17T04:03:21Z" +} diff --git a/configs/016_rmp_sam_test/pip-clean.txt b/configs/016_rmp_sam_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7638ecdf6a8eef1d78d6525742e246677cb8821 --- /dev/null +++ b/configs/016_rmp_sam_test/pip-clean.txt @@ -0,0 +1,464 @@ +absl-py==2.3.1 +accelerate==0.24.1 +addict==2.4.0 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +mmcv==2.1.0 +mmdet==3.3.0 +mmengine==0.10.7 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +opencv-python==4.13.0.92 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +platformdirs==4.3.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +termcolor==2.4.0 +terminaltables==3.1.10 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomli==2.4.1 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +yapf==0.43.0 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/016_rmp_sam_test/pip-freeze.txt b/configs/016_rmp_sam_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..c7638ecdf6a8eef1d78d6525742e246677cb8821 --- /dev/null +++ b/configs/016_rmp_sam_test/pip-freeze.txt @@ -0,0 +1,464 @@ +absl-py==2.3.1 +accelerate==0.24.1 +addict==2.4.0 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +mmcv==2.1.0 +mmdet==3.3.0 +mmengine==0.10.7 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +opencv-python==4.13.0.92 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +platformdirs==4.3.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +termcolor==2.4.0 +terminaltables==3.1.10 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomli==2.4.1 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +yapf==0.43.0 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/020_test/editable.txt b/configs/020_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/020_test/env.yml b/configs/020_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..31196a2477a55c421246e317a33e022996646c33 --- /dev/null +++ b/configs/020_test/env.yml @@ -0,0 +1,188 @@ +name: 020_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alsa-lib=1.2.14 + - aom=3.9.1 + - brotli-python=1.1.0 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - cairo=1.18.4 + - certifi=2025.8.3 + - contourpy=1.2.1 + - cycler=0.12.1 + - cyrus-sasl=2.1.28 + - dav1d=1.2.1 + - dbus=1.16.2 + - expat=2.7.1 + - fontconfig=2.15.0 + - fonttools=4.59.2 + - freetype=2.14.1 + - fribidi=1.0.16 + - graphite2=1.3.14 + - harfbuzz=10.2.0 + - icu=73.2 + - importlib-resources=6.5.2 + - importlib_resources=6.5.2 + - joblib=1.5.1 + - jpeg=9e + - keyutils=1.6.3 + - kiwisolver=1.4.4 + - krb5=1.21.3 + - lcms2=2.16 + - ld_impl_linux-64=2.44 + - lerc=4.0.0 + - libabseil=20250127.0 + - libavif=1.3.0 + - libavif16=1.3.0 + - libblas=3.9.0 + - libcblas=3.9.0 + - libclang13=20.1.8 + - libcups=2.4.2 + - libdeflate=1.22 + - libdrm=2.4.125 + - libedit=3.1.20250104 + - libegl=1.7.0 + - libevent=2.1.12 + - libexpat=2.7.1 + - libffi=3.4.6 + - libfreetype=2.14.1 + - libfreetype6=2.14.1 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgfortran=15.1.0 + - libgfortran-ng=15.1.0 + - libgfortran5=15.1.0 + - libgl=1.7.0 + - libglib=2.84.2 + - libglvnd=1.7.0 + - libglx=1.7.0 + - libgomp=15.1.0 + - libiconv=1.18 + - libkrb5=1.21.3 + - liblapack=3.9.0 + - libllvm15=15.0.7 + - libllvm20=20.1.8 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libntlm=1.8 + - libopenblas=0.3.30 + - libopus=1.5.2 + - libpciaccess=0.18 + - libpng=1.6.50 + - libpq=17.4 + - libre2-11=2024.07.02 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libtiff=4.7.0 + - libuuid=2.41.2 + - libvpx=1.13.1 + - libwebp-base=1.6.0 + - libxcb=1.17.0 + - libxcrypt=4.4.36 + - libxkbcommon=1.11.0 + - libxkbfile=1.1.0 + - libxml2=2.13.8 + - libxslt=1.1.43 + - libzlib=1.3.1 + - lmdb=0.9.31 + - matplotlib=3.9.4 + - matplotlib-base=3.9.4 + - mesalib=25.1.5 + - mysql-common=9.3.0 + - mysql-libs=9.3.0 + - ncurses=6.5 + - nspr=4.37 + - nss=3.116 + - numpy=2.0.2 + - openjpeg=2.5.2 + - openldap=2.6.10 + - openssl=3.5.4 + - packaging=25.0 + - pandas=2.2.3 + - patsy=1.0.1 + - pcre2=10.42 + - pillow=11.3.0 + - pip=25.2 + - pixman=0.46.4 + - pthread-stubs=0.4 + - pyparsing=3.1.4 + - pyside6=6.9.2 + - python=3.9.23 + - python-dateutil=2.9.0.post0 + - python-tzdata=2025.2 + - python_abi=3.9 + - pytz=2025.2 + - qhull=2020.2 + - qtbase=6.9.2 + - qtdeclarative=6.9.2 + - qtshadertools=6.9.2 + - qtsvg=6.9.2 + - qttools=6.9.2 + - qtwebchannel=6.9.2 + - qtwebengine=6.9.2 + - qtwebsockets=6.9.2 + - rav1e=0.7.1 + - re2=2024.07.02 + - readline=8.2 + - scikit-learn=1.6.1 + - scipy=1.13.1 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - setuptools=80.9.0 + - six=1.17.0 + - snappy=1.2.2 + - spirv-tools=2025.1 + - sqlite=3.50.4 + - statsmodels=0.14.5 + - svt-av1=3.1.2 + - threadpoolctl=3.6.0 + - tk=8.6.13 + - tornado=6.5.2 + - tzdata=2025b + - unicodedata2=16.0.0 + - wheel=0.45.1 + - xcb-util=0.4.1 + - xcb-util-cursor=0.1.5 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.1 + - xcb-util-renderutil=0.3.10 + - xcb-util-wm=0.4.2 + - xkeyboard-config=2.45 + - xorg-libice=1.1.2 + - xorg-libsm=1.2.6 + - xorg-libx11=1.8.12 + - xorg-libxau=1.0.12 + - xorg-libxcomposite=0.4.6 + - xorg-libxdamage=1.1.6 + - xorg-libxdmcp=1.1.5 + - xorg-libxext=1.3.6 + - xorg-libxfixes=6.0.2 + - xorg-libxi=1.8.2 + - xorg-libxrandr=1.5.4 + - xorg-libxrender=0.9.12 + - xorg-libxshmfence=1.3.3 + - xorg-libxtst=1.2.5 + - xorg-libxxf86vm=1.1.6 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zipp=3.23.0 + - zlib=1.3.1 + - zstd=1.5.7 + - pip: + - filelock==3.13.1 + - fsspec==2024.6.1 + - jinja2==3.1.4 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.2.1 + - sympy==1.13.3 + - torch==2.8.0+cpu + - typing-extensions==4.12.2 +prefix: /home/lily/yz979/anaconda3/envs/020_test diff --git a/configs/020_test/explicit.txt b/configs/020_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..6e439cfef7c581a992032345ac98f932fe4d97af --- /dev/null +++ b/configs/020_test/explicit.txt @@ -0,0 +1,177 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/noarch/python_abi-3.9-8_cp39.conda#c2f0c4bf417925c27b62ab50264baa98 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda#76df83c2a9035c54df5d04ff81bcc02d +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda#f9f81ea472684d75b9dd8d0b328cf655 +https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.22-hb9d3cd8_0.conda#b422943d5d772b7cc858b36ad2a92db5 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda#4211416ecba1866fab0c6470986c22d6 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba +https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libntlm-1.8-hb9d3cd8_0.conda#7c7927b404672409d9917d49bff5f2d6 +https://conda.anaconda.org/conda-forge/linux-64/libopus-1.5.2-hd0c01bc_0.conda#b64523fb87ac6f87f0790f324ad43046 +https://conda.anaconda.org/conda-forge/linux-64/libpciaccess-0.18-hb9d3cd8_0.conda#70e3400cbbfa03e96dcde7fc13e38c7b +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_5.conda#4e02a49aaa9d5190cb630fa43528fbe6 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda#aea31d2e5b1091feca96fcfe945c3cf9 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0 +https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e +https://conda.anaconda.org/conda-forge/linux-64/rav1e-0.7.1-h8fae777_3.conda#2c42649888aac645608191ffdc80d13a +https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda#fb901ff28063514abb6046c9ec2c4a45 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb9d3cd8_0.conda#f6ebe2cb3f82ba6c057dde5d9debe4f7 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxshmfence-1.3.3-hb9d3cd8_0.conda#9a809ce9f65460195777f2f2116bae02 +https://conda.anaconda.org/conda-forge/linux-64/dav1d-1.2.1-hd590300_0.conda#418c6ca5929a611cbd69204907a83995 +https://conda.anaconda.org/conda-forge/linux-64/expat-2.7.1-hecca717_0.conda#6033d8c2bb9b460929d00ba54154614c +https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda#2cd94587f3a401ae05e03a6caf09539d +https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h0b41bf4_3.conda#c7a069243e1fbe9a556ed2ec030e6407 +https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835 +https://conda.anaconda.org/conda-forge/linux-64/libdrm-2.4.125-hb03c661_1.conda#9314bc5a1fe7d1044dc9dfd3ef400535 +https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b +https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.12-hf998b51_1.conda#a1cfcc585f0c42bf8d5546bb1dfb668d +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_5.conda#8bba50c7f4679f08c861b597ad2bda6b +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/libxkbfile-1.1.0-h166bdaf_1.conda#c6274d38be57ac8b059b8e33d406aaf6 +https://conda.anaconda.org/conda-forge/linux-64/lmdb-0.9.31-hd590300_1.conda#55a44a03f31a494eb674c9444b5f1918 +https://conda.anaconda.org/conda-forge/linux-64/mysql-common-9.3.0-h266115a_0.conda#9693774d2822c39a9541f2a80c346e30 +https://conda.anaconda.org/conda-forge/linux-64/nspr-4.37-h29cc59b_0.conda#d73ccc379297a67ed921bd55b38a6c6a +https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.42-hcad00b1_0.conda#679c8961826aa4b50653bce17ee52abe +https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda#c01af13bdc553d1a8fbfff6e8db075f0 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+https://repo.anaconda.com/pkgs/main/linux-64/qtwebengine-6.9.2-h2da6924_0.conda#b7b2c24c2772a0ea68527b0599632da2 +https://repo.anaconda.com/pkgs/main/linux-64/pyside6-6.9.2-py39h2ddcaae_0.conda#6006b94c834de07cf7d4a505b20a616d +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.9.4-py39hf3d152e_0.conda#922f2edd2f9ff0a95c83eb781bacad5e diff --git a/configs/020_test/meta.json b/configs/020_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..483941f295a7753a55a849a600d224ae1f59c354 --- /dev/null +++ b/configs/020_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "020_test", + "python_version": "3.9.23", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/020_test", + "exported_at": "2026-05-17T04:03:33Z" +} diff --git a/configs/020_test/pip-clean.txt b/configs/020_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2546692e785ee1d0371ea15d4becc23b352a9599 --- /dev/null +++ b/configs/020_test/pip-clean.txt @@ -0,0 +1,11 @@ +filelock==3.13.1 +fsspec==2024.6.1 +Jinja2==3.1.4 +MarkupSafe==2.1.5 +matplotlib==3.9.4 +mpmath==1.3.0 +PySide6==6.9.2 +shiboken6==6.9.2 +sympy==1.13.3 +torch==2.8.0+cpu +typing_extensions==4.12.2 diff --git a/configs/020_test/pip-freeze.txt b/configs/020_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..a1b1caa006089eb9972fc6d0d178294e59792da3 --- /dev/null +++ b/configs/020_test/pip-freeze.txt @@ -0,0 +1,38 @@ +Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1749229842835/work +certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1754231422783/work/certifi +contourpy @ file:///croot/contourpy_1738160616259/work +cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1733332471406/work +filelock==3.13.1 +fonttools @ file:///home/task_175879159822283/conda-bld/fonttools_1758791613454/work +fsspec==2024.6.1 +importlib_resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1736252299705/work +Jinja2==3.1.4 +joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1748019130050/work +kiwisolver @ file:///croot/kiwisolver_1672387140495/work +MarkupSafe==2.1.5 +matplotlib==3.9.4 +mpmath==1.3.0 +networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work +numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1732314280888/work/dist/numpy-2.0.2-cp39-cp39-linux_x86_64.whl#sha256=62d98eb3da9f13e6b227c430d01026b7427f341b3fdcb838430f2a9e520417b1 +packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1745345660/work +pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1744430470408/work +patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1733792384640/work +pillow @ file:///croot/pillow_1752524526621/work +pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work +PySide6==6.9.2 +python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_python-dateutil_1751104122/work +pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1742920838005/work +scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1736496755362/work/dist/scikit_learn-1.6.1-cp39-cp39-linux_x86_64.whl#sha256=e8f978e37bb47e04e1337a63f75697b723d6d25f58e477734555faed033884ba +scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1716470218293/work/dist/scipy-1.13.1-cp39-cp39-linux_x86_64.whl#sha256=e6696cb8683d94467891b7648e068a3970f6bc0a1b3c1aa7f9bc89458eafd2f0 +seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1733730015268/work +shiboken6==6.9.2 +six @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_six_1753199211/work +statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1751917446772/work +sympy==1.13.3 +threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1741878222898/work +torch==2.8.0+cpu +tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1754731992698/work +typing_extensions==4.12.2 +tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1742745135198/work +unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1736692503055/work +zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1749421620841/work diff --git a/configs/026_test/editable.txt b/configs/026_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/026_test/env.yml b/configs/026_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..9d27a374d25d9b7ff86ac4b6e8e8b9a8063a8ab8 --- /dev/null +++ b/configs/026_test/env.yml @@ -0,0 +1,47 @@ +name: 026_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.3 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - filelock==3.13.1 + - fsspec==2024.6.1 + - idna==3.10 + - jinja2==3.1.4 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.0 + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1+cpu + - typing-extensions==4.12.2 +prefix: /home/lily/yz979/anaconda3/envs/026_test diff --git a/configs/026_test/explicit.txt b/configs/026_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/026_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/026_test/meta.json b/configs/026_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..844768cd8f9d8b37f5b7f3bf18f2045e88c8f848 --- /dev/null +++ b/configs/026_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "026_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/026_test", + "exported_at": "2026-05-17T04:03:31Z" +} diff --git a/configs/026_test/pip-clean.txt b/configs/026_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae72d020abac43e97af9b9a363c9d17fa5657487 --- /dev/null +++ b/configs/026_test/pip-clean.txt @@ -0,0 +1,449 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.13.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.0 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/026_test/pip-freeze.txt b/configs/026_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae72d020abac43e97af9b9a363c9d17fa5657487 --- /dev/null +++ b/configs/026_test/pip-freeze.txt @@ -0,0 +1,449 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.13.