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  1. configs/003_knowledge_entropy_test/editable.txt +0 -0
  2. configs/003_knowledge_entropy_test/env.yml +98 -0
  3. configs/003_knowledge_entropy_test/explicit.txt +94 -0
  4. configs/003_knowledge_entropy_test/meta.json +8 -0
  5. configs/003_knowledge_entropy_test/pip-clean.txt +444 -0
  6. configs/003_knowledge_entropy_test/pip-freeze.txt +456 -0
  7. configs/024_test/editable.txt +0 -0
  8. configs/024_test/env.yml +46 -0
  9. configs/024_test/explicit.txt +31 -0
  10. configs/024_test/meta.json +8 -0
  11. configs/024_test/pip-clean.txt +448 -0
  12. configs/024_test/pip-freeze.txt +448 -0
  13. configs/037_test/editable.txt +0 -0
  14. configs/037_test/env.yml +38 -0
  15. configs/037_test/explicit.txt +31 -0
  16. configs/037_test/meta.json +8 -0
  17. configs/037_test/pip-clean.txt +444 -0
  18. configs/037_test/pip-freeze.txt +444 -0
  19. configs/051_test/editable.txt +0 -0
  20. configs/051_test/env.yml +59 -0
  21. configs/051_test/explicit.txt +31 -0
  22. configs/051_test/meta.json +8 -0
  23. configs/051_test/pip-clean.txt +461 -0
  24. configs/051_test/pip-freeze.txt +461 -0
  25. configs/s41467_024_45642_z_test/editable.txt +0 -0
  26. configs/s41467_024_45642_z_test/explicit.txt +80 -0
  27. configs/s41467_024_45642_z_test/meta.json +8 -0
  28. configs/s41467_024_45642_z_test/pip-clean.txt +445 -0
  29. configs/s41467_024_45642_z_test/pip-freeze.txt +454 -0
  30. configs/s41467_024_48567_9_test/editable.txt +1 -0
  31. configs/s41467_024_48567_9_test/explicit.txt +31 -0
  32. configs/s41467_024_48567_9_test/meta.json +8 -0
  33. configs/s41467_024_48567_9_test/pip-clean.txt +464 -0
  34. configs/s41467_024_48567_9_test/pip-freeze.txt +464 -0
  35. configs/s41467_024_50317_w_test/env.yml +49 -0
  36. configs/s41467_024_50317_w_test/explicit.txt +31 -0
  37. configs/s41467_024_50317_w_test/meta.json +8 -0
  38. configs/s41467_024_50317_w_test/pip-clean.txt +450 -0
  39. configs/s41467_024_50317_w_test/pip-freeze.txt +450 -0
  40. configs/s41467_024_51933_2_test/editable.txt +0 -0
  41. configs/s41467_024_51933_2_test/env.yml +57 -0
  42. configs/s41467_024_51933_2_test/explicit.txt +31 -0
  43. configs/s41467_024_51933_2_test/meta.json +8 -0
  44. configs/s41467_024_51933_2_test/pip-clean.txt +459 -0
  45. configs/s41467_024_51933_2_test/pip-freeze.txt +459 -0
  46. configs/s41467_025_56348_1_test/editable.txt +0 -0
  47. configs/s41467_025_56348_1_test/env.yml +60 -0
  48. configs/s41467_025_56348_1_test/explicit.txt +45 -0
  49. configs/s41467_025_56348_1_test/meta.json +8 -0
  50. configs/s41467_025_56348_1_test/pip-clean.txt +449 -0
configs/003_knowledge_entropy_test/editable.txt ADDED
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configs/003_knowledge_entropy_test/env.yml ADDED
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+ name: 003_knowledge_entropy_test
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+ channels:
3
+ - conda-forge
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+ - defaults
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+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - blas=2.136
9
+ - blas-devel=3.9.0
10
+ - brotli-python=1.1.0
11
+ - bzip2=1.0.8
12
+ - ca-certificates=2025.8.3
13
+ - certifi=2024.2.2
14
+ - charset-normalizer=3.3.2
15
+ - colorama=0.4.6
16
+ - cycler=0.12.1
17
+ - freetype=2.14.1
18
+ - idna=3.10
19
+ - joblib=1.4.2
20
+ - kiwisolver=1.4.4
21
+ - lcms2=2.17
22
+ - ld_impl_linux-64=2.44
23
+ - lerc=4.0.0
24
+ - libblas=3.9.0
25
+ - libcblas=3.9.0
26
+ - libdeflate=1.24
27
+ - libffi=3.4.6
28
+ - libfreetype=2.14.1
29
+ - libfreetype6=2.14.1
30
+ - libgcc=15.1.0
31
+ - libgcc-ng=15.1.0
32
+ - libgfortran=15.1.0
33
+ - libgfortran-ng=15.1.0
34
+ - libgfortran5=15.1.0
35
+ - libgomp=15.1.0
36
+ - libjpeg-turbo=3.1.0
37
+ - liblapack=3.9.0
38
+ - liblapacke=3.9.0
39
+ - liblzma=5.8.1
40
+ - liblzma-devel=5.8.1
41
+ - libnsl=2.0.1
42
+ - libopenblas=0.3.30
43
+ - libpng=1.6.50
44
+ - libsqlite=3.50.4
45
+ - libstdcxx=15.1.0
46
+ - libstdcxx-ng=15.1.0
47
+ - libtiff=4.7.1
48
+ - libuuid=2.41.2
49
+ - libwebp-base=1.6.0
50
+ - libxcb=1.17.0
51
+ - libxcrypt=4.4.36
52
+ - libzlib=1.3.1
53
+ - matplotlib-base=3.4.3
54
+ - ncurses=6.5
55
+ - networkx=2.8.8
56
+ - numpy=1.24.4
57
+ - openblas=0.3.30
58
+ - openjpeg=2.5.4
59
+ - openssl=3.5.4
60
+ - packaging=25.0
61
+ - pandas=2.0.3
62
+ - patsy=0.5.6
63
+ - pillow=10.4.0
64
+ - pip=22.1.2
65
+ - plotly=5.24.1
66
+ - pthread-stubs=0.4
67
+ - pyparsing=3.1.4
68
+ - pysocks=1.7.1
69
+ - python=3.8.20
70
+ - python-dateutil=2.8.2
71
+ - python-tzdata=2025.2
72
+ - python_abi=3.8
73
+ - pytz=2024.2
74
+ - readline=8.2
75
+ - requests=2.32.3
76
+ - scikit-learn=1.3.2
77
+ - scipy=1.9.3
78
+ - seaborn=0.13.2
79
+ - seaborn-base=0.13.2
80
+ - setuptools=70.3.0
81
+ - statsmodels=0.13.5
82
+ - tenacity=8.5.0
83
+ - threadpoolctl=3.3.0
84
+ - tk=8.6.13
85
+ - tornado=6.2
86
+ - tqdm=4.67.1
87
+ - urllib3=2.2.1
88
+ - wheel=0.45.1
89
+ - xorg-libxau=1.0.12
90
+ - xorg-libxdmcp=1.1.5
91
+ - xz=5.8.1
92
+ - xz-gpl-tools=5.8.1
93
+ - xz-tools=5.8.1
94
+ - zstd=1.5.7
95
+ - pip:
96
+ - six==1.17.0
97
+ - torch==2.4.1+cpu
98
+ prefix: /home/lily/yz979/anaconda3/envs/003_knowledge_entropy_test
configs/003_knowledge_entropy_test/explicit.txt ADDED
@@ -0,0 +1,94 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
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+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
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+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
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+ https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
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+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
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+ types-requests==2.31.0.20240406
410
+ typing-inspect==0.9.0
411
+ typing-utils==0.1.0
412
+ typing_extensions==4.13.2
413
+ tzdata==2024.1
414
+ tzlocal==5.2
415
+ umap-learn==0.5.7
416
+ Unidecode==1.3.2
417
+ unittest-xml-reporting==3.2.0
418
+ unstructured==0.11.0
419
+ unstructured-client==0.22.0
420
+ unstructured-inference==0.7.15
421
+ unstructured.pytesseract==0.3.12
422
+ uvicorn==0.29.0
423
+ uvloop==0.21.0
424
+ validators==0.28.1
425
+ vllm==0.2.7
426
+ vtk==9.3.1
427
+ wandb==0.22.0
428
+ watchdog==3.0.0
429
+ watchfiles==0.21.0
430
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431
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432
+ websocket-client==1.8.0
433
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434
+ Werkzeug==2.0.2
435
+ word2number==1.1
436
+ xlrd==2.0.1
437
+ XlsxWriter==3.0.2
438
+ xxhash==2.0.2
439
+ Yapsy==1.12.2
440
+ yarl==1.15.2
441
+ youtube-search==2.1.2
442
+ zipp==3.20.2
443
+ zope.event==4.5.0
444
+ zstandard==0.23.0
configs/003_knowledge_entropy_test/pip-freeze.txt ADDED
@@ -0,0 +1,456 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
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6
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7
+ aiosignal==1.3.1
8
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9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
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28
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29
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30
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31
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32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
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39
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40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
43
+ cffi==1.15.0
44
+ cftime==1.6.4.post1
45
+ chaospy==3.3.9
46
+ charset-normalizer==3.4.7
47
+ chex==0.1.7
48
+ chroma-hnswlib==0.7.3
49
+ chromadb==0.4.15
50
+ click==8.1.7
51
+ cloudpathlib==0.16.0
52
+ cobra==0.29.1
53
+ cohere==5.3.3
54
+ colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
55
+ coloredlogs==15.0.1
56
+ confection==0.1.4
57
+ ConfigArgParse==1.5.3
58
+ conllu==0.11
59
+ coverage==7.6.1
60
+ cpm-kernels==1.0.11
61
+ cryptography==42.0.5
62
+ cvxopt==1.3.2
63
+ cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
64
+ cymem==2.0.8
65
+ Cython==0.29.30
66
+ dataclasses==0.6
67
+ dataclasses-json==0.6.4
68
+ datasets==2.19.0
69
+ deepdiff==7.0.1
70
+ Deprecated==1.2.14
71
+ deprecation==2.1.0
72
+ dill==0.3.8
73
+ distro==1.9.0
74
+ dm-tree==0.1.8
75
+ dnspython==2.6.1
76
+ docstring_parser==0.17.0
77
+ docutils==0.15.2
78
+ dotenv==0.9.9
79
+ duckduckgo-search==3.9.9
80
+ editdistance==0.6.0
81
+ effdet==0.4.1
82
+ einops==0.7.0
83
+ email-validator==2.3.0
84
+ emoji==2.11.1
85
+ equinox==0.10.4
86
+ et-xmlfile==1.1.0
87
+ eval_type_backport==0.2.2
88
+ exceptiongroup==1.2.1
89
+ fairseq==0.10.2
90
+ faiss-cpu==1.7.4
91
+ faiss-gpu==1.7.2
92
+ fancy-einsum==0.0.3
93
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94
+ fastapi-sso==0.16.0
95
+ fastavro==1.9.4
96
+ fastuuid==0.13.5
97
+ fbpca==1.0
98
+ feedparser==6.0.10
99
+ ffmpy==0.3.2
100
+ filetype==1.2.0
101
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
102
+ flaky==3.7.0
103
+ Flask-Cors==3.0.10
104
+ frozenlist==1.4.1
105
+ fschat==0.2.35
106
+ fsspec==2025.3.0
107
+ ftfy==6.0.3
108
+ future==0.18.2
109
+ fuzzywuzzy==0.18.0
110
+ gdown==5.2.0
111
+ geosketch==1.3
112
+ geotorch==0.3.0
113
+ get-annotations==0.1.2
114
+ gevent==21.12.0
115
+ gitdb==4.0.11
116
+ GitPython==3.1.43
117
+ google-pasta==0.2.0
118
+ googleapis-common-protos==1.63.0
119
+ gpustat==1.1.1
120
+ gpytorch==1.10
121
+ gradio_client==0.16.0
122
+ graphlib_backport==1.1.0
123
+ greenlet==1.1.2
124
+ gunicorn==23.0.0
125
+ h11==0.14.0
126
+ h2==4.1.0
127
+ hf-xet==1.2.0
128
+ hf_transfer==0.1.9
129
+ hpack==4.0.0
130
+ httpcore==1.0.5
131
+ httptools==0.6.1
132
+ httpx==0.28.1
133
+ httpx-sse==0.4.0
134
+ huggingface_hub==0.36.1
135
+ humanfriendly==10.0
136
+ hyperframe==6.0.1
137
+ icetk==0.0.4
138
+ idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work
139
+ igraph==0.11.8
140
+ imageio==2.35.1
141
+ imagesize==1.3.0
142
+ imgaug==0.4.0
143
+ importlib-metadata==7.0.0
144
+ importlib_resources==6.4.5
145
+ inequalipy==1.0.5
146
+ iniconfig==1.1.1
147
+ inquirerpy==0.3.4
148
+ iopath==0.1.10
149
+ isodate==0.7.2
150
+ itsdangerous==2.0.1
151
+ jax==0.4.13
152
+ jaxlib==0.4.13
153
+ jaxtyping==0.2.19
154
+ Jinja2==3.1.6
155
+ jiter==0.9.1
156
+ jmespath==0.10.0
157
+ joblib==1.4.2
158
+ jsonnet==0.17.0
159
+ jsonpatch==1.33
160
+ jsonpath-python==1.0.6
161
+ jsonpickle==2.0.0
162
+ jsonschema==4.23.0
163
+ jsonschema-specifications==2023.12.1
164
+ kaggle==1.7.4.5
165
+ Keras-Preprocessing==1.1.2
166
+ kiwisolver @ file:///croot/kiwisolver_1672387140495/work
167
+ kubernetes==29.0.0
168
+ langchain==0.1.16
169
+ langchain-community==0.0.34
170
+ langchain-core==0.1.46
171
+ langchain-experimental==0.0.57
172
+ langchain-text-splitters==0.0.1
173
+ langcodes==3.4.0
174
+ langdetect==1.0.9
175
+ langsmith==0.1.51
176
+ language_data==1.2.0
177
+ layoutparser==0.3.4
178
+ lazy_loader==0.4
179
+ leidenalg==0.10.2
180
+ Levenshtein==0.25.1
181
+ linear-operator==0.4.0
182
+ litellm==1.77.4
183
+ litellm-enterprise==0.1.20
184
+ litellm-proxy-extras==0.2.19
185
+ llama-index==0.9.35
186
+ llvmlite==0.41.1
187
+ lmdb==1.7.3
188
+ lxml==5.2.1
189
+ madoka==0.7.1
190
+ marisa-trie==1.1.0
191
+ Markdown==3.3.6
192
+ markdown-it-py==3.0.0
193
+ markdown2==2.4.13
194
+ markdownify==0.11.6
195
+ MarkupSafe==2.1.5
196
+ marshmallow==3.21.1
197
+ matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work
198
+ mdtex2html==1.3.0
199
+ mdurl==0.1.2
200
+ metaphor-python==0.1.23
201
+ ml-dtypes==0.2.0
202
+ monotonic==1.6
203
+ mrcfile==1.5.4
204
+ msal==1.36.0
205
+ msal-extensions==1.3.0
206
+ msg-parser==1.2.0
207
+ msgpack==1.0.8
208
+ msgpack-numpy==0.4.3.2
209
+ multidict==6.0.5
210
+ multipledispatch==1.0.0
211
+ multiprocess==0.70.16
212
+ murmurhash==1.0.10
213
+ mypy-extensions==1.0.0
214
+ narwhals==1.42.1
215
+ natsort==8.4.0
216
+ nest-asyncio==1.6.0
217
+ netCDF4==1.7.2
218
+ networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work
219
+ neuroHarmonize==2.4.5
220
+ nh3==0.2.17
221
+ ninja==1.11.1.1
222
+ nltk==3.8.1
223
+ numba==0.58.1
224
+ numexpr==2.8.6
225
+ numpoly==1.0.6
226
+ numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1687808301083/work
227
+ numpydoc==1.1.0
228
+ nvidia-ml-py==12.535.133
229
+ nvitop==1.3.2
230
+ oauthlib==3.2.2
231
+ onnx==1.16.0
232
+ onnxruntime==1.15.1
233
+ openai==1.101.0
234
+ openpyxl==3.0.9
235
+ opentelemetry-api==1.24.0
236
+ opentelemetry-exporter-otlp-proto-common==1.24.0
237
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
238
+ opentelemetry-proto==1.24.0
239
+ opentelemetry-sdk==1.24.0
240
+ opentelemetry-semantic-conventions==0.45b0
241
+ opt-einsum==3.3.0
242
+ optax==0.1.5
243
+ ordered-set==4.1.0
244
+ orjson==3.10.1
245
+ overrides==7.7.0
246
+ packaging==26.2
247
+ pandas==2.0.3
248
+ pandas-stubs==1.2.0.45
249
+ parsimonious==0.8.1
250
+ pathlib==1.0.1
251
+ patsy==1.0.1
252
+ pdf2image==1.17.0
253
+ pfzy==0.3.4
254
+ PICOS==2.6.1
255
+ pikepdf==8.4.1
256
+ pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
257
+ pip-search==0.0.12
258
+ pkgutil_resolve_name==1.3.10
259
+ plac==0.9.6
260
+ plotly==6.3.0
261
+ pluggy==1.5.0
262
+ ply==3.11
263
+ pondpond==1.4.1
264
+ pooch==1.8.2
265
+ portalocker==2.4.0
266
+ posthog==3.5.0
267
+ preshed==3.0.9
268
+ prettytable==3.11.0
269
+ primer3-py==2.2.0
270
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271
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272
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273
+ pulsar-client==3.5.0
274
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275
+ pyarrow-hotfix==0.6
276
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277
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278
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279
+ pydantic==2.10.6
280
+ pydantic_core==2.27.2
281
+ pydeck==0.9.0b1
282
+ pyDOE2==1.3.0
283
+ pydub==0.25.1
284
+ pyfaidx==0.9.0.1
285
+ Pygments==2.19.2
286
+ PyJWT==2.8.0
287
+ pymodbus==3.6.9
288
+ PyMuPDF==1.23.16
289
+ PyMuPDFb==1.23.9
290
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291
+ pynndescent==0.5.13
292
+ Pyomo==6.8.2
293
+ pyOpenSSL==24.1.0
294
+ pypandoc==1.13
295
+ pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
296
+ pypdf==4.2.0
297
+ pypdfium2==4.29.0
298
+ PyPika==0.48.9
299
+ PyQt5==5.15.7
300
+ PyQt5-Qt5==5.15.17
301
+ PyQt5_sip==12.15.0
302
+ pyro-api==0.1.2
303
+ pyro-ppl==1.9.1
304
+ pysam==0.23.3
305
+ PySocks==1.7.1
306
+ pysqlite3-binary==0.5.2.post3
307
+ pystan==2.19.1.1
308
+ pytesseract==0.3.10
309
+ pytest-cov==5.0.0
310
+ python-dateutil==2.9.0.post0
311
+ python-decouple==3.8
312
+ python-docx==1.1.0
313
+ python-dotenv==1.0.1
314
+ python-iso639==2024.4.27
315
+ python-Levenshtein==0.25.1
316
+ python-multipart==0.0.18
317
+ python-pptx==0.6.23
318
+ python-slugify==8.0.4
319
+ pytorch-pretrained-bert==0.6.2
320
+ pytz==2025.2
321
+ pyvista==0.44.2
322
+ PyWavelets==1.4.1
323
+ PyYAML==6.0.3
324
+ quantile-python==1.1
325
+ rapidfuzz==3.8.1
326
+ rapidocr-onnxruntime==1.3.8
327
+ ray==2.10.0
328
+ rdkit==2024.3.5
329
+ redis==6.1.1
330
+ referencing==0.35.1
331
+ regex==2022.4.24
332
+ requests==2.32.4
333
+ requests-oauthlib==1.3.0
334
+ responses==0.16.0
335
+ rich==13.7.1
336
+ rouge-score==0.1.2
337
+ rpds-py==0.20.1
338
+ rq==2.3.3
339
+ rsa==4.7.2
340
+ ruff==0.4.2
341
+ rustworkx==0.15.1
342
+ s3transfer==0.11.3
343
+ sacrebleu==2.1.0
344
+ sacremoses==0.0.46
345
+ safetensors==0.4.3
346
+ scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
347
+ scipy==1.9.3
348
+ scooby==0.10.1
349
+ seaborn==0.13.2
350
+ semantic-version==2.10.0
351
+ sentence-transformers==2.2.2
352
+ sentencepiece==0.1.91
353
+ sentry-sdk==2.39.0
354
+ session_info==1.0.1
355
+ sgmllib3k==1.0.0
356
+ shapely==2.0.4
357
+ shellingham==1.5.4
358
+ shortuuid==1.0.13
359
+ six==1.17.0
360
+ smart-open==6.4.0
361
+ smmap==5.0.1
362
+ sniffio==1.3.1
363
+ snowballstemmer==2.2.0
364
+ sobol-seq==0.2.0
365
+ socksio==1.0.0
366
+ soupsieve==2.5
367
+ spacy-legacy==3.0.12
368
+ spacy-loggers==1.0.5
369
+ Sphinx==4.3.1
370
+ sphinxcontrib-applehelp==1.0.2
371
+ sphinxcontrib-devhelp==1.0.2
372
+ sphinxcontrib-htmlhelp==2.0.0
373
+ sphinxcontrib-jsmath==1.0.1
374
+ sphinxcontrib-qthelp==1.0.3
375
+ sphinxcontrib-serializinghtml==1.1.5
376
+ SQLAlchemy==2.0.19
377
+ sqlparse==0.4.2
378
+ sse-starlette==1.8.2
379
+ starlette==0.44.0
380
+ statsmodels==0.14.1
381
+ stdlib-list==0.10.0
382
+ streamlit==1.30.0
383
+ streamlit-aggrid==0.3.4.post3
384
+ streamlit-antd-components==0.3.1
385
+ streamlit-chatbox==1.1.11
386
+ streamlit-feedback==0.1.3
387
+ streamlit-modal==0.1.0
388
+ streamlit-option-menu==0.3.12
389
+ strsimpy==0.2.1
390
+ svgwrite==1.4.3
391
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
392
+ tabulate==0.8.9
393
+ tenacity==8.2.3
394
+ tensorboard-plugin-wit==1.8.0
395
+ tensorboardX==2.4.1
396
+ text-unidecode==1.3
397
+ texttable==1.7.0
398
+ thefuzz==0.22.1
399
+ threadpoolctl==3.5.0
400
+ tifffile==2023.7.10
401
+ tiktoken==0.7.0
402
+ timm==0.9.16
403
+ tk==0.1.0
404
+ tokenizers==0.20.3
405
+ toml==0.10.2
406
+ tomlkit==0.12.0
407
+ toolz==0.12.1
408
+ torch==2.4.1+cpu
409
+ torch-geometric==2.6.1
410
+ torchaudio==2.1.2+cu118
411
+ torchtext==0.4.0
412
+ tornado==6.4
413
+ tqdm==4.67.1
414
+ transformer-lens==2.16.1
415
+ transformers==4.46.3
416
+ transformers-stream-generator==0.0.5
417
+ typed-argument-parser==1.10.1
418
+ typeguard==4.4.0
419
+ typer==0.9.4
420
+ types-requests==2.31.0.20240406
421
+ typing-inspect==0.9.0
422
+ typing-utils==0.1.0
423
+ typing_extensions==4.13.2
424
+ tzdata==2024.1
425
+ tzlocal==5.2
426
+ umap-learn==0.5.7
427
+ Unidecode==1.3.2
428
+ unittest-xml-reporting==3.2.0
429
+ unstructured==0.11.0
430
+ unstructured-client==0.22.0
431
+ unstructured-inference==0.7.15
432
+ unstructured.pytesseract==0.3.12
433
+ urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work
434
+ uvicorn==0.29.0
435
+ uvloop==0.21.0
436
+ validators==0.28.1
437
+ vllm==0.2.7
438
+ vtk==9.3.1
439
+ wandb==0.22.0
440
+ watchdog==3.0.0
441
+ watchfiles==0.21.0
442
+ wavedrom==2.0.3.post3
443
+ weasel==0.3.4
444
+ websocket-client==1.8.0
445
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configs/024_test/env.yml ADDED
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1
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configs/024_test/explicit.txt ADDED
