Add files using upload-large-folder tool

configs/005_trust_align_test/pip-freeze.txt

@@ -0,0 +1,455 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1726459485162/work
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver @ file:///croot/kiwisolver_1672387140495/work
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1632416634429/work
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1667391556261/work
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy @ file:///home/conda/feedstock_root/build_artifacts/numpy_1687808301083/work
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1719903565503/work
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1724616129934/work
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1701931997682/work
+scipy==1.9.3
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
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+transformer-lens==2.16.1
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+transformers-stream-generator==0.0.5
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+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1708239446578/work
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0

configs/031_test/env.yml

@@ -0,0 +1,47 @@
+name: 031_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.3
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - filelock==3.13.1
+    - fsspec==2024.6.1
+    - geotorch==0.3.0
+    - jinja2==3.1.4
+    - markupsafe==2.1.5
+    - mpmath==1.3.0
+    - networkx==3.0
+    - numpy==1.24.4
+    - packaging==25.0
+    - six==1.17.0
+    - sympy==1.13.3
+    - torch==2.4.1+cpu
+    - typing-extensions==4.12.2
+prefix: /home/lily/yz979/anaconda3/envs/031_test

configs/031_test/explicit.txt

@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96

configs/031_test/meta.json

@@ -0,0 +1,8 @@
+{
+  "env": "031_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/031_test",
+  "exported_at": "2026-05-17T04:03:42Z"
+}

configs/031_test/pip-clean.txt

@@ -0,0 +1,448 @@
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configs/031_test/pip-freeze.txt

@@ -0,0 +1,448 @@
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+narwhals==1.42.1
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+netCDF4==1.7.2
+networkx==3.0
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+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
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+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
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+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
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+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
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+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
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+pooch==1.8.2
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+pyarrow-hotfix==0.6
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+pyDOE2==1.3.0
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+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
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+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
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+python-slugify==8.0.4
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configs/071_test/explicit.txt

@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-ha97dd6f_2.conda#14bae321b8127b63cba276bd53fac237
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda#dcd5ff1940cd38f6df777cac86819d60
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda#264fbfba7fb20acf3b29cde153e345ce
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda#069afdf8ea72504e48d23ae1171d951c
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.3-h26f9b46_1.conda#4fc6c4c88da64c0219c0c6c0408cedd4
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96

configs/071_test/meta.json

@@ -0,0 +1,8 @@
+{
+  "env": "071_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/071_test",
+  "exported_at": "2026-05-17T04:04:18Z"
+}

configs/071_test/pip-clean.txt

@@ -0,0 +1,464 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.2.25
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
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+fbpca==1.0
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+filelock==3.16.1
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
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+fschat==0.2.35
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+ftfy==6.0.3
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+geosketch==1.3
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+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
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+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
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+h11==0.14.0
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+httpx-sse==0.4.0
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+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+idna==3.10
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+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
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+jiter==0.9.1
+jmespath==0.10.0
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+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
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+langchain-experimental==0.0.57
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+langcodes==3.4.0
+langdetect==1.0.9
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+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
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+multipledispatch==1.0.0
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+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
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+nltk==3.8.1
+numba==0.58.1
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+numpydoc==1.1.0
+nvidia-cublas-cu12==12.9.2.10
+nvidia-cuda-cupti-cu12==12.9.79
+nvidia-cuda-nvrtc-cu12==12.9.86
+nvidia-cuda-runtime-cu12==12.9.79
+nvidia-cudnn-cu12==8.9.2.26
+nvidia-cufft-cu12==11.4.1.4
+nvidia-curand-cu12==10.3.10.19
+nvidia-cusparse-cu12==12.5.10.65
+nvidia-ml-py==12.535.133
+nvidia-nccl-cu12==2.18.1
+nvidia-nvjitlink-cu12==12.9.86
+nvidia-nvtx-cu12==12.9.79
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
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+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
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+ordered-set==4.1.0
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+overrides==7.7.0
+packaging==26.2
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+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
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+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
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+primer3-py==2.2.0
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+pydeck==0.9.0b1
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+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
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+pypandoc==1.13
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+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
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+python-dateutil==2.9.0.post0
+python-decouple==3.8
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+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
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+PyWavelets==1.4.1
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+ray==2.10.0
+rdkit==2024.3.5
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+streamlit-modal==0.1.0
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+svgwrite==1.4.3
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+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
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+toml==0.10.2
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+toolz==0.12.1
+torch==2.1.2
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+torchaudio==2.1.2+cu118
+torchtext==0.4.0
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+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
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+typeguard==4.4.0
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+typing-utils==0.1.0
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+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
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+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0

configs/071_test/pip-freeze.txt

@@ -0,0 +1,464 @@
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+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
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+certifi==2026.2.25
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
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+click==8.1.7
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+confection==0.1.4
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+coverage==7.6.1
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+cryptography==42.0.5
+cvxopt==1.3.2
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+Cython==0.29.30
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+Deprecated==1.2.14
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+editdistance==0.6.0
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+einops==0.7.0
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+emoji==2.11.1
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+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
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+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+sympy==1.13.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch==2.1.2
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+triton==2.1.0
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+urllib3==2.2.3
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0