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.0 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/032_test/editable.txt b/configs/032_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/032_test/env.yml b/configs/032_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..99836817f4708f5b0e08bafe3f06bc356de32944 --- /dev/null +++ b/configs/032_test/env.yml @@ -0,0 +1,37 @@ +name: 032_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.3 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/032_test diff --git a/configs/032_test/explicit.txt b/configs/032_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/032_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/032_test/meta.json b/configs/032_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..c83b19ecf353edf644cbbed67ed9b19014ae79af --- /dev/null +++ b/configs/032_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "032_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/032_test", + "exported_at": "2026-05-17T04:03:39Z" +} diff --git a/configs/032_test/pip-clean.txt b/configs/032_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/032_test/pip-clean.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 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git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 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+zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/032_test/pip-freeze.txt b/configs/032_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/032_test/pip-freeze.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/041_test/editable.txt b/configs/041_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/041_test/env.yml b/configs/041_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..29e640c47dd22aabb98c839120a0a68164f01154 --- /dev/null +++ b/configs/041_test/env.yml @@ -0,0 +1,72 @@ +name: 041_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.3 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.2.25 + - filelock==3.13.1 + - fsspec==2024.6.1 + - idna==3.10 + - jinja2==3.1.4 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.0 + - numpy==1.24.4 + - nvidia-cublas-cu11==11.10.3.66 + - nvidia-cublas-cu12==12.1.3.1 + - nvidia-cuda-cupti-cu12==12.1.105 + - nvidia-cuda-nvrtc-cu11==11.7.99 + - nvidia-cuda-nvrtc-cu12==12.1.105 + - nvidia-cuda-runtime-cu11==11.7.99 + - nvidia-cuda-runtime-cu12==12.1.105 + - nvidia-cudnn-cu11==8.5.0.96 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-cusparse-cu12==12.1.0.106 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.1.105 + - packaging==25.0 + - pillow==10.4.0 + - pyyaml==6.0.3 + - requests==2.32.4 + - rouge-score==0.1.2 + - scikit-learn==1.3.2 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1 + - torchvision==0.19.1 + - triton==3.0.0 + - typing-extensions==4.12.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/041_test diff --git a/configs/041_test/explicit.txt b/configs/041_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/041_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/041_test/meta.json b/configs/041_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..f0b1e2da8a3b70af7f6c673a264a451b3ca6f1eb --- /dev/null +++ b/configs/041_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "041_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/041_test", + "exported_at": "2026-05-17T04:03:47Z" +} diff --git a/configs/041_test/pip-clean.txt b/configs/041_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..21d74f22e7970ad24c75bdb776559860526ee685 --- /dev/null +++ b/configs/041_test/pip-clean.txt @@ -0,0 +1,471 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.2.25 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.13.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.0 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu11==11.10.3.66 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvrtc-cu11==11.7.99 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu11==11.7.99 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu11==8.5.0.96 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-cusparse-cu12==12.1.0.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.1.105 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +torchvision==0.19.1 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/041_test/pip-freeze.txt b/configs/041_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..21d74f22e7970ad24c75bdb776559860526ee685 --- /dev/null +++ b/configs/041_test/pip-freeze.txt @@ -0,0 +1,471 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.2.25 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.13.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.0 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu11==11.10.3.66 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvrtc-cu11==11.7.99 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu11==11.7.99 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu11==8.5.0.96 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-cusparse-cu12==12.1.0.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.1.105 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +torchvision==0.19.1 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/053_test/editable.txt b/configs/053_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/053_test/env.yml b/configs/053_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..b7abf69baf5f6db7fafcbfd5f59793cd8c4b8e59 --- /dev/null +++ b/configs/053_test/env.yml @@ -0,0 +1,65 @@ +name: 053_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.3 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.2.25 + - filelock==3.16.1 + - fsspec==2024.3.1 + - idna==3.10 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.9.2.10 + - nvidia-cuda-cupti-cu12==12.9.79 + - nvidia-cuda-nvrtc-cu12==12.9.86 + - nvidia-cuda-runtime-cu12==12.9.79 + - nvidia-cudnn-cu12==8.9.2.26 + - nvidia-cufft-cu12==11.4.1.4 + - nvidia-curand-cu12==10.3.10.19 + - nvidia-cusparse-cu12==12.5.10.65 + - nvidia-nccl-cu12==2.18.1 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.9.79 + - packaging==25.0 + - python-dateutil==2.9.0.post0 + - pyyaml==6.0.3 + - requests==2.32.4 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.1.0 + - triton==2.1.0 + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/053_test diff --git a/configs/053_test/explicit.txt b/configs/053_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/053_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/053_test/meta.json b/configs/053_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..35a7711dc9a39a7ae6095b30556963c468f2f6bd --- /dev/null +++ b/configs/053_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "053_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/053_test", + "exported_at": "2026-05-17T04:04:02Z" +} diff --git a/configs/053_test/pip-clean.txt b/configs/053_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..213322672575602dbc5962d125fa13e6cf93e3cc --- /dev/null +++ b/configs/053_test/pip-clean.txt @@ -0,0 +1,464 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.2.25 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.9.2.10 +nvidia-cuda-cupti-cu12==12.9.79 +nvidia-cuda-nvrtc-cu12==12.9.86 +nvidia-cuda-runtime-cu12==12.9.79 +nvidia-cudnn-cu12==8.9.2.26 +nvidia-cufft-cu12==11.4.1.4 +nvidia-curand-cu12==10.3.10.19 +nvidia-cusparse-cu12==12.5.10.65 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.18.1 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.9.79 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.1.0 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==2.1.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/053_test/pip-freeze.txt b/configs/053_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..213322672575602dbc5962d125fa13e6cf93e3cc --- /dev/null +++ b/configs/053_test/pip-freeze.txt @@ -0,0 +1,464 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.2.25 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.9.2.10 +nvidia-cuda-cupti-cu12==12.9.79 +nvidia-cuda-nvrtc-cu12==12.9.86 +nvidia-cuda-runtime-cu12==12.9.79 +nvidia-cudnn-cu12==8.9.2.26 +nvidia-cufft-cu12==11.4.1.4 +nvidia-curand-cu12==10.3.10.19 +nvidia-cusparse-cu12==12.5.10.65 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.18.1 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.9.79 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.1.0 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==2.1.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/060_test/editable.txt b/configs/060_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/060_test/env.yml b/configs/060_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..66a93238e61c21e1bf70ea24462da14eb3013400 --- /dev/null +++ b/configs/060_test/env.yml @@ -0,0 +1,65 @@ +name: 060_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.3 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.4.22 + - cli-exit-tools==1.2.7 + - filelock==3.16.1 + - httpx==0.28.1 + - idna==3.10 + - jinja2==3.1.6 + - lib-detect-testenv==2.0.8 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.9.2.10 + - nvidia-cuda-cupti-cu12==12.9.79 + - nvidia-cuda-nvrtc-cu12==12.9.86 + - nvidia-cuda-runtime-cu12==12.9.79 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.4.1.4 + - nvidia-curand-cu12==10.3.10.19 + - nvidia-cusparse-cu12==12.5.10.65 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.9.79 + - packaging==25.0 + - pytest==8.3.5 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1 + - triton==3.0.0 + - wrapt==2.0.1 + - wrapt-timeout-decorator==1.5.1 +prefix: /home/lily/yz979/anaconda3/envs/060_test diff --git a/configs/060_test/explicit.txt b/configs/060_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/060_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/060_test/meta.json b/configs/060_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..724081948c21ee6b49663005f319b10ead6668f2 --- /dev/null +++ b/configs/060_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "060_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/060_test", + "exported_at": "2026-05-17T04:04:06Z" +} diff --git a/configs/060_test/pip-clean.txt b/configs/060_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..8952e2216bbe6bdcc3981c528905a9882b8a5d8b --- /dev/null +++ b/configs/060_test/pip-clean.txt @@ -0,0 +1,468 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.4.22 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +cli_exit_tools==1.2.7 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +lib-detect-testenv==2.0.8 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.9.2.10 +nvidia-cuda-cupti-cu12==12.9.79 +nvidia-cuda-nvrtc-cu12==12.9.86 +nvidia-cuda-runtime-cu12==12.9.79 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.4.1.4 +nvidia-curand-cu12==10.3.10.19 +nvidia-cusparse-cu12==12.5.10.65 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.9.79 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest==8.3.5 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +wrapt==2.0.1 +wrapt_timeout_decorator==1.5.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/060_test/pip-freeze.txt b/configs/060_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..8952e2216bbe6bdcc3981c528905a9882b8a5d8b --- /dev/null +++ b/configs/060_test/pip-freeze.txt @@ -0,0 +1,468 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.4.22 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +cli_exit_tools==1.2.7 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +lib-detect-testenv==2.0.8 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.9.2.10 +nvidia-cuda-cupti-cu12==12.9.79 +nvidia-cuda-nvrtc-cu12==12.9.86 +nvidia-cuda-runtime-cu12==12.9.79 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.4.1.4 +nvidia-curand-cu12==10.3.10.19 +nvidia-cusparse-cu12==12.5.10.65 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.9.79 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest==8.3.5 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +wrapt==2.0.1 +wrapt_timeout_decorator==1.5.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/064_test/editable.txt b/configs/064_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/064_test/env.yml b/configs/064_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..bf656579d27e8d8c839e6123666f2bd1aa440e92 --- /dev/null +++ b/configs/064_test/env.yml @@ -0,0 +1,57 @@ +name: 064_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.4 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - filelock==3.16.1 + - fsspec==2025.3.0 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.9.2.10 + - nvidia-cuda-cupti-cu12==12.9.79 + - nvidia-cuda-nvrtc-cu12==12.9.86 + - nvidia-cuda-runtime-cu12==12.9.79 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.4.1.4 + - nvidia-curand-cu12==10.3.10.19 + - nvidia-cusparse-cu12==12.5.10.65 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.9.79 + - packaging==25.0 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1 + - triton==3.0.0 +prefix: /home/lily/yz979/anaconda3/envs/064_test diff --git a/configs/064_test/explicit.txt b/configs/064_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..519dd4c543792147b565413766e3de659c7414ad --- /dev/null +++ b/configs/064_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/064_test/meta.json b/configs/064_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..40b8ed93a6382ca0022dc58b9b8d97bf46415510 --- /dev/null +++ b/configs/064_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "064_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/064_test", + "exported_at": "2026-05-17T04:04:13Z" +} diff --git a/configs/064_test/pip-clean.txt b/configs/064_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..7fc1e4e508ca31d9f244ccef325fcbc3573b99dd --- /dev/null +++ b/configs/064_test/pip-clean.txt @@ -0,0 +1,460 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.9.2.10 +nvidia-cuda-cupti-cu12==12.9.79 +nvidia-cuda-nvrtc-cu12==12.9.86 +nvidia-cuda-runtime-cu12==12.9.79 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.4.1.4 +nvidia-curand-cu12==10.3.10.19 +nvidia-cusparse-cu12==12.5.10.65 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.9.79 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/064_test/pip-freeze.txt b/configs/064_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..7fc1e4e508ca31d9f244ccef325fcbc3573b99dd --- /dev/null +++ b/configs/064_test/pip-freeze.txt @@ -0,0 +1,460 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.9.2.10 +nvidia-cuda-cupti-cu12==12.9.79 +nvidia-cuda-nvrtc-cu12==12.9.86 +nvidia-cuda-runtime-cu12==12.9.79 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.4.1.4 +nvidia-curand-cu12==10.3.10.19 +nvidia-cusparse-cu12==12.5.10.65 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.9.79 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/067_test/editable.txt b/configs/067_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/067_test/env.yml b/configs/067_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..31f390b377565779b30e34a86574bfedca5d89e8 --- /dev/null +++ b/configs/067_test/env.yml @@ -0,0 +1,169 @@ +name: 067_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alsa-lib=1.2.14 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - cairo=1.18.4 + - cycler=0.12.1 + - cyrus-sasl=2.1.28 + - dbus=1.16.2 + - double-conversion=3.3.1 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.15.0 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - freetype=2.14.1 + - graphite2=1.3.14 + - harfbuzz=12.1.0 + - icu=75.1 + - joblib=1.5.2 + - keyutils=1.6.3 + - krb5=1.21.3 + - lcms2=2.17 + - ld_impl_linux-64=2.44 + - lerc=4.0.0 + - libblas=3.9.