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1
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2
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configs/024_test/meta.json ADDED
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1
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configs/024_test/pip-clean.txt ADDED
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306
+ python-docx==1.1.0
307
+ python-dotenv==1.0.1
308
+ python-iso639==2024.4.27
309
+ python-Levenshtein==0.25.1
310
+ python-multipart==0.0.18
311
+ python-pptx==0.6.23
312
+ python-slugify==8.0.4
313
+ pytorch-pretrained-bert==0.6.2
314
+ pytz==2025.2
315
+ pyvista==0.44.2
316
+ PyWavelets==1.4.1
317
+ PyYAML==6.0.3
318
+ quantile-python==1.1
319
+ rapidfuzz==3.8.1
320
+ rapidocr-onnxruntime==1.3.8
321
+ ray==2.10.0
322
+ rdkit==2024.3.5
323
+ redis==6.1.1
324
+ referencing==0.35.1
325
+ regex==2022.4.24
326
+ requests==2.32.4
327
+ requests-oauthlib==1.3.0
328
+ responses==0.16.0
329
+ rich==13.7.1
330
+ rouge-score==0.1.2
331
+ rpds-py==0.20.1
332
+ rq==2.3.3
333
+ rsa==4.7.2
334
+ ruff==0.4.2
335
+ rustworkx==0.15.1
336
+ s3transfer==0.11.3
337
+ sacrebleu==2.1.0
338
+ sacremoses==0.0.46
339
+ safetensors==0.4.3
340
+ scooby==0.10.1
341
+ seaborn==0.13.2
342
+ semantic-version==2.10.0
343
+ sentence-transformers==2.2.2
344
+ sentencepiece==0.1.91
345
+ sentry-sdk==2.39.0
346
+ session_info==1.0.1
347
+ sgmllib3k==1.0.0
348
+ shapely==2.0.4
349
+ shellingham==1.5.4
350
+ shortuuid==1.0.13
351
+ six==1.17.0
352
+ smart-open==6.4.0
353
+ smmap==5.0.1
354
+ sniffio==1.3.1
355
+ snowballstemmer==2.2.0
356
+ sobol-seq==0.2.0
357
+ socksio==1.0.0
358
+ soupsieve==2.5
359
+ spacy-legacy==3.0.12
360
+ spacy-loggers==1.0.5
361
+ Sphinx==4.3.1
362
+ sphinxcontrib-applehelp==1.0.2
363
+ sphinxcontrib-devhelp==1.0.2
364
+ sphinxcontrib-htmlhelp==2.0.0
365
+ sphinxcontrib-jsmath==1.0.1
366
+ sphinxcontrib-qthelp==1.0.3
367
+ sphinxcontrib-serializinghtml==1.1.5
368
+ SQLAlchemy==2.0.19
369
+ sqlparse==0.4.2
370
+ sse-starlette==1.8.2
371
+ starlette==0.44.0
372
+ statsmodels==0.14.1
373
+ stdlib-list==0.10.0
374
+ streamlit==1.30.0
375
+ streamlit-aggrid==0.3.4.post3
376
+ streamlit-antd-components==0.3.1
377
+ streamlit-chatbox==1.1.11
378
+ streamlit-feedback==0.1.3
379
+ streamlit-modal==0.1.0
380
+ streamlit-option-menu==0.3.12
381
+ strsimpy==0.2.1
382
+ svgwrite==1.4.3
383
+ sympy==1.13.3
384
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
385
+ tabulate==0.8.9
386
+ tenacity==8.2.3
387
+ tensorboard-plugin-wit==1.8.0
388
+ tensorboardX==2.4.1
389
+ text-unidecode==1.3
390
+ texttable==1.7.0
391
+ thefuzz==0.22.1
392
+ threadpoolctl==3.5.0
393
+ tifffile==2023.7.10
394
+ tiktoken==0.7.0
395
+ timm==0.9.16
396
+ tk==0.1.0
397
+ tokenizers==0.20.3
398
+ toml==0.10.2
399
+ tomlkit==0.12.0
400
+ toolz==0.12.1
401
+ torch==2.4.1+cpu
402
+ torch-geometric==2.6.1
403
+ torchaudio==2.1.2+cu118
404
+ torchtext==0.4.0
405
+ tornado==6.4
406
+ tqdm==4.67.1
407
+ transformer-lens==2.16.1
408
+ transformers==4.46.3
409
+ transformers-stream-generator==0.0.5
410
+ typed-argument-parser==1.10.1
411
+ typeguard==4.4.0
412
+ typer==0.9.4
413
+ types-requests==2.31.0.20240406
414
+ typing-inspect==0.9.0
415
+ typing-utils==0.1.0
416
+ typing_extensions==4.13.2
417
+ tzdata==2024.1
418
+ tzlocal==5.2
419
+ umap-learn==0.5.7
420
+ Unidecode==1.3.2
421
+ unittest-xml-reporting==3.2.0
422
+ unstructured==0.11.0
423
+ unstructured-client==0.22.0
424
+ unstructured-inference==0.7.15
425
+ unstructured.pytesseract==0.3.12
426
+ uvicorn==0.29.0
427
+ uvloop==0.21.0
428
+ validators==0.28.1
429
+ vllm==0.2.7
430
+ vtk==9.3.1
431
+ wandb==0.22.0
432
+ watchdog==3.0.0
433
+ watchfiles==0.21.0
434
+ wavedrom==2.0.3.post3
435
+ weasel==0.3.4
436
+ websocket-client==1.8.0
437
+ websockets==13.1
438
+ Werkzeug==2.0.2
439
+ word2number==1.1
440
+ xlrd==2.0.1
441
+ XlsxWriter==3.0.2
442
+ xxhash==2.0.2
443
+ Yapsy==1.12.2
444
+ yarl==1.15.2
445
+ youtube-search==2.1.2
446
+ zipp==3.20.2
447
+ zope.event==4.5.0
448
+ zstandard==0.23.0
configs/024_test/pip-freeze.txt ADDED
@@ -0,0 +1,448 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filelock==3.13.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
+ google-pasta==0.2.0
116
+ googleapis-common-protos==1.63.0
117
+ gpustat==1.1.1
118
+ gpytorch==1.10
119
+ gradio_client==0.16.0
120
+ graphlib_backport==1.1.0
121
+ greenlet==1.1.2
122
+ gunicorn==23.0.0
123
+ h11==0.14.0
124
+ h2==4.1.0
125
+ hf-xet==1.2.0
126
+ hf_transfer==0.1.9
127
+ hpack==4.0.0
128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ igraph==0.11.8
137
+ imageio==2.35.1
138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
+ llvmlite==0.41.1
183
+ lmdb==1.7.3
184
+ lxml==5.2.1
185
+ madoka==0.7.1
186
+ marisa-trie==1.1.0
187
+ Markdown==3.3.6
188
+ markdown-it-py==3.0.0
189
+ markdown2==2.4.13
190
+ markdownify==0.11.6
191
+ MarkupSafe==2.1.5
192
+ marshmallow==3.21.1
193
+ mdtex2html==1.3.0
194
+ mdurl==0.1.2
195
+ metaphor-python==0.1.23
196
+ ml-dtypes==0.2.0
197
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198
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199
+ mrcfile==1.5.4
200
+ msal==1.36.0
201
+ msal-extensions==1.3.0
202
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203
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204
+ msgpack-numpy==0.4.3.2
205
+ multidict==6.0.5
206
+ multipledispatch==1.0.0
207
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208
+ murmurhash==1.0.10
209
+ mypy-extensions==1.0.0
210
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211
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212
+ nest-asyncio==1.6.0
213
+ netCDF4==1.7.2
214
+ networkx==3.0
215
+ neuroHarmonize==2.4.5
216
+ nh3==0.2.17
217
+ ninja==1.11.1.1
218
+ nltk==3.8.1
219
+ numba==0.58.1
220
+ numexpr==2.8.6
221
+ numpoly==1.0.6
222
+ numpy==1.24.4
223
+ numpydoc==1.1.0
224
+ nvidia-ml-py==12.535.133
225
+ nvitop==1.3.2
226
+ oauthlib==3.2.2
227
+ onnx==1.16.0
228
+ onnxruntime==1.15.1
229
+ openai==1.101.0
230
+ openpyxl==3.0.9
231
+ opentelemetry-api==1.24.0
232
+ opentelemetry-exporter-otlp-proto-common==1.24.0
233
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
234
+ opentelemetry-proto==1.24.0
235
+ opentelemetry-sdk==1.24.0
236
+ opentelemetry-semantic-conventions==0.45b0
237
+ opt-einsum==3.3.0
238
+ optax==0.1.5
239
+ ordered-set==4.1.0
240
+ orjson==3.10.1
241
+ overrides==7.7.0
242
+ packaging==26.2
243
+ pandas==2.0.3
244
+ pandas-stubs==1.2.0.45
245
+ parsimonious==0.8.1
246
+ pathlib==1.0.1
247
+ patsy==1.0.1
248
+ pdf2image==1.17.0
249
+ pfzy==0.3.4
250
+ PICOS==2.6.1
251
+ pikepdf==8.4.1
252
+ pip-search==0.0.12
253
+ pkgutil_resolve_name==1.3.10
254
+ plac==0.9.6
255
+ plotly==6.3.0
256
+ pluggy==1.5.0
257
+ ply==3.11
258
+ pondpond==1.4.1
259
+ pooch==1.8.2
260
+ portalocker==2.4.0
261
+ posthog==3.5.0
262
+ preshed==3.0.9
263
+ prettytable==3.11.0
264
+ primer3-py==2.2.0
265
+ prompt-toolkit==3.0.43
266
+ propcache==0.2.0
267
+ PuLP==3.1.1
268
+ pulsar-client==3.5.0
269
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270
+ pyarrow-hotfix==0.6
271
+ pyclipper==1.3.0.post5
272
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273
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274
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275
+ pydantic_core==2.27.2
276
+ pydeck==0.9.0b1
277
+ pyDOE2==1.3.0
278
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279
+ pyfaidx==0.9.0.1
280
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281
+ PyJWT==2.8.0
282
+ pymodbus==3.6.9
283
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284
+ PyMuPDFb==1.23.9
285
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286
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287
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288
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289
+ pypandoc==1.13
290
+ pypdf==4.2.0
291
+ pypdfium2==4.29.0
292
+ PyPika==0.48.9
293
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294
+ PyQt5-Qt5==5.15.17
295
+ PyQt5_sip==12.15.0
296
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297
+ pyro-ppl==1.9.1
298
+ pysam==0.23.3
299
+ PySocks==1.7.1
300
+ pysqlite3-binary==0.5.2.post3
301
+ pystan==2.19.1.1
302
+ pytesseract==0.3.10
303
+ pytest-cov==5.0.0
304
+ python-dateutil==2.9.0.post0
305
+ python-decouple==3.8
306
+ python-docx==1.1.0
307
+ python-dotenv==1.0.1
308
+ python-iso639==2024.4.27
309
+ python-Levenshtein==0.25.1
310
+ python-multipart==0.0.18
311
+ python-pptx==0.6.23
312
+ python-slugify==8.0.4
313
+ pytorch-pretrained-bert==0.6.2
314
+ pytz==2025.2
315
+ pyvista==0.44.2
316
+ PyWavelets==1.4.1
317
+ PyYAML==6.0.3
318
+ quantile-python==1.1
319
+ rapidfuzz==3.8.1
320
+ rapidocr-onnxruntime==1.3.8
321
+ ray==2.10.0
322
+ rdkit==2024.3.5
323
+ redis==6.1.1
324
+ referencing==0.35.1
325
+ regex==2022.4.24
326
+ requests==2.32.4
327
+ requests-oauthlib==1.3.0
328
+ responses==0.16.0
329
+ rich==13.7.1
330
+ rouge-score==0.1.2
331
+ rpds-py==0.20.1
332
+ rq==2.3.3
333
+ rsa==4.7.2
334
+ ruff==0.4.2
335
+ rustworkx==0.15.1
336
+ s3transfer==0.11.3
337
+ sacrebleu==2.1.0
338
+ sacremoses==0.0.46
339
+ safetensors==0.4.3
340
+ scooby==0.10.1
341
+ seaborn==0.13.2
342
+ semantic-version==2.10.0
343
+ sentence-transformers==2.2.2
344
+ sentencepiece==0.1.91
345
+ sentry-sdk==2.39.0
346
+ session_info==1.0.1
347
+ sgmllib3k==1.0.0
348
+ shapely==2.0.4
349
+ shellingham==1.5.4
350
+ shortuuid==1.0.13
351
+ six==1.17.0
352
+ smart-open==6.4.0
353
+ smmap==5.0.1
354
+ sniffio==1.3.1
355
+ snowballstemmer==2.2.0
356
+ sobol-seq==0.2.0
357
+ socksio==1.0.0
358
+ soupsieve==2.5
359
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362
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363
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364
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365
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366
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367
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369
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372
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375
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383
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384
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385
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393
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397
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398
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402
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403
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405
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406
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409
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415
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418
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419
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421
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429
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432
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433
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434
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442
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445
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446
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447
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448
+ zstandard==0.23.0
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File without changes
configs/037_test/env.yml ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: 037_test
2
+ channels:
3
+ - conda-forge
4
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5
+ dependencies:
6
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7
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8
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9
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11
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13
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14
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15
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19
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20
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24
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25
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26
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27
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28
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33
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34
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35
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36
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37
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38
+ prefix: /home/lily/yz979/anaconda3/envs/037_test
configs/037_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
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9
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21
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26
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configs/037_test/meta.json ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "env": "037_test",
3
+ "python_version": "3.8.20",
4
+ "has_cuda_hint": false,
5
+ "editable_count": 0,
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+ "source_prefix": "/home/lily/yz979/anaconda3/envs/037_test",
7
+ "exported_at": "2026-05-17T04:03:41Z"
8
+ }
configs/037_test/pip-clean.txt ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
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232
+ opentelemetry-sdk==1.24.0
233
+ opentelemetry-semantic-conventions==0.45b0
234
+ opt-einsum==3.3.0
235
+ optax==0.1.5
236
+ ordered-set==4.1.0
237
+ orjson==3.10.1
238
+ overrides==7.7.0
239
+ packaging==26.2
240
+ pandas==2.0.3
241
+ pandas-stubs==1.2.0.45
242
+ parsimonious==0.8.1
243
+ pathlib==1.0.1
244
+ patsy==1.0.1
245
+ pdf2image==1.17.0
246
+ pfzy==0.3.4
247
+ PICOS==2.6.1
248
+ pikepdf==8.4.1
249
+ pip-search==0.0.12
250
+ pkgutil_resolve_name==1.3.10
251
+ plac==0.9.6
252
+ plotly==6.3.0
253
+ pluggy==1.5.0
254
+ ply==3.11
255
+ pondpond==1.4.1
256
+ pooch==1.8.2
257
+ portalocker==2.4.0
258
+ posthog==3.5.0
259
+ preshed==3.0.9
260
+ prettytable==3.11.0
261
+ primer3-py==2.2.0
262
+ prompt-toolkit==3.0.43
263
+ propcache==0.2.0
264
+ PuLP==3.1.1
265
+ pulsar-client==3.5.0
266
+ pyarrow==17.0.0
267
+ pyarrow-hotfix==0.6
268
+ pyclipper==1.3.0.post5
269
+ pycocotools==2.0.7
270
+ pycparser==2.21
271
+ pydantic==2.10.6
272
+ pydantic_core==2.27.2
273
+ pydeck==0.9.0b1
274
+ pyDOE2==1.3.0
275
+ pydub==0.25.1
276
+ pyfaidx==0.9.0.1
277
+ Pygments==2.19.2
278
+ PyJWT==2.8.0
279
+ pymodbus==3.6.9
280
+ PyMuPDF==1.23.16
281
+ PyMuPDFb==1.23.9
282
+ PyNaCl==1.6.2
283
+ pynndescent==0.5.13
284
+ Pyomo==6.8.2
285
+ pyOpenSSL==24.1.0
286
+ pypandoc==1.13
287
+ pypdf==4.2.0
288
+ pypdfium2==4.29.0
289
+ PyPika==0.48.9
290
+ PyQt5==5.15.7
291
+ PyQt5-Qt5==5.15.17
292
+ PyQt5_sip==12.15.0
293
+ pyro-api==0.1.2
294
+ pyro-ppl==1.9.1
295
+ pysam==0.23.3
296
+ PySocks==1.7.1
297
+ pysqlite3-binary==0.5.2.post3
298
+ pystan==2.19.1.1
299
+ pytesseract==0.3.10
300
+ pytest-cov==5.0.0
301
+ python-dateutil==2.9.0.post0
302
+ python-decouple==3.8
303
+ python-docx==1.1.0
304
+ python-dotenv==1.0.1
305
+ python-iso639==2024.4.27
306
+ python-Levenshtein==0.25.1
307
+ python-multipart==0.0.18
308
+ python-pptx==0.6.23
309
+ python-slugify==8.0.4
310
+ pytorch-pretrained-bert==0.6.2
311
+ pytz==2025.2
312
+ pyvista==0.44.2
313
+ PyWavelets==1.4.1
314
+ PyYAML==6.0.3
315
+ quantile-python==1.1
316
+ rapidfuzz==3.8.1
317
+ rapidocr-onnxruntime==1.3.8
318
+ ray==2.10.0
319
+ rdkit==2024.3.5
320
+ redis==6.1.1
321
+ referencing==0.35.1
322
+ regex==2022.4.24
323
+ requests==2.32.4
324
+ requests-oauthlib==1.3.0
325
+ responses==0.16.0
326
+ rich==13.7.1
327
+ rouge-score==0.1.2
328
+ rpds-py==0.20.1
329
+ rq==2.3.3
330
+ rsa==4.7.2
331
+ ruff==0.4.2
332
+ rustworkx==0.15.1
333
+ s3transfer==0.11.3
334
+ sacrebleu==2.1.0
335
+ sacremoses==0.0.46
336
+ safetensors==0.4.3
337
+ scipy==1.10.1
338
+ scooby==0.10.1
339
+ seaborn==0.13.2
340
+ semantic-version==2.10.0
341
+ sentence-transformers==2.2.2
342
+ sentencepiece==0.1.91
343
+ sentry-sdk==2.39.0
344
+ session_info==1.0.1
345
+ sgmllib3k==1.0.0
346
+ shapely==2.0.4
347
+ shellingham==1.5.4
348
+ shortuuid==1.0.13
349
+ six==1.17.0
350
+ smart-open==6.4.0
351
+ smmap==5.0.1
352
+ sniffio==1.3.1
353
+ snowballstemmer==2.2.0
354
+ sobol-seq==0.2.0
355
+ socksio==1.0.0
356
+ soupsieve==2.5
357
+ spacy-legacy==3.0.12
358
+ spacy-loggers==1.0.5
359
+ Sphinx==4.3.1
360
+ sphinxcontrib-applehelp==1.0.2
361
+ sphinxcontrib-devhelp==1.0.2
362
+ sphinxcontrib-htmlhelp==2.0.0
363
+ sphinxcontrib-jsmath==1.0.1
364
+ sphinxcontrib-qthelp==1.0.3
365
+ sphinxcontrib-serializinghtml==1.1.5
366
+ SQLAlchemy==2.0.19
367
+ sqlparse==0.4.2
368
+ sse-starlette==1.8.2
369
+ starlette==0.44.0
370
+ statsmodels==0.14.1
371
+ stdlib-list==0.10.0
372
+ streamlit==1.30.0
373
+ streamlit-aggrid==0.3.4.post3
374
+ streamlit-antd-components==0.3.1
375
+ streamlit-chatbox==1.1.11
376
+ streamlit-feedback==0.1.3
377
+ streamlit-modal==0.1.0
378
+ streamlit-option-menu==0.3.12
379
+ strsimpy==0.2.1
380
+ svgwrite==1.4.3
381
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
382
+ tabulate==0.8.9
383
+ tenacity==8.2.3
384
+ tensorboard-plugin-wit==1.8.0
385
+ tensorboardX==2.4.1
386
+ text-unidecode==1.3
387
+ texttable==1.7.0
388
+ thefuzz==0.22.1
389
+ threadpoolctl==3.5.0
390
+ tifffile==2023.7.10
391
+ tiktoken==0.7.0
392
+ timm==0.9.16
393
+ tk==0.1.0
394
+ tokenizers==0.20.3
395
+ toml==0.10.2
396
+ tomlkit==0.12.0
397
+ toolz==0.12.1
398
+ torch-geometric==2.6.1
399
+ torchaudio==2.1.2+cu118
400
+ torchtext==0.4.0
401
+ tornado==6.4
402
+ tqdm==4.67.1
403
+ transformer-lens==2.16.1
404
+ transformers==4.46.3
405
+ transformers-stream-generator==0.0.5
406
+ typed-argument-parser==1.10.1
407
+ typeguard==4.4.0
408
+ typer==0.9.4
409
+ types-requests==2.31.0.20240406
410
+ typing-inspect==0.9.0
411
+ typing-utils==0.1.0
412
+ typing_extensions==4.13.2
413
+ tzdata==2024.1
414
+ tzlocal==5.2
415
+ umap-learn==0.5.7
416
+ Unidecode==1.3.2
417
+ unittest-xml-reporting==3.2.0
418
+ unstructured==0.11.0
419
+ unstructured-client==0.22.0
420
+ unstructured-inference==0.7.15
421
+ unstructured.pytesseract==0.3.12
422
+ uvicorn==0.29.0
423