configs/r_test_env/env.yml

@@ -0,0 +1,375 @@
+name: r_test_env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - _r-mutex=1.0.1
+  - binutils_impl_linux-64=2.44
+  - binutils_linux-64=2.44
+  - bwidget=1.10.1
+  - bzip2=1.0.8
+  - c-ares=1.34.5
+  - ca-certificates=2026.4.22
+  - cairo=1.18.4
+  - curl=8.14.1
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.15.0
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - freetype=2.13.3
+  - fribidi=1.0.10
+  - gcc_impl_linux-64=13.3.0
+  - gcc_linux-64=13.3.0
+  - gfortran_impl_linux-64=13.3.0
+  - glpk=5.0
+  - gmp=6.3.0
+  - graphite2=1.3.14
+  - gsl=2.7.1
+  - gxx_impl_linux-64=13.3.0
+  - gxx_linux-64=13.3.0
+  - harfbuzz=11.4.5
+  - icu=75.1
+  - kernel-headers_linux-64=2.6.32
+  - keyutils=1.6.3
+  - krb5=1.21.3
+  - ld_impl_linux-64=2.44
+  - lerc=4.0.0
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcurl=8.14.1
+  - libdeflate=1.24
+  - libedit=3.1.20250104
+  - libev=4.33
+  - libexpat=2.7.1
+  - libffi=3.4.6
+  - libfreetype=2.13.3
+  - libfreetype6=2.13.3
+  - libgcc=15.1.0
+  - libgcc-devel_linux-64=13.3.0
+  - libgcc-ng=15.1.0
+  - libgfortran=15.1.0
+  - libgfortran-ng=15.1.0
+  - libgfortran5=15.1.0
+  - libgit2=1.9.1
+  - libglib=2.84.3
+  - libgomp=15.1.0
+  - libiconv=1.18
+  - libjpeg-turbo=3.1.0
+  - liblapack=3.9.0
+  - liblzma=5.8.1
+  - libmpdec=4.0.0
+  - libnghttp2=1.64.0
+  - libopenblas=0.3.30
+  - libpng=1.6.50
+  - libsanitizer=13.3.0
+  - libsqlite=3.50.4
+  - libssh2=1.11.1
+  - libstdcxx=15.1.0
+  - libstdcxx-devel_linux-64=13.3.0
+  - libstdcxx-ng=15.1.0
+  - libtiff=4.7.0
+  - libuuid=2.38.1
+  - libuv=1.51.0
+  - libwebp-base=1.6.0
+  - libxcb=1.17.0
+  - libxml2=2.13.8
+  - libzlib=1.3.1
+  - make=4.4.1
+  - ncurses=6.5
+  - nlopt=2.9.0
+  - numpy=2.3.2
+  - openjdk=8.0.472
+  - openssl=3.6.2
+  - pandoc=3.7.0.2
+  - pango=1.56.4
+  - pcre2=10.45
+  - pip=25.2
+  - pixman=0.46.4
+  - pthread-stubs=0.4
+  - python=3.13.5
+  - python_abi=3.13
+  - r-abind=1.4_5
+  - r-ape=5.8_1
+  - r-askpass=1.2.1
+  - r-backports=1.5.0
+  - r-base=4.3.3
+  - r-base64enc=0.1_3
+  - r-bh=1.87.0_1
+  - r-bit=4.6.0
+  - r-bit64=4.6.0_1
+  - r-bitops=1.0_9
+  - r-boot=1.3_32
+  - r-brew=1.0_10
+  - r-brio=1.1.5
+  - r-broom=1.0.9
+  - r-bslib=0.9.0
+  - r-cachem=1.1.0
+  - r-callr=3.7.6
+  - r-car=3.1_3
+  - r-cardata=3.0_5
+  - r-caret=6.0_94
+  - r-catools=1.18.3
+  - r-checkmate=2.3.3
+  - r-class=7.3_23
+  - r-cli=3.6.5
+  - r-clipr=0.8.0
+  - r-clock=0.7.3
+  - r-cluster=2.1.8.1
+  - r-codetools=0.2_20
+  - r-colorspace=2.1_1
+  - r-commonmark=2.0.0
+  - r-conquer=1.3.3
+  - r-corrplot=0.95
+  - r-cowplot=1.2.0
+  - r-cpp11=0.5.2
+  - r-crayon=1.5.3
+  - r-credentials=2.0.3
+  - r-crosstalk=1.2.2
+  - r-curl=7.0.0
+  - r-data.table=1.17.8
+  - r-deldir=2.0_4
+  - r-deriv=4.2.0
+  - r-desc=1.4.3
+  - r-devtools=2.4.5
+  - r-diagram=1.6.5
+  - r-diffobj=0.3.6
+  - r-digest=0.6.37
+  - r-doby=4.7.0
+  - r-dotcall64=1.2
+  - r-downlit=0.4.4
+  - r-dplyr=1.1.4
+  - r-dqrng=0.3.2
+  - r-e1071=1.7_16
+  - r-ellipsis=0.3.2
+  - r-evaluate=1.0.5
+  - r-fansi=1.0.6
+  - r-farver=2.1.2
+  - r-fastmap=1.2.0
+  - r-fitdistrplus=1.2_4
+  - r-fnn=1.1.4.1
+  - r-fontawesome=0.5.3
+  - r-foreach=1.5.2
+  - r-formula=1.2_5
+  - r-fs=1.6.6
+  - r-future=1.67.0
+  - r-future.apply=1.20.0
+  - r-gbrd=0.4.12
+  - r-gcdnet=1.0.6
+  - r-generics=0.1.4
+  - r-geometry=0.5.2
+  - r-gert=2.1.5
+  - r-ggplot2=3.5.2
+  - r-ggpubr=0.6.1
+  - r-ggrepel=0.9.6
+  - r-ggridges=0.5.7
+  - r-ggsci=3.2.0
+  - r-ggsignif=0.6.4
+  - r-gh=1.5.0
+  - r-gitcreds=0.1.2
+  - r-glmnet=4.1_10
+  - r-globals=0.18.0
+  - r-glue=1.8.0
+  - r-gmp=0.7_2
+  - r-goftest=1.2_3
+  - r-gower=1.0.1
+  - r-gplots=3.2.0
+  - r-gridextra=2.3
+  - r-gtable=0.3.6
+  - r-gtools=3.9.5
+  - r-h2o=3.44.0.3
+  - r-hardhat=1.4.2
+  - r-here=1.0.1
+  - r-highr=0.11
+  - r-hms=1.1.3
+  - r-htmltools=0.5.8.1
+  - r-htmlwidgets=1.6.4
+  - r-httpuv=1.6.16
+  - r-httr=1.4.7