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcblas=3.9.0 + - libclang-cpp21.1=21.1.2 + - libclang13=21.1.2 + - libcups=2.3.3 + - libdeflate=1.24 + - libdrm=2.4.125 + - libedit=3.1.20250104 + - libegl=1.7.0 + - libexpat=2.7.1 + - libffi=3.4.6 + - libfreetype=2.14.1 + - libfreetype6=2.14.1 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgfortran=15.1.0 + - libgfortran5=15.1.0 + - libgl=1.7.0 + - libglib=2.86.0 + - libglvnd=1.7.0 + - libglx=1.7.0 + - libgomp=15.1.0 + - libiconv=1.18 + - libjpeg-turbo=3.1.0 + - liblapack=3.9.0 + - libllvm21=21.1.2 + - liblzma=5.8.1 + - libnsl=2.0.1 + - libntlm=1.8 + - libopenblas=0.3.30 + - libopengl=1.7.0 + - libpciaccess=0.18 + - libpng=1.6.50 + - libpq=18.0 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libtiff=4.7.1 + - libuuid=2.41.2 + - libvulkan-loader=1.4.313.0 + - libwebp-base=1.6.0 + - libxcb=1.17.0 + - libxcrypt=4.4.36 + - libxkbcommon=1.11.0 + - libxml2=2.15.0 + - libxml2-16=2.15.0 + - libxslt=1.1.43 + - libzlib=1.3.1 + - matplotlib-base=3.10.6 + - munkres=1.1.4 + - ncurses=6.5 + - openjpeg=2.5.4 + - openldap=2.6.10 + - openssl=3.5.4 + - packaging=25.0 + - patsy=1.0.1 + - pcre2=10.46 + - pip=25.2 + - pixman=0.46.4 + - pthread-stubs=0.4 + - pyparsing=3.2.5 + - pyside6=6.9.3 + - python=3.10.18 + - python-dateutil=2.9.0.post0 + - python-tzdata=2025.2 + - python_abi=3.10 + - pytz=2025.2 + - qhull=2020.2 + - qt6-main=6.9.3 + - readline=8.2 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - setuptools=80.9.0 + - six=1.17.0 + - threadpoolctl=3.6.0 + - tk=8.6.13 + - tzdata=2025b + - wayland=1.24.0 + - wheel=0.45.1 + - xcb-util=0.4.1 + - xcb-util-cursor=0.1.5 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.1 + - xcb-util-renderutil=0.3.10 + - xcb-util-wm=0.4.2 + - xkeyboard-config=2.45 + - xorg-libice=1.1.2 + - xorg-libsm=1.2.6 + - xorg-libx11=1.8.12 + - xorg-libxau=1.0.12 + - xorg-libxcomposite=0.4.6 + - xorg-libxcursor=1.2.3 + - xorg-libxdamage=1.1.6 + - xorg-libxdmcp=1.1.5 + - xorg-libxext=1.3.6 + - xorg-libxfixes=6.0.2 + - xorg-libxi=1.8.2 + - xorg-libxrandr=1.5.4 + - xorg-libxrender=0.9.12 + - xorg-libxtst=1.2.5 + - xorg-libxxf86vm=1.1.6 + - zstd=1.5.7 + - pip: + - contourpy==1.3.1 + - exceptiongroup==1.3.1 + - filelock==3.13.1 + - fonttools==4.60.1 + - fsspec==2024.6.1 + - iniconfig==2.3.0 + - jinja2==3.1.4 + - kiwisolver==1.4.9 + - markupsafe==2.1.5 + - matplotlib==3.10.6 + - mpmath==1.3.0 + - networkx==3.3 + - numpy==1.26.4 + - pandas==2.3.3 + - pillow==11.3.0 + - pluggy==1.6.0 + - pygments==2.20.0 + - pytest==9.0.3 + - scikit-learn==1.7.2 + - scipy==1.15.2 + - statsmodels==0.14.5 + - sympy==1.13.3 + - tomli==2.4.1 + - torch==2.8.0+cpu + - tornado==6.5.2 + - triton==3.6.0 + - typing-extensions==4.15.0 + - unicodedata2==16.0.0 +prefix: /home/lily/yz979/anaconda3/envs/067_test diff --git a/configs/067_test/explicit.txt b/configs/067_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..7940aab702acd746cc8ac87588c0e28e1c178a9d --- /dev/null +++ b/configs/067_test/explicit.txt @@ -0,0 +1,151 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237 +https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-6_cp310.conda#01f0f2104b8466714804a72e511de599 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048 +https://conda.anaconda.org/conda-forge/linux-64/libopengl-1.7.0-ha4b6fd6_2.conda#7df50d44d4a14d6c31a2c54f2cd92157 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda#76df83c2a9035c54df5d04ff81bcc02d +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hb03c661_4.conda#1d29d2e33fe59954af82ef54a8af3fe1 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda#4211416ecba1866fab0c6470986c22d6 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba +https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88 +https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638 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+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hb03c661_4.conda#5cb5a1c9a94a78f5b23684bcb845338d +https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hb03c661_4.conda#2e55011fa483edb8bfe3fd92e860cd79 +https://conda.anaconda.org/conda-forge/linux-64/libdrm-2.4.125-hb03c661_1.conda#9314bc5a1fe7d1044dc9dfd3ef400535 +https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c 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a/configs/cpp_test_env/editable.txt b/configs/cpp_test_env/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/cpp_test_env/env.yml b/configs/cpp_test_env/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..1675f7661b406b635adaa1aea242c50882109493 --- /dev/null +++ b/configs/cpp_test_env/env.yml @@ -0,0 +1,194 @@ +name: cpp_test_env +channels: + - bioconda + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alsa-lib=1.2.14 + - bamtools=2.5.3 + - binutils_impl_linux-64=2.44 + - binutils_linux-64=2.44 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - bzip2=1.0.8 + - c-ares=1.34.5 + - ca-certificates=2026.2.25 + - cairo=1.18.4 + - charset-normalizer=3.4.7 + - cmake=4.1.1 + - contourpy=1.3.3 + - cycler=0.12.1 + - cyrus-sasl=2.1.28 + - dbus=1.16.2 + - double-conversion=3.3.1 + - eigen=5.0.1 + - fftw=3.3.10 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.15.0 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - fonttools=4.60.1 + - freetype=2.14.1 + - freetype-py=2.3.0 + - gcc_impl_linux-64=15.1.0 + - gcc_linux-64=15.1.0 + - graphite2=1.3.14 + - greenlet=3.4.0 + - gtest=1.17.0 + - gxx_impl_linux-64=15.1.0 + - gxx_linux-64=15.1.0 + - harfbuzz=12.1.0 + - icu=75.1 + - joblib=1.5.2 + - jsoncpp=1.9.6 + - kernel-headers_linux-64=2.6.32 + - keyutils=1.6.3 + - kiwisolver=1.4.9 + - krb5=1.21.3 + - lcms2=2.17 + - ld_impl_linux-64=2.44 + - lerc=4.0.0 + - libblas=3.9.0 + - libboost=1.86.0 + - libboost-python=1.86.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcblas=3.9.0 + - libclang-cpp21.1=21.1.2 + - libclang13=21.1.2 + - libcups=2.3.3 + - libcurl=8.14.1 + - libdeflate=1.24 + - libdrm=2.4.125 + - libedit=3.1.20250104 + - libegl=1.7.0 + - libev=4.33 + - libexpat=2.7.1 + - libffi=3.4.6 + - libfreetype=2.14.1 + - libfreetype6=2.14.1 + - libgcc=15.1.0 + - libgcc-devel_linux-64=15.1.0 + - libgcc-ng=15.1.0 + - libgfortran=15.1.0 + - libgfortran-ng=15.1.0 + - libgfortran5=15.1.0 + - libgl=1.7.0 + - libglib=2.86.0 + - libglvnd=1.7.0 + - libglx=1.7.0 + - libgomp=15.1.0 + - libiconv=1.18 + - libjpeg-turbo=3.1.0 + - liblapack=3.9.0 + - liblapacke=3.9.0 + - libllvm21=21.1.2 + - liblzma=5.8.1 + - libmpdec=4.0.0 + - libnghttp2=1.67.0 + - libntlm=1.8 + - libopenblas=0.3.30 + - libopengl=1.7.0 + - libpciaccess=0.18 + - libpng=1.6.50 + - libpq=18.0 + - librdkit=2025.09.1 + - librdkit-dev=2025.09.1 + - libsanitizer=15.1.0 + - libsqlite=3.50.4 + - libssh2=1.11.1 + - libstdcxx=15.1.0 + - libstdcxx-devel_linux-64=15.1.0 + - libstdcxx-ng=15.1.0 + - libtiff=4.7.1 + - libuuid=2.41.2 + - libuv=1.51.0 + - libvulkan-loader=1.4.313.0 + - libwebp-base=1.6.0 + - libxcb=1.17.0 + - libxcrypt=4.4.36 + - libxkbcommon=1.11.0 + - libxml2=2.15.0 + - libxml2-16=2.15.0 + - libxslt=1.1.43 + - libzlib=1.3.1 + - matplotlib=3.10.6 + - matplotlib-base=3.10.6 + - munkres=1.1.4 + - ncurses=6.5 + - networkx=2.8.8 + - numpy=2.3.3 + - openjpeg=2.5.4 + - openldap=2.6.10 + - openssl=3.6.2 + - packaging=25.0 + - pandas=2.3.3 + - patsy=1.0.1 + - pcre2=10.46 + - pillow=11.3.0 + - pip=26.0.1 + - pixman=0.46.4 + - pthread-stubs=0.4 + - pycairo=1.29.0 + - pyparsing=3.2.5 + - pyside6=6.9.3 + - python=3.13.7 + - python-dateutil=2.9.0.post0 + - python-tzdata=2025.2 + - python_abi=3.13 + - pytz=2025.2 + - qhull=2020.2 + - qt6-main=6.9.3 + - rdkit=2025.09.1 + - readline=8.2 + - reportlab=4.4.10 + - rhash=1.4.6 + - rlpycairo=0.4.0 + - scikit-learn=1.7.2 + - scipy=1.16.2 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - seqan-library=2.4.0 + - setuptools=80.9.0 + - six=1.17.0 + - sqlalchemy=2.0.49 + - statsmodels=0.14.5 + - sysroot_linux-64=2.12 + - threadpoolctl=3.6.0 + - tk=8.6.13 + - tornado=6.5.2 + - typing-extensions=4.15.0 + - typing_extensions=4.15.0 + - tzdata=2025b + - wayland=1.24.0 + - xcb-util=0.4.1 + - xcb-util-cursor=0.1.5 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.1 + - xcb-util-renderutil=0.3.10 + - xcb-util-wm=0.4.2 + - xkeyboard-config=2.45 + - xorg-libice=1.1.2 + - xorg-libsm=1.2.6 + - xorg-libx11=1.8.12 + - xorg-libxau=1.0.12 + - xorg-libxcomposite=0.4.6 + - xorg-libxcursor=1.2.3 + - xorg-libxdamage=1.1.6 + - xorg-libxdmcp=1.1.5 + - xorg-libxext=1.3.6 + - xorg-libxfixes=6.0.2 + - xorg-libxi=1.8.2 + - xorg-libxrandr=1.5.4 + - xorg-libxrender=0.9.12 + - xorg-libxtst=1.2.5 + - xorg-libxxf86vm=1.1.6 + - zlib=1.3.1 + - zstd=1.5.7 +prefix: /home/lily/yz979/anaconda3/envs/cpp_test_env diff --git a/configs/cpp_test_env/explicit.txt b/configs/cpp_test_env/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae40b15befa8ef8acd2abd3a44ea70a33594f06d --- /dev/null +++ b/configs/cpp_test_env/explicit.txt @@ -0,0 +1,191 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/eigen-5.0.1-hc65338a_0.conda#fcc98d38ae074ee72ee9152e357bcbf2 +https://conda.anaconda.org/conda-forge/linux-64/seqan-library-2.4.0-ha770c72_0.conda#f748d65b0168c289c3aace8956664bb7 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda#4492fd26db29495f0ba23f146cd5638d +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce +https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-15.1.0-h4c094af_105.conda#a38922dbdf037d78b3d00d6d0a0399da +https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60 +https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-15.1.0-h4c094af_105.conda#3bc809fa9c4b2cd49ed38fe555af5f99 +https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda#94305520c52a4aa3f6c2b1ff6008d9f8 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h8577fbf_1.conda#e4e8496b68cf5f25e76fbe67f3856550 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda#a7970cd949a077b7cb9696379d338681 +https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048 +https://conda.anaconda.org/conda-forge/linux-64/libopengl-1.7.0-ha4b6fd6_2.conda#7df50d44d4a14d6c31a2c54f2cd92157 +https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda#76df83c2a9035c54df5d04ff81bcc02d +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885 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+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda#b2895afaf55bf96a8c8282a2e47a5de0 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb03c661_1.conda#1dafce8548e38671bea82e3f5c6ce22f +https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.3.1-h5888daf_0.conda#bfd56492d8346d669010eccafe0ba058 +https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda#2cd94587f3a401ae05e03a6caf09539d +https://conda.anaconda.org/conda-forge/linux-64/gtest-1.17.0-h84d6215_1.conda#55e29b72a71339bc651f9975492db71f +https://conda.anaconda.org/conda-forge/linux-64/jsoncpp-1.9.6-hf42df4d_1.conda#7bdc5e2cc11cb0a0f795bdad9732b0f2 +https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hb03c661_4.conda#5cb5a1c9a94a78f5b23684bcb845338d 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+pillow @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pillow_1758208668/work +pycairo==1.29.0 +pyparsing @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pyparsing_1758436411/work +PySide6==6.9.3 +python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_python-dateutil_1751104122/work +pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1742920838005/work +rdkit @ file:///home/conda/feedstock_root/build_artifacts/rdkit-meta_1760596024977/work +reportlab @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_reportlab_1771171345/work +rlPyCairo @ file:///home/conda/feedstock_root/build_artifacts/rlpycairo_1756864152814/work +scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1757406014136/work/dist/scikit_learn-1.7.2-cp313-cp313-linux_x86_64.whl#sha256=57a01e14089134138162e1d97e88306d884f79ffcdb68a7ec41d3c3eb56ae97a +scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1757681044632/work/dist/scipy-1.16.2-cp313-cp313-linux_x86_64.whl#sha256=0a1104325b56a664a1c608c286d76f7d19815da3f0a5fbd29472eab99b3879d3 +seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1733730015268/work +setuptools==80.9.0 +shiboken6==6.9.3 +six @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_six_1753199211/work +SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_sqlalchemy_1775241332/work +statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1759296941273/work +threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1741878222898/work +tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1762506745858/work +typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_typing_extensions_1756220668/work +tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1742745135198/work diff --git a/configs/s41467_024_45514_6_test/editable.txt b/configs/s41467_024_45514_6_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_45514_6_test/env.yml b/configs/s41467_024_45514_6_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..8efa7b8bb55b4dd1b52d4013f13312c17714ea71 --- /dev/null +++ b/configs/s41467_024_45514_6_test/env.yml @@ -0,0 +1,41 @@ +name: s41467_024_45514_6_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - coverage==7.6.1 + - numpy==1.24.4 + - packaging==25.0 + - pytest-cov==5.0.0 + - scipy==1.10.1 + - six==1.17.0 + - unittest-xml-reporting==3.2.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45514_6_test diff --git a/configs/s41467_024_45514_6_test/explicit.txt b/configs/s41467_024_45514_6_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_45514_6_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_45514_6_test/pip-clean.txt b/configs/s41467_024_45514_6_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7 --- /dev/null +++ b/configs/s41467_024_45514_6_test/pip-clean.txt @@ -0,0 +1,444 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_45514_6_test/pip-freeze.txt b/configs/s41467_024_45514_6_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..0e7a0a5e93c8fc31f50ffa5b995a1d3b75e9c7c7 --- /dev/null +++ b/configs/s41467_024_45514_6_test/pip-freeze.txt @@ -0,0 +1,444 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_45598_0_test/editable.txt b/configs/s41467_024_45598_0_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_45598_0_test/env.yml b/configs/s41467_024_45598_0_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..ee0d0fd6cb202fa03fb956a36e53421adc518da3 --- /dev/null +++ b/configs/s41467_024_45598_0_test/env.yml @@ -0,0 +1,47 @@ +name: s41467_024_45598_0_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - networkx=2.8.8 + - openssl=3.5.4 + - packaging=25.0 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - coverage==7.6.1 + - imbalanced-learn==0.12.4 + - numpy==1.24.4 + - pandas==2.0.3 + - pytest-cov==5.0.0 + - python-dateutil==2.9.0.post0 + - pytz==2025.2 + - scikit-learn==1.3.2 + - scipy==1.10.1 + - six==1.17.0 + - unittest-xml-reporting==3.2.