+ uvloop==0.21.0
424
+ validators==0.28.1
425
+ vllm==0.2.7
426
+ vtk==9.3.1
427
+ wandb==0.22.0
428
+ watchdog==3.0.0
429
+ watchfiles==0.21.0
430
+ wavedrom==2.0.3.post3
431
+ weasel==0.3.4
432
+ websocket-client==1.8.0
433
+ websockets==13.1
434
+ Werkzeug==2.0.2
435
+ word2number==1.1
436
+ xlrd==2.0.1
437
+ XlsxWriter==3.0.2
438
+ xxhash==2.0.2
439
+ Yapsy==1.12.2
440
+ yarl==1.15.2
441
+ youtube-search==2.1.2
442
+ zipp==3.20.2
443
+ zope.event==4.5.0
444
+ zstandard==0.23.0
configs/037_test/pip-freeze.txt ADDED
@@ -0,0 +1,444 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filetype==1.2.0
98
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
99
+ flaky==3.7.0
100
+ Flask-Cors==3.0.10
101
+ frozenlist==1.4.1
102
+ fschat==0.2.35
103
+ fsspec==2025.3.0
104
+ ftfy==6.0.3
105
+ future==0.18.2
106
+ fuzzywuzzy==0.18.0
107
+ gdown==5.2.0
108
+ geosketch==1.3
109
+ geotorch==0.3.0
110
+ get-annotations==0.1.2
111
+ gevent==21.12.0
112
+ gitdb==4.0.11
113
+ GitPython==3.1.43
114
+ google-pasta==0.2.0
115
+ googleapis-common-protos==1.63.0
116
+ gpustat==1.1.1
117
+ gpytorch==1.10
118
+ gradio_client==0.16.0
119
+ graphlib_backport==1.1.0
120
+ greenlet==1.1.2
121
+ gunicorn==23.0.0
122
+ h11==0.14.0
123
+ h2==4.1.0
124
+ hf-xet==1.2.0
125
+ hf_transfer==0.1.9
126
+ hpack==4.0.0
127
+ httpcore==1.0.5
128
+ httptools==0.6.1
129
+ httpx==0.28.1
130
+ httpx-sse==0.4.0
131
+ huggingface_hub==0.36.1
132
+ humanfriendly==10.0
133
+ hyperframe==6.0.1
134
+ icetk==0.0.4
135
+ igraph==0.11.8
136
+ imageio==2.35.1
137
+ imagesize==1.3.0
138
+ imgaug==0.4.0
139
+ importlib-metadata==7.0.0
140
+ importlib_resources==6.4.5
141
+ inequalipy==1.0.5
142
+ iniconfig==1.1.1
143
+ inquirerpy==0.3.4
144
+ iopath==0.1.10
145
+ isodate==0.7.2
146
+ itsdangerous==2.0.1
147
+ jax==0.4.13
148
+ jaxlib==0.4.13
149
+ jaxtyping==0.2.19
150
+ Jinja2==3.1.6
151
+ jiter==0.9.1
152
+ jmespath==0.10.0
153
+ joblib==1.4.2
154
+ jsonnet==0.17.0
155
+ jsonpatch==1.33
156
+ jsonpath-python==1.0.6
157
+ jsonpickle==2.0.0
158
+ jsonschema==4.23.0
159
+ jsonschema-specifications==2023.12.1
160
+ kaggle==1.7.4.5
161
+ Keras-Preprocessing==1.1.2
162
+ kubernetes==29.0.0
163
+ langchain==0.1.16
164
+ langchain-community==0.0.34
165
+ langchain-core==0.1.46
166
+ langchain-experimental==0.0.57
167
+ langchain-text-splitters==0.0.1
168
+ langcodes==3.4.0
169
+ langdetect==1.0.9
170
+ langsmith==0.1.51
171
+ language_data==1.2.0
172
+ layoutparser==0.3.4
173
+ lazy_loader==0.4
174
+ leidenalg==0.10.2
175
+ Levenshtein==0.25.1
176
+ linear-operator==0.4.0
177
+ litellm==1.77.4
178
+ litellm-enterprise==0.1.20
179
+ litellm-proxy-extras==0.2.19
180
+ llama-index==0.9.35
181
+ llvmlite==0.41.1
182
+ lmdb==1.7.3
183
+ lxml==5.2.1
184
+ madoka==0.7.1
185
+ marisa-trie==1.1.0
186
+ Markdown==3.3.6
187
+ markdown-it-py==3.0.0
188
+ markdown2==2.4.13
189
+ markdownify==0.11.6
190
+ MarkupSafe==2.1.5
191
+ marshmallow==3.21.1
192
+ mdtex2html==1.3.0
193
+ mdurl==0.1.2
194
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195
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196
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197
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198
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199
+ msal-extensions==1.3.0
200
+ msg-parser==1.2.0
201
+ msgpack==1.0.8
202
+ msgpack-numpy==0.4.3.2
203
+ multidict==6.0.5
204
+ multipledispatch==1.0.0
205
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206
+ murmurhash==1.0.10
207
+ mypy-extensions==1.0.0
208
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209
+ natsort==8.4.0
210
+ nest-asyncio==1.6.0
211
+ netCDF4==1.7.2
212
+ neuroHarmonize==2.4.5
213
+ nh3==0.2.17
214
+ ninja==1.11.1.1
215
+ nltk==3.8.1
216
+ numba==0.58.1
217
+ numexpr==2.8.6
218
+ numpoly==1.0.6
219
+ numpy==1.24.4
220
+ numpydoc==1.1.0
221
+ nvidia-ml-py==12.535.133
222
+ nvitop==1.3.2
223
+ oauthlib==3.2.2
224
+ onnx==1.16.0
225
+ onnxruntime==1.15.1
226
+ openai==1.101.0
227
+ openpyxl==3.0.9
228
+ opentelemetry-api==1.24.0
229
+ opentelemetry-exporter-otlp-proto-common==1.24.0
230
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
231
+ opentelemetry-proto==1.24.0
232
+ opentelemetry-sdk==1.24.0
233
+ opentelemetry-semantic-conventions==0.45b0
234
+ opt-einsum==3.3.0
235
+ optax==0.1.5
236
+ ordered-set==4.1.0
237
+ orjson==3.10.1
238
+ overrides==7.7.0
239
+ packaging==26.2
240
+ pandas==2.0.3
241
+ pandas-stubs==1.2.0.45
242
+ parsimonious==0.8.1
243
+ pathlib==1.0.1
244
+ patsy==1.0.1
245
+ pdf2image==1.17.0
246
+ pfzy==0.3.4
247
+ PICOS==2.6.1
248
+ pikepdf==8.4.1
249
+ pip-search==0.0.12
250
+ pkgutil_resolve_name==1.3.10
251
+ plac==0.9.6
252
+ plotly==6.3.0
253
+ pluggy==1.5.0
254
+ ply==3.11
255
+ pondpond==1.4.1
256
+ pooch==1.8.2
257
+ portalocker==2.4.0
258
+ posthog==3.5.0
259
+ preshed==3.0.9
260
+ prettytable==3.11.0
261
+ primer3-py==2.2.0
262
+ prompt-toolkit==3.0.43
263
+ propcache==0.2.0
264
+ PuLP==3.1.1
265
+ pulsar-client==3.5.0
266
+ pyarrow==17.0.0
267
+ pyarrow-hotfix==0.6
268
+ pyclipper==1.3.0.post5
269
+ pycocotools==2.0.7
270
+ pycparser==2.21
271
+ pydantic==2.10.6
272
+ pydantic_core==2.27.2
273
+ pydeck==0.9.0b1
274
+ pyDOE2==1.3.0
275
+ pydub==0.25.1
276
+ pyfaidx==0.9.0.1
277
+ Pygments==2.19.2
278
+ PyJWT==2.8.0
279
+ pymodbus==3.6.9
280
+ PyMuPDF==1.23.16
281
+ PyMuPDFb==1.23.9
282
+ PyNaCl==1.6.2
283
+ pynndescent==0.5.13
284
+ Pyomo==6.8.2
285
+ pyOpenSSL==24.1.0
286
+ pypandoc==1.13
287
+ pypdf==4.2.0
288
+ pypdfium2==4.29.0
289
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290
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291
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292
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293
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294
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295
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296
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297
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298
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299
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300
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301
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302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
+ rdkit==2024.3.5
320
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321
+ referencing==0.35.1
322
+ regex==2022.4.24
323
+ requests==2.32.4
324
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325
+ responses==0.16.0
326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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337
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338
+ scooby==0.10.1
339
+ seaborn==0.13.2
340
+ semantic-version==2.10.0
341
+ sentence-transformers==2.2.2
342
+ sentencepiece==0.1.91
343
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344
+ session_info==1.0.1
345
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346
+ shapely==2.0.4
347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
+ spacy-loggers==1.0.5
359
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360
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361
+ sphinxcontrib-devhelp==1.0.2
362
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363
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364
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365
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366
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367
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368
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369
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370
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371
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372
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373
+ streamlit-aggrid==0.3.4.post3
374
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375
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376
+ streamlit-feedback==0.1.3
377
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378
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379
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380
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381
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
382
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383
+ tenacity==8.2.3
384
+ tensorboard-plugin-wit==1.8.0
385
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386
+ text-unidecode==1.3
387
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388
+ thefuzz==0.22.1
389
+ threadpoolctl==3.5.0
390
+ tifffile==2023.7.10
391
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392
+ timm==0.9.16
393
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394
+ tokenizers==0.20.3
395
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396
+ tomlkit==0.12.0
397
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398
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399
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400
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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
+ unittest-xml-reporting==3.2.0
418
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419
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420
+ unstructured-inference==0.7.15
421
+ unstructured.pytesseract==0.3.12
422
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423
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424
+ validators==0.28.1
425
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426
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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439
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440
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441
+ youtube-search==2.1.2
442
+ zipp==3.20.2
443
+ zope.event==4.5.0
444
+ zstandard==0.23.0
configs/051_test/editable.txt ADDED
File without changes
configs/051_test/env.yml ADDED
@@ -0,0 +1,59 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: 051_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - bzip2=1.0.8
9
+ - ca-certificates=2025.8.3
10
+ - ld_impl_linux-64=2.44
11
+ - libffi=3.4.6
12
+ - libgcc=15.1.0
13
+ - libgcc-ng=15.1.0
14
+ - libgomp=15.1.0
15
+ - liblzma=5.8.1
16
+ - liblzma-devel=5.8.1
17
+ - libnsl=2.0.1
18
+ - libsqlite=3.50.4
19
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20
+ - libxcrypt=4.4.36
21
+ - libzlib=1.3.1
22
+ - ncurses=6.5
23
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24
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25
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26
+ - readline=8.2
27
+ - setuptools=70.3.0
28
+ - tk=8.6.13
29
+ - wheel=0.45.1
30
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31
+ - xz-gpl-tools=5.8.1
32
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33
+ - pip:
34
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35
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36
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37
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38
+ - markupsafe==2.1.5
39
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40
+ - networkx==3.1
41
+ - numpy==1.24.4
42
+ - nvidia-cublas-cu12==12.9.2.10
43
+ - nvidia-cuda-cupti-cu12==12.9.79
44
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45
+ - nvidia-cuda-runtime-cu12==12.9.79
46
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47
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48
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49
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50
+ - nvidia-nccl-cu12==2.20.5
51
+ - nvidia-nvjitlink-cu12==12.9.86
52
+ - nvidia-nvtx-cu12==12.9.79
53
+ - packaging==25.0
54
+ - six==1.17.0
55
+ - sympy==1.13.3
56
+ - torch==2.4.1
57
+ - triton==3.0.0
58
+ - typing-extensions==4.13.2
59
+ prefix: /home/lily/yz979/anaconda3/envs/051_test
configs/051_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
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8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
10
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
11
+ https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
12
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
13
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
14
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
15
+ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
16
+ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
17
+ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
18
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
19
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
20
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21
+ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
22
+ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
23
+ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
24
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25
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26
+ https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
27
+ https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
28
+ https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
29
+ https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
30
+ https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
31
+ https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
configs/051_test/meta.json ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "env": "051_test",
3
+ "python_version": "3.8.20",
4
+ "has_cuda_hint": false,
5
+ "editable_count": 0,
6
+ "source_prefix": "/home/lily/yz979/anaconda3/envs/051_test",
7
+ "exported_at": "2026-05-17T04:04:02Z"
8
+ }
configs/051_test/pip-clean.txt ADDED
@@ -0,0 +1,461 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
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4
+ aiohappyeyeballs==2.4.4
5
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6
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7
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8
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9
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10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
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16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
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19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
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22
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23
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24
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25
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26
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27
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28
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29
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30
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31
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32
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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57
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58
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59
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62
+ Cython==0.29.30
63
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64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
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68
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69
+ dill==0.3.8
70
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71
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73
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74
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75
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77
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80
+ email-validator==2.3.0
81
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82
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83
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84
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85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
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89
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90
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91
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92
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93
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94
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95
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96
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97
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98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
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101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
+ llvmlite==0.41.1
183
+ lmdb==1.7.3
184
+ loguru==0.7.3
185
+ lxml==5.2.1
186
+ madoka==0.7.1
187
+ marisa-trie==1.1.0
188
+ Markdown==3.3.6
189
+ markdown-it-py==3.0.0
190
+ markdown2==2.4.13
191
+ markdownify==0.11.6
192
+ MarkupSafe==2.1.5
193
+ marshmallow==3.21.1
194
+ mdtex2html==1.3.0
195
+ mdurl==0.1.2
196
+ metaphor-python==0.1.23
197
+ ml-dtypes==0.2.0
198
+ monotonic==1.6
199
+ mpmath==1.3.0
200
+ mrcfile==1.5.4
201
+ msal==1.36.0
202
+ msal-extensions==1.3.0
203
+ msg-parser==1.2.0
204
+ msgpack==1.0.8
205
+ msgpack-numpy==0.4.3.2
206
+ multidict==6.0.5
207
+ multipledispatch==1.0.0
208
+ multiprocess==0.70.16
209
+ murmurhash==1.0.10
210
+ mypy-extensions==1.0.0
211
+ narwhals==1.42.1
212
+ natsort==8.4.0
213
+ nest-asyncio==1.6.0
214
+ netCDF4==1.7.2
215
+ networkx==3.1
216
+ neuroHarmonize==2.4.5
217
+ nh3==0.2.17
218
+ ninja==1.11.1.1
219
+ nltk==3.8.1
220
+ numba==0.58.1
221
+ numexpr==2.8.6
222
+ numpoly==1.0.6
223
+ numpy==1.24.4
224
+ numpydoc==1.1.0
225
+ nvidia-cublas-cu12==12.9.2.10
226
+ nvidia-cuda-cupti-cu12==12.9.79
227
+ nvidia-cuda-nvrtc-cu12==12.9.86
228
+ nvidia-cuda-runtime-cu12==12.9.79
229
+ nvidia-cudnn-cu12==9.1.0.70
230
+ nvidia-cufft-cu12==11.4.1.4
231
+ nvidia-curand-cu12==10.3.10.19
232
+ nvidia-cusparse-cu12==12.5.10.65
233
+ nvidia-ml-py==12.535.133
234
+ nvidia-nccl-cu12==2.20.5
235
+ nvidia-nvjitlink-cu12==12.9.86
236
+ nvidia-nvtx-cu12==12.9.79
237
+ nvitop==1.3.2
238
+ oauthlib==3.2.2
239
+ onnx==1.16.0
240
+ onnxruntime==1.15.1
241
+ openai==1.101.0
242
+ openpyxl==3.0.9
243
+ opentelemetry-api==1.24.0
244
+ opentelemetry-exporter-otlp-proto-common==1.24.0
245
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