+  - r-httr2=1.2.1
+  - r-ica=1.0_3
+  - r-igraph=2.1.4
+  - r-ini=0.3.1
+  - r-ipred=0.9_15
+  - r-irlba=2.3.5.1
+  - r-isoband=0.2.7
+  - r-iterators=1.0.14
+  - r-jquerylib=0.1.4
+  - r-jsonlite=2.0.0
+  - r-kernsmooth=2.23_26
+  - r-knitr=1.50
+  - r-labeling=0.4.3
+  - r-later=1.4.4
+  - r-lattice=0.22_7
+  - r-lava=1.8.1
+  - r-lazyeval=0.2.2
+  - r-lbfgs=1.2.1.2
+  - r-leiden=0.4.3.1
+  - r-lifecycle=1.0.4
+  - r-linprog=0.9_4
+  - r-listenv=0.9.1
+  - r-lme4=1.1_37
+  - r-lmtest=0.9_40
+  - r-lpsolve=5.6.23
+  - r-lubridate=1.9.4
+  - r-magic=1.6_1
+  - r-magrittr=2.0.3
+  - r-mass=7.3_60
+  - r-matrix=1.6_5
+  - r-matrixmodels=0.5_4
+  - r-matrixstats=1.5.0
+  - r-memoise=2.0.1
+  - r-mgcv=1.9_3
+  - r-microbenchmark=1.5.0
+  - r-mime=0.13
+  - r-miniui=0.1.2
+  - r-minqa=1.2.8
+  - r-modelmetrics=1.2.2.2
+  - r-modelr=0.1.11
+  - r-munsell=0.5.1
+  - r-nlme=3.1_168
+  - r-nloptr=2.2.1
+  - r-nnet=7.3_20
+  - r-numderiv=2016.8_1.1
+  - r-openssl=2.3.3
+  - r-parallelly=1.45.1
+  - r-patchwork=1.3.2
+  - r-pbapply=1.7_4
+  - r-pbkrtest=0.5.5
+  - r-permute=0.9_4
+  - r-picante=1.8.2
+  - r-pillar=1.11.0
+  - r-pkgbuild=1.4.8
+  - r-pkgconfig=2.0.3
+  - r-pkgdown=2.1.3
+  - r-pkgload=1.4.0
+  - r-plotly=4.10.2
+  - r-plyr=1.8.9
+  - r-png=0.1_8
+  - r-polyclip=1.10_7
+  - r-polynom=1.4_1
+  - r-praise=1.0.0
+  - r-prettyunits=1.2.0
+  - r-proc=1.19.0.1
+  - r-processx=3.8.6
+  - r-prodlim=2025.04.28
+  - r-profvis=0.4.0
+  - r-progress=1.2.3
+  - r-progressr=0.15.1
+  - r-promises=1.3.3
+  - r-proxy=0.4_27
+  - r-ps=1.9.1
+  - r-purrr=1.1.0
+  - r-quantreg=6.1
+  - r-r6=2.6.1
+  - r-ragg=1.5.0
+  - r-rann=2.6.2
+  - r-rappdirs=0.3.3
+  - r-rbibutils=2.3
+  - r-rcmdcheck=1.4.0
+  - r-rcolorbrewer=1.1_3
+  - r-rcpp=1.1.0
+  - r-rcppannoy=0.0.22
+  - r-rcpparmadillo=15.0.1_1
+  - r-rcppeigen=0.3.4.0.2
+  - r-rcppprogress=0.4.2
+  - r-rcpptoml=0.2.3
+  - r-rcurl=1.98_1.12
+  - r-rdpack=2.6.4
+  - r-readr=2.1.5
+  - r-recipes=1.3.1
+  - r-reformulas=0.4.1
+  - r-registry=0.5_1
+  - r-rematch2=2.1.2
+  - r-remotes=2.5.0
+  - r-reshape2=1.4.4
+  - r-reticulate=1.43.0
+  - r-rlang=1.1.6
+  - r-rmarkdown=2.29
+  - r-rocr=1.0_11
+  - r-roi=1.0_1
+  - r-roxygen2=7.3.3
+  - r-rpart=4.1.24
+  - r-rprojroot=2.1.1
+  - r-rsample=0.0.2
+  - r-rstatix=0.7.2
+  - r-rstudioapi=0.17.1
+  - r-rtsne=0.17
+  - r-rversions=2.1.2
+  - r-sass=0.4.10
+  - r-scales=1.4.0
+  - r-scattermore=1.2
+  - r-sctransform=0.4.2
+  - r-sessioninfo=1.2.3
+  - r-seurat=4.4.0
+  - r-seuratobject=5.2.0
+  - r-shape=1.4.6.1
+  - r-shiny=1.11.1
+  - r-sitmo=2.0.2
+  - r-slam=0.1_55
+  - r-sourcetools=0.1.7_1
+  - r-sp=2.2_0
+  - r-spam=2.11_1
+  - r-spamm=4.4.0
+  - r-sparsem=1.84_2
+  - r-sparsevctrs=0.3.4
+  - r-spatstat.data=3.1_8
+  - r-spatstat.explore=3.2_3
+  - r-spatstat.geom=3.2_5
+  - r-spatstat.random=3.1_6
+  - r-spatstat.sparse=3.1_0
+  - r-spatstat.utils=3.1_5
+  - r-squarem=2021.1
+  - r-stringi=1.8.7
+  - r-stringr=1.5.1
+  - r-survival=3.8_3
+  - r-sys=3.4.3
+  - r-systemfonts=1.2.3
+  - r-tensor=1.5.1
+  - r-testthat=3.2.3
+  - r-textshaping=1.0.3
+  - r-tibble=3.3.0
+  - r-tidyr=1.3.1
+  - r-tidyselect=1.2.1
+  - r-timechange=0.3.0
+  - r-timedate=4041.110
+  - r-tinytex=0.57
+  - r-tzdb=0.5.0
+  - r-urlchecker=1.0.1
+  - r-usethis=3.2.1
+  - r-utf8=1.2.6
+  - r-uwot=0.1.16
+  - r-vctrs=0.6.5
+  - r-vegan=2.6_4
+  - r-viridislite=0.4.2
+  - r-vroom=1.6.5
+  - r-waldo=0.6.2
+  - r-whisker=0.4.1
+  - r-withr=3.0.2
+  - r-xfun=0.53
+  - r-xml2=1.4.0
+  - r-xopen=1.0.1
+  - r-xtable=1.8_4
+  - r-yaml=2.3.10
+  - r-zip=2.3.3
+  - r-zoo=1.8_14
+  - readline=8.2
+  - sed=4.9
+  - sysroot_linux-64=2.12
+  - tk=8.6.13
+  - tktable=2.10
+  - tzdata=2025b
+  - xorg-libice=1.1.2
+  - xorg-libsm=1.2.6
+  - xorg-libx11=1.8.12
+  - xorg-libxau=1.0.12
+  - xorg-libxdmcp=1.1.5
+  - xorg-libxext=1.3.6
+  - xorg-libxrender=0.9.12
+  - xorg-libxt=1.3.1
+  - zstd=1.5.7
+prefix: /home/lily/yz979/anaconda3/envs/r_test_env

