diff --git a/configs/012_oscillatory_state_space_models_test/editable.txt b/configs/012_oscillatory_state_space_models_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/012_oscillatory_state_space_models_test/env.yml b/configs/012_oscillatory_state_space_models_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..b4e7c7f0742cc2e51d9325a6831d9f3d91ac9402 --- /dev/null +++ b/configs/012_oscillatory_state_space_models_test/env.yml @@ -0,0 +1,37 @@ +name: 012_oscillatory_state_space_models_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/012_oscillatory_state_space_models_test diff --git a/configs/012_oscillatory_state_space_models_test/explicit.txt b/configs/012_oscillatory_state_space_models_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/012_oscillatory_state_space_models_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/012_oscillatory_state_space_models_test/meta.json b/configs/012_oscillatory_state_space_models_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..01f0bd230feecb37212eba88e5977dbdd6a128b7 --- /dev/null +++ b/configs/012_oscillatory_state_space_models_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "012_oscillatory_state_space_models_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/012_oscillatory_state_space_models_test", + "exported_at": "2026-05-17T04:03:15Z" +} diff --git a/configs/012_oscillatory_state_space_models_test/pip-clean.txt b/configs/012_oscillatory_state_space_models_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/012_oscillatory_state_space_models_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/012_oscillatory_state_space_models_test/pip-freeze.txt b/configs/012_oscillatory_state_space_models_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..2a9a868cef1868a39cbc6662cecfc900fcd5c1cb --- /dev/null +++ b/configs/012_oscillatory_state_space_models_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/023_test/editable.txt b/configs/023_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/023_test/explicit.txt b/configs/023_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/023_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/023_test/meta.json b/configs/023_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..5e7672ca54612053e1b5498c7d75602c96af2aaf --- /dev/null +++ b/configs/023_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "023_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/023_test", + "exported_at": "2026-05-17T04:03:31Z" +} diff --git a/configs/023_test/pip-clean.txt b/configs/023_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..697d35f015c1c5c496fc7fe2e60233c7b85246c5 --- /dev/null +++ b/configs/023_test/pip-clean.txt @@ -0,0 +1,450 @@ +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 +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 +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+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/023_test/pip-freeze.txt b/configs/023_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..697d35f015c1c5c496fc7fe2e60233c7b85246c5 --- /dev/null +++ b/configs/023_test/pip-freeze.txt @@ -0,0 +1,450 @@ +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 +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 +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+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/027_test/editable.txt b/configs/027_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/027_test/env.yml b/configs/027_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..c8d3bbbc19d5bf77349edf03ed2cbe2f0898be3e --- /dev/null +++ b/configs/027_test/env.yml @@ -0,0 +1,47 @@ +name: 027_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/027_test diff --git a/configs/027_test/explicit.txt b/configs/027_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/027_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/027_test/meta.json b/configs/027_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..e61e03a53b9f54b4e4b76fec6f13f6994f649b18 --- /dev/null +++ b/configs/027_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "027_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/027_test", + "exported_at": "2026-05-17T04:03:33Z" +} diff --git a/configs/027_test/pip-clean.txt b/configs/027_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae72d020abac43e97af9b9a363c9d17fa5657487 --- /dev/null +++ b/configs/027_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/027_test/pip-freeze.txt b/configs/027_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..ae72d020abac43e97af9b9a363c9d17fa5657487 --- /dev/null +++ b/configs/027_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/044_test/editable.txt b/configs/044_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/044_test/env.yml b/configs/044_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..370d5f7cf5c31eb5f70ef3bcf2c2b337dca4a1b6 --- /dev/null +++ b/configs/044_test/env.yml @@ -0,0 +1,119 @@ +name: 044_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - appdirs=1.4.4 + - brotli-python=1.1.0 + - bzip2=1.0.8 + - ca-certificates=2026.4.22 + - certifi=2024.2.2 + - charset-normalizer=3.3.2 + - cycler=0.12.1 + - freetype=2.14.1 + - idna=3.10 + - joblib=1.4.2 + - kiwisolver=1.4.4 + - lcms2=2.17 + - ld_impl_linux-64=2.44 + - lerc=4.0.0 + - libblas=3.9.0 + - libcblas=3.9.0 + - libdeflate=1.24 + - 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 + - libgomp=15.1.0 + - libjpeg-turbo=3.1.0 + - liblapack=3.9.