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45598_0_test diff --git a/configs/s41467_024_45598_0_test/explicit.txt b/configs/s41467_024_45598_0_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..85e70ec6cf34584814ec48b5e324b0b639953bcd --- /dev/null +++ b/configs/s41467_024_45598_0_test/explicit.txt @@ -0,0 +1,33 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/networkx-2.8.8-pyhd8ed1ab_0.tar.bz2#bb45ff9deddb045331fd039949f39650 +https://conda.anaconda.org/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda#58335b26c38bf4a20f399384c33cbcf9 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_45598_0_test/meta.json b/configs/s41467_024_45598_0_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..32c2887301b3dd2100d321b9faa52a09da450a56 --- /dev/null +++ b/configs/s41467_024_45598_0_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_45598_0_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_45598_0_test", + "exported_at": "2026-05-17T04:04:38Z" +} diff --git a/configs/s41467_024_45598_0_test/pip-clean.txt b/configs/s41467_024_45598_0_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..fe39a9d66e527f3c55a78cd1db65aa379e8d4225 --- /dev/null +++ b/configs/s41467_024_45598_0_test/pip-clean.txt @@ -0,0 +1,446 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imbalanced-learn==0.12.4 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_45598_0_test/pip-freeze.txt b/configs/s41467_024_45598_0_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..8de7d6ed4a0121535c421ff6152b9916b5cdc47a --- /dev/null +++ b/configs/s41467_024_45598_0_test/pip-freeze.txt @@ -0,0 +1,447 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imbalanced-learn==0.12.4 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_45733_x_test/editable.txt b/configs/s41467_024_45733_x_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_45733_x_test/env.yml b/configs/s41467_024_45733_x_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..32c078479b600f3fc7786efdb6526ec6c02bc079 --- /dev/null +++ b/configs/s41467_024_45733_x_test/env.yml @@ -0,0 +1,79 @@ +name: s41467_024_45733_x_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libblas=3.9.0 + - libcblas=3.9.0 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgfortran=15.1.0 + - libgfortran5=15.1.0 + - libgomp=15.1.0 + - liblapack=3.9.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libopenblas=0.3.30 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - python_abi=3.8 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.2.25 + - charset-normalizer==3.4.3 + - coverage==7.6.1 + - flatbuffers==25.2.10 + - gast==0.7.0 + - google-auth==2.40.3 + - google-auth-oauthlib==1.0.0 + - h5py==3.11.0 + - idna==3.10 + - jax==0.4.13 + - keras==2.13.1 + - libclang==18.1.1 + - ml-dtypes==0.2.0 + - numpy==1.23.5 + - packaging==25.0 + - pandas==2.0.3 + - protobuf==4.25.8 + - pyasn1==0.6.1 + - pyasn1-modules==0.4.2 + - pytest-cov==5.0.0 + - python-dateutil==2.9.0.post0 + - pytz==2025.2 + - requests==2.32.4 + - scipy==1.10.1 + - six==1.17.0 + - tensorboard==2.13.0 + - tensorboard-data-server==0.7.2 + - tensorflow==2.12.0 + - tensorflow-cpu==2.13.1 + - tensorflow-estimator==2.13.0 + - tensorflow-io-gcs-filesystem==0.34.0 + - termcolor==2.4.0 + - typing-extensions==4.5.0 + - unittest-xml-reporting==3.2.0 + - urllib3==2.2.3 + - wrapt==1.14.2 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45733_x_test diff --git a/configs/s41467_024_45733_x_test/explicit.txt b/configs/s41467_024_45733_x_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..da5e17bac11f80895c744eff98f8ff6f76bf5f75 --- /dev/null +++ b/configs/s41467_024_45733_x_test/explicit.txt @@ -0,0 +1,42 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 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0000000000000000000000000000000000000000..0207932f2a9c27bf936b35cb4ccf2bb1add9ebd3 --- /dev/null +++ b/configs/s41467_024_45733_x_test/pip-freeze.txt @@ -0,0 +1,465 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.2.25 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +flatbuffers==25.2.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gast==0.7.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-auth==2.40.3 +google-auth-oauthlib==1.0.0 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +h5py==3.11.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.10 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +keras==2.13.1 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +libclang==18.1.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.23.5 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +protobuf==4.25.8 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyasn1==0.6.1 +pyasn1_modules==0.4.2 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard==2.13.0 +tensorboard-data-server==0.7.2 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +tensorflow==2.12.0 +tensorflow-cpu==2.13.1 +tensorflow-estimator==2.13.0 +tensorflow-io-gcs-filesystem==0.34.0 +termcolor==2.4.0 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +wrapt==1.14.2 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_46027_y_test/editable.txt b/configs/s41467_024_46027_y_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_46027_y_test/env.yml b/configs/s41467_024_46027_y_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..2047c37b474a4e03b318c11f48468424ef3a1ab2 --- /dev/null +++ b/configs/s41467_024_46027_y_test/env.yml @@ -0,0 +1,37 @@ +name: s41467_024_46027_y_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46027_y_test diff --git a/configs/s41467_024_46027_y_test/explicit.txt b/configs/s41467_024_46027_y_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_46027_y_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_46027_y_test/meta.json b/configs/s41467_024_46027_y_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..80fde947f84f233d8625a8a774965858d3f2913f --- /dev/null +++ b/configs/s41467_024_46027_y_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_46027_y_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46027_y_test", + "exported_at": "2026-05-17T04:04:46Z" +} diff --git a/configs/s41467_024_46027_y_test/pip-clean.txt b/configs/s41467_024_46027_y_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/s41467_024_46027_y_test/pip-clean.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 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+hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_46399_1_test/editable.txt b/configs/s41467_024_46399_1_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_46399_1_test/explicit.txt b/configs/s41467_024_46399_1_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_46399_1_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_46399_1_test/meta.json b/configs/s41467_024_46399_1_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..3f5d7ba9e72ec65d967d0c3ca1761313ffc57346 --- /dev/null +++ b/configs/s41467_024_46399_1_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_46399_1_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46399_1_test", + "exported_at": "2026-05-17T04:04:51Z" +} diff --git a/configs/s41467_024_46399_1_test/pip-clean.txt b/configs/s41467_024_46399_1_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..db7455f93c5a63b0465aa2622166f3964e3e7420 --- /dev/null +++ b/configs/s41467_024_46399_1_test/pip-clean.txt @@ -0,0 +1,447 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-image==0.21.0 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_47447_6_test/editable.txt b/configs/s41467_024_47447_6_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_47447_6_test/env.yml b/configs/s41467_024_47447_6_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..4f14f789cf16563fb4df96a1e92e1168a90ae2ff --- /dev/null +++ b/configs/s41467_024_47447_6_test/env.yml @@ -0,0 +1,47 @@ +name: s41467_024_47447_6_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - brukeropusreader==1.3.4 + - contourpy==1.1.1 + - cycler==0.12.1 + - fonttools==4.57.0 + - importlib-resources==6.4.5 + - kiwisolver==1.4.7 + - matplotlib==3.7.5 + - numpy==1.24.4 + - packaging==25.0 + - pillow==10.4.0 + - pyparsing==3.1.4 + - scipy==1.10.1 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_47447_6_test diff --git a/configs/s41467_024_47447_6_test/explicit.txt b/configs/s41467_024_47447_6_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_47447_6_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_47447_6_test/meta.json b/configs/s41467_024_47447_6_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..2e118048010babd73b70407b301d095523da7561 --- /dev/null +++ b/configs/s41467_024_47447_6_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_47447_6_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_47447_6_test", + "exported_at": "2026-05-17T04:05:05Z" +} diff --git a/configs/s41467_024_47447_6_test/pip-clean.txt b/configs/s41467_024_47447_6_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2984daaa0e336998ff8206b4c49a96824ed05ba7 --- /dev/null +++ b/configs/s41467_024_47447_6_test/pip-clean.txt @@ -0,0 +1,452 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +brukeropusreader==1.3.4 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_47447_6_test/pip-freeze.txt b/configs/s41467_024_47447_6_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..2984daaa0e336998ff8206b4c49a96824ed05ba7 --- /dev/null +++ b/configs/s41467_024_47447_6_test/pip-freeze.txt @@ -0,0 +1,452 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +brukeropusreader==1.3.4 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_47459_2_test/editable.txt b/configs/s41467_024_47459_2_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_47459_2_test/env.yml b/configs/s41467_024_47459_2_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..6957cacc02f8996f1f31be838801edd47bcc1b78 --- /dev/null +++ b/configs/s41467_024_47459_2_test/env.yml @@ -0,0 +1,37 @@ +name: s41467_024_47459_2_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_47459_2_test diff --git a/configs/s41467_024_47459_2_test/explicit.txt b/configs/s41467_024_47459_2_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_47459_2_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_47459_2_test/meta.json b/configs/s41467_024_47459_2_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..69ec7898f3e5a6fff58ad38db6e6686045f809cf --- /dev/null +++ b/configs/s41467_024_47459_2_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_47459_2_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_47459_2_test", + "exported_at": "2026-05-17T04:05:05Z" +} diff --git a/configs/s41467_024_47459_2_test/pip-clean.txt b/configs/s41467_024_47459_2_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/s41467_024_47459_2_test/pip-clean.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_47459_2_test/pip-freeze.txt b/configs/s41467_024_47459_2_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/s41467_024_47459_2_test/pip-freeze.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_47659_w_test/editable.txt b/configs/s41467_024_47659_w_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_47659_w_test/env.yml b/configs/s41467_024_47659_w_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..fe6d2f8ae5557a4f1089df92ca18492b9d4ff9c1 --- /dev/null +++ b/configs/s41467_024_47659_w_test/env.yml @@ -0,0 +1,49 @@ +name: s41467_024_47659_w_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - asteval==1.0.5 + - contourpy==1.1.1 + - cycler==0.12.1 + - fonttools==4.57.0 + - importlib-resources==6.4.5 + - kiwisolver==1.4.7 + - lmfit==1.3.2 + - matplotlib==3.7.5 + - numpy==1.24.4 + - packaging==25.0 + - pillow==10.4.0 + - pyparsing==3.1.4 + - scipy==1.10.1 + - six==1.17.0 + - uncertainties==3.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_47659_w_test diff --git a/configs/s41467_024_47659_w_test/explicit.txt b/configs/s41467_024_47659_w_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_47659_w_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_47659_w_test/meta.json b/configs/s41467_024_47659_w_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..055f20dd6e37db761d4dca59fb9a745066aed9ef --- /dev/null +++ b/configs/s41467_024_47659_w_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_47659_w_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_47659_w_test", + "exported_at": "2026-05-17T04:05:07Z" +} diff --git a/configs/s41467_024_47659_w_test/pip-clean.txt b/configs/s41467_024_47659_w_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b60e68f54a25d54b579bca03cea50520bcb3570 --- /dev/null +++ b/configs/s41467_024_47659_w_test/pip-clean.txt @@ -0,0 +1,454 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +asteval==1.0.5 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lmfit==1.3.2 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +uncertainties==3.2.3 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_47659_w_test/pip-freeze.txt b/configs/s41467_024_47659_w_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..3b60e68f54a25d54b579bca03cea50520bcb3570 --- /dev/null +++ b/configs/s41467_024_47659_w_test/pip-freeze.txt @@ -0,0 +1,454 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +asteval==1.0.5 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lmfit==1.3.2 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +uncertainties==3.2.3 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_48578_6_test/editable.txt b/configs/s41467_024_48578_6_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6af45a4f9cdb1ad0bcff31c97ca79231f32ad8b --- /dev/null +++ b/configs/s41467_024_48578_6_test/editable.txt @@ -0,0 +1 @@ +hypergraphx-1.7.8.egg-link /data/lily/yz979/xx/Python/s41467-024-48578-6/hypergraphx diff --git a/configs/s41467_024_48578_6_test/env.yml b/configs/s41467_024_48578_6_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..1aa0ac0781ee20321c495f4548f9f2310032c65d --- /dev/null +++ b/configs/s41467_024_48578_6_test/env.yml @@ -0,0 +1,166 @@ +name: s41467_024_48578_6_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - alsa-lib=1.2.14 + - brotli=1.1.0 + - brotli-bin=1.1.0 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - cairo=1.18.4 + - cycler=0.12.1 + - cyrus-sasl=2.1.28 + - dbus=1.16.2 + - double-conversion=3.3.1 + - font-ttf-dejavu-sans-mono=2.37 + - font-ttf-inconsolata=3.000 + - font-ttf-source-code-pro=2.038 + - font-ttf-ubuntu=0.83 + - fontconfig=2.15.0 + - fonts-conda-ecosystem=1 + - fonts-conda-forge=1 + - freetype=2.14.1 + - graphite2=1.3.14 + - harfbuzz=12.1.0 + - icu=75.1 + - keyutils=1.6.3 + - krb5=1.21.3 + - lcms2=2.17 + - ld_impl_linux-64=2.44 + - lerc=4.0.0 + - libblas=3.9.0 + - libbrotlicommon=1.1.0 + - libbrotlidec=1.1.0 + - libbrotlienc=1.1.0 + - libcblas=3.9.0 + - libclang-cpp21.1=21.1.2 + - libclang13=21.1.2 + - libcups=2.3.3 + - libdeflate=1.24 + - libdrm=2.4.125 + - libedit=3.1.20250104 + - libegl=1.7.0 + - libexpat=2.7.1 + - libffi=3.4.6 + - libfreetype=2.14.1 + - libfreetype6=2.14.1 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgfortran=15.1.0 + - libgfortran5=15.1.0 + - libgl=1.7.0 + - libglib=2.86.0 + - libglvnd=1.7.0 + - libglx=1.7.0 + - libgomp=15.1.0 + - libiconv=1.18 + - libjpeg-turbo=3.1.0 + - liblapack=3.9.0 + - libllvm21=21.1.2 + - liblzma=5.8.1 + - libnsl=2.0.1 + - libntlm=1.8 + - libopenblas=0.3.30 + - libopengl=1.7.0 + - libpciaccess=0.18 + - libpng=1.6.50 + - libpq=18.0 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libtiff=4.7.1 + - libuuid=2.38.1 + - libvulkan-loader=1.4.313.0 + - libwebp-base=1.6.0 + - libxcb=1.17.0 + - libxcrypt=4.4.36 + - libxkbcommon=1.11.0 + - libxml2=2.15.0 + - libxml2-16=2.15.0 + - libxslt=1.1.43 + - libzlib=1.3.1 + - matplotlib-base=3.10.6 + - munkres=1.1.4 + - ncurses=6.5 + - networkx=2.8.8 + - openjpeg=2.5.4 + - openldap=2.6.10 + - openssl=3.5.4 + - packaging=25.0 + - patsy=1.0.1 + - pcre2=10.46 + - pip=25.2 + - pixman=0.46.4 + - pthread-stubs=0.4 + - pyparsing=3.2.5 + - pyside6=6.9.3 + - python=3.10.18 + - python-dateutil=2.9.0.post0 + - python-tzdata=2025.2 + - python_abi=3.10 + - pytz=2025.2 + - qhull=2020.2 + - qt6-main=6.9.3 + - readline=8.2 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - setuptools=80.9.0 + - six=1.17.0 + - tk=8.6.13 + - tzdata=2025b + - wayland=1.24.0 + - wheel=0.45.1 + - xcb-util=0.4.1 + - xcb-util-cursor=0.1.5 + - xcb-util-image=0.4.0 + - xcb-util-keysyms=0.4.1 + - xcb-util-renderutil=0.3.10 + - xcb-util-wm=0.4.2 + - xkeyboard-config=2.45 + - xorg-libice=1.1.2 + - xorg-libsm=1.2.6 + - xorg-libx11=1.8.12 + - xorg-libxau=1.0.12 + - xorg-libxcomposite=0.4.6 + - xorg-libxcursor=1.2.3 + - xorg-libxdamage=1.1.6 + - xorg-libxdmcp=1.1.5 + - xorg-libxext=1.3.6 + - xorg-libxfixes=6.0.2 + - xorg-libxi=1.8.2 + - xorg-libxrandr=1.5.4 + - xorg-libxrender=0.9.12 + - xorg-libxtst=1.2.5 + - xorg-libxxf86vm=1.1.6 + - zstd=1.5.7 + - pip: + - contourpy==1.3.1 + - coverage==7.10.4 + - exceptiongroup==1.3.0 + - fonttools==4.60.1 + - hypergraphx==1.7.8 + - iniconfig==2.1.0 + - joblib==1.5.1 + - kiwisolver==1.4.9 + - lxml==6.0.0 + - matplotlib==3.10.6 + - numpy==2.2.6 + - pandas==2.3.3 + - pillow==11.3.0 + - pluggy==1.6.0 + - pygments==2.19.2 + - pytest==8.4.1 + - pytest-cov==6.2.1 + - scikit-learn==1.7.1 + - scipy==1.15.3 + - statsmodels==0.14.5 + - threadpoolctl==3.6.0 + - tomli==2.2.1 + - tornado==6.5.2 + - typing-extensions==4.14.1 + - unicodedata2==16.0.0 + - unittest-xml-reporting==3.2.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_48578_6_test diff --git a/configs/s41467_024_48578_6_test/explicit.txt b/configs/s41467_024_48578_6_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..d7f095a31c06efd5d4a7765fb7008995506c2432 --- /dev/null +++ b/configs/s41467_024_48578_6_test/explicit.txt @@ -0,0 +1,148 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda#434ca7e50e40f4918ab701e3facd59a0 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-6_cp310.conda#01f0f2104b8466714804a72e511de599 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/linux-64/libegl-1.7.0-ha4b6fd6_2.conda#c151d5eb730e9b7480e6d48c0fc44048 +https://conda.anaconda.org/conda-forge/linux-64/libopengl-1.7.0-ha4b6fd6_2.conda#7df50d44d4a14d6c31a2c54f2cd92157 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda#76df83c2a9035c54df5d04ff81bcc02d +https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlicommon-1.1.0-hb03c661_4.conda#1d29d2e33fe59954af82ef54a8af3fe1 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda#4211416ecba1866fab0c6470986c22d6 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba +https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88 +https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libntlm-1.8-hb9d3cd8_0.conda#7c7927b404672409d9917d49bff5f2d6 +https://conda.anaconda.org/conda-forge/linux-64/libpciaccess-0.18-hb9d3cd8_0.conda#70e3400cbbfa03e96dcde7fc13e38c7b +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab +https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda#aea31d2e5b1091feca96fcfe945c3cf9 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0 +https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e +https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda#fb901ff28063514abb6046c9ec2c4a45 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb9d3cd8_0.conda#f6ebe2cb3f82ba6c057dde5d9debe4f7 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/double-conversion-3.3.1-h5888daf_0.conda#bfd56492d8346d669010eccafe0ba058 +https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda#2cd94587f3a401ae05e03a6caf09539d +https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835 +https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.1.0-hb03c661_4.conda#5cb5a1c9a94a78f5b23684bcb845338d +https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.1.0-hb03c661_4.conda#2e55011fa483edb8bfe3fd92e860cd79 +https://conda.anaconda.org/conda-forge/linux-64/libdrm-2.4.125-hb03c661_1.conda#9314bc5a1fe7d1044dc9dfd3ef400535 +https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_4.conda#2d34729cbc1da0ec988e57b13b712067 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda#c01af13bdc553d1a8fbfff6e8db075f0 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 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+https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.10.6-py310hfde16b3_1.conda#65d3af47b03c91d9d2bb69dd8307a661 +https://conda.anaconda.org/conda-forge/linux-64/statsmodels-0.14.5-py310hf779ad0_1.conda#60c940dc2baf2dac42ca194340681798 +https://conda.anaconda.org/conda-forge/linux-64/qt6-main-6.9.3-h5c1c036_0.conda#cc0bffcaf6410aba9c6581dfdc18012d +https://conda.anaconda.org/conda-forge/noarch/seaborn-base-0.13.2-pyhd8ed1ab_3.conda#fd96da444e81f9e6fcaac38590f3dd42 +https://conda.anaconda.org/conda-forge/linux-64/pyside6-6.9.3-py310h2007e60_1.conda#81c1ead40d87777cab2747cb6714e771 +https://conda.anaconda.org/conda-forge/noarch/seaborn-0.13.2-hd8ed1ab_3.conda#62afb877ca2c2b4b6f9ecb37320085b6 +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.10.6-py310hff52083_1.conda#0c662281a74b7fa5e3063bc78508d763 diff --git a/configs/s41467_024_48578_6_test/meta.json b/configs/s41467_024_48578_6_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..36ad633bb098b93da422a1b84177c7e564f29e7f --- /dev/null +++ b/configs/s41467_024_48578_6_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_48578_6_test", + "python_version": "3.10.18", + "has_cuda_hint": false, + "editable_count": 1, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_48578_6_test", + "exported_at": "2026-05-17T04:05:22Z" +} diff --git a/configs/s41467_024_48578_6_test/pip-clean.txt b/configs/s41467_024_48578_6_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..bfcfcb292c7f1b7eee9fde818bcdbeeedd0c4480 --- /dev/null +++ b/configs/s41467_024_48578_6_test/pip-clean.txt @@ -0,0 +1,19 @@ +coverage==7.10.4 +exceptiongroup==1.3.0 +-e git+https://github.com/HGX-Team/hypergraphx.git@832c77d7e70c62ade3589a2dcf2c69ec4ed4b97a#egg=hypergraphx +iniconfig==2.1.0 +joblib==1.5.1 +lxml==6.0.0 +matplotlib==3.10.6 +munkres==1.1.4 +pluggy==1.6.0 +Pygments==2.19.2 +PySide6==6.9.3 +pytest==8.4.1 +pytest-cov==6.2.1 +scikit-learn==1.7.1 +shiboken6==6.9.3 +threadpoolctl==3.6.0 +tomli==2.2.1 +typing_extensions==4.14.1 +unittest-xml-reporting==3.2.0 diff --git a/configs/s41467_024_48578_6_test/pip-freeze.txt b/configs/s41467_024_48578_6_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..b56d21d1d3e8ad3ed4fc7c2ec32b78a87c75bca0 --- /dev/null +++ b/configs/s41467_024_48578_6_test/pip-freeze.txt @@ -0,0 +1,39 @@ +contourpy @ file:///croot/contourpy_1732540045555/work +coverage==7.10.4 +cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1733332471406/work +exceptiongroup==1.3.0 +fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1759187078489/work +-e git+https://github.com/HGX-Team/hypergraphx.git@832c77d7e70c62ade3589a2dcf2c69ec4ed4b97a#egg=hypergraphx +iniconfig==2.1.0 +joblib==1.5.1 +kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_kiwisolver_1756467543/work +lxml==6.0.0 +matplotlib==3.10.6 +munkres==1.1.4 +networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work +numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1747544640217/work/dist/numpy-2.2.6-cp310-cp310-linux_x86_64.whl#sha256=d6d964caeef85d00073d27cd62b46883d275b3d8162f723f0fcabbd0b3cc3f9d +packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1745345660/work +pandas @ file:///home/conda/feedstock_root/build_artifacts/pandas_1759265530216/work +patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1733792384640/work +pillow @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pillow_1758208668/work +pluggy==1.6.0 +Pygments==2.19.2 +pyparsing @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_pyparsing_1758436411/work +PySide6==6.9.3 +pytest==8.4.1 +pytest-cov==6.2.1 +python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_python-dateutil_1751104122/work +pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1742920838005/work +scikit-learn==1.7.1 +scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1739790642651/work/dist/scipy-1.15.2-cp310-cp310-linux_x86_64.whl#sha256=9e52bad6c3294d1a5b04a13632118ca2157130603c6c018c2d710162b223b27e +seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1733730015268/work +shiboken6==6.9.3 +six @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_six_1753199211/work +statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1759296953068/work +threadpoolctl==3.6.0 +tomli==2.2.1 +tornado @ file:///home/conda/feedstock_root/build_artifacts/tornado_1756854848849/work +typing_extensions==4.14.1 +tzdata @ file:///home/conda/feedstock_root/build_artifacts/python-tzdata_1742745135198/work +unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1756494453687/work +unittest-xml-reporting==3.2.0 diff --git a/configs/s41467_024_49957_9_test/editable.txt b/configs/s41467_024_49957_9_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_49957_9_test/env.yml b/configs/s41467_024_49957_9_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..2c87196bf85b3a2ed2cc30ba9bf035c5cc2105c4 --- /dev/null +++ b/configs/s41467_024_49957_9_test/env.yml @@ -0,0 +1,62 @@ +name: s41467_024_49957_9_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - brotli-python=1.1.0 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - certifi=2024.2.2 + - charset-normalizer=3.3.2 + - idna=3.10 + - ld_impl_linux-64=2.44 + - libblas=3.9.0 + - libcblas=3.9.0 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgfortran=15.1.0 + - libgfortran-ng=15.1.0 + - libgfortran5=15.1.0 + - libgomp=15.1.0 + - liblapack=3.9.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libopenblas=0.3.25 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - numpy=1.24.4 + - openssl=3.5.2 + - packaging=25.0 + - pandas=2.0.3 + - pip=22.1.2 + - platformdirs=4.2.2 + - pooch=1.8.2 + - pysocks=1.7.1 + - python=3.8.20 + - python-dateutil=2.8.2 + - python-tzdata=2025.2 + - python_abi=3.8 + - pytz=2024.2 + - readline=8.2 + - requests=2.32.3 + - scipy=1.10.1 + - setuptools=70.3.0 + - six=1.16.0 + - tk=8.6.13 + - urllib3=2.2.1 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - tqdm==4.67.1 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_49957_9_test diff --git a/configs/s41467_024_49957_9_test/explicit.txt b/configs/s41467_024_49957_9_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..aee555ba2849b0511ff80682d82dbb02c813ca28 --- /dev/null +++ b/configs/s41467_024_49957_9_test/explicit.txt @@ -0,0 +1,58 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d 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+aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1687808301083/work +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1715777629804/work +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy-split_1683900206454/work/base/dist/scipy-1.10.1-cp38-cp38-linux_x86_64.whl#sha256=13ab5c17dedeb97a65ba90de1c51475f2d3ae0fe50bc43e9b018cc2943541de4 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_50605_5_test/editable.txt b/configs/s41467_024_50605_5_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_50605_5_test/env.yml b/configs/s41467_024_50605_5_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..330c29fb4f1d3c2e818bb63cf6babd570f642e05 --- /dev/null +++ b/configs/s41467_024_50605_5_test/env.yml @@ -0,0 +1,64 @@ +name: s41467_024_50605_5_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.10.5 + - ld_impl_linux-64=2.44 + - libffi=3.5.2 + - libgcc=15.2.0 + - libgcc-ng=15.2.0 + - libgomp=15.2.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libstdcxx=15.2.0 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.4 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zstd=1.5.7 + - pip: + - emmet-core==0.68.0 + - fonttools==4.57.0 + - idna==3.11 + - joblib==1.4.2 + - kiwisolver==1.4.7 + - latexcodec==3.0.0 + - monty==2023.9.25 + - mp-api==0.35.1 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - packaging==25.0 + - palettable==3.3.3 + - pybtex==0.25.1 + - pydantic==1.10.24 + - pymatgen==2023.8.10 + - pyparsing==3.1.4 + - python-dateutil==2.9.0.post0 + - ruamel-yaml==0.18.16 + - ruamel-yaml-clib==0.2.8 + - scipy==1.10.1 + - six==1.17.0 + - spglib==2.4.0 + - sympy==1.13.3 + - tqdm==4.67.1 + - typing-extensions==4.13.2 + - uncertainties==3.2.3 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50605_5_test diff --git a/configs/s41467_024_50605_5_test/explicit.txt b/configs/s41467_024_50605_5_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..841563ed8102f8148502b2bad8b2091f5ec4404e --- /dev/null +++ b/configs/s41467_024_50605_5_test/explicit.txt @@ -0,0 +1,33 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a 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0000000000000000000000000000000000000000..f0a70654ec839afebf4698acaebf65a326630984 --- /dev/null +++ b/configs/s41467_024_50605_5_test/pip-clean.txt @@ -0,0 +1,463 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 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+uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_50605_5_test/pip-freeze.txt b/configs/s41467_024_50605_5_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..f0a70654ec839afebf4698acaebf65a326630984 --- /dev/null +++ b/configs/s41467_024_50605_5_test/pip-freeze.txt @@ -0,0 +1,463 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emmet-core==0.68.