configs/r_test_env/explicit.txt

@@ -0,0 +1,373 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2026.4.22-hbd8a1cb_0.conda#e18ad67cf881dcadee8b8d9e2f8e5f73
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.3.0-hc03c837_102.conda#4c1d6961a6a54f602ae510d9bf31fa60
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.3.0-hc03c837_102.conda#aa38de2738c5f4a72a880e3d31ffe8b4
+https://conda.anaconda.org/conda-forge/linux-64/openjdk-8.0.472-h4d9bdce_0.conda#814b49910a4cd9da2a1f31144386a309
+https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.7.0.2-ha770c72_0.conda#db0c1632047d38997559ce2c4741dd91
+https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-8_cp313.conda#94305520c52a4aa3f6c2b1ff6008d9f8
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.44-h4bf12b8_1.conda#e45cfedc8ca5630e02c106ea36d2c5c6
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
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configs/r_test_env/meta.json

@@ -0,0 +1,8 @@
+{
+  "env": "r_test_env",
+  "python_version": "3.13.5",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/r_test_env",
+  "exported_at": "2026-05-17T04:04:36Z"
+}

configs/r_test_env/pip-clean.txt

@@ -0,0 +1,15 @@
+contourpy==1.3.3
+cycler==0.12.1
+fonttools==4.60.1
+kiwisolver==1.4.9
+matplotlib==3.10.6
+nlopt==2.9.0
+packaging==25.0
+pandas==2.3.3
+pillow==11.3.0
+pyparsing==3.2.5
+python-dateutil==2.9.0.post0
+pytz==2025.2
+scipy==1.16.2
+six==1.17.0
+tzdata==2025.2

configs/r_test_env/pip-freeze.txt

@@ -0,0 +1,16 @@
+contourpy==1.3.3
+cycler==0.12.1
+fonttools==4.60.1
+kiwisolver==1.4.9
+matplotlib==3.10.6
+nlopt==2.9.0
+numpy @ file:///home/conda/feedstock_root/build_artifacts/bld/rattler-build_numpy_1756343073/work/dist/numpy-2.3.2-cp313-cp313-linux_x86_64.whl#sha256=396b87a0e28b5d5ec2d3d9f083d74196522440c4f4b53de8610398c1a7ae4945
+packaging==25.0
+pandas==2.3.3
+pillow==11.3.0
+pyparsing==3.2.5
+python-dateutil==2.9.0.post0
+pytz==2025.2
+scipy==1.16.2
+six==1.17.0
+tzdata==2025.2

configs/s41467_024_50505_8_test/env.yml

@@ -0,0 +1,47 @@
+name: s41467_024_50505_8_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - contourpy==1.1.1
+    - cycler==0.12.1
+    - fonttools==4.57.0
+    - importlib-resources==6.4.5
+    - kiwisolver==1.4.7
+    - matplotlib==3.7.5
+    - numpy==1.24.4
+    - packaging==25.0
+    - pillow==10.4.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scipy==1.10.1
+    - six==1.17.0
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_50505_8_test