246
+ opentelemetry-proto==1.24.0
247
+ opentelemetry-sdk==1.24.0
248
+ opentelemetry-semantic-conventions==0.45b0
249
+ opt-einsum==3.3.0
250
+ optax==0.1.5
251
+ ordered-set==4.1.0
252
+ orjson==3.10.1
253
+ overrides==7.7.0
254
+ packaging==26.2
255
+ pandas==2.0.3
256
+ pandas-stubs==1.2.0.45
257
+ parsimonious==0.8.1
258
+ pathlib==1.0.1
259
+ patsy==1.0.1
260
+ pdf2image==1.17.0
261
+ pfzy==0.3.4
262
+ PICOS==2.6.1
263
+ pikepdf==8.4.1
264
+ pip-search==0.0.12
265
+ pkgutil_resolve_name==1.3.10
266
+ plac==0.9.6
267
+ plotly==6.3.0
268
+ pluggy==1.5.0
269
+ ply==3.11
270
+ pondpond==1.4.1
271
+ pooch==1.8.2
272
+ portalocker==2.4.0
273
+ posthog==3.5.0
274
+ preshed==3.0.9
275
+ prettytable==3.11.0
276
+ primer3-py==2.2.0
277
+ prompt-toolkit==3.0.43
278
+ propcache==0.2.0
279
+ PuLP==3.1.1
280
+ pulsar-client==3.5.0
281
+ pyarrow==17.0.0
282
+ pyarrow-hotfix==0.6
283
+ pyclipper==1.3.0.post5
284
+ pycocotools==2.0.7
285
+ pycparser==2.21
286
+ pydantic==2.10.6
287
+ pydantic_core==2.27.2
288
+ pydeck==0.9.0b1
289
+ pyDOE2==1.3.0
290
+ pydub==0.25.1
291
+ pyfaidx==0.9.0.1
292
+ Pygments==2.19.2
293
+ PyJWT==2.8.0
294
+ pymodbus==3.6.9
295
+ PyMuPDF==1.23.16
296
+ PyMuPDFb==1.23.9
297
+ PyNaCl==1.6.2
298
+ pynndescent==0.5.13
299
+ Pyomo==6.8.2
300
+ pyOpenSSL==24.1.0
301
+ pypandoc==1.13
302
+ pypdf==4.2.0
303
+ pypdfium2==4.29.0
304
+ PyPika==0.48.9
305
+ PyQt5==5.15.7
306
+ PyQt5-Qt5==5.15.17
307
+ PyQt5_sip==12.15.0
308
+ pyro-api==0.1.2
309
+ pyro-ppl==1.9.1
310
+ pysam==0.23.3
311
+ PySocks==1.7.1
312
+ pysqlite3-binary==0.5.2.post3
313
+ pystan==2.19.1.1
314
+ pytesseract==0.3.10
315
+ pytest-cov==5.0.0
316
+ python-dateutil==2.9.0.post0
317
+ python-decouple==3.8
318
+ python-docx==1.1.0
319
+ python-dotenv==1.0.1
320
+ python-iso639==2024.4.27
321
+ python-Levenshtein==0.25.1
322
+ python-multipart==0.0.18
323
+ python-pptx==0.6.23
324
+ python-slugify==8.0.4
325
+ pytorch-pretrained-bert==0.6.2
326
+ pytz==2025.2
327
+ pyvista==0.44.2
328
+ PyWavelets==1.4.1
329
+ PyYAML==6.0.3
330
+ quantile-python==1.1
331
+ rapidfuzz==3.8.1
332
+ rapidocr-onnxruntime==1.3.8
333
+ ray==2.10.0
334
+ rdkit==2024.3.5
335
+ redis==6.1.1
336
+ referencing==0.35.1
337
+ regex==2022.4.24
338
+ requests==2.32.4
339
+ requests-oauthlib==1.3.0
340
+ responses==0.16.0
341
+ rich==13.7.1
342
+ rouge-score==0.1.2
343
+ rpds-py==0.20.1
344
+ rq==2.3.3
345
+ rsa==4.7.2
346
+ ruff==0.4.2
347
+ rustworkx==0.15.1
348
+ s3transfer==0.11.3
349
+ sacrebleu==2.1.0
350
+ sacremoses==0.0.46
351
+ safetensors==0.4.3
352
+ scooby==0.10.1
353
+ seaborn==0.13.2
354
+ semantic-version==2.10.0
355
+ sentence-transformers==2.2.2
356
+ sentencepiece==0.1.91
357
+ sentry-sdk==2.39.0
358
+ session_info==1.0.1
359
+ sgmllib3k==1.0.0
360
+ shapely==2.0.4
361
+ shellingham==1.5.4
362
+ shortuuid==1.0.13
363
+ six==1.17.0
364
+ smart-open==6.4.0
365
+ smmap==5.0.1
366
+ sniffio==1.3.1
367
+ snowballstemmer==2.2.0
368
+ sobol-seq==0.2.0
369
+ socksio==1.0.0
370
+ soupsieve==2.5
371
+ spacy-legacy==3.0.12
372
+ spacy-loggers==1.0.5
373
+ Sphinx==4.3.1
374
+ sphinxcontrib-applehelp==1.0.2
375
+ sphinxcontrib-devhelp==1.0.2
376
+ sphinxcontrib-htmlhelp==2.0.0
377
+ sphinxcontrib-jsmath==1.0.1
378
+ sphinxcontrib-qthelp==1.0.3
379
+ sphinxcontrib-serializinghtml==1.1.5
380
+ SQLAlchemy==2.0.19
381
+ sqlparse==0.4.2
382
+ sse-starlette==1.8.2
383
+ starlette==0.44.0
384
+ statsmodels==0.14.1
385
+ stdlib-list==0.10.0
386
+ streamlit==1.30.0
387
+ streamlit-aggrid==0.3.4.post3
388
+ streamlit-antd-components==0.3.1
389
+ streamlit-chatbox==1.1.11
390
+ streamlit-feedback==0.1.3
391
+ streamlit-modal==0.1.0
392
+ streamlit-option-menu==0.3.12
393
+ strsimpy==0.2.1
394
+ svgwrite==1.4.3
395
+ sympy==1.13.3
396
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
397
+ tabulate==0.8.9
398
+ tenacity==8.2.3
399
+ tensorboard-plugin-wit==1.8.0
400
+ tensorboardX==2.4.1
401
+ text-unidecode==1.3
402
+ texttable==1.7.0
403
+ thefuzz==0.22.1
404
+ threadpoolctl==3.5.0
405
+ tifffile==2023.7.10
406
+ tiktoken==0.7.0
407
+ timm==0.9.16
408
+ tk==0.1.0
409
+ tokenizers==0.20.3
410
+ toml==0.10.2
411
+ tomlkit==0.12.0
412
+ toolz==0.12.1
413
+ torch==2.4.1
414
+ torch-geometric==2.6.1
415
+ torchaudio==2.1.2+cu118
416
+ torchtext==0.4.0
417
+ tornado==6.4
418
+ tqdm==4.67.1
419
+ transformer-lens==2.16.1
420
+ transformers==4.46.3
421
+ transformers-stream-generator==0.0.5
422
+ triton==3.0.0
423
+ typed-argument-parser==1.10.1
424
+ typeguard==4.4.0
425
+ typer==0.9.4
426
+ types-requests==2.31.0.20240406
427
+ typing-inspect==0.9.0
428
+ typing-utils==0.1.0
429
+ typing_extensions==4.13.2
430
+ tzdata==2024.1
431
+ tzlocal==5.2
432
+ umap-learn==0.5.7
433
+ Unidecode==1.3.2
434
+ unittest-xml-reporting==3.2.0
435
+ unstructured==0.11.0
436
+ unstructured-client==0.22.0
437
+ unstructured-inference==0.7.15
438
+ unstructured.pytesseract==0.3.12
439
+ uvicorn==0.29.0
440
+ uvloop==0.21.0
441
+ validators==0.28.1
442
+ vllm==0.2.7
443
+ vtk==9.3.1
444
+ wandb==0.22.0
445
+ watchdog==3.0.0
446
+ watchfiles==0.21.0
447
+ wavedrom==2.0.3.post3
448
+ weasel==0.3.4
449
+ websocket-client==1.8.0
450
+ websockets==13.1
451
+ Werkzeug==2.0.2
452
+ word2number==1.1
453
+ xlrd==2.0.1
454
+ XlsxWriter==3.0.2
455
+ xxhash==2.0.2
456
+ Yapsy==1.12.2
457
+ yarl==1.15.2
458
+ youtube-search==2.1.2
459
+ zipp==3.20.2
460
+ zope.event==4.5.0
461
+ zstandard==0.23.0
configs/051_test/pip-freeze.txt ADDED
@@ -0,0 +1,461 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filelock==3.16.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
+ google-pasta==0.2.0
116
+ googleapis-common-protos==1.63.0
117
+ gpustat==1.1.1
118
+ gpytorch==1.10
119
+ gradio_client==0.16.0
120
+ graphlib_backport==1.1.0
121
+ greenlet==1.1.2
122
+ gunicorn==23.0.0
123
+ h11==0.14.0
124
+ h2==4.1.0
125
+ hf-xet==1.2.0
126
+ hf_transfer==0.1.9
127
+ hpack==4.0.0
128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ igraph==0.11.8
137
+ imageio==2.35.1
138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
+ llvmlite==0.41.1
183
+ lmdb==1.7.3
184
+ loguru==0.7.3
185
+ lxml==5.2.1
186
+ madoka==0.7.1
187
+ marisa-trie==1.1.0
188
+ Markdown==3.3.6
189
+ markdown-it-py==3.0.0
190
+ markdown2==2.4.13
191
+ markdownify==0.11.6
192
+ MarkupSafe==2.1.5
193
+ marshmallow==3.21.1
194
+ mdtex2html==1.3.0
195
+ mdurl==0.1.2
196
+ metaphor-python==0.1.23
197
+ ml-dtypes==0.2.0
198
+ monotonic==1.6
199
+ mpmath==1.3.0
200
+ mrcfile==1.5.4
201
+ msal==1.36.0
202
+ msal-extensions==1.3.0
203
+ msg-parser==1.2.0
204
+ msgpack==1.0.8
205
+ msgpack-numpy==0.4.3.2
206
+ multidict==6.0.5
207
+ multipledispatch==1.0.0
208
+ multiprocess==0.70.16
209
+ murmurhash==1.0.10
210
+ mypy-extensions==1.0.0
211
+ narwhals==1.42.1
212
+ natsort==8.4.0
213
+ nest-asyncio==1.6.0
214
+ netCDF4==1.7.2
215
+ networkx==3.1
216
+ neuroHarmonize==2.4.5
217
+ nh3==0.2.17
218
+ ninja==1.11.1.1
219
+ nltk==3.8.1
220
+ numba==0.58.1
221
+ numexpr==2.8.6
222
+ numpoly==1.0.6
223
+ numpy==1.24.4
224
+ numpydoc==1.1.0
225
+ nvidia-cublas-cu12==12.9.2.10
226
+ nvidia-cuda-cupti-cu12==12.9.79
227
+ nvidia-cuda-nvrtc-cu12==12.9.86
228
+ nvidia-cuda-runtime-cu12==12.9.79
229
+ nvidia-cudnn-cu12==9.1.0.70
230
+ nvidia-cufft-cu12==11.4.1.4
231
+ nvidia-curand-cu12==10.3.10.19
232
+ nvidia-cusparse-cu12==12.5.10.65
233
+ nvidia-ml-py==12.535.133
234
+ nvidia-nccl-cu12==2.20.5
235
+ nvidia-nvjitlink-cu12==12.9.86
236
+ nvidia-nvtx-cu12==12.9.79
237
+ nvitop==1.3.2
238
+ oauthlib==3.2.2
239
+ onnx==1.16.0
240
+ onnxruntime==1.15.1
241
+ openai==1.101.0
242
+ openpyxl==3.0.9
243
+ opentelemetry-api==1.24.0
244
+ opentelemetry-exporter-otlp-proto-common==1.24.0
245
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
246
+ opentelemetry-proto==1.24.0
247
+ opentelemetry-sdk==1.24.0
248
+ opentelemetry-semantic-conventions==0.45b0
249
+ opt-einsum==3.3.0
250
+ optax==0.1.5
251
+ ordered-set==4.1.0
252
+ orjson==3.10.1
253
+ overrides==7.7.0
254
+ packaging==26.2
255
+ pandas==2.0.3
256
+ pandas-stubs==1.2.0.45
257
+ parsimonious==0.8.1
258
+ pathlib==1.0.1
259
+ patsy==1.0.1
260
+ pdf2image==1.17.0
261
+ pfzy==0.3.4
262
+ PICOS==2.6.1
263
+ pikepdf==8.4.1
264
+ pip-search==0.0.12
265
+ pkgutil_resolve_name==1.3.10
266
+ plac==0.9.6
267
+ plotly==6.3.0
268
+ pluggy==1.5.0
269
+ ply==3.11
270
+ pondpond==1.4.1
271
+ pooch==1.8.2
272
+ portalocker==2.4.0
273
+ posthog==3.5.0
274
+ preshed==3.0.9
275
+ prettytable==3.11.0
276
+ primer3-py==2.2.0
277
+ prompt-toolkit==3.0.43
278
+ propcache==0.2.0
279
+ PuLP==3.1.1
280
+ pulsar-client==3.5.0
281
+ pyarrow==17.0.0
282
+ pyarrow-hotfix==0.6
283
+ pyclipper==1.3.0.post5
284
+ pycocotools==2.0.7
285
+ pycparser==2.21
286
+ pydantic==2.10.6
287
+ pydantic_core==2.27.2
288
+ pydeck==0.9.0b1
289
+ pyDOE2==1.3.0
290
+ pydub==0.25.1
291
+ pyfaidx==0.9.0.1
292
+ Pygments==2.19.2
293
+ PyJWT==2.8.0
294
+ pymodbus==3.6.9
295
+ PyMuPDF==1.23.16
296
+ PyMuPDFb==1.23.9
297
+ PyNaCl==1.6.2
298
+ pynndescent==0.5.13
299
+ Pyomo==6.8.2
300
+ pyOpenSSL==24.1.0
301
+ pypandoc==1.13
302
+ pypdf==4.2.0
303
+ pypdfium2==4.29.0
304
+ PyPika==0.48.9
305
+ PyQt5==5.15.7
306
+ PyQt5-Qt5==5.15.17
307
+ PyQt5_sip==12.15.0
308
+ pyro-api==0.1.2
309
+ pyro-ppl==1.9.1
310
+ pysam==0.23.3
311
+ PySocks==1.7.1
312
+ pysqlite3-binary==0.5.2.post3
313
+ pystan==2.19.1.1
314
+ pytesseract==0.3.10
315
+ pytest-cov==5.0.0
316
+ python-dateutil==2.9.0.post0
317
+ python-decouple==3.8
318
+ python-docx==1.1.0
319
+ python-dotenv==1.0.1
320
+ python-iso639==2024.4.27
321
+ python-Levenshtein==0.25.1
322
+ python-multipart==0.0.18
323
+ python-pptx==0.6.23
324
+ python-slugify==8.0.4
325
+ pytorch-pretrained-bert==0.6.2
326
+ pytz==2025.2
327
+ pyvista==0.44.2
328
+ PyWavelets==1.4.1
329
+ PyYAML==6.0.3
330
+ quantile-python==1.1
331
+ rapidfuzz==3.8.1
332
+ rapidocr-onnxruntime==1.3.8
333
+ ray==2.10.0
334
+ rdkit==2024.3.5
335
+ redis==6.1.1
336
+ referencing==0.35.1
337
+ regex==2022.4.24
338
+ requests==2.32.4
339
+ requests-oauthlib==1.3.0
340
+ responses==0.16.0
341
+ rich==13.7.1
342
+ rouge-score==0.1.2
343
+ rpds-py==0.20.1
344
+ rq==2.3.3
345
+ rsa==4.7.2
346
+ ruff==0.4.2
347
+ rustworkx==0.15.1
348
+ s3transfer==0.11.3
349
+ sacrebleu==2.1.0
350
+ sacremoses==0.0.46
351
+ safetensors==0.4.3
352
+ scooby==0.10.1
353
+ seaborn==0.13.2
354
+ semantic-version==2.10.0
355
+ sentence-transformers==2.2.2
356
+ sentencepiece==0.1.91
357
+ sentry-sdk==2.39.0
358
+ session_info==1.0.1
359
+ sgmllib3k==1.0.0
360
+ shapely==2.0.4
361
+ shellingham==1.5.4
362
+ shortuuid==1.0.13
363
+ six==1.17.0
364
+ smart-open==6.4.0
365
+ smmap==5.0.1
366
+ sniffio==1.3.1
367
+ snowballstemmer==2.2.0
368
+ sobol-seq==0.2.0
369
+ socksio==1.0.0
370
+ soupsieve==2.5
371
+ spacy-legacy==3.0.12
372
+ spacy-loggers==1.0.5
373
+ Sphinx==4.3.1
374
+ sphinxcontrib-applehelp==1.0.2
375
+ sphinxcontrib-devhelp==1.0.2
376
+ sphinxcontrib-htmlhelp==2.0.0
377
+ sphinxcontrib-jsmath==1.0.1
378
+ sphinxcontrib-qthelp==1.0.3
379
+ sphinxcontrib-serializinghtml==1.1.5
380
+ SQLAlchemy==2.0.19
381
+ sqlparse==0.4.2
382
+ sse-starlette==1.8.2
383
+ starlette==0.44.0
384
+ statsmodels==0.14.1
385
+ stdlib-list==0.10.0
386
+ streamlit==1.30.0
387
+ streamlit-aggrid==0.3.4.post3
388
+ streamlit-antd-components==0.3.1
389
+ streamlit-chatbox==1.1.11
390
+ streamlit-feedback==0.1.3
391
+ streamlit-modal==0.1.0
392
+ streamlit-option-menu==0.3.12
393
+ strsimpy==0.2.1
394
+ svgwrite==1.4.3
395
+ sympy==1.13.3
396
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
397
+ tabulate==0.8.9
398
+ tenacity==8.2.3
399
+ tensorboard-plugin-wit==1.8.0
400
+ tensorboardX==2.4.1
401
+ text-unidecode==1.3
402
+ texttable==1.7.0
403
+ thefuzz==0.22.1
404
+ threadpoolctl==3.5.0
405
+ tifffile==2023.7.10
406
+ tiktoken==0.7.0
407
+ timm==0.9.16
408
+ tk==0.1.0
409
+ tokenizers==0.20.3
410
+ toml==0.10.2
411
+ tomlkit==0.12.0
412
+ toolz==0.12.1
413
+ torch==2.4.1
414
+ torch-geometric==2.6.1
415
+ torchaudio==2.1.2+cu118
416
+ torchtext==0.4.0
417
+ tornado==6.4
418
+ tqdm==4.67.1
419
+ transformer-lens==2.16.1
420
+ transformers==4.46.3
421
+ transformers-stream-generator==0.0.5
422
+ triton==3.0.0
423
+ typed-argument-parser==1.10.1
424
+ typeguard==4.4.0
425
+ typer==0.9.4
426
+ types-requests==2.31.0.20240406
427
+ typing-inspect==0.9.0
428
+ typing-utils==0.1.0
429
+ typing_extensions==4.13.2
430
+ tzdata==2024.1
431
+ tzlocal==5.2
432
+ umap-learn==0.5.7
433
+ Unidecode==1.3.2
434
+ unittest-xml-reporting==3.2.0
435
+ unstructured==0.11.0
436
+ unstructured-client==0.22.0
437
+ unstructured-inference==0.7.15
438
+ unstructured.pytesseract==0.3.12
439
+ uvicorn==0.29.0
440
+ uvloop==0.21.0
441
+ validators==0.28.1
442
+ vllm==0.2.7
443
+ vtk==9.3.1
444
+ wandb==0.22.0
445
+ watchdog==3.0.0
446
+ watchfiles==0.21.0
447
+ wavedrom==2.0.3.post3
448
+ weasel==0.3.4
449
+ websocket-client==1.8.0
450
+ websockets==13.1
451
+ Werkzeug==2.0.2
452
+ word2number==1.1
453
+ xlrd==2.0.1
454
+ XlsxWriter==3.0.2
455
+ xxhash==2.0.2
456
+ Yapsy==1.12.2
457
+ yarl==1.15.2
458
+ youtube-search==2.1.2
459
+ zipp==3.20.2
460
+ zope.event==4.5.0
461
+ zstandard==0.23.0
configs/s41467_024_45642_z_test/editable.txt ADDED
File without changes
configs/s41467_024_45642_z_test/explicit.txt ADDED
@@ -0,0 +1,80 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
9
+ https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
10
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
11
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
12
+ https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
13
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
14
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
15
+ https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
16
+ https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638
17
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
18
+ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
19
+ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
20
+ https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda#aea31d2e5b1091feca96fcfe945c3cf9
21
+ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
22
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
23
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
24
+ https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e
25
+ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb9d3cd8_0.conda#f6ebe2cb3f82ba6c057dde5d9debe4f7
26
+ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480
27
+ https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
28
+ https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835
29
+ https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b
30
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
31
+ https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.50-h421ea60_1.conda#7af8e91b0deb5f8e25d1a595dea79614
32
+ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
33
+ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_4.conda#2d34729cbc1da0ec988e57b13b712067
34
+ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
35
+ https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7
36
+ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
37
+ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
38
+ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
39
+ https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
40
+ https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
41
+ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
42
+ https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.1-h73754d4_0.conda#8e7251989bca326a28f4a5ffbd74557a
43
+ https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-15.1.0-h69a702a_5.conda#41a5893c957ffed7f82b4005bc24866c
44
+ https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.1-h8261f1e_0.conda#72b531694ebe4e8aa6f5745d1015c1b4
45
+ https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
46
+ https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471
47
+ https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda#f4084e4e6577797150f9b04a4560ceb0
48
+ https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.25-pthreads_h413a1c8_0.conda#d172b34a443b95f86089e8229ddc9a17
49
+ https://conda.anaconda.org/conda-forge/linux-64/openjpeg-2.5.4-h55fea9a_0.conda#11b3379b191f63139e29c0d19dee24cd
50
+ https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
51
+ https://conda.anaconda.org/conda-forge/noarch/certifi-2024.2.2-pyhd8ed1ab_0.conda#0876280e409658fc6f9e75d035960333
52
+ https://conda.anaconda.org/conda-forge/noarch/cycler-0.12.1-pyhd8ed1ab_0.conda#5cd86562580f274031ede6aa6aa24441
53
+ https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda#4afc585cd97ba8a23809406cd8a9eda8
54
+ https://repo.anaconda.com/pkgs/main/linux-64/kiwisolver-1.4.4-py38h6a678d5_0.conda#7424aa335d22974192800ec19a68486e
55
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376
+ streamlit-chatbox==1.1.11
377
+ streamlit-feedback==0.1.3
378
+ streamlit-modal==0.1.0
379
+ streamlit-option-menu==0.3.12
380
+ strsimpy==0.2.1
381
+ svgwrite==1.4.3
382
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
383
+ tabulate==0.8.9
384
+ tenacity==8.2.3
385
+ tensorboard-plugin-wit==1.8.0
386
+ tensorboardX==2.4.1
387
+ text-unidecode==1.3
388
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389
+ thefuzz==0.22.1
390
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391
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392
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393
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394
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395
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396
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397
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398
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399
+ torch-geometric==2.6.1
400
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401
+ torchtext==0.4.0
402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
+ unstructured==0.11.0
420
+ unstructured-client==0.22.0
421
+ unstructured-inference==0.7.15
422
+ unstructured.pytesseract==0.3.12
423
+ uvicorn==0.29.0
424
+ uvloop==0.21.0
425
+ validators==0.28.1
426
+ vllm==0.2.7
427
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428
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429
+ watchdog==3.0.0
430
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431
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432
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433
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434
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435