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.11 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +latexcodec==3.0.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +monty==2023.9.25 +mp-api==0.35.1 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +palettable==3.3.3 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pybtex==0.25.1 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymatgen==2023.8.10 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruamel.yaml==0.18.16 +ruamel.yaml.clib==0.2.8 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +spglib==2.4.0 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +uncertainties==3.2.3 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_50903_y_test/env.yml b/configs/s41467_024_50903_y_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..b66127fb4ff7839c5cd900cff24da45ce088ef74 --- /dev/null +++ b/configs/s41467_024_50903_y_test/env.yml @@ -0,0 +1,65 @@ +name: s41467_024_50903_y_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.2.25 + - charset-normalizer==3.4.7 + - filelock==3.16.1 + - fsspec==2025.3.0 + - idna==3.11 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.1.3.1 + - nvidia-cuda-cupti-cu12==12.1.105 + - nvidia-cuda-nvrtc-cu12==12.1.105 + - nvidia-cuda-runtime-cu12==12.1.105 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.1.105 + - packaging==25.0 + - python-dateutil==2.9.0.post0 + - pyyaml==6.0.3 + - requests==2.32.4 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1+cpu + - tqdm==4.67.1 + - triton==3.0.0 + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50903_y_test diff --git a/configs/s41467_024_51639_5_test/editable.txt b/configs/s41467_024_51639_5_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_51639_5_test/env.yml b/configs/s41467_024_51639_5_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..937db1568d8c54baabbddf7158ebd4084003b168 --- /dev/null +++ b/configs/s41467_024_51639_5_test/env.yml @@ -0,0 +1,57 @@ +name: s41467_024_51639_5_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - filelock==3.16.1 + - fsspec==2025.3.0 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.1.3.1 + - nvidia-cuda-cupti-cu12==12.1.105 + - nvidia-cuda-nvrtc-cu12==12.1.105 + - nvidia-cuda-runtime-cu12==12.1.105 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.1.105 + - packaging==25.0 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1+cpu + - triton==3.0.0 + - typing-extensions==4.13.2 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51639_5_test diff --git a/configs/s41467_024_51639_5_test/explicit.txt b/configs/s41467_024_51639_5_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_51639_5_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT 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0000000000000000000000000000000000000000..e7b2a7c6319c079b872a26715e90b38f1c31ed4c --- /dev/null +++ b/configs/s41467_024_51639_5_test/pip-clean.txt @@ -0,0 +1,459 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 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+unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_51639_5_test/pip-freeze.txt b/configs/s41467_024_51639_5_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7b2a7c6319c079b872a26715e90b38f1c31ed4c --- /dev/null +++ b/configs/s41467_024_51639_5_test/pip-freeze.txt @@ -0,0 +1,459 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.1.105 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_52414_2_test/editable.txt b/configs/s41467_024_52414_2_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_52414_2_test/env.yml b/configs/s41467_024_52414_2_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..ffe73e04a8772860a71c11d49b53230895ad83b3 --- /dev/null +++ b/configs/s41467_024_52414_2_test/env.yml @@ -0,0 +1,55 @@ +name: s41467_024_52414_2_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.4.22 + - filelock==3.13.1 + - fsspec==2024.6.1 + - idna==3.13 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - monai==1.3.2 + - mpmath==1.3.0 + - networkx==3.0 + - numpy==1.24.4 + - packaging==25.0 + - pillow==10.4.0 + - pyyaml==6.0.3 + - requests==2.32.4 + - scikit-image==0.21.0 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1+cpu + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_52414_2_test diff --git a/configs/s41467_024_52414_2_test/explicit.txt b/configs/s41467_024_52414_2_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_52414_2_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_52414_2_test/meta.json b/configs/s41467_024_52414_2_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..6837aacd1a642cab39dd9f24a31ef7f67f0b55c3 --- /dev/null +++ b/configs/s41467_024_52414_2_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_52414_2_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_52414_2_test", + "exported_at": "2026-05-17T04:05:48Z" +} diff --git a/configs/s41467_024_52414_2_test/pip-clean.txt b/configs/s41467_024_52414_2_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5926ffb215f070a8e7b7dc4d447b42e92680763 --- /dev/null +++ b/configs/s41467_024_52414_2_test/pip-clean.txt @@ -0,0 +1,455 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +certifi==2026.4.22 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 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+einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.13.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 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+litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monai==1.3.2 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.0 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-image==0.21.0 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_52580_3_test/editable.txt b/configs/s41467_024_52580_3_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_52580_3_test/env.yml b/configs/s41467_024_52580_3_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..f12a39c57d84571981f98e631a13ac9faccc606c --- /dev/null +++ b/configs/s41467_024_52580_3_test/env.yml @@ -0,0 +1,43 @@ +name: s41467_024_52580_3_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - joblib==1.4.2 + - numpy==1.24.4 + - packaging==25.0 + - python-dateutil==2.9.0.post0 + - scikit-learn==1.3.2 + - scipy==1.10.1 + - six==1.17.0 + - threadpoolctl==3.5.0 + - tqdm==4.67.1 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_52580_3_test diff --git a/configs/s41467_024_52580_3_test/explicit.txt b/configs/s41467_024_52580_3_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_52580_3_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_52580_3_test/meta.json b/configs/s41467_024_52580_3_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..746b1ee1debb12d646bba5f25670b524ed309043 --- /dev/null +++ b/configs/s41467_024_52580_3_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_52580_3_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_52580_3_test", + "exported_at": "2026-05-17T04:05:45Z" +} diff --git a/configs/s41467_024_52580_3_test/pip-clean.txt b/configs/s41467_024_52580_3_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..276a0249f6af3a89bac3295490cfff98fb66a023 --- /dev/null +++ b/configs/s41467_024_52580_3_test/pip-clean.txt @@ -0,0 +1,445 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_52580_3_test/pip-freeze.txt b/configs/s41467_024_52580_3_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..276a0249f6af3a89bac3295490cfff98fb66a023 --- /dev/null +++ b/configs/s41467_024_52580_3_test/pip-freeze.txt @@ -0,0 +1,445 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_024_55594_z_test/editable.txt b/configs/s41467_024_55594_z_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_55594_z_test/env.yml b/configs/s41467_024_55594_z_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..a1429a3d3c99bbccde67a0fd42943fa18008a7ff --- /dev/null +++ b/configs/s41467_024_55594_z_test/env.yml @@ -0,0 +1,42 @@ +name: s41467_024_55594_z_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - idna==3.11 + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 + - torch==1.13.1+cpu + - torchvision==0.14.1+cpu + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_55594_z_test diff --git a/configs/s41467_024_55594_z_test/explicit.txt b/configs/s41467_024_55594_z_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_55594_z_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_024_55594_z_test/meta.json b/configs/s41467_024_55594_z_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..0b29a8f74895ff369975b0d3cfa729c8c7cff92c --- /dev/null +++ b/configs/s41467_024_55594_z_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_55594_z_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_55594_z_test", + "exported_at": "2026-05-17T04:06:05Z" +} diff --git a/configs/s41467_024_55594_z_test/pip-freeze.txt b/configs/s41467_024_55594_z_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..f5acfec541568e356c83667aefd1ae39befc8cf8 --- /dev/null +++ b/configs/s41467_024_55594_z_test/pip-freeze.txt @@ -0,0 +1,447 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +idna==3.11 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==1.13.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +torchvision==0.14.1+cpu +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +urllib3==2.2.3 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_56424_6_test/editable.txt b/configs/s41467_025_56424_6_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_56424_6_test/env.yml b/configs/s41467_025_56424_6_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..0106015d61b9465033e34c57db27fb24e6c4f79b --- /dev/null +++ b/configs/s41467_025_56424_6_test/env.yml @@ -0,0 +1,57 @@ +name: s41467_025_56424_6_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - filelock==3.16.1 + - fsspec==2025.3.0 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.1.3.1 + - nvidia-cuda-cupti-cu12==12.1.105 + - nvidia-cuda-nvrtc-cu12==12.1.105 + - nvidia-cuda-runtime-cu12==12.1.105 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.1.105 + - packaging==25.0 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1+cpu + - triton==3.0.0 + - typing-extensions==4.13.2 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56424_6_test diff --git a/configs/s41467_025_56424_6_test/explicit.txt b/configs/s41467_025_56424_6_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_025_56424_6_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_56424_6_test/meta.json b/configs/s41467_025_56424_6_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..67abb54734fe7baa3bed17d23a330cf804e430fa --- /dev/null +++ b/configs/s41467_025_56424_6_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_56424_6_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56424_6_test", + "exported_at": "2026-05-17T04:06:17Z" +} diff --git a/configs/s41467_025_56424_6_test/pip-clean.txt b/configs/s41467_025_56424_6_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7b2a7c6319c079b872a26715e90b38f1c31ed4c --- /dev/null +++ b/configs/s41467_025_56424_6_test/pip-clean.txt @@ -0,0 +1,459 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.1.105 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_56424_6_test/pip-freeze.txt b/configs/s41467_025_56424_6_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..e7b2a7c6319c079b872a26715e90b38f1c31ed4c --- /dev/null +++ b/configs/s41467_025_56424_6_test/pip-freeze.txt @@ -0,0 +1,459 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filelock==3.16.1 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +networkx==3.1 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu12==9.1.0.70 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.9.86 +nvidia-nvtx-cu12==12.1.105 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==2.4.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +triton==3.0.0 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_56623_1_test/editable.txt b/configs/s41467_025_56623_1_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_56623_1_test/env.yml b/configs/s41467_025_56623_1_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..a9943b8a32918f6d0547c75688f4d1fb4caf537d --- /dev/null +++ b/configs/s41467_025_56623_1_test/env.yml @@ -0,0 +1,50 @@ +name: s41467_025_56623_1_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - contourpy==1.1.1 + - cycler==0.12.1 + - fonttools==4.57.0 + - importlib-resources==6.4.5 + - joblib==1.4.2 + - kiwisolver==1.4.7 + - matplotlib==3.7.5 + - numpy==1.24.4 + - packaging==25.0 + - pandas==2.0.3 + - pillow==10.4.0 + - pyparsing==3.1.4 + - python-dateutil==2.9.0.post0 + - scipy==1.10.1 + - six==1.17.0 + - threadpoolctl==3.5.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56623_1_test diff --git a/configs/s41467_025_56623_1_test/explicit.txt b/configs/s41467_025_56623_1_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_025_56623_1_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_56623_1_test/meta.json b/configs/s41467_025_56623_1_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..0657476b69f3a120d11eba2bd2ede9a13c77d94a --- /dev/null +++ b/configs/s41467_025_56623_1_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_56623_1_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56623_1_test", + "exported_at": "2026-05-17T04:06:15Z" +} diff --git a/configs/s41467_025_56623_1_test/pip-clean.txt b/configs/s41467_025_56623_1_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644 --- /dev/null +++ b/configs/s41467_025_56623_1_test/pip-clean.txt @@ -0,0 +1,451 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_56623_1_test/pip-freeze.txt b/configs/s41467_025_56623_1_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644 --- /dev/null +++ b/configs/s41467_025_56623_1_test/pip-freeze.txt @@ -0,0 +1,451 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +contourpy==1.1.1 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cycler==0.12.1 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +fonttools==4.57.0 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kiwisolver==1.4.7 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +matplotlib==3.7.5 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow==10.4.0 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pyparsing==3.1.4 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_57007_1_test/editable.txt b/configs/s41467_025_57007_1_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_57007_1_test/env.yml b/configs/s41467_025_57007_1_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..71b2687e72ff86c607210214128ca726605ca4cd --- /dev/null +++ b/configs/s41467_025_57007_1_test/env.yml @@ -0,0 +1,39 @@ +name: s41467_025_57007_1_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - mpmath==1.3.0 + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 + - sympy==1.13.