configs/s41467_024_51026_0_test/env.yml

@@ -0,0 +1,48 @@
+name: s41467_024_51026_0_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.8.3
+  - ld_impl_linux-64=2.44
+  - libffi=3.4.6
+  - libgcc=15.1.0
+  - libgcc-ng=15.1.0
+  - libgomp=15.1.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.50.4
+  - libuuid=2.38.1
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.5.2
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - pip:
+    - anndata==0.9.2
+    - fonttools==4.57.0
+    - joblib==1.4.2
+    - kiwisolver==1.4.7
+    - networkx==3.1
+    - numpy==1.24.4
+    - packaging==25.0
+    - pyparsing==3.1.4
+    - python-dateutil==2.9.0.post0
+    - scanpy==1.9.8
+    - scipy==1.10.1
+    - six==1.17.0
+    - threadpoolctl==3.5.0
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_024_51026_0_test

configs/s41467_024_51026_0_test/explicit.txt

@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96

configs/s41467_024_51026_0_test/meta.json

@@ -0,0 +1,8 @@
+{
+  "env": "s41467_024_51026_0_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_024_51026_0_test",
+  "exported_at": "2026-05-17T04:05:33Z"
+}

configs/s41467_024_51026_0_test/pip-clean.txt

@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+anndata==0.9.2
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
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+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
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+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
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+hpack==4.0.0
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+httpx==0.28.1
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+huggingface_hub==0.36.1
+humanfriendly==10.0
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+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
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+jmespath==0.10.0
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+jsonpickle==2.0.0
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
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+Levenshtein==0.25.1
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+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
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+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0