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436
+ word2number==1.1
437
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438
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439
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440
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441
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442
+ youtube-search==2.1.2
443
+ zipp==3.20.2
444
+ zope.event==4.5.0
445
+ zstandard==0.23.0
configs/s41467_024_45642_z_test/pip-freeze.txt ADDED
@@ -0,0 +1,454 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
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3
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4
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5
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6
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7
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8
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9
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10
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11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
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14
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15
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16
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17
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18
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19
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20
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21
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22
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23
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24
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25
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26
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27
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28
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29
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30
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31
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32
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33
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34
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35
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36
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37
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38
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39
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40
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41
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42
+ certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
+ confection==0.1.4
56
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57
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58
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59
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60
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61
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62
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63
+ cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
64
+ cymem==2.0.8
65
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66
+ dataclasses==0.6
67
+ dataclasses-json==0.6.4
68
+ datasets==2.19.0
69
+ deepdiff==7.0.1
70
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71
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72
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73
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74
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75
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76
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77
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78
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79
+ duckduckgo-search==3.9.9
80
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81
+ effdet==0.4.1
82
+ einops==0.7.0
83
+ email-validator==2.3.0
84
+ emoji==2.11.1
85
+ equinox==0.10.4
86
+ et-xmlfile==1.1.0
87
+ eval_type_backport==0.2.2
88
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89
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90
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91
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92
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93
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94
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95
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96
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97
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98
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99
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100
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101
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
+ huggingface_hub==0.36.1
135
+ humanfriendly==10.0
136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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149
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150
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151
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152
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153
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154
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155
+ jmespath==0.10.0
156
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157
+ jsonnet==0.17.0
158
+ jsonpatch==1.33
159
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160
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161
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162
+ jsonschema-specifications==2023.12.1
163
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164
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165
+ kiwisolver @ file:///croot/kiwisolver_1672387140495/work
166
+ kubernetes==29.0.0
167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
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211
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212
+ mypy-extensions==1.0.0
213
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214
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215
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216
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217
+ networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work
218
+ neuroHarmonize==2.4.5
219
+ nh3==0.2.17
220
+ ninja==1.11.1.1
221
+ nltk==3.8.1
222
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223
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224
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225
+ numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1687808301083/work
226
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227
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228
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229
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230
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231
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232
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233
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234
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235
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236
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237
+ opentelemetry-proto==1.24.0
238
+ opentelemetry-sdk==1.24.0
239
+ opentelemetry-semantic-conventions==0.45b0
240
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241
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242
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243
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244
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245
+ packaging==26.2
246
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247
+ pandas-stubs==1.2.0.45
248
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249
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250
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251
+ pdf2image==1.17.0
252
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253
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254
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255
+ pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
256
+ pip-search==0.0.12
257
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258
+ plac==0.9.6
259
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260
+ pluggy==1.5.0
261
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262
+ pondpond==1.4.1
263
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264
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265
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266
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267
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268
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269
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270
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271
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272
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273
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274
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275
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276
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277
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278
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279
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280
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281
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282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
+ pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
296
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297
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298
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299
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300
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301
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302
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303
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304
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305
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306
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307
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308
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309
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310
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311
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312
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313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
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343
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344
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
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360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
+ sphinxcontrib-devhelp==1.0.2
372
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373
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374
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375
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377
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378
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379
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380
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381
+ stdlib-list==0.10.0
382
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383
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384
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385
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386
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387
+ streamlit-modal==0.1.0
388
+ streamlit-option-menu==0.3.12
389
+ strsimpy==0.2.1
390
+ svgwrite==1.4.3
391
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
392
+ tabulate==0.8.9
393
+ tenacity==8.2.3
394
+ tensorboard-plugin-wit==1.8.0
395
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396
+ text-unidecode==1.3
397
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398
+ thefuzz==0.22.1
399
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400
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401
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402
+ timm==0.9.16
403
+ tk==0.1.0
404
+ tokenizers==0.20.3
405
+ toml==0.10.2
406
+ tomlkit==0.12.0
407
+ toolz==0.12.1
408
+ torch-geometric==2.6.1
409
+ torchaudio==2.1.2+cu118
410
+ torchtext==0.4.0
411
+ tornado==6.4
412
+ tqdm==4.67.1
413
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317
+ python-decouple==3.8
318
+ python-docx==1.1.0
319
+ python-dotenv==1.0.1
320
+ python-iso639==2024.4.27
321
+ python-Levenshtein==0.25.1
322
+ python-multipart==0.0.18
323
+ python-pptx==0.6.23
324
+ python-slugify==8.0.4
325
+ pytorch-pretrained-bert==0.6.2
326
+ pytz==2025.2
327
+ pyvista==0.44.2
328
+ PyWavelets==1.4.1
329
+ PyYAML==6.0.3
330
+ quantile-python==1.1
331
+ rapidfuzz==3.8.1
332
+ rapidocr-onnxruntime==1.3.8
333
+ ray==2.10.0
334
+ rdkit==2024.3.5
335
+ redis==6.1.1
336
+ referencing==0.35.1
337
+ regex==2022.4.24
338
+ requests==2.32.4
339
+ requests-oauthlib==1.3.0
340
+ responses==0.16.0
341
+ rich==13.7.1
342
+ rouge-score==0.1.2
343
+ rpds-py==0.20.1
344
+ rq==2.3.3
345
+ rsa==4.7.2
346
+ ruff==0.4.2
347
+ rustworkx==0.15.1
348
+ s3transfer==0.11.3
349
+ sacrebleu==2.1.0
350
+ sacremoses==0.0.46
351
+ safetensors==0.4.3
352
+ -e git+https://github.com/m-gallegos/SchNet4AIM.git@9e6be59a313099d4af6c013a55734ff72df76d7a#egg=SchNet4AIM
353
+ scipy==1.10.1
354
+ scooby==0.10.1
355
+ seaborn==0.13.2
356
+ semantic-version==2.10.0
357
+ sentence-transformers==2.2.2
358
+ sentencepiece==0.1.91
359
+ sentry-sdk==2.39.0
360
+ session_info==1.0.1
361
+ sgmllib3k==1.0.0
362
+ shapely==2.0.4
363
+ shellingham==1.5.4
364
+ shortuuid==1.0.13
365
+ six==1.17.0
366
+ smart-open==6.4.0
367
+ smmap==5.0.1
368
+ sniffio==1.3.1
369
+ snowballstemmer==2.2.0
370
+ sobol-seq==0.2.0
371
+ socksio==1.0.0
372
+ soupsieve==2.5
373
+ spacy-legacy==3.0.12
374
+ spacy-loggers==1.0.5
375
+ Sphinx==4.3.1
376
+ sphinxcontrib-applehelp==1.0.2
377
+ sphinxcontrib-devhelp==1.0.2
378
+ sphinxcontrib-htmlhelp==2.0.0
379
+ sphinxcontrib-jsmath==1.0.1
380
+ sphinxcontrib-qthelp==1.0.3
381
+ sphinxcontrib-serializinghtml==1.1.5
382
+ SQLAlchemy==2.0.19
383
+ sqlparse==0.4.2
384
+ sse-starlette==1.8.2
385
+ starlette==0.44.0
386
+ statsmodels==0.14.1
387
+ stdlib-list==0.10.0
388
+ streamlit==1.30.0
389
+ streamlit-aggrid==0.3.4.post3
390
+ streamlit-antd-components==0.3.1
391
+ streamlit-chatbox==1.1.11
392
+ streamlit-feedback==0.1.3
393
+ streamlit-modal==0.1.0
394
+ streamlit-option-menu==0.3.12
395
+ strsimpy==0.2.1
396
+ svgwrite==1.4.3
397
+ sympy==1.13.3
398
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
399
+ tabulate==0.8.9
400
+ tenacity==8.2.3
401
+ tensorboard-plugin-wit==1.8.0
402
+ tensorboardX==2.4.1
403
+ text-unidecode==1.3
404
+ texttable==1.7.0
405
+ thefuzz==0.22.1
406
+ threadpoolctl==3.5.0
407
+ tifffile==2023.7.10
408
+ tiktoken==0.7.0
409
+ timm==0.9.16
410
+ tk==0.1.0
411
+ tokenizers==0.20.3
412
+ toml==0.10.2
413
+ tomlkit==0.12.0
414
+ toolz==0.12.1
415
+ torch==1.13.1
416
+ torch-geometric==2.6.1
417
+ torchaudio==2.1.2+cu118
418
+ torchtext==0.4.0
419
+ torchvision==0.14.1
420
+ tornado==6.4
421
+ tqdm==4.67.1
422
+ transformer-lens==2.16.1
423
+ transformers==4.46.3
424
+ transformers-stream-generator==0.0.5
425
+ typed-argument-parser==1.10.1
426
+ typeguard==4.4.0
427
+ typer==0.9.4
428
+ types-requests==2.31.0.20240406
429
+ typing-inspect==0.9.0
430
+ typing-utils==0.1.0
431
+ typing_extensions==4.13.2
432
+ tzdata==2024.1
433
+ tzlocal==5.2
434
+ umap-learn==0.5.7
435
+ Unidecode==1.3.2
436
+ unittest-xml-reporting==3.2.0
437
+ unstructured==0.11.0
438
+ unstructured-client==0.22.0
439
+ unstructured-inference==0.7.15
440
+ unstructured.pytesseract==0.3.12
441
+ urllib3==2.2.3
442
+ uvicorn==0.29.0
443
+ uvloop==0.21.0
444
+ validators==0.28.1
445
+ vllm==0.2.7
446
+ vtk==9.3.1
447
+ wandb==0.22.0
448
+ watchdog==3.0.0
449
+ watchfiles==0.21.0
450
+ wavedrom==2.0.3.post3
451
+ weasel==0.3.4
452
+ websocket-client==1.8.0
453
+ websockets==13.1
454
+ Werkzeug==2.0.2
455
+ word2number==1.1
456
+ xlrd==2.0.1
457
+ XlsxWriter==3.0.2
458
+ xxhash==2.0.2
459
+ Yapsy==1.12.2
460
+ yarl==1.15.2
461
+ youtube-search==2.1.2
462
+ zipp==3.20.2
463
+ zope.event==4.5.0
464
+ zstandard==0.23.0
configs/s41467_024_48567_9_test/pip-freeze.txt ADDED
@@ -0,0 +1,464 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ ase==3.22.1
16
+ astunparse==1.6.3
17
+ async-timeout==4.0.3
18
+ attrs==25.3.0
19
+ autograd==1.7.0
20
+ autoray==0.6.12
21
+ awscli==1.32.93
22
+ azure-core==1.33.0
23
+ azure-identity==1.21.0
24
+ azure-storage-blob==12.26.0
25
+ Babel==2.9.1
26
+ backoff==2.2.1
27
+ backports.zoneinfo==0.2.1
28
+ bcrypt==4.1.2
29
+ beartype==0.14.1
30
+ better-abc==0.0.3
31
+ biopython==1.83
32
+ bitarray==2.5.1
33
+ bitsandbytes==0.43.1
34
+ blessed==1.20.0
35
+ blis==0.7.11
36
+ boto3==1.36.0
37
+ botocore==1.36.26
38
+ botorch==0.8.5
39
+ bpl==0.1.1
40
+ Brotli==1.1.0
41
+ bs4==0.0.2
42
+ cachetools==4.2.4
43
+ certifi==2026.2.25
44
+ cffi==1.15.0
45
+ cftime==1.6.4.post1
46
+ chaospy==3.3.9
47
+ charset-normalizer==3.4.7
48
+ chex==0.1.7
49
+ chroma-hnswlib==0.7.3
50
+ chromadb==0.4.15
51
+ click==8.1.7
52
+ cloudpathlib==0.16.0
53
+ cobra==0.29.1
54
+ cohere==5.3.3
55
+ coloredlogs==15.0.1
56
+ confection==0.1.4
57
+ ConfigArgParse==1.5.3
58
+ conllu==0.11
59
+ coverage==7.6.1
60
+ cpm-kernels==1.0.11
61
+ cryptography==42.0.5
62
+ cvxopt==1.3.2
63
+ cymem==2.0.8
64
+ Cython==0.29.30
65
+ dataclasses==0.6
66
+ dataclasses-json==0.6.4
67
+ datasets==2.19.0
68
+ deepdiff==7.0.1
69
+ Deprecated==1.2.14
70
+ deprecation==2.1.0
71
+ dill==0.3.8
72
+ distro==1.9.0
73
+ dm-tree==0.1.8
74
+ dnspython==2.6.1
75
+ docstring_parser==0.17.0
76
+ docutils==0.15.2
77
+ dotenv==0.9.9
78
+ duckduckgo-search==3.9.9
79
+ editdistance==0.6.0
80
+ effdet==0.4.1
81
+ einops==0.7.0
82
+ email-validator==2.3.0
83
+ emoji==2.11.1
84
+ equinox==0.10.4
85
+ et-xmlfile==1.1.0
86
+ eval_type_backport==0.2.2
87
+ exceptiongroup==1.2.1
88
+ fairseq==0.10.2
89
+ faiss-cpu==1.7.4
90
+ faiss-gpu==1.7.2
91
+ fancy-einsum==0.0.3
92
+ fastapi==0.115.14
93