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libopenblas=0.3.25 + - libpng=1.6.50 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libtiff=4.7.1 + - libuuid=2.41.2 + - libwebp-base=1.6.0 + - libxcb=1.17.0 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - matplotlib-base=3.4.3 + - ncurses=6.5 + - numpy=1.24.4 + - openjpeg=2.5.4 + - openssl=3.6.2 + - packaging=25.0 + - pandas=2.0.3 + - patsy=0.5.6 + - pillow=10.4.0 + - pip=22.1.2 + - pooch=0.6.0 + - pthread-stubs=0.4 + - pyparsing=3.1.4 + - 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 + - scikit-learn=1.3.2 + - scipy=1.10.1 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - setuptools=70.3.0 + - statsmodels=0.13.5 + - threadpoolctl=3.3.0 + - tk=8.6.13 + - tornado=6.2 + - urllib3=2.2.1 + - wheel=0.45.1 + - xorg-libxau=1.0.12 + - xorg-libxdmcp=1.1.5 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zstd=1.5.7 + - pip: + - asttokens==3.0.0 + - backcall==0.2.0 + - decorator==5.2.1 + - executing==2.2.1 + - filelock==3.13.1 + - fsspec==2024.6.1 + - ipdb==0.13.13 + - ipython==8.12.3 + - jedi==0.19.2 + - jinja2==3.1.4 + - lightning-utilities==0.11.9 + - markupsafe==2.1.5 + - matplotlib-inline==0.1.7 + - mpmath==1.3.0 + - networkx==3.0 + - parso==0.8.5 + - pexpect==4.9.0 + - pickleshare==0.7.5 + - ptyprocess==0.7.0 + - pure-eval==0.2.3 + - pytorch-lightning==2.4.0 + - pyyaml==6.0.3 + - six==1.17.0 + - stack-data==0.6.3 + - sympy==1.13.3 + - torch==2.4.1+cpu + - torchmetrics==1.5.2 + - traitlets==5.14.3 + - typing-extensions==4.12.2 + - wcwidth==0.2.14 +prefix: /home/lily/yz979/anaconda3/envs/044_test diff --git a/configs/044_test/explicit.txt b/configs/044_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..2b0edb8dc9717aa8dbc319a73a30c75c46dea967 --- /dev/null +++ b/configs/044_test/explicit.txt @@ -0,0 +1,87 @@ +# 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-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73 +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/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_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/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8 +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/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/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-3.6.2-h35e630c_0.conda#da1b85b6a87e141f5140bb9924cecab0 +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-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/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835 +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/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/libfreetype6-2.14.1-h73754d4_0.conda#8e7251989bca326a28f4a5ffbd74557a +https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_5.conda#41a5893c957ffed7f82b4005bc24866c +https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h8261f1e_0.conda#72b531694ebe4e8aa6f5745d1015c1b4 +https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d +https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471 +https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda#f4084e4e6577797150f9b04a4560ceb0 +https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17 +https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda#11b3379b191f63139e29c0d19dee24cd +https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7 +https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2#5f095bc6454094e96f146491fd03633b +https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py38h17151c0_1.conda#7a5a699c8992fc51ef25e980f4502c2a +https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333 +https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.3.2-pyhd8ed1ab_0.conda#7f4a9e3fcff3f6356ae99244a014da6a +https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441 +https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda#4afc585cd97ba8a23809406cd8a9eda8 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+++ b/configs/044_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "044_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/044_test", + "exported_at": "2026-05-17T04:03:53Z" +} diff --git a/configs/044_test/pip-clean.txt b/configs/044_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..f2792aecf78c45e6fbb9c634e2d4337f4d4fa69b --- /dev/null +++ b/configs/044_test/pip-clean.txt @@ -0,0 +1,466 @@ +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 +asttokens==3.0.0 +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 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+++ b/configs/044_test/pip-freeze.txt @@ -0,0 +1,478 @@ +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 +appdirs @ file:///home/conda/feedstock_root/build_artifacts/appdirs_1603108395799/work +APScheduler==3.11.2 +arxiv==2.1.0 +asttokens==3.0.0 +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 +backcall==0.2.0 +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 +cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work +cymem==2.0.8 +Cython==0.29.30 +dataclasses==0.6 +dataclasses-json==0.6.4 +datasets==2.19.0 +decorator==5.2.1 +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 +executing==2.2.1 +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 @ 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 +ipdb==0.13.13 +ipython==8.12.3 +isodate==0.7.2 +itsdangerous==2.0.1 +jax==0.4.13 +jaxlib==0.4.13 +jaxtyping==0.2.19 +jedi==0.19.2 +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 @ file:///croot/kiwisolver_1672387140495/work +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 +lightning-utilities==0.11.9 +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 @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work +matplotlib-inline==0.1.7 +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 @ 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 +parso==0.8.5 +pathlib==1.0.1 +patsy==1.0.1 +pdf2image==1.17.0 +pexpect==4.9.0 +pfzy==0.3.4 +pickleshare==0.7.5 +PICOS==2.6.1 +pikepdf==8.4.1 +pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work +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 +ptyprocess==0.7.0 +PuLP==3.1.1 +pulsar-client==3.5.0 +pure_eval==0.2.3 +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 @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work +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-lightning==2.4.0 +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 @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work +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 +stack-data==0.6.3 +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 +torchmetrics==1.5.2 +torchtext==0.4.0 +tornado==6.4 +tqdm==4.67.1 +traitlets==5.14.3 +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 +wcwidth==0.2.14 +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/046_test/editable.txt b/configs/046_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/046_test/env.yml b/configs/046_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..1be6a126e7bd60c54b789e5506f7be428b1f0b54 --- /dev/null +++ b/configs/046_test/env.yml @@ -0,0 +1,68 @@ +name: 046_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: + - antlr4-python3-runtime==4.9.3 + - 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==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 + - omegaconf==2.3.0 + - packaging==25.0 + - platformdirs==4.3.6 + - protobuf==5.29.6 + - pyyaml==6.0.3 + - requests==2.32.4 + - six==1.17.0 + - sympy==1.13.3 + - tensor-parallel==2.0.0 + - torch==2.4.1 + - triton==3.0.0 + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/046_test diff --git a/configs/046_test/explicit.txt b/configs/046_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/046_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 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+allennlp==0.8.4 +altair==5.3.0 +annotated-types==0.6.0 +antlr4-python3-runtime==4.9.3 +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==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 +omegaconf==2.3.0 +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==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 +protobuf==5.29.6 +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 +tensor-parallel==2.0.0 +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 +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/049_test/editable.txt b/configs/049_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/049_test/env.yml b/configs/049_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..b67bccd9248cd3bdf80248b1952191b9a2e9f364 --- /dev/null +++ b/configs/049_test/env.yml @@ -0,0 +1,59 @@ +name: 049_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==3.16.1 + - 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 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1 + - triton==3.0.0 + - typing-extensions==4.13.2 +prefix: /home/lily/yz979/anaconda3/envs/049_test diff --git a/configs/049_test/explicit.txt b/configs/049_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/049_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/049_test/meta.json b/configs/049_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..a451726de38b350f42df91fcf3577c734365a243 --- /dev/null +++ b/configs/049_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "049_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/049_test", + "exported_at": "2026-05-17T04:03:56Z" +} diff --git a/configs/049_test/pip-clean.txt b/configs/049_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..b272c6e2eadf05c531e952b835bc1e9338257699 --- /dev/null +++ b/configs/049_test/pip-clean.txt @@ -0,0 +1,461 @@ +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 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+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 +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 +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/055_test/editable.txt b/configs/055_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/055_test/env.yml b/configs/055_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..db9a155f05908b74ff686cc63176bcd76e99c1bc --- /dev/null +++ b/configs/055_test/env.yml @@ -0,0 +1,65 @@ +name: 055_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 + - ema-pytorch==0.7.7 + - filelock==3.16.1 + - fsspec==2025.3.0 + - gin-config==0.5.0 + - 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 + - pyyaml==6.0.3 + - requests==2.32.4 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.1.2 + - triton==2.1.0 + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/055_test diff --git a/configs/055_test/explicit.txt b/configs/055_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/055_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/055_test/meta.json b/configs/055_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..3a3a8fa7fa5f869cbf762fe3a6f3950c8df30d9c --- /dev/null +++ b/configs/055_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "055_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/055_test", + "exported_at": "2026-05-17T04:04:04Z" +} diff --git a/configs/055_test/pip-clean.txt b/configs/055_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a14741fd72043506648db468586a3abb9872920 --- /dev/null +++ b/configs/055_test/pip-clean.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 +ema-pytorch==0.7.7 +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 +gin-config==0.5.0 +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 +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==2.1.2 +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/055_test/pip-freeze.txt b/configs/055_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..0a14741fd72043506648db468586a3abb9872920 --- /dev/null +++ b/configs/055_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 +ema-pytorch==0.7.7 +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 +gin-config==0.5.0 +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 +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==2.1.2 +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/061_test/editable.txt b/configs/061_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/061_test/env.yml b/configs/061_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..d0af8aeb36888b4a43032ded1be8cdd95db9df51 --- /dev/null +++ b/configs/061_test/env.yml @@ -0,0 +1,51 @@ +name: 061_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 + - charset-normalizer==3.4.7 + - filelock==3.16.1 + - fsspec==2024.6.1 + - idna==3.10 + - jinja2==3.1.6 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - numpy==1.24.4 + - packaging==25.0 + - pyyaml==6.0.3 + - requests==2.32.4 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.1.2+cpu + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/061_test diff --git a/configs/061_test/explicit.txt b/configs/061_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..0903a6ac3107e1edc379dce49bc293a499bf34cf --- /dev/null +++ b/configs/061_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/061_test/meta.json b/configs/061_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..32eee7ad31f4322eed123b54f646d177156aa6b7 --- /dev/null +++ b/configs/061_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "061_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/061_test", + "exported_at": "2026-05-17T04:04:08Z" +} diff --git a/configs/061_test/pip-clean.txt b/configs/061_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6ce0c82966680eb8feb788c80974e2cb6b790c1 --- /dev/null +++ b/configs/061_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 +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 +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 +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==2.1.2+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/061_test/pip-freeze.txt b/configs/061_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6ce0c82966680eb8feb788c80974e2cb6b790c1 --- /dev/null +++ b/configs/061_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 +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 +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 +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==2.1.2+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_45642_z_test/env.yml b/configs/s41467_024_45642_z_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..ad04141b3b8cec3b6f9ca81432f7edd218a2e094 --- /dev/null +++ b/configs/s41467_024_45642_z_test/env.yml @@ -0,0 +1,89 @@ +name: s41467_024_45642_z_test +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1 + - _openmp_mutex=4.5 + - bzip2=1.0.8 + - ca-certificates=2025.8.3 + - certifi=2024.2.2 + - cycler=0.12.1 + - freetype=2.14.1 + - joblib=1.4.2 + - kiwisolver=1.4.4 + - lcms2=2.17 + - ld_impl_linux-64=2.44 + - lerc=4.0.0 + - libblas=3.9.0 + - libcblas=3.9.0 + - libdeflate=1.24 + - 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 + - libgomp=15.1.0 + - libjpeg-turbo=3.1.0 + - liblapack=3.9.0 + - liblzma=5.8.1 + - liblzma-devel=5.8.1 + - libnsl=2.0.1 + - libopenblas=0.3.25 + - libpng=1.6.50 + - libsqlite=3.50.4 + - libstdcxx=15.1.0 + - libstdcxx-ng=15.1.0 + - libtiff=4.7.1 + - libuuid=2.38.1 + - libwebp-base=1.6.0 + - libxcb=1.17.0 + - libxcrypt=4.4.36 + - libzlib=1.3.1 + - matplotlib-base=3.4.3 + - ncurses=6.5 + - networkx=2.8.8 + - numpy=1.24.4 + - openjpeg=2.5.4 + - openssl=3.5.4 + - packaging=25.0 + - pandas=2.0.3 + - patsy=0.5.6 + - pillow=10.4.0 + - pip=22.1.2 + - pthread-stubs=0.4 + - pyparsing=3.1.4 + - python=3.8.20 + - python-tzdata=2025.2 + - python_abi=3.8 + - pytz=2024.2 + - readline=8.2 + - scikit-learn=1.3.2 + - seaborn=0.13.2 + - seaborn-base=0.13.2 + - setuptools=70.3.0 + - statsmodels=0.13.5 + - threadpoolctl=3.3.0 + - tk=8.6.13 + - tornado=6.2 + - wheel=0.45.1 + - xorg-libxau=1.0.12 + - xorg-libxdmcp=1.1.5 + - xz=5.8.1 + - xz-gpl-tools=5.8.1 + - xz-tools=5.8.1 + - zstd=1.5.7 + - pip: + - contourpy==1.1.1 + - coverage==7.6.1 + - matplotlib==3.7.5 + - pyctem==0.0.1 + - pytest-cov==5.0.0 + - python-dateutil==2.9.0.post0 + - scipy==1.10.1 + - six==1.17.0 + - unittest-xml-reporting==3.2.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_45642_z_test diff --git a/configs/s41467_024_46773_z_test/editable.txt b/configs/s41467_024_46773_z_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_46773_z_test/env.yml b/configs/s41467_024_46773_z_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..4c81f2fa5d7438029b099fce3dc973bb530db9a2 --- /dev/null +++ b/configs/s41467_024_46773_z_test/env.yml @@ -0,0 +1,48 @@ +name: s41467_024_46773_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: + - anndata==0.9.2 + - coverage==7.6.1 + - h5py==3.11.0 + - natsort==8.4.0 + - numpy==1.24.4 + - packaging==25.0 + - pandas==2.0.3 + - pytest-cov==5.0.0 + - scikit-learn==1.3.2 + - scipy==1.10.1 + - six==1.17.0 + - sketchkh==0.1.3 + - tqdm-joblib==0.0.4 + - unittest-xml-reporting==3.2.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46773_z_test diff --git a/configs/s41467_024_46773_z_test/explicit.txt b/configs/s41467_024_46773_z_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_46773_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_46773_z_test/meta.json b/configs/s41467_024_46773_z_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..a24e918eb206b454235cd8d4983c7970991751b5 --- /dev/null +++ b/configs/s41467_024_46773_z_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_46773_z_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46773_z_test", + "exported_at": "2026-05-17T04:04:59Z" +} diff --git a/configs/s41467_024_46773_z_test/pip-clean.txt b/configs/s41467_024_46773_z_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e0e8121311c7e86d32ef2b7c2660c285f954df2 --- /dev/null +++ b/configs/s41467_024_46773_z_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 +anndata==0.9.2 +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 +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 +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 +sketchKH==0.1.3 +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 +tqdm_joblib==0.0.4 +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_46773_z_test/pip-freeze.txt b/configs/s41467_024_46773_z_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..4e0e8121311c7e86d32ef2b7c2660c285f954df2 --- /dev/null +++ b/configs/s41467_024_46773_z_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 +anndata==0.9.2 +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 +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 +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 +sketchKH==0.1.3 +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 +tqdm_joblib==0.0.4 +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_46946_w_test/editable.txt