configs/s41467_024_51026_0_test/pip-freeze.txt

@@ -0,0 +1,450 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+anndata==0.9.2
+annotated-types==0.6.0
+anyio==3.7.1
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
+bitarray==2.5.1
+bitsandbytes==0.43.1
+blessed==1.20.0
+blis==0.7.11
+boto3==1.36.0
+botocore==1.36.26
+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
+charset-normalizer==3.4.7
+chex==0.1.7
+chroma-hnswlib==0.7.3
+chromadb==0.4.15
+click==8.1.7
+cloudpathlib==0.16.0
+cobra==0.29.1
+cohere==5.3.3
+coloredlogs==15.0.1
+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
+docstring_parser==0.17.0
+docutils==0.15.2
+dotenv==0.9.9
+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
+fastapi==0.115.14
+fastapi-sso==0.16.0
+fastavro==1.9.4
+fastuuid==0.13.5
+fbpca==1.0
+feedparser==6.0.10
+ffmpy==0.3.2
+filetype==1.2.0
+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
+Flask-Cors==3.0.10
+fonttools==4.57.0
+frozenlist==1.4.1
+fschat==0.2.35
+fsspec==2025.3.0
+ftfy==6.0.3
+future==0.18.2
+fuzzywuzzy==0.18.0
+gdown==5.2.0
+geosketch==1.3
+geotorch==0.3.0
+get-annotations==0.1.2
+gevent==21.12.0
+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
+greenlet==1.1.2
+gunicorn==23.0.0
+h11==0.14.0
+h2==4.1.0
+hf-xet==1.2.0
+hf_transfer==0.1.9
+hpack==4.0.0
+httpcore==1.0.5
+httptools==0.6.1
+httpx==0.28.1
+httpx-sse==0.4.0
+huggingface_hub==0.36.1
+humanfriendly==10.0
+hyperframe==6.0.1
+icetk==0.0.4
+igraph==0.11.8
+imageio==2.35.1
+imagesize==1.3.0
+imgaug==0.4.0
+importlib-metadata==7.0.0
+importlib_resources==6.4.5
+inequalipy==1.0.5
+iniconfig==1.1.1
+inquirerpy==0.3.4
+iopath==0.1.10
+isodate==0.7.2
+itsdangerous==2.0.1
+jax==0.4.13
+jaxlib==0.4.13
+jaxtyping==0.2.19
+Jinja2==3.1.6
+jiter==0.9.1
+jmespath==0.10.0
+joblib==1.4.2
+jsonnet==0.17.0
+jsonpatch==1.33
+jsonpath-python==1.0.6
+jsonpickle==2.0.0
+jsonschema==4.23.0
+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kiwisolver==1.4.7
+kubernetes==29.0.0
+langchain==0.1.16
+langchain-community==0.0.34
+langchain-core==0.1.46
+langchain-experimental==0.0.57
+langchain-text-splitters==0.0.1
+langcodes==3.4.0
+langdetect==1.0.9
+langsmith==0.1.51
+language_data==1.2.0
+layoutparser==0.3.4
+lazy_loader==0.4
+leidenalg==0.10.2
+Levenshtein==0.25.1
+linear-operator==0.4.0
+litellm==1.77.4
+litellm-enterprise==0.1.20
+litellm-proxy-extras==0.2.19
+llama-index==0.9.35
+llvmlite==0.41.1
+lmdb==1.7.3
+lxml==5.2.1
+madoka==0.7.1
+marisa-trie==1.1.0
+Markdown==3.3.6
+markdown-it-py==3.0.0
+markdown2==2.4.13
+markdownify==0.11.6
+MarkupSafe==2.1.5
+marshmallow==3.21.1
+mdtex2html==1.3.0
+mdurl==0.1.2
+metaphor-python==0.1.23
+ml-dtypes==0.2.0
+monotonic==1.6
+mrcfile==1.5.4
+msal==1.36.0
+msal-extensions==1.3.0
+msg-parser==1.2.0
+msgpack==1.0.8
+msgpack-numpy==0.4.3.2
+multidict==6.0.5
+multipledispatch==1.0.0
+multiprocess==0.70.16
+murmurhash==1.0.10
+mypy-extensions==1.0.0
+narwhals==1.42.1
+natsort==8.4.0
+nest-asyncio==1.6.0
+netCDF4==1.7.2
+networkx==3.1
+neuroHarmonize==2.4.5
+nh3==0.2.17
+ninja==1.11.1.1
+nltk==3.8.1
+numba==0.58.1
+numexpr==2.8.6
+numpoly==1.0.6
+numpy==1.24.4
+numpydoc==1.1.0
+nvidia-ml-py==12.535.133
+nvitop==1.3.2
+oauthlib==3.2.2
+onnx==1.16.0
+onnxruntime==1.15.1
+openai==1.101.0
+openpyxl==3.0.9
+opentelemetry-api==1.24.0
+opentelemetry-exporter-otlp-proto-common==1.24.0
+opentelemetry-exporter-otlp-proto-grpc==1.24.0
+opentelemetry-proto==1.24.0
+opentelemetry-sdk==1.24.0
+opentelemetry-semantic-conventions==0.45b0
+opt-einsum==3.3.0
+optax==0.1.5
+ordered-set==4.1.0
+orjson==3.10.1
+overrides==7.7.0
+packaging==26.2
+pandas==2.0.3
+pandas-stubs==1.2.0.45
+parsimonious==0.8.1
+pathlib==1.0.1
+patsy==1.0.1
+pdf2image==1.17.0
+pfzy==0.3.4
+PICOS==2.6.1
+pikepdf==8.4.1
+pip-search==0.0.12
+pkgutil_resolve_name==1.3.10
+plac==0.9.6
+plotly==6.3.0
+pluggy==1.5.0
+ply==3.11
+pondpond==1.4.1
+pooch==1.8.2
+portalocker==2.4.0
+posthog==3.5.0
+preshed==3.0.9
+prettytable==3.11.0
+primer3-py==2.2.0
+prompt-toolkit==3.0.43
+propcache==0.2.0
+PuLP==3.1.1
+pulsar-client==3.5.0
+pyarrow==17.0.0
+pyarrow-hotfix==0.6
+pyclipper==1.3.0.post5
+pycocotools==2.0.7
+pycparser==2.21
+pydantic==2.10.6
+pydantic_core==2.27.2
+pydeck==0.9.0b1
+pyDOE2==1.3.0
+pydub==0.25.1
+pyfaidx==0.9.0.1
+Pygments==2.19.2
+PyJWT==2.8.0
+pymodbus==3.6.9
+PyMuPDF==1.23.16
+PyMuPDFb==1.23.9
+PyNaCl==1.6.2
+pynndescent==0.5.13
+Pyomo==6.8.2
+pyOpenSSL==24.1.0
+pypandoc==1.13
+pyparsing==3.1.4
+pypdf==4.2.0
+pypdfium2==4.29.0
+PyPika==0.48.9
+PyQt5==5.15.7
+PyQt5-Qt5==5.15.17
+PyQt5_sip==12.15.0
+pyro-api==0.1.2
+pyro-ppl==1.9.1
+pysam==0.23.3
+PySocks==1.7.1
+pysqlite3-binary==0.5.2.post3
+pystan==2.19.1.1
+pytesseract==0.3.10
+pytest-cov==5.0.0
+python-dateutil==2.9.0.post0
+python-decouple==3.8
+python-docx==1.1.0
+python-dotenv==1.0.1
+python-iso639==2024.4.27
+python-Levenshtein==0.25.1
+python-multipart==0.0.18
+python-pptx==0.6.23
+python-slugify==8.0.4
+pytorch-pretrained-bert==0.6.2
+pytz==2025.2
+pyvista==0.44.2
+PyWavelets==1.4.1
+PyYAML==6.0.3
+quantile-python==1.1
+rapidfuzz==3.8.1
+rapidocr-onnxruntime==1.3.8
+ray==2.10.0
+rdkit==2024.3.5
+redis==6.1.1
+referencing==0.35.1
+regex==2022.4.24
+requests==2.32.4
+requests-oauthlib==1.3.0
+responses==0.16.0
+rich==13.7.1
+rouge-score==0.1.2
+rpds-py==0.20.1
+rq==2.3.3
+rsa==4.7.2
+ruff==0.4.2
+rustworkx==0.15.1
+s3transfer==0.11.3
+sacrebleu==2.1.0
+sacremoses==0.0.46
+safetensors==0.4.3
+scanpy==1.9.8
+scipy==1.10.1
+scooby==0.10.1
+seaborn==0.13.2
+semantic-version==2.10.0
+sentence-transformers==2.2.2
+sentencepiece==0.1.91
+sentry-sdk==2.39.0
+session_info==1.0.1
+sgmllib3k==1.0.0
+shapely==2.0.4
+shellingham==1.5.4
+shortuuid==1.0.13
+six==1.17.0
+smart-open==6.4.0
+smmap==5.0.1
+sniffio==1.3.1
+snowballstemmer==2.2.0
+sobol-seq==0.2.0
+socksio==1.0.0
+soupsieve==2.5
+spacy-legacy==3.0.12
+spacy-loggers==1.0.5
+Sphinx==4.3.1
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+SQLAlchemy==2.0.19
+sqlparse==0.4.2
+sse-starlette==1.8.2
+starlette==0.44.0
+statsmodels==0.14.1
+stdlib-list==0.10.0
+streamlit==1.30.0
+streamlit-aggrid==0.3.4.post3
+streamlit-antd-components==0.3.1
+streamlit-chatbox==1.1.11
+streamlit-feedback==0.1.3
+streamlit-modal==0.1.0
+streamlit-option-menu==0.3.12
+strsimpy==0.2.1
+svgwrite==1.4.3
+tabnet @ git+https://github.com/titu1994/tf-TabNet.git@53b144b4dd47184c3ee891501dcd90fb37683ab7
+tabulate==0.8.9
+tenacity==8.2.3
+tensorboard-plugin-wit==1.8.0
+tensorboardX==2.4.1
+text-unidecode==1.3
+texttable==1.7.0
+thefuzz==0.22.1
+threadpoolctl==3.5.0
+tifffile==2023.7.10
+tiktoken==0.7.0
+timm==0.9.16
+tk==0.1.0
+tokenizers==0.20.3
+toml==0.10.2
+tomlkit==0.12.0
+toolz==0.12.1
+torch-geometric==2.6.1
+torchaudio==2.1.2+cu118
+torchtext==0.4.0
+tornado==6.4
+tqdm==4.67.1
+transformer-lens==2.16.1
+transformers==4.46.3
+transformers-stream-generator==0.0.5
+typed-argument-parser==1.10.1
+typeguard==4.4.0
+typer==0.9.4
+types-requests==2.31.0.20240406
+typing-inspect==0.9.0
+typing-utils==0.1.0
+typing_extensions==4.13.2
+tzdata==2024.1
+tzlocal==5.2
+umap-learn==0.5.7
+Unidecode==1.3.2
+unittest-xml-reporting==3.2.0
+unstructured==0.11.0
+unstructured-client==0.22.0
+unstructured-inference==0.7.15
+unstructured.pytesseract==0.3.12
+uvicorn==0.29.0
+uvloop==0.21.0
+validators==0.28.1
+vllm==0.2.7
+vtk==9.3.1
+wandb==0.22.0
+watchdog==3.0.0
+watchfiles==0.21.0
+wavedrom==2.0.3.post3
+weasel==0.3.4
+websocket-client==1.8.0
+websockets==13.1
+Werkzeug==2.0.2
+word2number==1.1
+xlrd==2.0.1
+XlsxWriter==3.0.2
+xxhash==2.0.2
+Yapsy==1.12.2
+yarl==1.15.2
+youtube-search==2.1.2
+zipp==3.20.2
+zope.event==4.5.0
+zstandard==0.23.0