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_57007_1_test diff --git a/configs/s41467_025_57007_1_test/explicit.txt b/configs/s41467_025_57007_1_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_025_57007_1_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_57007_1_test/meta.json b/configs/s41467_025_57007_1_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..58d7db6ce8e7bca301701d7eea1fbcd549c839e9 --- /dev/null +++ b/configs/s41467_025_57007_1_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_57007_1_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_57007_1_test", + "exported_at": "2026-05-17T04:06:20Z" +} diff --git a/configs/s41467_025_57007_1_test/pip-clean.txt b/configs/s41467_025_57007_1_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..64088fce78eff2e53dab6e813ce2ebb24fcc9af9 --- /dev/null +++ b/configs/s41467_025_57007_1_test/pip-clean.txt @@ -0,0 +1,445 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_57007_1_test/pip-freeze.txt b/configs/s41467_025_57007_1_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..64088fce78eff2e53dab6e813ce2ebb24fcc9af9 --- /dev/null +++ b/configs/s41467_025_57007_1_test/pip-freeze.txt @@ -0,0 +1,445 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mpmath==1.3.0 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +sympy==1.13.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_57031_1_test/env.yml b/configs/s41467_025_57031_1_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..3a9caa1379580da69cf239e72fa8fbc516022cca --- /dev/null +++ b/configs/s41467_025_57031_1_test/env.yml @@ -0,0 +1,67 @@ +name: s41467_025_57031_1_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - filelock==3.16.1 + - fonttools==4.57.0 + - fsspec==2025.3.0 + - jinja2==3.1.6 + - joblib==1.4.2 + - kiwisolver==1.4.7 + - markupsafe==2.1.5 + - matplotlib==3.7.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - nvidia-cublas-cu12==12.1.3.1 + - nvidia-cuda-cupti-cu12==12.1.105 + - nvidia-cuda-nvrtc-cu12==12.1.105 + - nvidia-cuda-runtime-cu12==12.1.105 + - nvidia-cudnn-cu12==9.1.0.70 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-nccl-cu12==2.20.5 + - nvidia-nvjitlink-cu12==12.9.86 + - nvidia-nvtx-cu12==12.1.105 + - packaging==25.0 + - pandas==2.0.3 + - pyparsing==3.1.4 + - python-dateutil==2.9.0.post0 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - threadpoolctl==3.5.0 + - torch==2.4.1+cpu + - tqdm==4.67.1 + - triton==3.0.0 + - typing-extensions==4.13.2 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_57031_1_test diff --git a/configs/s41467_025_58231_5_test/editable.txt b/configs/s41467_025_58231_5_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_58231_5_test/env.yml b/configs/s41467_025_58231_5_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..11efc56e6ce4b7344d183039997e88876a55865f --- /dev/null +++ b/configs/s41467_025_58231_5_test/env.yml @@ -0,0 +1,37 @@ +name: s41467_025_58231_5_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.10.5 + - ld_impl_linux-64=2.44 + - libffi=3.5.2 + - libgcc=15.2.0 + - libgcc-ng=15.2.0 + - libgomp=15.2.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.51.0 + - libstdcxx=15.2.0 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.6.0 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zstd=1.5.7 + - pip: + - numpy==1.24.4 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58231_5_test diff --git a/configs/s41467_025_58231_5_test/explicit.txt b/configs/s41467_025_58231_5_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e0def4cef8bb7c59c3e7becdcd5d90d7370f54a2 --- /dev/null +++ b/configs/s41467_025_58231_5_test/explicit.txt @@ -0,0 +1,33 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.0-h0c1763c_0.conda#a3205ecbffb255ca27e0540c8494a2ee +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1aa0949_5.conda#511ed8935448c1875776b60ad3daf3a1 +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_58231_5_test/meta.json b/configs/s41467_025_58231_5_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..fb4b4699aa2d27597e588022e054bd819077c7aa --- /dev/null +++ b/configs/s41467_025_58231_5_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_58231_5_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58231_5_test", + "exported_at": "2026-05-17T04:06:31Z" +} diff --git a/configs/s41467_025_58231_5_test/pip-clean.txt b/configs/s41467_025_58231_5_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/s41467_025_58231_5_test/pip-clean.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_58231_5_test/pip-freeze.txt b/configs/s41467_025_58231_5_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/s41467_025_58231_5_test/pip-freeze.txt @@ -0,0 +1,443 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_58586_9_test/editable.txt b/configs/s41467_025_58586_9_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_58586_9_test/env.yml b/configs/s41467_025_58586_9_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..9b6785da79c36f3ce5d685d0cd8b390f5e057440 --- /dev/null +++ b/configs/s41467_025_58586_9_test/env.yml @@ -0,0 +1,39 @@ +name: s41467_025_58586_9_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - certifi==2026.2.25 + - numpy==1.24.4 + - packaging==25.0 + - python-dateutil==2.9.0.post0 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58586_9_test diff --git a/configs/s41467_025_58586_9_test/explicit.txt b/configs/s41467_025_58586_9_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_025_58586_9_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_58586_9_test/meta.json b/configs/s41467_025_58586_9_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..0e66e17153bcaceb4fb57be80217caefbd6f21c4 --- /dev/null +++ b/configs/s41467_025_58586_9_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_58586_9_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58586_9_test", + "exported_at": "2026-05-17T04:06:33Z" +} diff --git a/configs/s41467_025_58586_9_test/pip-clean.txt b/configs/s41467_025_58586_9_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..ccbd6cdf67e3b822e781b876f9f50dae6460cdfa --- /dev/null +++ b/configs/s41467_025_58586_9_test/pip-clean.txt @@ -0,0 +1,444 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 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git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_58586_9_test/pip-freeze.txt b/configs/s41467_025_58586_9_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..ccbd6cdf67e3b822e781b876f9f50dae6460cdfa --- /dev/null +++ b/configs/s41467_025_58586_9_test/pip-freeze.txt @@ -0,0 +1,444 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 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+leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_60646_z_test/editable.txt b/configs/s41467_025_60646_z_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_60646_z_test/env.yml b/configs/s41467_025_60646_z_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..ce6694a280c75c2a0437953d49d56a079f082226 --- /dev/null +++ b/configs/s41467_025_60646_z_test/env.yml @@ -0,0 +1,39 @@ +name: s41467_025_60646_z_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.11.12 + - ld_impl_linux-64=2.45 + - libffi=3.5.2 + - libgcc=15.2.0 + - libgcc-ng=15.2.0 + - libgomp=15.2.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.51.0 + - libstdcxx=15.2.0 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.6.0 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zstd=1.5.7 + - pip: + - numpy==1.24.4 + - scipy==1.10.1 + - torch==1.12.1+cpu +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60646_z_test diff --git a/configs/s41467_025_60646_z_test/pip-clean.txt b/configs/s41467_025_60646_z_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b2969592a66fcc9e9bc6f1125ccd5c646389a6d --- /dev/null +++ b/configs/s41467_025_60646_z_test/pip-clean.txt @@ -0,0 +1,445 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==1.12.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_60646_z_test/pip-freeze.txt b/configs/s41467_025_60646_z_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..1b2969592a66fcc9e9bc6f1125ccd5c646389a6d --- /dev/null +++ b/configs/s41467_025_60646_z_test/pip-freeze.txt @@ -0,0 +1,445 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch==1.12.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_60872_5_test/editable.txt b/configs/s41467_025_60872_5_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_60872_5_test/env.yml b/configs/s41467_025_60872_5_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..cac5a190346e2e8d990d17e5d9c753f0855272f0 --- /dev/null +++ b/configs/s41467_025_60872_5_test/env.yml @@ -0,0 +1,35 @@ +name: s41467_025_60872_5_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.11.12 + - ld_impl_linux-64=2.45 + - libffi=3.5.2 + - libgcc=15.2.0 + - libgcc-ng=15.2.0 + - libgomp=15.2.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.51.0 + - libstdcxx=15.2.0 + - libuuid=2.41.2 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.6.0 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zstd=1.5.7 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60872_5_test diff --git a/configs/s41467_025_60872_5_test/explicit.txt b/configs/s41467_025_60872_5_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..7867afd6690437631ec3bec7dfc9b816817b7bc7 --- /dev/null +++ b/configs/s41467_025_60872_5_test/explicit.txt @@ -0,0 +1,33 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda#f0991f0f84902f6b6009b4d2350a83aa +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.0-h0c1763c_0.conda#a3205ecbffb255ca27e0540c8494a2ee +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_ha0e22de_103.conda#86bc20552bf46075e3d92b67f089172d +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45-h1aa0949_0.conda#1450224b3e7d17dfeb985364b77a4d47 +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_60872_5_test/meta.json b/configs/s41467_025_60872_5_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..7e4b878ec90a0be553c13b822a54a776f570d87d --- /dev/null +++ b/configs/s41467_025_60872_5_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_60872_5_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_60872_5_test", + "exported_at": "2026-05-17T04:06:59Z" +} diff --git a/configs/s41467_025_60872_5_test/pip-clean.txt b/configs/s41467_025_60872_5_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..c99e608869aee722f181038aca65fc6f371c3864 --- /dev/null +++ b/configs/s41467_025_60872_5_test/pip-clean.txt @@ -0,0 +1,442 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_60872_5_test/pip-freeze.txt b/configs/s41467_025_60872_5_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..c99e608869aee722f181038aca65fc6f371c3864 --- /dev/null +++ b/configs/s41467_025_60872_5_test/pip-freeze.txt @@ -0,0 +1,442 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_60878_z_test/editable.txt b/configs/s41467_025_60878_z_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_60878_z_test/env.yml b/configs/s41467_025_60878_z_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..874510e6a45c392f10867f92620525548b9cd227 --- /dev/null +++ b/configs/s41467_025_60878_z_test/env.yml @@ -0,0 +1,100 @@ +name: s41467_025_60878_z_test +channels: + - conda-forge + - defaults +dependencies: + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2026.2.25 + - ld_impl_linux-64=2.45.1 + - libexpat=2.7.5 + - libffi=3.5.2 + - libgcc=15.2.0 + - libgcc-ng=15.2.0 + - libgomp=15.2.0 + - liblzma=5.8.3 + - liblzma-devel=5.8.3 + - libnsl=2.0.1 + - libsqlite=3.53.0 + - libuuid=2.42 + - libxcrypt=4.4.36 + - libzlib=1.3.2 + - ncurses=6.5 + - openssl=3.6.2 + - packaging=26.1 + - pip=26.0.1 + - python=3.11.8 + - readline=8.3 + - tk=8.6.13 + - tzdata=2025c + - wheel=0.46.3 + - xz=5.8.3 + - xz-gpl-tools=5.8.3 + - xz-tools=5.8.3 + - zstd=1.5.7 + - pip: + - aiohappyeyeballs==2.6.1 + - aiohttp==3.13.5 + - aiosignal==1.4.0 + - antlr4-python3-runtime==4.9.3 + - attrs==26.1.0 + - audioread==3.1.0 + - certifi==2026.4.22 + - cffi==2.0.0 + - charset-normalizer==3.4.7 + - contourpy==1.3.3 + - cycler==0.12.1 + - decorator==5.2.1 + - expelliarmus==1.1.12 + - filelock==3.25.2 + - fonttools==4.62.1 + - frozenlist==1.8.0 + - fsspec==2026.2.0 + - h5py==3.16.0 + - hydra-core==1.3.2 + - idna==3.11 + - importrosbag==1.0.4 + - jinja2==3.1.6 + - joblib==1.5.3 + - kiwisolver==1.5.0 + - lazy-loader==0.5 + - librosa==0.11.0 + - lightning-utilities==0.15.3 + - llvmlite==0.47.0 + - markupsafe==3.0.3 + - matplotlib==3.10.8 + - mpmath==1.3.0 + - msgpack==1.1.2 + - multidict==6.7.1 + - networkx==3.6.1 + - numba==0.65.1 + - numpy==1.26.4 + - omegaconf==2.3.0 + - pbr==7.0.3 + - pillow==12.2.0 + - platformdirs==4.9.6 + - pooch==1.9.0 + - propcache==0.4.1 + - pycparser==3.0 + - pyparsing==3.3.2 + - python-dateutil==2.9.0.post0 + - pytorch-lightning==2.6.1 + - pyyaml==6.0.3 + - requests==2.33.1 + - scikit-learn==1.8.0 + - scipy==1.17.1 + - setuptools==70.2.0 + - six==1.17.0 + - soundfile==0.13.1 + - soxr==1.0.0 + - sympy==1.14.0 + - threadpoolctl==3.6.0 + - tonic==1.6.0 + - torch==2.11.0+cpu + - torchaudio==2.11.0+cpu + - torchmetrics==1.9.0 + - tqdm==4.67.3 + - typing-extensions==4.15.0 + - urllib3==2.6.3 + - yarl==1.23.