b/configs/s41467_024_46946_w_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_46946_w_test/env.yml b/configs/s41467_024_46946_w_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..854aab1d24765fdf9f958bff909184e0be8a2134 --- /dev/null +++ b/configs/s41467_024_46946_w_test/env.yml @@ -0,0 +1,60 @@ +name: s41467_024_46946_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: + - 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==8.9.2.26 + - nvidia-cufft-cu12==11.0.2.54 + - nvidia-curand-cu12==10.3.2.106 + - nvidia-nccl-cu12==2.18.1 + - 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 + - torchvision==0.19.1+cpu + - triton==2.1.0 + - typing-extensions==4.13.2 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_46946_w_test diff --git a/configs/s41467_024_46946_w_test/explicit.txt b/configs/s41467_024_46946_w_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_46946_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_46946_w_test/meta.json b/configs/s41467_024_46946_w_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..2b1c8ff10611ab78beb58d3aebdbc176b2dc8b1b --- /dev/null +++ b/configs/s41467_024_46946_w_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_46946_w_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_46946_w_test", + "exported_at": "2026-05-17T04:05:03Z" +} diff --git a/configs/s41467_024_46946_w_test/pip-clean.txt b/configs/s41467_024_46946_w_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..08ddc8f8b2e2ef9d7243d63da162bd96bcb4b233 --- /dev/null +++ b/configs/s41467_024_46946_w_test/pip-clean.txt @@ -0,0 +1,462 @@ +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 +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 +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==8.9.2.26 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.18.1 +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 +torchvision==0.19.1+cpu +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/s41467_024_46946_w_test/pip-freeze.txt b/configs/s41467_024_46946_w_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..08ddc8f8b2e2ef9d7243d63da162bd96bcb4b233 --- /dev/null +++ b/configs/s41467_024_46946_w_test/pip-freeze.txt @@ -0,0 +1,462 @@ +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 +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 +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==8.9.2.26 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu12==10.3.2.106 +nvidia-ml-py==12.535.133 +nvidia-nccl-cu12==2.18.1 +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 +torchvision==0.19.1+cpu +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/s41467_024_48567_9_test/env.yml b/configs/s41467_024_48567_9_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..8cdb8a6adb005f8d0ef383a880ed3712c1dc9ff9 --- /dev/null +++ b/configs/s41467_024_48567_9_test/env.yml @@ -0,0 +1,66 @@ +name: s41467_024_48567_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: + - ase==3.22.1 + - certifi==2026.2.25 + - filelock==3.13.1 + - fonttools==4.38.0 + - fsspec==2024.6.1 + - idna==3.11 + - jinja2==3.1.6 + - joblib==1.3.2 + - kiwisolver==1.4.4 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.0 + - numpy==1.23.5 + - nvidia-cublas-cu11==11.10.3.66 + - nvidia-cuda-nvrtc-cu11==11.7.99 + - nvidia-cuda-runtime-cu11==11.7.99 + - nvidia-cudnn-cu11==8.5.0.96 + - packaging==23.1 + - pillow==10.4.0 + - psutil==5.9.7 + - pyparsing==3.1.0 + - python-dateutil==2.8.2 + - requests==2.32.4 + - scipy==1.10.1 + - six==1.16.0 + - sympy==1.13.3 + - threadpoolctl==3.2.0 + - torch==1.13.1 + - torchvision==0.14.1 + - tqdm==4.65.0 + - typing-extensions==4.7.1 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_48567_9_test diff --git a/configs/s41467_024_48673_8_test/editable.txt b/configs/s41467_024_48673_8_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_48673_8_test/env.yml b/configs/s41467_024_48673_8_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..ae48fd0fb26d0bc91451223f6d108c7f1b96f661 --- /dev/null +++ b/configs/s41467_024_48673_8_test/env.yml @@ -0,0 +1,61 @@ +name: s41467_024_48673_8_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: + - attridict==0.0.9 + - contourpy==1.1.1 + - cycler==0.12.1 + - filelock==3.13.1 + - fonttools==4.57.0 + - fsspec==2024.6.1 + - h5py==3.11.0 + - importlib-resources==6.4.5 + - jinja2==3.1.6 + - kiwisolver==1.4.7 + - markupsafe==2.1.5 + - matplotlib==3.7.5 + - mpmath==1.3.0 + - networkx==3.0 + - numpy==1.24.4 + - ont-fast5-api==4.1.3 + - packaging==25.0 + - pillow==10.4.0 + - progressbar33==2.4 + - pyparsing==3.1.4 + - python-dateutil==2.9.0.post0 + - pyyaml==6.0.3 + - six==1.17.0 + - sympy==1.13.3 + - torch==2.4.1+cpu + - torchinfo==1.8.0 + - typing-extensions==4.12.2 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_48673_8_test diff --git a/configs/s41467_024_48673_8_test/explicit.txt b/configs/s41467_024_48673_8_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_48673_8_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_48673_8_test/meta.json b/configs/s41467_024_48673_8_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..61bec83b1bebe49a3d75d398d8e26992b773c23f --- /dev/null +++ b/configs/s41467_024_48673_8_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_48673_8_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_48673_8_test", + "exported_at": "2026-05-17T04:05:19Z" +} diff --git a/configs/s41467_024_48673_8_test/pip-clean.txt b/configs/s41467_024_48673_8_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f7c695349a70f5b610e972f233a54d7692956ed --- /dev/null +++ b/configs/s41467_024_48673_8_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 +attridict==0.0.9 +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 +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 +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 +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 +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 +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 +ont-fast5-api==4.1.3 +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 +progressbar33==2.4 +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 +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 +torchinfo==1.8.0 +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_48673_8_test/pip-freeze.txt b/configs/s41467_024_48673_8_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..5f7c695349a70f5b610e972f233a54d7692956ed --- /dev/null +++ b/configs/s41467_024_48673_8_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 +attridict==0.0.9 +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 +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 +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 +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 +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 +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 +ont-fast5-api==4.1.3 +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 +progressbar33==2.4 +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 +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 +torchinfo==1.8.0 +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_49339_1_test/editable.txt b/configs/s41467_024_49339_1_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_49339_1_test/env.yml b/configs/s41467_024_49339_1_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..41dcfdc4756bb386efbe661a2ccab905b30beae3 --- /dev/null +++ b/configs/s41467_024_49339_1_test/env.yml @@ -0,0 +1,47 @@ +name: s41467_024_49339_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 + - kiwisolver==1.4.7 + - matplotlib==3.7.5 + - numpy==1.24.4 + - packaging==25.0 + - pillow==10.4.0 + - pyparsing==3.1.4 + - python-dateutil==2.9.0.post0 + - scipy==1.10.1 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_49339_1_test diff --git a/configs/s41467_024_49339_1_test/explicit.txt b/configs/s41467_024_49339_1_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_49339_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_49339_1_test/meta.json b/configs/s41467_024_49339_1_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..a0a6ec2c7ecd22caa2a307f5611c435aed13a512 --- /dev/null +++ b/configs/s41467_024_49339_1_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_49339_1_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_49339_1_test", + "exported_at": "2026-05-17T04:05:21Z" +} diff --git a/configs/s41467_024_49339_1_test/pip-clean.txt b/configs/s41467_024_49339_1_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644 --- /dev/null +++ b/configs/s41467_024_49339_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_024_49339_1_test/pip-freeze.txt b/configs/s41467_024_49339_1_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e52e0af6fd7e2a81e3c4fa2d0219dbb56d14644 --- /dev/null +++ b/configs/s41467_024_49339_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_024_50317_w_test/editable.txt b/configs/s41467_024_50317_w_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_50381_2_test/editable.txt b/configs/s41467_024_50381_2_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_50381_2_test/env.yml b/configs/s41467_024_50381_2_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..dad64e39ee541990e7f696b49c6851c0877a2f96 --- /dev/null +++ b/configs/s41467_024_50381_2_test/env.yml @@ -0,0 +1,55 @@ +name: s41467_024_50381_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 + - cmocean==4.0.3 + - contourpy==1.1.1 + - cycler==0.12.1 + - dtw-python==1.5.3 + - 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 + - pillow==10.4.0 + - pyparsing==3.1.4 + - 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 + - tslearn==0.6.4 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50381_2_test diff --git a/configs/s41467_024_50381_2_test/explicit.txt b/configs/s41467_024_50381_2_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_50381_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 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+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 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0000000000000000000000000000000000000000..6ee7e9e8d08508f2a4a13653ba979416bf23bdab --- /dev/null +++ b/configs/s41467_024_50381_2_test/pip-clean.txt @@ -0,0 +1,456 @@ +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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+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 +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 +tslearn==0.6.4 +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_51477_5_test/editable.txt b/configs/s41467_024_51477_5_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_51477_5_test/env.yml b/configs/s41467_024_51477_5_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..42c0dec2a2d08a105e7a59d0f15597019792bcf8 --- /dev/null +++ b/configs/s41467_024_51477_5_test/env.yml @@ -0,0 +1,49 @@ +name: s41467_024_51477_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: + - cached-property==2.0.1 + - cloudpickle==3.1.1 + - decorator==5.2.1 + - etils==1.3.0 + - flax==0.7.2 + - numpy==1.24.4 + - optax==0.1.8 + - orbax-checkpoint==0.2.3 + - packaging==25.0 + - pyyaml==6.0.3 + - scipy==1.10.1 + - six==1.17.0 + - tensorflow-probability==0.21.0 + - tensorstore==0.1.45 + - typing-extensions==4.5.