+ fastapi-sso==0.16.0
94
+ fastavro==1.9.4
95
+ fastuuid==0.13.5
96
+ fbpca==1.0
97
+ feedparser==6.0.10
98
+ ffmpy==0.3.2
99
+ filelock==3.13.1
100
+ filetype==1.2.0
101
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
102
+ flaky==3.7.0
103
+ Flask-Cors==3.0.10
104
+ fonttools==4.38.0
105
+ frozenlist==1.4.1
106
+ fschat==0.2.35
107
+ fsspec==2025.3.0
108
+ ftfy==6.0.3
109
+ future==0.18.2
110
+ fuzzywuzzy==0.18.0
111
+ gdown==5.2.0
112
+ geosketch==1.3
113
+ geotorch==0.3.0
114
+ get-annotations==0.1.2
115
+ gevent==21.12.0
116
+ gitdb==4.0.11
117
+ GitPython==3.1.43
118
+ google-pasta==0.2.0
119
+ googleapis-common-protos==1.63.0
120
+ gpustat==1.1.1
121
+ gpytorch==1.10
122
+ gradio_client==0.16.0
123
+ graphlib_backport==1.1.0
124
+ greenlet==1.1.2
125
+ gunicorn==23.0.0
126
+ h11==0.14.0
127
+ h2==4.1.0
128
+ hf-xet==1.2.0
129
+ hf_transfer==0.1.9
130
+ hpack==4.0.0
131
+ httpcore==1.0.5
132
+ httptools==0.6.1
133
+ httpx==0.28.1
134
+ httpx-sse==0.4.0
135
+ huggingface_hub==0.36.1
136
+ humanfriendly==10.0
137
+ hyperframe==6.0.1
138
+ icetk==0.0.4
139
+ idna==3.11
140
+ igraph==0.11.8
141
+ imageio==2.35.1
142
+ imagesize==1.3.0
143
+ imgaug==0.4.0
144
+ importlib-metadata==7.0.0
145
+ importlib_resources==6.4.5
146
+ inequalipy==1.0.5
147
+ iniconfig==1.1.1
148
+ inquirerpy==0.3.4
149
+ iopath==0.1.10
150
+ isodate==0.7.2
151
+ itsdangerous==2.0.1
152
+ jax==0.4.13
153
+ jaxlib==0.4.13
154
+ jaxtyping==0.2.19
155
+ Jinja2==3.1.6
156
+ jiter==0.9.1
157
+ jmespath==0.10.0
158
+ joblib==1.4.2
159
+ jsonnet==0.17.0
160
+ jsonpatch==1.33
161
+ jsonpath-python==1.0.6
162
+ jsonpickle==2.0.0
163
+ jsonschema==4.23.0
164
+ jsonschema-specifications==2023.12.1
165
+ kaggle==1.7.4.5
166
+ Keras-Preprocessing==1.1.2
167
+ kiwisolver==1.4.4
168
+ kubernetes==29.0.0
169
+ langchain==0.1.16
170
+ langchain-community==0.0.34
171
+ langchain-core==0.1.46
172
+ langchain-experimental==0.0.57
173
+ langchain-text-splitters==0.0.1
174
+ langcodes==3.4.0
175
+ langdetect==1.0.9
176
+ langsmith==0.1.51
177
+ language_data==1.2.0
178
+ layoutparser==0.3.4
179
+ lazy_loader==0.4
180
+ leidenalg==0.10.2
181
+ Levenshtein==0.25.1
182
+ linear-operator==0.4.0
183
+ litellm==1.77.4
184
+ litellm-enterprise==0.1.20
185
+ litellm-proxy-extras==0.2.19
186
+ llama-index==0.9.35
187
+ llvmlite==0.41.1
188
+ lmdb==1.7.3
189
+ lxml==5.2.1
190
+ madoka==0.7.1
191
+ marisa-trie==1.1.0
192
+ Markdown==3.3.6
193
+ markdown-it-py==3.0.0
194
+ markdown2==2.4.13
195
+ markdownify==0.11.6
196
+ MarkupSafe==2.1.5
197
+ marshmallow==3.21.1
198
+ mdtex2html==1.3.0
199
+ mdurl==0.1.2
200
+ metaphor-python==0.1.23
201
+ ml-dtypes==0.2.0
202
+ monotonic==1.6
203
+ mpmath==1.3.0
204
+ mrcfile==1.5.4
205
+ msal==1.36.0
206
+ msal-extensions==1.3.0
207
+ msg-parser==1.2.0
208
+ msgpack==1.0.8
209
+ msgpack-numpy==0.4.3.2
210
+ multidict==6.0.5
211
+ multipledispatch==1.0.0
212
+ multiprocess==0.70.16
213
+ murmurhash==1.0.10
214
+ mypy-extensions==1.0.0
215
+ narwhals==1.42.1
216
+ natsort==8.4.0
217
+ nest-asyncio==1.6.0
218
+ netCDF4==1.7.2
219
+ networkx==3.0
220
+ neuroHarmonize==2.4.5
221
+ nh3==0.2.17
222
+ ninja==1.11.1.1
223
+ nltk==3.8.1
224
+ numba==0.58.1
225
+ numexpr==2.8.6
226
+ numpoly==1.0.6
227
+ numpy==1.23.5
228
+ numpydoc==1.1.0
229
+ nvidia-cublas-cu11==11.10.3.66
230
+ nvidia-cuda-nvrtc-cu11==11.7.99
231
+ nvidia-cuda-runtime-cu11==11.7.99
232
+ nvidia-cudnn-cu11==8.5.0.96
233
+ nvidia-ml-py==12.535.133
234
+ nvitop==1.3.2
235
+ oauthlib==3.2.2
236
+ onnx==1.16.0
237
+ onnxruntime==1.15.1
238
+ openai==1.101.0
239
+ openpyxl==3.0.9
240
+ opentelemetry-api==1.24.0
241
+ opentelemetry-exporter-otlp-proto-common==1.24.0
242
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
243
+ opentelemetry-proto==1.24.0
244
+ opentelemetry-sdk==1.24.0
245
+ opentelemetry-semantic-conventions==0.45b0
246
+ opt-einsum==3.3.0
247
+ optax==0.1.5
248
+ ordered-set==4.1.0
249
+ orjson==3.10.1
250
+ overrides==7.7.0
251
+ packaging==26.2
252
+ pandas==2.0.3
253
+ pandas-stubs==1.2.0.45
254
+ parsimonious==0.8.1
255
+ pathlib==1.0.1
256
+ patsy==1.0.1
257
+ pdf2image==1.17.0
258
+ pfzy==0.3.4
259
+ PICOS==2.6.1
260
+ pikepdf==8.4.1
261
+ pillow==10.4.0
262
+ pip-search==0.0.12
263
+ pkgutil_resolve_name==1.3.10
264
+ plac==0.9.6
265
+ plotly==6.3.0
266
+ pluggy==1.5.0
267
+ ply==3.11
268
+ pondpond==1.4.1
269
+ pooch==1.8.2
270
+ portalocker==2.4.0
271
+ posthog==3.5.0
272
+ preshed==3.0.9
273
+ prettytable==3.11.0
274
+ primer3-py==2.2.0
275
+ prompt-toolkit==3.0.43
276
+ propcache==0.2.0
277
+ psutil==5.9.7
278
+ PuLP==3.1.1
279
+ pulsar-client==3.5.0
280
+ pyarrow==17.0.0
281
+ pyarrow-hotfix==0.6
282
+ pyclipper==1.3.0.post5
283
+ pycocotools==2.0.7
284
+ pycparser==2.21
285
+ pydantic==2.10.6
286
+ pydantic_core==2.27.2
287
+ pydeck==0.9.0b1
288
+ pyDOE2==1.3.0
289
+ pydub==0.25.1
290
+ pyfaidx==0.9.0.1
291
+ Pygments==2.19.2
292
+ PyJWT==2.8.0
293
+ pymodbus==3.6.9
294
+ PyMuPDF==1.23.16
295
+ PyMuPDFb==1.23.9
296
+ PyNaCl==1.6.2
297
+ pynndescent==0.5.13
298
+ Pyomo==6.8.2
299
+ pyOpenSSL==24.1.0
300
+ pypandoc==1.13
301
+ pyparsing==3.1.0
302
+ pypdf==4.2.0
303
+ pypdfium2==4.29.0
304
+ PyPika==0.48.9
305
+ PyQt5==5.15.7
306
+ PyQt5-Qt5==5.15.17
307
+ PyQt5_sip==12.15.0
308
+ pyro-api==0.1.2
309
+ pyro-ppl==1.9.1
310
+ pysam==0.23.3
311
+ PySocks==1.7.1
312
+ pysqlite3-binary==0.5.2.post3
313
+ pystan==2.19.1.1
314
+ pytesseract==0.3.10
315
+ pytest-cov==5.0.0
316
+ python-dateutil==2.9.0.post0
317
+ python-decouple==3.8
318
+ python-docx==1.1.0
319
+ python-dotenv==1.0.1
320
+ python-iso639==2024.4.27
321
+ python-Levenshtein==0.25.1
322
+ python-multipart==0.0.18
323
+ python-pptx==0.6.23
324
+ python-slugify==8.0.4
325
+ pytorch-pretrained-bert==0.6.2
326
+ pytz==2025.2
327
+ pyvista==0.44.2
328
+ PyWavelets==1.4.1
329
+ PyYAML==6.0.3
330
+ quantile-python==1.1
331
+ rapidfuzz==3.8.1
332
+ rapidocr-onnxruntime==1.3.8
333
+ ray==2.10.0
334
+ rdkit==2024.3.5
335
+ redis==6.1.1
336
+ referencing==0.35.1
337
+ regex==2022.4.24
338
+ requests==2.32.4
339
+ requests-oauthlib==1.3.0
340
+ responses==0.16.0
341
+ rich==13.7.1
342
+ rouge-score==0.1.2
343
+ rpds-py==0.20.1
344
+ rq==2.3.3
345
+ rsa==4.7.2
346
+ ruff==0.4.2
347
+ rustworkx==0.15.1
348
+ s3transfer==0.11.3
349
+ sacrebleu==2.1.0
350
+ sacremoses==0.0.46
351
+ safetensors==0.4.3
352
+ -e git+https://github.com/m-gallegos/SchNet4AIM.git@9e6be59a313099d4af6c013a55734ff72df76d7a#egg=SchNet4AIM
353
+ scipy==1.10.1
354
+ scooby==0.10.1
355
+ seaborn==0.13.2
356
+ semantic-version==2.10.0
357
+ sentence-transformers==2.2.2
358
+ sentencepiece==0.1.91
359
+ sentry-sdk==2.39.0
360
+ session_info==1.0.1
361
+ sgmllib3k==1.0.0
362
+ shapely==2.0.4
363
+ shellingham==1.5.4
364
+ shortuuid==1.0.13
365
+ six==1.17.0
366
+ smart-open==6.4.0
367
+ smmap==5.0.1
368
+ sniffio==1.3.1
369
+ snowballstemmer==2.2.0
370
+ sobol-seq==0.2.0
371
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372
+ soupsieve==2.5
373
+ spacy-legacy==3.0.12
374
+ spacy-loggers==1.0.5
375
+ Sphinx==4.3.1
376
+ sphinxcontrib-applehelp==1.0.2
377
+ sphinxcontrib-devhelp==1.0.2
378
+ sphinxcontrib-htmlhelp==2.0.0
379
+ sphinxcontrib-jsmath==1.0.1
380
+ sphinxcontrib-qthelp==1.0.3
381
+ sphinxcontrib-serializinghtml==1.1.5
382
+ SQLAlchemy==2.0.19
383
+ sqlparse==0.4.2
384
+ sse-starlette==1.8.2
385
+ starlette==0.44.0
386
+ statsmodels==0.14.1
387
+ stdlib-list==0.10.0
388
+ streamlit==1.30.0
389
+ streamlit-aggrid==0.3.4.post3
390
+ streamlit-antd-components==0.3.1
391
+ streamlit-chatbox==1.1.11
392
+ streamlit-feedback==0.1.3
393
+ streamlit-modal==0.1.0
394
+ streamlit-option-menu==0.3.12
395
+ strsimpy==0.2.1
396
+ svgwrite==1.4.3
397
+ sympy==1.13.3
398
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
399
+ tabulate==0.8.9
400
+ tenacity==8.2.3
401
+ tensorboard-plugin-wit==1.8.0
402
+ tensorboardX==2.4.1
403
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404
+ texttable==1.7.0
405
+ thefuzz==0.22.1
406
+ threadpoolctl==3.5.0
407
+ tifffile==2023.7.10
408
+ tiktoken==0.7.0
409
+ timm==0.9.16
410
+ tk==0.1.0
411
+ tokenizers==0.20.3
412
+ toml==0.10.2
413
+ tomlkit==0.12.0
414
+ toolz==0.12.1
415
+ torch==1.13.1
416
+ torch-geometric==2.6.1
417
+ torchaudio==2.1.2+cu118
418
+ torchtext==0.4.0
419
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420
+ tornado==6.4
421
+ tqdm==4.67.1
422
+ transformer-lens==2.16.1
423
+ transformers==4.46.3
424
+ transformers-stream-generator==0.0.5
425
+ typed-argument-parser==1.10.1
426
+ typeguard==4.4.0
427
+ typer==0.9.4
428
+ types-requests==2.31.0.20240406
429
+ typing-inspect==0.9.0
430
+ typing-utils==0.1.0
431
+ typing_extensions==4.13.2
432
+ tzdata==2024.1
433
+ tzlocal==5.2
434
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435
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436
+ unittest-xml-reporting==3.2.0
437
+ unstructured==0.11.0
438
+ unstructured-client==0.22.0
439
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440
+ unstructured.pytesseract==0.3.12
441
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442
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443
+ uvloop==0.21.0
444
+ validators==0.28.1
445
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446
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447
+ wandb==0.22.0
448
+ watchdog==3.0.0
449
+ watchfiles==0.21.0
450
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451
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452
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453
+ websockets==13.1
454
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455
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456
+ xlrd==2.0.1
457
+ XlsxWriter==3.0.2
458
+ xxhash==2.0.2
459
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460
+ yarl==1.15.2
461
+ youtube-search==2.1.2
462
+ zipp==3.20.2
463
+ zope.event==4.5.0
464
+ zstandard==0.23.0
configs/s41467_024_50317_w_test/env.yml ADDED
@@ -0,0 +1,49 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: s41467_024_50317_w_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - bzip2=1.0.8
9
+ - ca-certificates=2025.8.3
10
+ - ld_impl_linux-64=2.44
11
+ - libffi=3.4.6
12
+ - libgcc=15.1.0
13
+ - libgcc-ng=15.1.0
14
+ - libgomp=15.1.0
15
+ - liblzma=5.8.1
16
+ - liblzma-devel=5.8.1
17
+ - libnsl=2.0.1
18
+ - libsqlite=3.50.4
19
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20
+ - libxcrypt=4.4.36
21
+ - libzlib=1.3.1
22
+ - ncurses=6.5
23
+ - openssl=3.5.2
24
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25
+ - python=3.8.20
26
+ - readline=8.2
27
+ - setuptools=70.3.0
28
+ - tk=8.6.13
29
+ - wheel=0.45.1
30
+ - xz=5.8.1
31
+ - xz-gpl-tools=5.8.1
32
+ - xz-tools=5.8.1
33
+ - pip:
34
+ - filelock==3.13.1
35
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36
+ - jinja2==3.1.6
37
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38
+ - mpmath==1.3.0
39
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40
+ - numpy==1.24.4
41
+ - packaging==25.0
42
+ - python-dateutil==2.9.0.post0
43
+ - scipy==1.10.1
44
+ - six==1.17.0
45
+ - sympy==1.13.3
46
+ - torch==2.4.1+cpu
47
+ - torchvision==0.19.1+cpu
48
+ - typing-extensions==4.12.2
49
+ prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50317_w_test
configs/s41467_024_50317_w_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
10
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
11
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
12
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
13
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
14
+ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
15
+ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
16
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
17
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
18
+ https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
19
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
20
+ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
21
+ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
22
+ https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
23
+ https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
24
+ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
25
+ https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
26
+ https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
27
+ https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
28
+ https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
29
+ https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
30
+ https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
31
+ https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96
configs/s41467_024_50317_w_test/meta.json ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "env": "s41467_024_50317_w_test",
3
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4
+ "has_cuda_hint": false,
5
+ "editable_count": 0,
6
+ "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_50317_w_test",
7
+ "exported_at": "2026-05-17T04:05:29Z"
8
+ }
configs/s41467_024_50317_w_test/pip-clean.txt ADDED
@@ -0,0 +1,450 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
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6
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7
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8
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9
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10
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11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
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23
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24
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25
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26
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27
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28
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29
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30
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31
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32
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33
+ blessed==1.20.0
34
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35
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36
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37
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38
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39
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40
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41
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42
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43
+ cftime==1.6.4.post1
44
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45
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46
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47
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48
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49
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50
+ cloudpathlib==0.16.0
51
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52
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53
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54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
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57
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58
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59
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60
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61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
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71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
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75
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76
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77
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78
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79
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80
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81
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82
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83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
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92
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93
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94
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95
+ feedparser==6.0.10
96
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97
+ filelock==3.13.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
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104
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105
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106
+ future==0.18.2
107
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108
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109
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110
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111
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112
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113
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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183
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184
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185
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186
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187
+ Markdown==3.3.6
188
+ markdown-it-py==3.0.0
189
+ markdown2==2.4.13
190
+ markdownify==0.11.6
191
+ MarkupSafe==2.1.5
192
+ marshmallow==3.21.1
193
+ mdtex2html==1.3.0
194
+ mdurl==0.1.2
195
+ metaphor-python==0.1.23
196
+ ml-dtypes==0.2.0
197
+ monotonic==1.6
198
+ mpmath==1.3.0
199
+ mrcfile==1.5.4
200
+ msal==1.36.0
201
+ msal-extensions==1.3.0
202
+ msg-parser==1.2.0
203
+ msgpack==1.0.8
204
+ msgpack-numpy==0.4.3.2
205
+ multidict==6.0.5
206
+ multipledispatch==1.0.0
207
+ multiprocess==0.70.16
208
+ murmurhash==1.0.10
209
+ mypy-extensions==1.0.0
210
+ narwhals==1.42.1
211
+ natsort==8.4.0
212
+ nest-asyncio==1.6.0
213
+ netCDF4==1.7.2
214
+ networkx==3.0
215
+ neuroHarmonize==2.4.5
216
+ nh3==0.2.17
217
+ ninja==1.11.1.1
218
+ nltk==3.8.1
219
+ numba==0.58.1
220
+ numexpr==2.8.6
221
+ numpoly==1.0.6
222
+ numpy==1.24.4
223
+ numpydoc==1.1.0
224
+ nvidia-ml-py==12.535.133
225
+ nvitop==1.3.2
226
+ oauthlib==3.2.2
227
+ onnx==1.16.0
228
+ onnxruntime==1.15.1
229
+ openai==1.101.0
230
+ openpyxl==3.0.9
231
+ opentelemetry-api==1.24.0
232
+ opentelemetry-exporter-otlp-proto-common==1.24.0
233