configs/s41467_024_52081_3_test/explicit.txt

@@ -0,0 +1,31 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda#74784ee3d225fc3dca89edb635b4e5cc
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda#0be7c6e070c19105f966d3758448d018
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda#3baf8976c96134738bba224e9ef6b1e5
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda#f406dcbb2e7bef90d793e50e79a2882b
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda#28771437ffcd9f3417c66012dc49a3be
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.2-h26f9b46_0.conda#ffffb341206dd0dab0c36053c048d621
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda#0b367fad34931cb79e0d6b7e5c06bb1c
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96

configs/s41467_025_58227_1_test/env.yml

@@ -0,0 +1,56 @@
+name: s41467_025_58227_1_test
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=4.5
+  - bzip2=1.0.8
+  - ca-certificates=2025.10.5
+  - ld_impl_linux-64=2.44
+  - libffi=3.5.2
+  - libgcc=15.2.0
+  - libgcc-ng=15.2.0
+  - libgomp=15.2.0
+  - liblzma=5.8.1
+  - liblzma-devel=5.8.1
+  - libnsl=2.0.1
+  - libsqlite=3.51.0
+  - libstdcxx=15.2.0
+  - libuuid=2.41.2
+  - libxcrypt=4.4.36
+  - libzlib=1.3.1
+  - ncurses=6.5
+  - openssl=3.6.0
+  - pip=22.1.2
+  - python=3.8.20
+  - readline=8.2
+  - setuptools=70.3.0
+  - tk=8.6.13
+  - wheel=0.45.1
+  - xz=5.8.1
+  - xz-gpl-tools=5.8.1
+  - xz-tools=5.8.1
+  - zstd=1.5.7
+  - pip:
+    - appdirs==1.4.4
+    - certifi==2026.4.22
+    - depinfo==2.2.0
+    - diskcache==5.6.3
+    - gurobipy==11.0.3
+    - httpx==0.28.1
+    - idna==3.13
+    - importlib-resources==6.4.5
+    - mpmath==1.3.0
+    - numpy==1.24.4
+    - optlang==1.8.2
+    - pandas==2.0.3
+    - python-dateutil==2.9.0.post0
+    - python-libsbml==5.21.1
+    - ruamel-yaml==0.18.16
+    - ruamel-yaml-clib==0.2.8
+    - six==1.17.0
+    - swiglpk==5.0.13
+    - sympy==1.13.3
+    - tqdm==4.67.1
+prefix: /home/lily/yz979/anaconda3/envs/s41467_025_58227_1_test