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51477_5_test diff --git a/configs/s41467_024_51477_5_test/explicit.txt b/configs/s41467_024_51477_5_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_51477_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 +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_51477_5_test/meta.json b/configs/s41467_024_51477_5_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..78c031fd747d682bb0d9890593c7a77c3a148d8f --- /dev/null +++ b/configs/s41467_024_51477_5_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_51477_5_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_51477_5_test", + "exported_at": "2026-05-17T04:05:37Z" +} diff --git a/configs/s41467_024_51477_5_test/pip-clean.txt b/configs/s41467_024_51477_5_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..793bd0fd36d26bf4130ec491f3d333c719ca014e --- /dev/null +++ b/configs/s41467_024_51477_5_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 +bs4==0.0.2 +cached-property==2.0.1 +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 +cloudpickle==3.1.1 +cobra==0.29.1 +cohere==5.3.3 +coloredlogs==15.0.1 +confection==0.1.4 +ConfigArgParse==1.5.3 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a/configs/s41467_024_51477_5_test/pip-freeze.txt b/configs/s41467_024_51477_5_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..793bd0fd36d26bf4130ec491f3d333c719ca014e --- /dev/null +++ b/configs/s41467_024_51477_5_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 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+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 +flax==0.7.2 +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 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+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 +orbax-checkpoint==0.2.3 +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 +tensorflow-probability==0.21.0 +tensorstore==0.1.45 +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_52003_3_test/editable.txt b/configs/s41467_024_52003_3_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_024_52003_3_test/env.yml b/configs/s41467_024_52003_3_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..0e45c43691ad2e1088440263cdc39b12bbd3f99c --- /dev/null +++ b/configs/s41467_024_52003_3_test/env.yml @@ -0,0 +1,58 @@ +name: s41467_024_52003_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: + - certifi==2026.4.22 + - filelock==3.16.1 + - idna==3.13 + - jinja2==3.1.6 + - joblib==1.4.2 + - markupsafe==2.1.5 + - mpmath==1.3.0 + - networkx==3.1 + - numpy==1.24.4 + - packaging==25.0 + - pillow==10.4.0 + - python-dateutil==2.9.0.post0 + - requests==2.32.4 + - scikit-image==0.21.0 + - scikit-learn==1.3.2 + - scipy==1.10.1 + - six==1.17.0 + - sympy==1.13.3 + - threadpoolctl==3.5.0 + - torch==2.0.1+cpu + - torchvision==0.15.2+cpu + - torchxrayvision==1.4.0 + - tqdm==4.67.1 + - urllib3==2.2.3 +prefix: /home/lily/yz979/anaconda3/envs/s41467_024_52003_3_test diff --git a/configs/s41467_024_52003_3_test/explicit.txt b/configs/s41467_024_52003_3_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_024_52003_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_52003_3_test/meta.json b/configs/s41467_024_52003_3_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..ad59cb88adbf0574e75e271fba02f5da322b8b8c --- /dev/null +++ b/configs/s41467_024_52003_3_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_024_52003_3_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_52003_3_test", + "exported_at": "2026-05-17T04:05:48Z" +} diff --git a/configs/s41467_024_52003_3_test/pip-clean.txt b/configs/s41467_024_52003_3_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..06411028d11259048c5d2766ac3773a4c6485f03 --- /dev/null +++ b/configs/s41467_024_52003_3_test/pip-clean.txt @@ -0,0 +1,457 @@ +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 +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==3.13 +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-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 +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==2.0.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +torchvision==0.15.2+cpu +torchxrayvision==1.4.0 +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_52003_3_test/pip-freeze.txt b/configs/s41467_024_52003_3_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..06411028d11259048c5d2766ac3773a4c6485f03 --- /dev/null +++ b/configs/s41467_024_52003_3_test/pip-freeze.txt @@ -0,0 +1,457 @@ +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 +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==3.13 +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-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 +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==2.0.1+cpu +torch-geometric==2.6.1 +torchaudio==2.1.2+cu118 +torchtext==0.4.0 +torchvision==0.15.2+cpu +torchxrayvision==1.4.0 +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_025_56378_9_test/editable.txt b/configs/s41467_025_56378_9_test/editable.txt new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/configs/s41467_025_56378_9_test/env.yml b/configs/s41467_025_56378_9_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..18294a09dd6c87d93c4561a97b2997ffaab1adc5 --- /dev/null +++ b/configs/s41467_025_56378_9_test/env.yml @@ -0,0 +1,107 @@ +name: s41467_025_56378_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: + - argcomplete==3.6.2 + - argh==0.31.3 + - asciitree==0.3.3 + - bioframe==0.8.0 + - blosc2==2.0.0 + - bx-python==0.13.0 + - certifi==2026.2.25 + - charset-normalizer==3.4.7 + - contourpy==1.1.1 + - cooler==0.10.2 + - cooltools==0.7.1 + - cycler==0.12.1 + - cytoolz==1.0.1 + - dill==0.4.0 + - filelock==3.16.1 + - fonttools==4.57.0 + - fsspec==2025.3.0 + - gffutils==0.13 + - h5py==3.11.0 + - hicmatrix==17.2 + - idna==3.11 + - importlib-resources==6.4.5 + - intervaltree==3.1.0 + - jinja2==3.1.6 + - joblib==1.4.2 + - kiwisolver==1.4.7 + - markupsafe==2.1.5 + - matplotlib==3.7.5 + - mpmath==1.3.0 + - multiprocess==0.70.18 + - ncls==0.0.70 + - 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 + - pillow==10.4.0 + - py-cpuinfo==9.0.0 + - pybedtools==0.12.0 + - pybigwig==0.3.22 + - pygenometracks==3.9 + - pyparsing==3.1.4 + - pyranges==0.1.4 + - pytabix==0.1 + - python-dateutil==2.9.0.post0 + - pyyaml==6.0.3 + - requests==2.32.4 + - scikit-image==0.21.0 + - scikit-learn==1.3.2 + - scipy==1.10.1 + - selene-sdk==0.5.1 + - simplejson==3.20.1 + - six==1.17.0 + - sorted-nearest==0.0.41 + - sortedcontainers==2.4.0 + - sympy==1.13.3 + - tables==3.8.0 + - threadpoolctl==3.5.0 + - torch==2.4.1+cpu + - torchvision==0.19.1+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_025_56378_9_test diff --git a/configs/s41467_025_56378_9_test/explicit.txt b/configs/s41467_025_56378_9_test/explicit.txt new file mode 100644 index 