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_60878_z_test diff --git a/configs/s41467_025_60878_z_test/explicit.txt b/configs/s41467_025_60878_z_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..5ccd11a00e77732482a161cc053d59e27c1c818e --- /dev/null +++ b/configs/s41467_025_60878_z_test/explicit.txt @@ -0,0 +1,33 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.2.25-hbd8a1cb_0.conda#4492fd26db29495f0ba23f146cd5638d +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.5-hecca717_0.conda#49f570f3bc4c874a06ea69b7225753af +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h3435931_0.conda#a360c33a5abe61c07959e449fa1453eb +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_18.conda#d5e96b1ed75ca01906b3d2469b4ce493 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.3-hb03c661_0.conda#b88d90cad08e6bc8ad540cb310a761fb +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.53.0-h0c1763c_0.conda#393c8b31bd128e3d979e7ec17e9507c6 +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.42-h5347b49_0.conda#38ffe67b78c9d4de527be8315e5ada2c +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda#cffd3bdd58090148f4cfcd831f4b26ab +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.3-hb03c661_0.conda#55c20edec8e90c4703787acaade60808 +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.3-h853b02a_0.conda#d7d95fc8287ea7bf33e0e7116d2b95ec +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.3-ha02ee65_0.conda#8f5e2c6726c1339287a3c76a2c138ac7 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.3-hb03c661_0.conda#b62b615caa60812640f24db3a8d0fc87 +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.3-ha02ee65_0.conda#6a1b6af49a334e4e06b9f103367762bf +https://conda.anaconda.org/conda-forge/linux-64/python-3.11.8-hab00c5b_0_cpython.conda#2fdc314ee058eda0114738a9309d3683 +https://conda.anaconda.org/conda-forge/noarch/packaging-26.1-pyhc364b38_0.conda#b8ae38639d323d808da535fb71e31be8 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.46.3-pyhd8ed1ab_0.conda#bdbd7385b4a67025ac2dba4ef8cb6a8f +https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh8b19718_0.conda#67bdec43082fd8a9cffb9484420b39a2 diff --git a/configs/s41467_025_60878_z_test/meta.json b/configs/s41467_025_60878_z_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..683737a1e1c14e05d47720ffb17672bef9a13bf9 --- /dev/null +++ b/configs/s41467_025_60878_z_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_60878_z_test", + "python_version": "3.11.8", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_60878_z_test", + "exported_at": "2026-05-17T04:07:08Z" +} diff --git a/configs/s41467_025_60878_z_test/pip-clean.txt b/configs/s41467_025_60878_z_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..a392880f81612228fbd4998a1d2fdff1886d0806 --- /dev/null +++ b/configs/s41467_025_60878_z_test/pip-clean.txt @@ -0,0 +1,63 @@ +aiohappyeyeballs==2.6.1 +aiohttp==3.13.5 +aiosignal==1.4.0 +antlr4-python3-runtime==4.9.3 +attrs==26.1.0 +audioread==3.1.0 +certifi==2026.4.22 +cffi==2.0.0 +charset-normalizer==3.4.7 +contourpy==1.3.3 +cycler==0.12.1 +decorator==5.2.1 +expelliarmus==1.1.12 +filelock==3.25.2 +fonttools==4.62.1 +frozenlist==1.8.0 +fsspec==2026.2.0 +h5py==3.16.0 +hydra-core==1.3.2 +idna==3.11 +importRosbag==1.0.4 +Jinja2==3.1.6 +joblib==1.5.3 +kiwisolver==1.5.0 +lazy-loader==0.5 +librosa==0.11.0 +lightning-utilities==0.15.3 +llvmlite==0.47.0 +MarkupSafe==3.0.3 +matplotlib==3.10.8 +mpmath==1.3.0 +msgpack==1.1.2 +multidict==6.7.1 +networkx==3.6.1 +numba==0.65.1 +numpy==1.26.4 +omegaconf==2.3.0 +pbr==7.0.3 +pillow==12.2.0 +platformdirs==4.9.6 +pooch==1.9.0 +propcache==0.4.1 +pycparser==3.0 +pyparsing==3.3.2 +python-dateutil==2.9.0.post0 +pytorch-lightning==2.6.1 +PyYAML==6.0.3 +requests==2.33.1 +scikit-learn==1.8.0 +scipy==1.17.1 +six==1.17.0 +soundfile==0.13.1 +soxr==1.0.0 +sympy==1.14.0 +threadpoolctl==3.6.0 +tonic==1.6.0 +torch==2.11.0+cpu +torchaudio==2.11.0+cpu +torchmetrics==1.9.0 +tqdm==4.67.3 +typing_extensions==4.15.0 +urllib3==2.6.3 +yarl==1.23.0 diff --git a/configs/s41467_025_60878_z_test/pip-freeze.txt b/configs/s41467_025_60878_z_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..d170ada3327a11d535e9dc60c0535a169252465c --- /dev/null +++ b/configs/s41467_025_60878_z_test/pip-freeze.txt @@ -0,0 +1,64 @@ +aiohappyeyeballs==2.6.1 +aiohttp==3.13.5 +aiosignal==1.4.0 +antlr4-python3-runtime==4.9.3 +attrs==26.1.0 +audioread==3.1.0 +certifi==2026.4.22 +cffi==2.0.0 +charset-normalizer==3.4.7 +contourpy==1.3.3 +cycler==0.12.1 +decorator==5.2.1 +expelliarmus==1.1.12 +filelock==3.25.2 +fonttools==4.62.1 +frozenlist==1.8.0 +fsspec==2026.2.0 +h5py==3.16.0 +hydra-core==1.3.2 +idna==3.11 +importRosbag==1.0.4 +Jinja2==3.1.6 +joblib==1.5.3 +kiwisolver==1.5.0 +lazy-loader==0.5 +librosa==0.11.0 +lightning-utilities==0.15.3 +llvmlite==0.47.0 +MarkupSafe==3.0.3 +matplotlib==3.10.8 +mpmath==1.3.0 +msgpack==1.1.2 +multidict==6.7.1 +networkx==3.6.1 +numba==0.65.1 +numpy==1.26.4 +omegaconf==2.3.0 +packaging @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_packaging_1776209387/work +pbr==7.0.3 +pillow==12.2.0 +platformdirs==4.9.6 +pooch==1.9.0 +propcache==0.4.1 +pycparser==3.0 +pyparsing==3.3.2 +python-dateutil==2.9.0.post0 +pytorch-lightning==2.6.1 +PyYAML==6.0.3 +requests==2.33.1 +scikit-learn==1.8.0 +scipy==1.17.1 +six==1.17.0 +soundfile==0.13.1 +soxr==1.0.0 +sympy==1.14.0 +threadpoolctl==3.6.0 +tonic==1.6.0 +torch==2.11.0+cpu +torchaudio==2.11.0+cpu +torchmetrics==1.9.0 +tqdm==4.67.3 +typing_extensions==4.15.0 +urllib3==2.6.3 +yarl==1.23.0 diff --git a/configs/s41467_025_61454_1_test/editable.txt b/configs/s41467_025_61454_1_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_61454_1_test/env.yml b/configs/s41467_025_61454_1_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..4089e3e2d35a33e41fc5b55b89cb23389ad16ea9 --- /dev/null +++ b/configs/s41467_025_61454_1_test/env.yml @@ -0,0 +1,38 @@ +name: s41467_025_61454_1_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - ld_impl_linux-64=2.44 + - libffi=3.4.6 + - libgcc=15.1.0 + - libgcc-ng=15.1.0 + - libgomp=15.1.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libsqlite=3.50.4 + - libuuid=2.38.1 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - ncurses=6.5 + - openssl=3.5.2 + - pip=22.1.2 + - python=3.8.20 + - readline=8.2 + - setuptools=70.3.0 + - tk=8.6.13 + - wheel=0.45.1 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - pip: + - gurobipy==11.0.3 + - numpy==1.24.4 + - packaging==25.0 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_61454_1_test diff --git a/configs/s41467_025_61454_1_test/explicit.txt b/configs/s41467_025_61454_1_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_025_61454_1_test/explicit.txt @@ -0,0 +1,31 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc +https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8 +https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8 +https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09 +https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627 +https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9 +https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96 diff --git a/configs/s41467_025_61454_1_test/meta.json b/configs/s41467_025_61454_1_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..c030178c285e1a9b5dc8880493bbb625787bcea5 --- /dev/null +++ b/configs/s41467_025_61454_1_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_61454_1_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_61454_1_test", + "exported_at": "2026-05-17T04:07:03Z" +} diff --git a/configs/s41467_025_61454_1_test/pip-clean.txt b/configs/s41467_025_61454_1_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..b74ee01c4a5690937cf7a21dd3795feca5f3b4ef --- /dev/null +++ b/configs/s41467_025_61454_1_test/pip-clean.txt @@ -0,0 +1,444 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +gurobipy==11.0.3 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0 diff --git a/configs/s41467_025_61454_1_test/pip-freeze.txt b/configs/s41467_025_61454_1_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..b74ee01c4a5690937cf7a21dd3795feca5f3b4ef --- /dev/null +++ b/configs/s41467_025_61454_1_test/pip-freeze.txt @@ -0,0 +1,444 @@ +absl-py==2.3.1 +accelerate==0.24.1 +aiofiles==23.2.1 +aiohappyeyeballs==2.4.4 +aiohttp==3.10.11 +aioprometheus==23.12.0 +aiosignal==1.3.1 +alabaster==0.7.12 +allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +anyio==3.7.1 +APScheduler==3.11.2 +arxiv==2.1.0 +astunparse==1.6.3 +async-timeout==4.0.3 +attrs==25.3.0 +autograd==1.7.0 +autoray==0.6.12 +awscli==1.32.93 +azure-core==1.33.0 +azure-identity==1.21.0 +azure-storage-blob==12.26.0 +Babel==2.9.1 +backoff==2.2.1 +backports.zoneinfo==0.2.1 +bcrypt==4.1.2 +beartype==0.14.1 +better-abc==0.0.3 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +cachetools==4.2.4 +cffi==1.15.0 +cftime==1.6.4.post1 +chaospy==3.3.9 +charset-normalizer==3.4.7 +chex==0.1.7 +chroma-hnswlib==0.7.3 +chromadb==0.4.15 +click==8.1.7 +cloudpathlib==0.16.0 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 +conllu==0.11 +coverage==7.6.1 +cpm-kernels==1.0.11 +cryptography==42.0.5 +cvxopt==1.3.2 +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +deepdiff==7.0.1 +Deprecated==1.2.14 +deprecation==2.1.0 +dill==0.3.8 +distro==1.9.0 +dm-tree==0.1.8 +dnspython==2.6.1 +docstring_parser==0.17.0 +docutils==0.15.2 +dotenv==0.9.9 +duckduckgo-search==3.9.9 +editdistance==0.6.0 +effdet==0.4.1 +einops==0.7.0 +email-validator==2.3.0 +emoji==2.11.1 +equinox==0.10.4 +et-xmlfile==1.1.0 +eval_type_backport==0.2.2 +exceptiongroup==1.2.1 +fairseq==0.10.2 +faiss-cpu==1.7.4 +faiss-gpu==1.7.2 +fancy-einsum==0.0.3 +fastapi==0.115.14 +fastapi-sso==0.16.0 +fastavro==1.9.4 +fastuuid==0.13.5 +fbpca==1.0 +feedparser==6.0.10 +ffmpy==0.3.2 +filetype==1.2.0 +finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c +flaky==3.7.0 +Flask-Cors==3.0.10 +frozenlist==1.4.1 +fschat==0.2.35 +fsspec==2025.3.0 +ftfy==6.0.3 +future==0.18.2 +fuzzywuzzy==0.18.0 +gdown==5.2.0 +geosketch==1.3 +geotorch==0.3.0 +get-annotations==0.1.2 +gevent==21.12.0 +gitdb==4.0.11 +GitPython==3.1.43 +google-pasta==0.2.0 +googleapis-common-protos==1.63.0 +gpustat==1.1.1 +gpytorch==1.10 +gradio_client==0.16.0 +graphlib_backport==1.1.0 +greenlet==1.1.2 +gunicorn==23.0.0 +gurobipy==11.0.3 +h11==0.14.0 +h2==4.1.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +hpack==4.0.0 +httpcore==1.0.5 +httptools==0.6.1 +httpx==0.28.1 +httpx-sse==0.4.0 +huggingface_hub==0.36.1 +humanfriendly==10.0 +hyperframe==6.0.1 +icetk==0.0.4 +igraph==0.11.8 +imageio==2.35.1 +imagesize==1.3.0 +imgaug==0.4.0 +importlib-metadata==7.0.0 +importlib_resources==6.4.5 +inequalipy==1.0.5 +iniconfig==1.1.1 +inquirerpy==0.3.4 +iopath==0.1.10 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +Jinja2==3.1.6 +jiter==0.9.1 +jmespath==0.10.0 +joblib==1.4.2 +jsonnet==0.17.0 +jsonpatch==1.33 +jsonpath-python==1.0.6 +jsonpickle==2.0.0 +jsonschema==4.23.0 +jsonschema-specifications==2023.12.1 +kaggle==1.7.4.5 +Keras-Preprocessing==1.1.2 +kubernetes==29.0.0 +langchain==0.1.16 +langchain-community==0.0.34 +langchain-core==0.1.46 +langchain-experimental==0.0.57 +langchain-text-splitters==0.0.1 +langcodes==3.4.0 +langdetect==1.0.9 +langsmith==0.1.51 +language_data==1.2.0 +layoutparser==0.3.4 +lazy_loader==0.4 +leidenalg==0.10.2 +Levenshtein==0.25.1 +linear-operator==0.4.0 +litellm==1.77.4 +litellm-enterprise==0.1.20 +litellm-proxy-extras==0.2.19 +llama-index==0.9.35 +llvmlite==0.41.1 +lmdb==1.7.3 +lxml==5.2.1 +madoka==0.7.1 +marisa-trie==1.1.0 +Markdown==3.3.6 +markdown-it-py==3.0.0 +markdown2==2.4.13 +markdownify==0.11.6 +MarkupSafe==2.1.5 +marshmallow==3.21.1 +mdtex2html==1.3.0 +mdurl==0.1.2 +metaphor-python==0.1.23 +ml-dtypes==0.2.0 +monotonic==1.6 +mrcfile==1.5.4 +msal==1.36.0 +msal-extensions==1.3.0 +msg-parser==1.2.0 +msgpack==1.0.8 +msgpack-numpy==0.4.3.2 +multidict==6.0.5 +multipledispatch==1.0.0 +multiprocess==0.70.16 +murmurhash==1.0.10 +mypy-extensions==1.0.0 +narwhals==1.42.1 +natsort==8.4.0 +nest-asyncio==1.6.0 +netCDF4==1.7.2 +neuroHarmonize==2.4.5 +nh3==0.2.17 +ninja==1.11.1.1 +nltk==3.8.1 +numba==0.58.1 +numexpr==2.8.6 +numpoly==1.0.6 +numpy==1.24.4 +numpydoc==1.1.0 +nvidia-ml-py==12.535.133 +nvitop==1.3.2 +oauthlib==3.2.2 +onnx==1.16.0 +onnxruntime==1.15.1 +openai==1.101.0 +openpyxl==3.0.9 +opentelemetry-api==1.24.0 +opentelemetry-exporter-otlp-proto-common==1.24.0 +opentelemetry-exporter-otlp-proto-grpc==1.24.0 +opentelemetry-proto==1.24.0 +opentelemetry-sdk==1.24.0 +opentelemetry-semantic-conventions==0.45b0 +opt-einsum==3.3.0 +optax==0.1.5 +ordered-set==4.1.0 +orjson==3.10.1 +overrides==7.7.0 +packaging==26.2 +pandas==2.0.3 +pandas-stubs==1.2.0.45 +parsimonious==0.8.1 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pfzy==0.3.4 +PICOS==2.6.1 +pikepdf==8.4.1 +pip-search==0.0.12 +pkgutil_resolve_name==1.3.10 +plac==0.9.6 +plotly==6.3.0 +pluggy==1.5.0 +ply==3.11 +pondpond==1.4.1 +pooch==1.8.2 +portalocker==2.4.0 +posthog==3.5.0 +preshed==3.0.9 +prettytable==3.11.0 +primer3-py==2.2.0 +prompt-toolkit==3.0.43 +propcache==0.2.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pyclipper==1.3.0.post5 +pycocotools==2.0.7 +pycparser==2.21 +pydantic==2.10.6 +pydantic_core==2.27.2 +pydeck==0.9.0b1 +pyDOE2==1.3.0 +pydub==0.25.1 +pyfaidx==0.9.0.1 +Pygments==2.19.2 +PyJWT==2.8.0 +pymodbus==3.6.9 +PyMuPDF==1.23.16 +PyMuPDFb==1.23.9 +PyNaCl==1.6.2 +pynndescent==0.5.13 +Pyomo==6.8.2 +pyOpenSSL==24.1.0 +pypandoc==1.13 +pypdf==4.2.0 +pypdfium2==4.29.0 +PyPika==0.48.9 +PyQt5==5.15.7 +PyQt5-Qt5==5.15.17 +PyQt5_sip==12.15.0 +pyro-api==0.1.2 +pyro-ppl==1.9.1 +pysam==0.23.3 +PySocks==1.7.1 +pysqlite3-binary==0.5.2.post3 +pystan==2.19.1.1 +pytesseract==0.3.10 +pytest-cov==5.0.0 +python-dateutil==2.9.0.post0 +python-decouple==3.8 +python-docx==1.1.0 +python-dotenv==1.0.1 +python-iso639==2024.4.27 +python-Levenshtein==0.25.1 +python-multipart==0.0.18 +python-pptx==0.6.23 +python-slugify==8.0.4 +pytorch-pretrained-bert==0.6.2 +pytz==2025.2 +pyvista==0.44.2 +PyWavelets==1.4.1 +PyYAML==6.0.3 +quantile-python==1.1 +rapidfuzz==3.8.1 +rapidocr-onnxruntime==1.3.8 +ray==2.10.0 +rdkit==2024.3.5 +redis==6.1.1 +referencing==0.35.1 +regex==2022.4.24 +requests==2.32.4 +requests-oauthlib==1.3.0 +responses==0.16.0 +rich==13.7.1 +rouge-score==0.1.2 +rpds-py==0.20.1 +rq==2.3.3 +rsa==4.7.2 +ruff==0.4.2 +rustworkx==0.15.1 +s3transfer==0.11.3 +sacrebleu==2.1.0 +sacremoses==0.0.46 +safetensors==0.4.3 +scooby==0.10.1 +seaborn==0.13.2 +semantic-version==2.10.0 +sentence-transformers==2.2.2 +sentencepiece==0.1.91 +sentry-sdk==2.39.0 +session_info==1.0.1 +sgmllib3k==1.0.0 +shapely==2.0.4 +shellingham==1.5.4 +shortuuid==1.0.13 +six==1.17.0 +smart-open==6.4.0 +smmap==5.0.1 +sniffio==1.3.1 +snowballstemmer==2.2.0 +sobol-seq==0.2.0 +socksio==1.0.0 +soupsieve==2.5 +spacy-legacy==3.0.12 +spacy-loggers==1.0.5 +Sphinx==4.3.1 +sphinxcontrib-applehelp==1.0.2 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.0 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +SQLAlchemy==2.0.19 +sqlparse==0.4.2 +sse-starlette==1.8.2 +starlette==0.44.0 +statsmodels==0.14.1 +stdlib-list==0.10.0 +streamlit==1.30.0 +streamlit-aggrid==0.3.4.post3 +streamlit-antd-components==0.3.1 +streamlit-chatbox==1.1.11 +streamlit-feedback==0.1.3 +streamlit-modal==0.1.0 +streamlit-option-menu==0.3.12 +strsimpy==0.2.1 +svgwrite==1.4.3 +tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7 +tabulate==0.8.9 +tenacity==8.2.3 +tensorboard-plugin-wit==1.8.0 +tensorboardX==2.4.1 +text-unidecode==1.3 +texttable==1.7.0 +thefuzz==0.22.1 +threadpoolctl==3.5.0 +tifffile==2023.7.10 +tiktoken==0.7.0 +timm==0.9.16 +tk==0.1.0 +tokenizers==0.20.3 +toml==0.10.2 +tomlkit==0.12.0 +toolz==0.12.1 +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +transformer-lens==2.16.1 +transformers==4.46.3 +transformers-stream-generator==0.0.5 +typed-argument-parser==1.10.1 +typeguard==4.4.0 +typer==0.9.4 +types-requests==2.31.0.20240406 +typing-inspect==0.9.0 +typing-utils==0.1.0 +typing_extensions==4.13.2 +tzdata==2024.1 +tzlocal==5.2 +umap-learn==0.5.7 +Unidecode==1.3.2 +unittest-xml-reporting==3.2.0 +unstructured==0.11.0 +unstructured-client==0.22.0 +unstructured-inference==0.7.15 +unstructured.pytesseract==0.3.12 +uvicorn==0.29.0 +uvloop==0.21.0 +validators==0.28.1 +vllm==0.2.7 +vtk==9.3.1 +wandb==0.22.0 +watchdog==3.0.0 +watchfiles==0.21.0 +wavedrom==2.0.3.post3 +weasel==0.3.4 +websocket-client==1.8.0 +websockets==13.1 +Werkzeug==2.0.2 +word2number==1.1 +xlrd==2.0.1 +XlsxWriter==3.0.2 +xxhash==2.0.2 +Yapsy==1.12.2 +yarl==1.15.2 +youtube-search==2.1.2 +zipp==3.20.2 +zope.event==4.5.0 +zstandard==0.23.0