configs/s41467_025_58227_1_test/explicit.txt

@@ -0,0 +1,33 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda#35f29eec58405aaf55e01cb470d8c26a
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hb9d3cd8_1.conda#d864d34357c3b65a4b731f78c0801dc4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda#80c07c68d2f6870250959dcc95b209d1
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda#9ee58d5c534af06558933af3c845a780
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda#f61edadbb301530bd65a32646bd81552
+https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.51.0-h0c1763c_0.conda#a3205ecbffb255ca27e0540c8494a2ee
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_hd72426e_102.conda#a0116df4f4ed05c303811a837d5b39d8
+https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.8.1-hbcc6ac9_2.conda#bf627c16aa26231720af037a2709ab09
+https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.8.1-hb9d3cd8_2.conda#1bad2995c8f1c8075c6c331bf96e46fb
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1aa0949_5.conda#511ed8935448c1875776b60ad3daf3a1
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.8.1-hbcc6ac9_2.conda#68eae977d7d1196d32b636a026dc015d
+https://conda.anaconda.org/conda-forge/linux-64/python-3.8.20-h4a871b0_2_cpython.conda#05ffff2f44ad60b94ecb53d029c6bdf7
+https://conda.anaconda.org/conda-forge/noarch/setuptools-70.3.0-pyhd8ed1ab_0.conda#693bb57e8f92120caa956898065f3627
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.45.1-pyhd8ed1ab_0.conda#bdb2f437ce62fd2f1fef9119a37a12d9
+https://conda.anaconda.org/conda-forge/noarch/pip-22.1.2-pyhd8ed1ab_0.tar.bz2#d29185c662a424f8bea1103270b85c96

configs/s41467_025_58227_1_test/meta.json

@@ -0,0 +1,8 @@
+{
+  "env": "s41467_025_58227_1_test",
+  "python_version": "3.8.20",
+  "has_cuda_hint": false,
+  "editable_count": 0,
+  "source_prefix": "/home/lily/yz979/anaconda3/envs/s41467_025_58227_1_test",
+  "exported_at": "2026-05-17T04:06:32Z"
+}

configs/s41467_025_58227_1_test/pip-clean.txt

@@ -0,0 +1,456 @@
+absl-py==2.3.1
+accelerate==0.24.1
+aiofiles==23.2.1
+aiohappyeyeballs==2.4.4
+aiohttp==3.10.11
+aioprometheus==23.12.0
+aiosignal==1.3.1
+alabaster==0.7.12
+allennlp==0.8.4
+altair==5.3.0
+annotated-types==0.6.0
+anyio==3.7.1
+appdirs==1.4.4
+APScheduler==3.11.2
+arxiv==2.1.0
+astunparse==1.6.3
+async-timeout==4.0.3
+attrs==25.3.0
+autograd==1.7.0
+autoray==0.6.12
+awscli==1.32.93
+azure-core==1.33.0
+azure-identity==1.21.0
+azure-storage-blob==12.26.0
+Babel==2.9.1
+backoff==2.2.1
+backports.zoneinfo==0.2.1
+bcrypt==4.1.2
+beartype==0.14.1
+better-abc==0.0.3
+biopython==1.83
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+bitsandbytes==0.43.1
+blessed==1.20.0
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+boto3==1.36.0
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+botorch==0.8.5
+bpl==0.1.1
+Brotli==1.1.0
+bs4==0.0.2
+cachetools==4.2.4
+certifi==2026.4.22
+cffi==1.15.0
+cftime==1.6.4.post1
+chaospy==3.3.9
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+chex==0.1.7
+chroma-hnswlib==0.7.3
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+cloudpathlib==0.16.0
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+confection==0.1.4
+ConfigArgParse==1.5.3
+conllu==0.11
+coverage==7.6.1
+cpm-kernels==1.0.11
+cryptography==42.0.5
+cvxopt==1.3.2
+cymem==2.0.8
+Cython==0.29.30
+dataclasses==0.6
+dataclasses-json==0.6.4
+datasets==2.19.0
+deepdiff==7.0.1
+depinfo==2.2.0
+Deprecated==1.2.14
+deprecation==2.1.0
+dill==0.3.8
+diskcache==5.6.3
+distro==1.9.0
+dm-tree==0.1.8
+dnspython==2.6.1
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+duckduckgo-search==3.9.9
+editdistance==0.6.0
+effdet==0.4.1
+einops==0.7.0
+email-validator==2.3.0
+emoji==2.11.1
+equinox==0.10.4
+et-xmlfile==1.1.0
+eval_type_backport==0.2.2
+exceptiongroup==1.2.1
+fairseq==0.10.2
+faiss-cpu==1.7.4
+faiss-gpu==1.7.2
+fancy-einsum==0.0.3
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+finch-clust @ git+https://github.com/ssarfraz/FINCH-Clustering.git@b18166999af5f93c66edba8bdbae096f8795e82c
+flaky==3.7.0
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+gitdb==4.0.11
+GitPython==3.1.43
+google-pasta==0.2.0
+googleapis-common-protos==1.63.0
+gpustat==1.1.1
+gpytorch==1.10
+gradio_client==0.16.0
+graphlib_backport==1.1.0
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+gunicorn==23.0.0
+gurobipy==11.0.3
+h11==0.14.0
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+httpcore==1.0.5
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+httpx-sse==0.4.0
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+importlib_resources==6.4.5
+inequalipy==1.0.5
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+jsonschema-specifications==2023.12.1
+kaggle==1.7.4.5
+Keras-Preprocessing==1.1.2
+kubernetes==29.0.0
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+langchain-community==0.0.34
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+pdf2image==1.17.0
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+PICOS==2.6.1
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