0000000000000000000000000000000000000000..e6bf6f30529304d9a6e549959469dbe2e50db8dc --- /dev/null +++ b/configs/s41467_025_56378_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_56378_9_test/meta.json b/configs/s41467_025_56378_9_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..87041ec33e239bbc1c92fd1fdbec6045cd39c1be --- /dev/null +++ b/configs/s41467_025_56378_9_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_56378_9_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_56378_9_test", + "exported_at": "2026-05-17T04:06:17Z" +} diff --git a/configs/s41467_025_56378_9_test/pip-clean.txt b/configs/s41467_025_56378_9_test/pip-clean.txt new file mode 100644 index 0000000000000000000000000000000000000000..13a4e25b6de3a27c9a68894933a951d306606ce6 --- /dev/null +++ b/configs/s41467_025_56378_9_test/pip-clean.txt @@ -0,0 +1,498 @@ +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 +argcomplete==3.6.2 +argh==0.31.3 +arxiv==2.1.0 +asciitree==0.3.3 +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 +bioframe==0.8.0 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +blosc2==2.0.0 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +bx-python==0.13.0 +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 +contourpy==1.1.1 +cooler==0.10.2 +cooltools==0.7.1 +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 +cytoolz==1.0.1 +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 +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 +gffutils==0.13 +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 +h5py==3.11.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +HiCMatrix==17.2 +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 +intervaltree==3.1.0 +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 +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 +ncls==0.0.70 +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 +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 +py-cpuinfo==9.0.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pybedtools==0.12.0 +pyBigWig==0.3.22 +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 +pyGenomeTracks==3.9 +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 +pyranges==0.1.4 +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 +pytabix==0.1 +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 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +selene-sdk==0.5.1 +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 +simplejson==3.20.1 +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 +sorted_nearest==0.0.41 +sortedcontainers==2.4.0 +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 +tables==3.8.0 +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 +torchvision==0.19.1+cpu +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/s41467_025_56378_9_test/pip-freeze.txt b/configs/s41467_025_56378_9_test/pip-freeze.txt new file mode 100644 index 0000000000000000000000000000000000000000..13a4e25b6de3a27c9a68894933a951d306606ce6 --- /dev/null +++ b/configs/s41467_025_56378_9_test/pip-freeze.txt @@ -0,0 +1,498 @@ +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 +argcomplete==3.6.2 +argh==0.31.3 +arxiv==2.1.0 +asciitree==0.3.3 +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 +bioframe==0.8.0 +biopython==1.83 +bitarray==2.5.1 +bitsandbytes==0.43.1 +blessed==1.20.0 +blis==0.7.11 +blosc2==2.0.0 +boto3==1.36.0 +botocore==1.36.26 +botorch==0.8.5 +bpl==0.1.1 +Brotli==1.1.0 +bs4==0.0.2 +bx-python==0.13.0 +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 +contourpy==1.1.1 +cooler==0.10.2 +cooltools==0.7.1 +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 +cytoolz==1.0.1 +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 +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 +gffutils==0.13 +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 +h5py==3.11.0 +hf-xet==1.2.0 +hf_transfer==0.1.9 +HiCMatrix==17.2 +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 +intervaltree==3.1.0 +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 +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 +ncls==0.0.70 +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 +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 +py-cpuinfo==9.0.0 +pyarrow==17.0.0 +pyarrow-hotfix==0.6 +pybedtools==0.12.0 +pyBigWig==0.3.22 +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 +pyGenomeTracks==3.9 +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 +pyranges==0.1.4 +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 +pytabix==0.1 +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 +scikit-learn==1.3.2 +scipy==1.10.1 +scooby==0.10.1 +seaborn==0.13.2 +selene-sdk==0.5.1 +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 +simplejson==3.20.1 +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 +sorted_nearest==0.0.41 +sortedcontainers==2.4.0 +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 +tables==3.8.0 +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 +torchvision==0.19.1+cpu +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/s41467_025_61475_w_test/env.yml b/configs/s41467_025_61475_w_test/env.yml new file mode 100644 index 0000000000000000000000000000000000000000..a68cc6cd0bb97bcb9acdd3031927816aa710842a --- /dev/null +++ b/configs/s41467_025_61475_w_test/env.yml @@ -0,0 +1,46 @@ +name: s41467_025_61475_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: + - 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 + - python-dateutil==2.9.0.post0 + - six==1.17.0 +prefix: /home/lily/yz979/anaconda3/envs/s41467_025_61475_w_test diff --git a/configs/s41467_025_61475_w_test/meta.json b/configs/s41467_025_61475_w_test/meta.json new file mode 100644 index 0000000000000000000000000000000000000000..d0489f8f7ccb36aa3c3e36ae5a8e0290d7e2ec54 --- /dev/null +++ b/configs/s41467_025_61475_w_test/meta.json @@ -0,0 +1,8 @@ +{ + "env": "s41467_025_61475_w_test", + "python_version": "3.8.20", + "has_cuda_hint": false, + "editable_count": 0, + "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_61475_w_test", + "exported_at": "2026-05-17T04:07:06Z" +}