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
234
+ opentelemetry-proto==1.24.0
235
+ opentelemetry-sdk==1.24.0
236
+ opentelemetry-semantic-conventions==0.45b0
237
+ opt-einsum==3.3.0
238
+ optax==0.1.5
239
+ ordered-set==4.1.0
240
+ orjson==3.10.1
241
+ overrides==7.7.0
242
+ packaging==26.2
243
+ pandas==2.0.3
244
+ pandas-stubs==1.2.0.45
245
+ parsimonious==0.8.1
246
+ pathlib==1.0.1
247
+ patsy==1.0.1
248
+ pdf2image==1.17.0
249
+ pfzy==0.3.4
250
+ PICOS==2.6.1
251
+ pikepdf==8.4.1
252
+ pip-search==0.0.12
253
+ pkgutil_resolve_name==1.3.10
254
+ plac==0.9.6
255
+ plotly==6.3.0
256
+ pluggy==1.5.0
257
+ ply==3.11
258
+ pondpond==1.4.1
259
+ pooch==1.8.2
260
+ portalocker==2.4.0
261
+ posthog==3.5.0
262
+ preshed==3.0.9
263
+ prettytable==3.11.0
264
+ primer3-py==2.2.0
265
+ prompt-toolkit==3.0.43
266
+ propcache==0.2.0
267
+ PuLP==3.1.1
268
+ pulsar-client==3.5.0
269
+ pyarrow==17.0.0
270
+ pyarrow-hotfix==0.6
271
+ pyclipper==1.3.0.post5
272
+ pycocotools==2.0.7
273
+ pycparser==2.21
274
+ pydantic==2.10.6
275
+ pydantic_core==2.27.2
276
+ pydeck==0.9.0b1
277
+ pyDOE2==1.3.0
278
+ pydub==0.25.1
279
+ pyfaidx==0.9.0.1
280
+ Pygments==2.19.2
281
+ PyJWT==2.8.0
282
+ pymodbus==3.6.9
283
+ PyMuPDF==1.23.16
284
+ PyMuPDFb==1.23.9
285
+ PyNaCl==1.6.2
286
+ pynndescent==0.5.13
287
+ Pyomo==6.8.2
288
+ pyOpenSSL==24.1.0
289
+ pypandoc==1.13
290
+ pypdf==4.2.0
291
+ pypdfium2==4.29.0
292
+ PyPika==0.48.9
293
+ PyQt5==5.15.7
294
+ PyQt5-Qt5==5.15.17
295
+ PyQt5_sip==12.15.0
296
+ pyro-api==0.1.2
297
+ pyro-ppl==1.9.1
298
+ pysam==0.23.3
299
+ PySocks==1.7.1
300
+ pysqlite3-binary==0.5.2.post3
301
+ pystan==2.19.1.1
302
+ pytesseract==0.3.10
303
+ pytest-cov==5.0.0
304
+ python-dateutil==2.9.0.post0
305
+ python-decouple==3.8
306
+ python-docx==1.1.0
307
+ python-dotenv==1.0.1
308
+ python-iso639==2024.4.27
309
+ python-Levenshtein==0.25.1
310
+ python-multipart==0.0.18
311
+ python-pptx==0.6.23
312
+ python-slugify==8.0.4
313
+ pytorch-pretrained-bert==0.6.2
314
+ pytz==2025.2
315
+ pyvista==0.44.2
316
+ PyWavelets==1.4.1
317
+ PyYAML==6.0.3
318
+ quantile-python==1.1
319
+ rapidfuzz==3.8.1
320
+ rapidocr-onnxruntime==1.3.8
321
+ ray==2.10.0
322
+ rdkit==2024.3.5
323
+ redis==6.1.1
324
+ referencing==0.35.1
325
+ regex==2022.4.24
326
+ requests==2.32.4
327
+ requests-oauthlib==1.3.0
328
+ responses==0.16.0
329
+ rich==13.7.1
330
+ rouge-score==0.1.2
331
+ rpds-py==0.20.1
332
+ rq==2.3.3
333
+ rsa==4.7.2
334
+ ruff==0.4.2
335
+ rustworkx==0.15.1
336
+ s3transfer==0.11.3
337
+ sacrebleu==2.1.0
338
+ sacremoses==0.0.46
339
+ safetensors==0.4.3
340
+ scipy==1.10.1
341
+ scooby==0.10.1
342
+ seaborn==0.13.2
343
+ semantic-version==2.10.0
344
+ sentence-transformers==2.2.2
345
+ sentencepiece==0.1.91
346
+ sentry-sdk==2.39.0
347
+ session_info==1.0.1
348
+ sgmllib3k==1.0.0
349
+ shapely==2.0.4
350
+ shellingham==1.5.4
351
+ shortuuid==1.0.13
352
+ six==1.17.0
353
+ smart-open==6.4.0
354
+ smmap==5.0.1
355
+ sniffio==1.3.1
356
+ snowballstemmer==2.2.0
357
+ sobol-seq==0.2.0
358
+ socksio==1.0.0
359
+ soupsieve==2.5
360
+ spacy-legacy==3.0.12
361
+ spacy-loggers==1.0.5
362
+ Sphinx==4.3.1
363
+ sphinxcontrib-applehelp==1.0.2
364
+ sphinxcontrib-devhelp==1.0.2
365
+ sphinxcontrib-htmlhelp==2.0.0
366
+ sphinxcontrib-jsmath==1.0.1
367
+ sphinxcontrib-qthelp==1.0.3
368
+ sphinxcontrib-serializinghtml==1.1.5
369
+ SQLAlchemy==2.0.19
370
+ sqlparse==0.4.2
371
+ sse-starlette==1.8.2
372
+ starlette==0.44.0
373
+ statsmodels==0.14.1
374
+ stdlib-list==0.10.0
375
+ streamlit==1.30.0
376
+ streamlit-aggrid==0.3.4.post3
377
+ streamlit-antd-components==0.3.1
378
+ streamlit-chatbox==1.1.11
379
+ streamlit-feedback==0.1.3
380
+ streamlit-modal==0.1.0
381
+ streamlit-option-menu==0.3.12
382
+ strsimpy==0.2.1
383
+ svgwrite==1.4.3
384
+ sympy==1.13.3
385
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
386
+ tabulate==0.8.9
387
+ tenacity==8.2.3
388
+ tensorboard-plugin-wit==1.8.0
389
+ tensorboardX==2.4.1
390
+ text-unidecode==1.3
391
+ texttable==1.7.0
392
+ thefuzz==0.22.1
393
+ threadpoolctl==3.5.0
394
+ tifffile==2023.7.10
395
+ tiktoken==0.7.0
396
+ timm==0.9.16
397
+ tk==0.1.0
398
+ tokenizers==0.20.3
399
+ toml==0.10.2
400
+ tomlkit==0.12.0
401
+ toolz==0.12.1
402
+ torch==2.4.1+cpu
403
+ torch-geometric==2.6.1
404
+ torchaudio==2.1.2+cu118
405
+ torchtext==0.4.0
406
+ torchvision==0.19.1+cpu
407
+ tornado==6.4
408
+ tqdm==4.67.1
409
+ transformer-lens==2.16.1
410
+ transformers==4.46.3
411
+ transformers-stream-generator==0.0.5
412
+ typed-argument-parser==1.10.1
413
+ typeguard==4.4.0
414
+ typer==0.9.4
415
+ types-requests==2.31.0.20240406
416
+ typing-inspect==0.9.0
417
+ typing-utils==0.1.0
418
+ typing_extensions==4.13.2
419
+ tzdata==2024.1
420
+ tzlocal==5.2
421
+ umap-learn==0.5.7
422
+ Unidecode==1.3.2
423
+ unittest-xml-reporting==3.2.0
424
+ unstructured==0.11.0
425
+ unstructured-client==0.22.0
426
+ unstructured-inference==0.7.15
427
+ unstructured.pytesseract==0.3.12
428
+ uvicorn==0.29.0
429
+ uvloop==0.21.0
430
+ validators==0.28.1
431
+ vllm==0.2.7
432
+ vtk==9.3.1
433
+ wandb==0.22.0
434
+ watchdog==3.0.0
435
+ watchfiles==0.21.0
436
+ wavedrom==2.0.3.post3
437
+ weasel==0.3.4
438
+ websocket-client==1.8.0
439
+ websockets==13.1
440
+ Werkzeug==2.0.2
441
+ word2number==1.1
442
+ xlrd==2.0.1
443
+ XlsxWriter==3.0.2
444
+ xxhash==2.0.2
445
+ Yapsy==1.12.2
446
+ yarl==1.15.2
447
+ youtube-search==2.1.2
448
+ zipp==3.20.2
449
+ zope.event==4.5.0
450
+ zstandard==0.23.0
configs/s41467_024_50317_w_test/pip-freeze.txt ADDED
@@ -0,0 +1,450 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filelock==3.13.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
+ google-pasta==0.2.0
116
+ googleapis-common-protos==1.63.0
117
+ gpustat==1.1.1
118
+ gpytorch==1.10
119
+ gradio_client==0.16.0
120
+ graphlib_backport==1.1.0
121
+ greenlet==1.1.2
122
+ gunicorn==23.0.0
123
+ h11==0.14.0
124
+ h2==4.1.0
125
+ hf-xet==1.2.0
126
+ hf_transfer==0.1.9
127
+ hpack==4.0.0
128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ igraph==0.11.8
137
+ imageio==2.35.1
138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
+ llvmlite==0.41.1
183
+ lmdb==1.7.3
184
+ lxml==5.2.1
185
+ madoka==0.7.1
186
+ marisa-trie==1.1.0
187
+ Markdown==3.3.6
188
+ markdown-it-py==3.0.0
189
+ markdown2==2.4.13
190
+ markdownify==0.11.6
191
+ MarkupSafe==2.1.5
192
+ marshmallow==3.21.1
193
+ mdtex2html==1.3.0
194
+ mdurl==0.1.2
195
+ metaphor-python==0.1.23
196
+ ml-dtypes==0.2.0
197
+ monotonic==1.6
198
+ mpmath==1.3.0
199
+ mrcfile==1.5.4
200
+ msal==1.36.0
201
+ msal-extensions==1.3.0
202
+ msg-parser==1.2.0
203
+ msgpack==1.0.8
204
+ msgpack-numpy==0.4.3.2
205
+ multidict==6.0.5
206
+ multipledispatch==1.0.0
207
+ multiprocess==0.70.16
208
+ murmurhash==1.0.10
209
+ mypy-extensions==1.0.0
210
+ narwhals==1.42.1
211
+ natsort==8.4.0
212
+ nest-asyncio==1.6.0
213
+ netCDF4==1.7.2
214
+ networkx==3.0
215
+ neuroHarmonize==2.4.5
216
+ nh3==0.2.17
217
+ ninja==1.11.1.1
218
+ nltk==3.8.1
219
+ numba==0.58.1
220
+ numexpr==2.8.6
221
+ numpoly==1.0.6
222
+ numpy==1.24.4
223
+ numpydoc==1.1.0
224
+ nvidia-ml-py==12.535.133
225
+ nvitop==1.3.2
226
+ oauthlib==3.2.2
227
+ onnx==1.16.0
228
+ onnxruntime==1.15.1
229
+ openai==1.101.0
230
+ openpyxl==3.0.9
231
+ opentelemetry-api==1.24.0
232
+ opentelemetry-exporter-otlp-proto-common==1.24.0
233
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
234
+ opentelemetry-proto==1.24.0
235
+ opentelemetry-sdk==1.24.0
236
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configs/s41467_024_51933_2_test/editable.txt ADDED
File without changes
configs/s41467_024_51933_2_test/env.yml ADDED
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1
+ name: s41467_024_51933_2_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
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9
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10
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11
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12
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13
+ - libgcc-ng=15.1.0
14
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15
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16
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17
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18
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25
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28
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39
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41
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42
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43
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44
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53
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+ - triton==3.0.0
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57
+ prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51933_2_test
configs/s41467_024_51933_2_test/explicit.txt ADDED
@@ -0,0 +1,31 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
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7
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8
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9
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
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+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
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13
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14
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15
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16
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17
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19
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20
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21
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22
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configs/s41467_024_51933_2_test/meta.json ADDED
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configs/s41467_024_51933_2_test/pip-clean.txt ADDED
@@ -0,0 +1,459 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filelock==3.16.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
+ google-pasta==0.2.0
116
+ googleapis-common-protos==1.63.0
117
+ gpustat==1.1.1
118
+ gpytorch==1.10
119
+ gradio_client==0.16.0
120
+ graphlib_backport==1.1.0
121
+ greenlet==1.1.2
122
+ gunicorn==23.0.0
123
+ h11==0.14.0
124
+ h2==4.1.0
125
+ hf-xet==1.2.0
126
+ hf_transfer==0.1.9
127
+ hpack==4.0.0
128
+ httpcore==1.0.5
129
+ httptools==0.6.1
130
+ httpx==0.28.1
131
+ httpx-sse==0.4.0
132
+ huggingface_hub==0.36.1
133
+ humanfriendly==10.0
134
+ hyperframe==6.0.1
135
+ icetk==0.0.4
136
+ igraph==0.11.8
137
+ imageio==2.35.1
138
+ imagesize==1.3.0
139
+ imgaug==0.4.0
140
+ importlib-metadata==7.0.0
141
+ importlib_resources==6.4.5
142
+ inequalipy==1.0.5
143
+ iniconfig==1.1.1
144
+ inquirerpy==0.3.4
145
+ iopath==0.1.10
146
+ isodate==0.7.2
147
+ itsdangerous==2.0.1
148
+ jax==0.4.13
149
+ jaxlib==0.4.13
150
+ jaxtyping==0.2.19
151
+ Jinja2==3.1.6
152
+ jiter==0.9.1
153
+ jmespath==0.10.0
154
+ joblib==1.4.2
155
+ jsonnet==0.17.0
156
+ jsonpatch==1.33
157
+ jsonpath-python==1.0.6
158
+ jsonpickle==2.0.0
159
+ jsonschema==4.23.0
160
+ jsonschema-specifications==2023.12.1
161
+ kaggle==1.7.4.5
162
+ Keras-Preprocessing==1.1.2
163
+ kubernetes==29.0.0
164
+ langchain==0.1.16
165
+ langchain-community==0.0.34
166
+ langchain-core==0.1.46
167
+ langchain-experimental==0.0.57
168
+ langchain-text-splitters==0.0.1
169
+ langcodes==3.4.0
170
+ langdetect==1.0.9
171
+ langsmith==0.1.51
172
+ language_data==1.2.0
173
+ layoutparser==0.3.4
174
+ lazy_loader==0.4
175
+ leidenalg==0.10.2
176
+ Levenshtein==0.25.1
177
+ linear-operator==0.4.0
178
+ litellm==1.77.4
179
+ litellm-enterprise==0.1.20
180
+ litellm-proxy-extras==0.2.19
181
+ llama-index==0.9.35
182
+ llvmlite==0.41.1
183
+ lmdb==1.7.3
184
+ lxml==5.2.1
185
+ madoka==0.7.1
186
+ marisa-trie==1.1.0
187
+ Markdown==3.3.6
188
+ markdown-it-py==3.0.0
189
+ markdown2==2.4.13
190
+ markdownify==0.11.6
191
+ MarkupSafe==2.1.5
192
+ marshmallow==3.21.1
193
+ mdtex2html==1.3.0
194
+ mdurl==0.1.2
195
+ metaphor-python==0.1.23
196
+ ml-dtypes==0.2.0
197
+ monotonic==1.6
198
+ mpmath==1.3.0
199
+ mrcfile==1.5.4
200
+ msal==1.36.0
201
+ msal-extensions==1.3.0
202
+ msg-parser==1.2.0
203
+ msgpack==1.0.8
204
+ msgpack-numpy==0.4.3.2
205
+ multidict==6.0.5
206
+ multipledispatch==1.0.0
207
+ multiprocess==0.70.16
208
+ murmurhash==1.0.10
209
+ mypy-extensions==1.0.0
210
+ narwhals==1.42.1
211
+ natsort==8.4.0
212
+ nest-asyncio==1.6.0
213
+ netCDF4==1.7.2
214
+ networkx==3.1
215
+ neuroHarmonize==2.4.5
216
+ nh3==0.2.17
217
+ ninja==1.11.1.1
218
+ nltk==3.8.1
219
+ numba==0.58.1
220
+ numexpr==2.8.6
221
+ numpoly==1.0.6
222
+ numpy==1.24.4
223
+ numpydoc==1.1.0
224
+ nvidia-cublas-cu12==12.1.3.1
225
+ nvidia-cuda-cupti-cu12==12.1.105
226
+ nvidia-cuda-nvrtc-cu12==12.1.105
227
+ nvidia-cuda-runtime-cu12==12.1.105
228
+ nvidia-cudnn-cu12==9.1.0.70
229
+ nvidia-cufft-cu12==11.0.2.54
230
+ nvidia-curand-cu12==10.3.2.106
231
+ nvidia-ml-py==12.535.133
232
+ nvidia-nccl-cu12==2.20.5
233
+ nvidia-nvjitlink-cu12==12.9.86
234
+ nvidia-nvtx-cu12==12.1.105
235
+ nvitop==1.3.2
236
+ oauthlib==3.2.2
237
+ onnx==1.16.0
238
+ onnxruntime==1.15.1
239
+ openai==1.101.0
240
+ openpyxl==3.0.9
241
+ opentelemetry-api==1.24.0
242
+ opentelemetry-exporter-otlp-proto-common==1.24.0
243
+ opentelemetry-exporter-otlp-proto-grpc==1.24.0
244
+ opentelemetry-proto==1.24.0
245
+ opentelemetry-sdk==1.24.0
246
+ opentelemetry-semantic-conventions==0.45b0
247
+ opt-einsum==3.3.0
248
+ optax==0.1.5
249
+ ordered-set==4.1.0
250
+ orjson==3.10.1
251
+ overrides==7.7.0
252
+ packaging==26.2
253
+ pandas==2.0.3
254
+ pandas-stubs==1.2.0.45
255
+ parsimonious==0.8.1
256
+ pathlib==1.0.1
257
+ patsy==1.0.1
258
+ pdf2image==1.17.0
259
+ pfzy==0.3.4
260
+ PICOS==2.6.1
261
+ pikepdf==8.4.1
262
+ pip-search==0.0.12
263
+ pkgutil_resolve_name==1.3.10
264
+ plac==0.9.6
265
+ plotly==6.3.0
266
+ pluggy==1.5.0
267
+ ply==3.11
268
+ pondpond==1.4.1
269
+ pooch==1.8.2
270
+ portalocker==2.4.0
271
+ posthog==3.5.0
272
+ preshed==3.0.9
273
+ prettytable==3.11.0
274
+ primer3-py==2.2.0
275
+ prompt-toolkit==3.0.43
276
+ propcache==0.2.0
277
+ PuLP==3.1.1
278
+ pulsar-client==3.5.0
279
+ pyarrow==17.0.0
280
+ pyarrow-hotfix==0.6
281
+ pyclipper==1.3.0.post5
282
+ pycocotools==2.0.7
283
+ pycparser==2.21
284
+ pydantic==2.10.6
285
+ pydantic_core==2.27.2
286
+ pydeck==0.9.0b1
287
+ pyDOE2==1.3.0
288
+ pydub==0.25.1
289
+ pyfaidx==0.9.0.1
290
+ Pygments==2.19.2
291
+ PyJWT==2.8.0
292
+ pymodbus==3.6.9
293
+ PyMuPDF==1.23.16
294
+ PyMuPDFb==1.23.9
295
+ PyNaCl==1.6.2
296
+ pynndescent==0.5.13
297
+ Pyomo==6.8.2
298
+ pyOpenSSL==24.1.0
299
+ pypandoc==1.13
300
+ pypdf==4.2.0
301
+ pypdfium2==4.29.0
302
+ PyPika==0.48.9
303
+ PyQt5==5.15.7
304
+ PyQt5-Qt5==5.15.17
305
+ PyQt5_sip==12.15.0
306
+ pyro-api==0.1.2
307
+ pyro-ppl==1.9.1
308
+ pysam==0.23.3
309
+ PySocks==1.7.1
310
+ pysqlite3-binary==0.5.2.post3
311
+ pystan==2.19.1.1
312
+ pytesseract==0.3.10
313
+ pytest-cov==5.0.0
314
+ python-dateutil==2.9.0.post0
315
+ python-decouple==3.8
316
+ python-docx==1.1.0
317
+ python-dotenv==1.0.1
318
+ python-iso639==2024.4.27
319
+ python-Levenshtein==0.25.1
320
+ python-multipart==0.0.18
321
+ python-pptx==0.6.23
322
+ python-slugify==8.0.4
323
+ pytorch-pretrained-bert==0.6.2
324
+ pytz==2025.2
325
+ pyvista==0.44.2
326
+ PyWavelets==1.4.1
327
+ PyYAML==6.0.3
328
+ quantile-python==1.1
329
+ rapidfuzz==3.8.1
330
+ rapidocr-onnxruntime==1.3.8
331
+ ray==2.10.0
332
+ rdkit==2024.3.5
333
+ redis==6.1.1
334
+ referencing==0.35.1
335
+ regex==2022.4.24
336
+ requests==2.32.4
337
+ requests-oauthlib==1.3.0
338
+ responses==0.16.0
339
+ rich==13.7.1
340
+ rouge-score==0.1.2
341
+ rpds-py==0.20.1
342
+ rq==2.3.3
343
+ rsa==4.7.2
344
+ ruff==0.4.2
345
+ rustworkx==0.15.1
346
+ s3transfer==0.11.3
347
+ sacrebleu==2.1.0
348
+ sacremoses==0.0.46
349
+ safetensors==0.4.3
350
+ scooby==0.10.1
351
+ seaborn==0.13.2
352
+ semantic-version==2.10.0
353
+ sentence-transformers==2.2.2
354
+ sentencepiece==0.1.91
355
+ sentry-sdk==2.39.0
356
+ session_info==1.0.1
357
+ sgmllib3k==1.0.0
358
+ shapely==2.0.4
359
+ shellingham==1.5.4
360
+ shortuuid==1.0.13
361
+ six==1.17.0
362
+ smart-open==6.4.0
363
+ smmap==5.0.1
364
+ sniffio==1.3.1
365
+ snowballstemmer==2.2.0
366
+ sobol-seq==0.2.0
367
+ socksio==1.0.0
368
+ soupsieve==2.5
369
+ spacy-legacy==3.0.12
370
+ spacy-loggers==1.0.5
371
+ Sphinx==4.3.1
372
+ sphinxcontrib-applehelp==1.0.2
373
+ sphinxcontrib-devhelp==1.0.2
374
+ sphinxcontrib-htmlhelp==2.0.0
375
+ sphinxcontrib-jsmath==1.0.1
376
+ sphinxcontrib-qthelp==1.0.3
377
+ sphinxcontrib-serializinghtml==1.1.5
378
+ SQLAlchemy==2.0.19
379
+ sqlparse==0.4.2
380
+ sse-starlette==1.8.2
381
+ starlette==0.44.0
382
+ statsmodels==0.14.1
383
+ stdlib-list==0.10.0
384
+ streamlit==1.30.0
385
+ streamlit-aggrid==0.3.4.post3
386
+ streamlit-antd-components==0.3.1
387
+ streamlit-chatbox==1.1.11
388
+ streamlit-feedback==0.1.3
389
+ streamlit-modal==0.1.0
390
+ streamlit-option-menu==0.3.12
391
+ strsimpy==0.2.1
392
+ svgwrite==1.4.3
393
+ sympy==1.13.3
394
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
395
+ tabulate==0.8.9
396
+ tenacity==8.2.3
397
+ tensorboard-plugin-wit==1.8.0
398
+ tensorboardX==2.4.1
399
+ text-unidecode==1.3
400
+ texttable==1.7.0
401
+ thefuzz==0.22.1
402
+ threadpoolctl==3.5.0
403
+ tifffile==2023.7.10
404
+ tiktoken==0.7.0
405
+ timm==0.9.16
406
+ tk==0.1.0
407
+ tokenizers==0.20.3
408
+ toml==0.10.2
409
+ tomlkit==0.12.0
410
+ toolz==0.12.1
411
+ torch==2.4.1+cpu
412
+ torch-geometric==2.6.1
413
+ torchaudio==2.1.2+cu118
414
+ torchtext==0.4.0
415
+ tornado==6.4
416
+ tqdm==4.67.1
417
+ transformer-lens==2.16.1
418
+ transformers==4.46.3
419
+ transformers-stream-generator==0.0.5
420
+ triton==3.0.0
421
+ typed-argument-parser==1.10.1
422
+ typeguard==4.4.0
423
+ typer==0.9.4
424
+ types-requests==2.31.0.20240406
425
+ typing-inspect==0.9.0
426
+ typing-utils==0.1.0
427
+ typing_extensions==4.13.2
428
+ tzdata==2024.1
429
+ tzlocal==5.2
430
+ umap-learn==0.5.7
431
+ Unidecode==1.3.2
432
+ unittest-xml-reporting==3.2.0
433
+ unstructured==0.11.0
434
+ unstructured-client==0.22.0
435
+ unstructured-inference==0.7.15
436
+ unstructured.pytesseract==0.3.12
437
+ uvicorn==0.29.0
438
+ uvloop==0.21.0
439
+ validators==0.28.1
440
+ vllm==0.2.7
441
+ vtk==9.3.1
442
+ wandb==0.22.0
443
+ watchdog==3.0.0
444
+ watchfiles==0.21.0
445
+ wavedrom==2.0.3.post3
446
+ weasel==0.3.4
447
+ websocket-client==1.8.0
448
+ websockets==13.1
449
+ Werkzeug==2.0.2
450
+ word2number==1.1
451
+ xlrd==2.0.1
452
+ XlsxWriter==3.0.2
453
+ xxhash==2.0.2
454
+ Yapsy==1.12.2
455
+ yarl==1.15.2
456
+ youtube-search==2.1.2
457
+ zipp==3.20.2
458
+ zope.event==4.5.0
459
+ zstandard==0.23.0
configs/s41467_024_51933_2_test/pip-freeze.txt ADDED
@@ -0,0 +1,459 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ absl-py==2.3.1
2
+ accelerate==0.24.1
3
+ aiofiles==23.2.1
4
+ aiohappyeyeballs==2.4.4
5
+ aiohttp==3.10.11
6
+ aioprometheus==23.12.0
7
+ aiosignal==1.3.1
8
+ alabaster==0.7.12
9
+ allennlp==0.8.4
10
+ altair==5.3.0
11
+ annotated-types==0.6.0
12
+ anyio==3.7.1
13
+ APScheduler==3.11.2
14
+ arxiv==2.1.0
15
+ astunparse==1.6.3
16
+ async-timeout==4.0.3
17
+ attrs==25.3.0
18
+ autograd==1.7.0
19
+ autoray==0.6.12
20
+ awscli==1.32.93
21
+ azure-core==1.33.0
22
+ azure-identity==1.21.0
23
+ azure-storage-blob==12.26.0
24
+ Babel==2.9.1
25
+ backoff==2.2.1
26
+ backports.zoneinfo==0.2.1
27
+ bcrypt==4.1.2
28
+ beartype==0.14.1
29
+ better-abc==0.0.3
30
+ biopython==1.83
31
+ bitarray==2.5.1
32
+ bitsandbytes==0.43.1
33
+ blessed==1.20.0
34
+ blis==0.7.11
35
+ boto3==1.36.0
36
+ botocore==1.36.26
37
+ botorch==0.8.5
38
+ bpl==0.1.1
39
+ Brotli==1.1.0
40
+ bs4==0.0.2
41
+ cachetools==4.2.4
42
+ cffi==1.15.0
43
+ cftime==1.6.4.post1
44
+ chaospy==3.3.9
45
+ charset-normalizer==3.4.7
46
+ chex==0.1.7
47
+ chroma-hnswlib==0.7.3
48
+ chromadb==0.4.15
49
+ click==8.1.7
50
+ cloudpathlib==0.16.0
51
+ cobra==0.29.1
52
+ cohere==5.3.3
53
+ coloredlogs==15.0.1
54
+ confection==0.1.4
55
+ ConfigArgParse==1.5.3
56
+ conllu==0.11
57
+ coverage==7.6.1
58
+ cpm-kernels==1.0.11
59
+ cryptography==42.0.5
60
+ cvxopt==1.3.2
61
+ cymem==2.0.8
62
+ Cython==0.29.30
63
+ dataclasses==0.6
64
+ dataclasses-json==0.6.4
65
+ datasets==2.19.0
66
+ deepdiff==7.0.1
67
+ Deprecated==1.2.14
68
+ deprecation==2.1.0
69
+ dill==0.3.8
70
+ distro==1.9.0
71
+ dm-tree==0.1.8
72
+ dnspython==2.6.1
73
+ docstring_parser==0.17.0
74
+ docutils==0.15.2
75
+ dotenv==0.9.9
76
+ duckduckgo-search==3.9.9
77
+ editdistance==0.6.0
78
+ effdet==0.4.1
79
+ einops==0.7.0
80
+ email-validator==2.3.0
81
+ emoji==2.11.1
82
+ equinox==0.10.4
83
+ et-xmlfile==1.1.0
84
+ eval_type_backport==0.2.2
85
+ exceptiongroup==1.2.1
86
+ fairseq==0.10.2
87
+ faiss-cpu==1.7.4
88
+ faiss-gpu==1.7.2
89
+ fancy-einsum==0.0.3
90
+ fastapi==0.115.14
91
+ fastapi-sso==0.16.0
92
+ fastavro==1.9.4
93
+ fastuuid==0.13.5
94
+ fbpca==1.0
95
+ feedparser==6.0.10
96
+ ffmpy==0.3.2
97
+ filelock==3.16.1
98
+ filetype==1.2.0
99
+ finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
100
+ flaky==3.7.0
101
+ Flask-Cors==3.0.10
102
+ frozenlist==1.4.1
103
+ fschat==0.2.35
104
+ fsspec==2025.3.0
105
+ ftfy==6.0.3
106
+ future==0.18.2
107
+ fuzzywuzzy==0.18.0
108
+ gdown==5.2.0
109
+ geosketch==1.3
110
+ geotorch==0.3.0
111
+ get-annotations==0.1.2
112
+ gevent==21.12.0
113
+ gitdb==4.0.11
114
+ GitPython==3.1.43
115
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116
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118
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119
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120
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121
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122
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124
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125
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126
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127
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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149
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150
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161
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162
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163
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164
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165
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166
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167
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168
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169
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170
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171
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172
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173
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174
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175
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176
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177
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178
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179
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180
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181
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
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211
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212
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213
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214
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215
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216
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217
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218
+ nltk==3.8.1
219
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220
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221
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222
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223
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224
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225
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226
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227
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228
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229
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230
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231
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232
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233
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234
+ nvidia-nvtx-cu12==12.1.105
235
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236
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237
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238
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239
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240
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241
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242
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243
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244
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245
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246
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247
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248
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249
+ ordered-set==4.1.0
250
+ orjson==3.10.1
251
+ overrides==7.7.0
252
+ packaging==26.2
253
+ pandas==2.0.3
254
+ pandas-stubs==1.2.0.45
255
+ parsimonious==0.8.1
256
+ pathlib==1.0.1
257
+ patsy==1.0.1
258
+ pdf2image==1.17.0
259
+ pfzy==0.3.4
260
+ PICOS==2.6.1
261
+ pikepdf==8.4.1
262
+ pip-search==0.0.12
263
+ pkgutil_resolve_name==1.3.10
264
+ plac==0.9.6
265
+ plotly==6.3.0
266
+ pluggy==1.5.0
267
+ ply==3.11
268
+ pondpond==1.4.1
269
+ pooch==1.8.2
270
+ portalocker==2.4.0
271
+ posthog==3.5.0
272
+ preshed==3.0.9
273
+ prettytable==3.11.0
274
+ primer3-py==2.2.0
275
+ prompt-toolkit==3.0.43
276
+ propcache==0.2.0
277
+ PuLP==3.1.1
278
+ pulsar-client==3.5.0
279
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280
+ pyarrow-hotfix==0.6
281
+ pyclipper==1.3.0.post5
282
+ pycocotools==2.0.7
283
+ pycparser==2.21
284
+ pydantic==2.10.6
285
+ pydantic_core==2.27.2
286
+ pydeck==0.9.0b1
287
+ pyDOE2==1.3.0
288
+ pydub==0.25.1
289
+ pyfaidx==0.9.0.1
290
+ Pygments==2.19.2
291
+ PyJWT==2.8.0
292
+ pymodbus==3.6.9
293
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294
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295
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296
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297
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298
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299
+ pypandoc==1.13
300
+ pypdf==4.2.0
301
+ pypdfium2==4.29.0
302
+ PyPika==0.48.9
303
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304
+ PyQt5-Qt5==5.15.17
305
+ PyQt5_sip==12.15.0
306
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307
+ pyro-ppl==1.9.1
308
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309
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310
+ pysqlite3-binary==0.5.2.post3
311
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312
+ pytesseract==0.3.10
313
+ pytest-cov==5.0.0
314
+ python-dateutil==2.9.0.post0
315
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316
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317
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318
+ python-iso639==2024.4.27
319
+ python-Levenshtein==0.25.1
320
+ python-multipart==0.0.18
321
+ python-pptx==0.6.23
322
+ python-slugify==8.0.4
323
+ pytorch-pretrained-bert==0.6.2
324
+ pytz==2025.2
325
+ pyvista==0.44.2
326
+ PyWavelets==1.4.1
327
+ PyYAML==6.0.3
328
+ quantile-python==1.1
329
+ rapidfuzz==3.8.1
330
+ rapidocr-onnxruntime==1.3.8
331
+ ray==2.10.0
332
+ rdkit==2024.3.5
333
+ redis==6.1.1
334
+ referencing==0.35.1
335
+ regex==2022.4.24
336
+ requests==2.32.4
337
+ requests-oauthlib==1.3.0
338
+ responses==0.16.0
339
+ rich==13.7.1
340
+ rouge-score==0.1.2
341
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342
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343
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344
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345
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346
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347
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348
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349
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350
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351
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352
+ semantic-version==2.10.0
353
+ sentence-transformers==2.2.2
354
+ sentencepiece==0.1.91
355
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356
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357
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358
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359
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360
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361
+ six==1.17.0
362
+ smart-open==6.4.0
363
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364
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365
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366
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367
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368
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369
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370
+ spacy-loggers==1.0.5
371
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372
+ sphinxcontrib-applehelp==1.0.2
373
+ sphinxcontrib-devhelp==1.0.2
374
+ sphinxcontrib-htmlhelp==2.0.0
375
+ sphinxcontrib-jsmath==1.0.1
376
+ sphinxcontrib-qthelp==1.0.3
377
+ sphinxcontrib-serializinghtml==1.1.5
378
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379
+ sqlparse==0.4.2
380
+ sse-starlette==1.8.2
381
+ starlette==0.44.0
382
+ statsmodels==0.14.1
383
+ stdlib-list==0.10.0
384
+ streamlit==1.30.0
385
+ streamlit-aggrid==0.3.4.post3
386
+ streamlit-antd-components==0.3.1
387
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388
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389
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390
+ streamlit-option-menu==0.3.12
391
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392
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393
+ sympy==1.13.3
394
+ tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
395
+ tabulate==0.8.9
396
+ tenacity==8.2.3
397
+ tensorboard-plugin-wit==1.8.0
398
+ tensorboardX==2.4.1
399
+ text-unidecode==1.3
400
+ texttable==1.7.0
401
+ thefuzz==0.22.1
402
+ threadpoolctl==3.5.0
403
+ tifffile==2023.7.10
404
+ tiktoken==0.7.0
405
+ timm==0.9.16
406
+ tk==0.1.0
407
+ tokenizers==0.20.3
408
+ toml==0.10.2
409
+ tomlkit==0.12.0
410
+ toolz==0.12.1
411
+ torch==2.4.1+cpu
412
+ torch-geometric==2.6.1
413
+ torchaudio==2.1.2+cu118
414
+ torchtext==0.4.0
415
+ tornado==6.4
416
+ tqdm==4.67.1
417
+ transformer-lens==2.16.1
418
+ transformers==4.46.3
419
+ transformers-stream-generator==0.0.5
420
+ triton==3.0.0
421
+ typed-argument-parser==1.10.1
422
+ typeguard==4.4.0
423
+ typer==0.9.4
424
+ types-requests==2.31.0.20240406
425
+ typing-inspect==0.9.0
426
+ typing-utils==0.1.0
427
+ typing_extensions==4.13.2
428
+ tzdata==2024.1
429
+ tzlocal==5.2
430
+ umap-learn==0.5.7
431
+ Unidecode==1.3.2
432
+ unittest-xml-reporting==3.2.0
433
+ unstructured==0.11.0
434
+ unstructured-client==0.22.0
435
+ unstructured-inference==0.7.15
436
+ unstructured.pytesseract==0.3.12
437
+ uvicorn==0.29.0
438
+ uvloop==0.21.0
439
+ validators==0.28.1
440
+ vllm==0.2.7
441
+ vtk==9.3.1
442
+ wandb==0.22.0
443
+ watchdog==3.0.0
444
+ watchfiles==0.21.0
445
+ wavedrom==2.0.3.post3
446
+ weasel==0.3.4
447
+ websocket-client==1.8.0
448
+ websockets==13.1
449
+ Werkzeug==2.0.2
450
+ word2number==1.1
451
+ xlrd==2.0.1
452
+ XlsxWriter==3.0.2
453
+ xxhash==2.0.2
454
+ Yapsy==1.12.2
455
+ yarl==1.15.2
456
+ youtube-search==2.1.2
457
+ zipp==3.20.2
458
+ zope.event==4.5.0
459
+ zstandard==0.23.0
configs/s41467_025_56348_1_test/editable.txt ADDED
File without changes
configs/s41467_025_56348_1_test/env.yml ADDED
@@ -0,0 +1,60 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name: s41467_025_56348_1_test
2
+ channels:
3
+ - conda-forge
4
+ - defaults
5
+ dependencies:
6
+ - _libgcc_mutex=0.1
7
+ - _openmp_mutex=4.5
8
+ - bzip2=1.0.8
9
+ - ca-certificates=2025.8.3
10
+ - ld_impl_linux-64=2.44
11
+ - libblas=3.9.0
12
+ - libcblas=3.9.0
13
+ - libffi=3.4.6
14
+ - libgcc=15.1.0
15
+ - libgcc-ng=15.1.0
16
+ - libgfortran=15.1.0
17
+ - libgfortran5=15.1.0
18
+ - libgomp=15.1.0
19
+ - liblapack=3.9.0
20
+ - liblzma=5.8.1
21
+ - liblzma-devel=5.8.1
22
+ - libnsl=2.0.1
23
+ - libopenblas=0.3.30
24
+ - libsqlite=3.50.4
25
+ - libstdcxx=15.1.0
26
+ - libstdcxx-ng=15.1.0
27
+ - libuuid=2.38.1
28
+ - libxcrypt=4.4.36
29
+ - libzlib=1.3.1
30
+ - ncurses=6.5
31
+ - numpy=1.24.4
32
+ - openssl=3.5.2
33
+ - pip=22.1.2
34
+ - python=3.8.20
35
+ - python-dateutil=2.8.2
36
+ - python-tzdata=2025.2
37
+ - python_abi=3.8
38
+ - pytz=2024.2
39
+ - readline=8.2
40
+ - setuptools=70.3.0
41
+ - tk=8.6.13
42
+ - wheel=0.45.1
43
+ - xz=5.8.1
44
+ - xz-gpl-tools=5.8.1
45
+ - xz-tools=5.8.1
46
+ - pip:
47
+ - cycler==0.12.1
48
+ - fonttools==4.57.0
49
+ - importlib-resources==6.4.5
50
+ - kiwisolver==1.4.7
51
+ - matplotlib==3.7.5
52
+ - narwhals==1.42.1
53
+ - packaging==25.0
54
+ - pandas==1.4.4
55
+ - pillow==10.4.0
56
+ - plotly==6.3.0
57
+ - pyparsing==3.1.4
58
+ - scipy==1.10.1
59
+ - six==1.17.0
60
+ prefix: /home/lily/yz979/anaconda3/envs/s41467_025_56348_1_test
configs/s41467_025_56348_1_test/explicit.txt ADDED
@@ -0,0 +1,45 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # This file may be used to create an environment using:
2
+ # $ conda create --name <env> --file <this file>
3
+ # platform: linux-64
4
+ @EXPLICIT
5
+ https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
6
+ https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
7
+ https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
8
+ https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
9
+ https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.8-6_cp38.conda#630d86b05404bb70a07dd078c99e671a
10
+ https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
11
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
12
+ https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
13
+ https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
14
+ https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.1.0-hcea5267_5.conda#fbd4008644add05032b6764807ee2cba
15
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
16
+ https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
17
+ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_4.conda#3c376af8888c386b9d3d1c2701e2f3ab
18
+ https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
19
+ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
20
+ https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
21
+ https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
22
+ https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.1.0-h69a702a_5.conda#0c91408b3dec0b97e8a3c694845bd63b
23
+ https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
24
+ https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
25
+ https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_4.conda#2d34729cbc1da0ec988e57b13b712067
26
+ https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
27
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404
+ torchaudio==2.1.2+cu118
405
+ torchtext==0.4.0
406
+ tornado==6.4
407
+ tqdm==4.67.1
408
+ transformer-lens==2.16.1
409
+ transformers==4.46.3
410
+ transformers-stream-generator==0.0.5
411
+ typed-argument-parser==1.10.1
412
+ typeguard==4.4.0
413
+ typer==0.9.4
414
+ types-requests==2.31.0.20240406
415
+ typing-inspect==0.9.0
416
+ typing-utils==0.1.0
417
+ typing_extensions==4.13.2
418
+ tzdata==2024.1
419
+ tzlocal==5.2
420
+ umap-learn==0.5.7
421
+ Unidecode==1.3.2
422
+ unittest-xml-reporting==3.2.0
423
+ unstructured==0.11.0
424
+ unstructured-client==0.22.0
425
+ unstructured-inference==0.7.15
426
+ unstructured.pytesseract==0.3.12
427
+ uvicorn==0.29.0
428
+ uvloop==0.21.0
429
+ validators==0.28.1
430
+ vllm==0.2.7
431
+ vtk==9.3.1
432
+ wandb==0.22.0
433
+ watchdog==3.0.0
434
+ watchfiles==0.21.0
435
+ wavedrom==2.0.3.post3
436
+ weasel==0.3.4
437
+ websocket-client==1.8.0
438
+ websockets==13.1
439
+ Werkzeug==2.0.2
440
+ word2number==1.1
441
+ xlrd==2.0.1
442
+ XlsxWriter==3.0.2
443
+ xxhash==2.0.2
444
+ Yapsy==1.12.2
445
+ yarl==1.15.2
446
+ youtube-search==2.1.2
447
+ zipp==3.20.2
448
+ zope.event==4.5.0
449
+ zstandard==0.23.0