env

environment.yml

@@ -4,7 +4,431 @@ channels:
   - omnia
   - defaults
 dependencies:
-  - python=3.10
-  - conda-forge::ripgrep
-  - git-lfs
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - bzip2=1.0.8=h5eee18b_6
+  - ca-certificates=2025.11.12=hbd8a1cb_0
+  - certifi=2025.11.12=pyhd8ed1ab_0
+  - expat=2.7.1=h6a678d5_0
+  - git-lfs=3.7.1=h6138981_0
+  - ld_impl_linux-64=2.40=h12ee557_0
+  - libffi=3.4.4=h6a678d5_1
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libuuid=1.41.5=h5eee18b_0
+  - libxcb=1.17.0=h9b100fa_0
+  - ncurses=6.5=h7934f7d_0
+  - openssl=3.0.17=h5eee18b_0
+  - pip=25.1=pyhc872135_2
+  - pthread-stubs=0.3=h0ce48e5_1
+  - python=3.10.18=h1a3bd86_0
+  - readline=8.3=hc2a1206_0
+  - ripgrep=13.0.0=h2f28480_2
+  - sqlite=3.50.2=hb25bd0a_1
+  - tk=8.6.15=h54e0aa7_0
+  - wheel=0.45.1=py310h06a4308_0
+  - xorg-libx11=1.8.12=h9b100fa_1
+  - xorg-libxau=1.0.12=h9b100fa_0
+  - xorg-libxdmcp=1.1.5=h9b100fa_0
+  - xorg-xorgproto=2024.1=h5eee18b_1
+  - xz=5.6.4=h5eee18b_1
+  - zlib=1.2.13=h5eee18b_1
+  - pip:
+      - about-time==4.2.1
+      - absl-py==2.3.1
+      - accelerate==1.10.0
+      - aiofiles==23.2.1
+      - aiohappyeyeballs==2.6.1
+      - aiohttp==3.12.15
+      - aiosignal==1.4.0
+      - alembic==1.17.2
+      - alive-progress==3.3.0
+      - anndata==0.11.4
+      - annotated-doc==0.0.3
+      - annotated-types==0.7.0
+      - antlr4-python3-runtime==4.9.3
+      - anyio==4.10.0
+      - argon2-cffi==25.1.0
+      - argon2-cffi-bindings==25.1.0
+      - array-api-compat==1.12.0
+      - arrow==1.3.0
+      - ase==3.26.0
+      - astroid==3.3.11
+      - asttokens==3.0.0
+      - astunparse==1.6.3
+      - async-lru==2.0.5
+      - async-timeout==5.0.1
+      - attrs==25.3.0
+      - autograd==1.8.0
+      - autopep8==2.0.4
+      - babel==2.17.0
+      - beautifulsoup4==4.13.4
+      - biopython==1.85
+      - biotite==0.41.2
+      - biotraj==1.2.2
+      - black==25.1.0
+      - bleach==6.2.0
+      - blosum==2.0.3
+      - bokeh==3.6.3
+      - brotli==1.2.0
+      - cachetools==6.2.3
+      - cffi==1.17.1
+      - cftime==1.6.4.post1
+      - charset-normalizer==3.4.3
+      - click==8.2.1
+      - cloudpathlib==0.23.0
+      - cloudpickle==3.1.2
+      - cma==4.4.0
+      - colorama==0.4.6
+      - colorcet==3.1.0
+      - colorlog==6.10.1
+      - comm==0.2.3
+      - contourpy==1.3.2
+      - cucim-cu12==25.12.0
+      - cuda-bindings==12.9.4
+      - cuda-core==0.3.2
+      - cuda-pathfinder==1.3.3
+      - cuda-python==12.9.4
+      - cuda-toolkit==12.9.1
+      - cudf-cu12==25.12.0
+      - cugraph-cu12==25.12.2
+      - cuml-cu12==25.12.0
+      - cupy-cuda12x==13.6.0
+      - cuvs-cu12==25.12.0
+      - cuxfilter-cu12==25.12.0
+      - cycler==0.12.1
+      - dask==2025.9.1
+      - dask-cuda==25.12.0
+      - dask-cudf-cu12==25.12.0
+      - datasets==4.0.0
+      - datashader==0.18.2
+      - debugpy==1.8.16
+      - decorator==5.2.1
+      - deeptime==0.4.5
+      - defusedxml==0.7.1
+      - deprecated==1.2.18
+      - dill==0.3.8
+      - distributed==2025.9.1
+      - distributed-ucxx-cu12==0.47.0
+      - docstring-to-markdown==0.17
+      - einops==0.8.1
+      - exceptiongroup==1.3.0
+      - executing==2.2.0
+      - fair-esm==2.0.0
+      - fastapi==0.121.0
+      - fastjsonschema==2.21.2
+      - fastprogress==1.0.3
+      - fastrlock==0.8.3
+      - ffmpy==0.6.4
+      - filelock==3.19.1
+      - flake8==7.1.2
+      - flatbuffers==25.9.23
+      - fonttools==4.60.0
+      - fqdn==1.5.1
+      - frozenlist==1.7.0
+      - fsspec==2025.3.0
+      - gast==0.6.0
+      - gensim==4.4.0
+      - geopandas==1.1.1
+      - gitdb==4.0.12
+      - gitpython==3.1.45
+      - google-pasta==0.2.0
+      - gradio==5.20.1
+      - gradio-client==1.7.2
+      - graphemeu==0.7.2
+      - greenlet==3.3.0
+      - groovy==0.1.2
+      - grpcio==1.76.0
+      - h11==0.16.0
+      - h5py==3.14.0
+      - hf-xet==1.1.8
+      - holoviews==1.20.2
+      - httpcore==1.0.9
+      - httpx==0.28.1
+      - huggingface-hub==0.35.3
+      - humanfriendly==10.0
+      - hydra-core==1.3.2
+      - idna==3.10
+      - igraph==1.0.0
+      - imageio==2.37.0
+      - importlib-metadata==8.7.0
+      - inquirerpy==0.3.4
+      - ipykernel==6.30.1
+      - ipython==8.37.0
+      - isoduration==20.11.0
+      - isort==6.0.1
+      - iterative-stratification==0.1.9
+      - jedi==0.19.2
+      - jinja2==3.1.6
+      - joblib==1.5.1
+      - json5==0.12.1
+      - jsonpointer==3.0.0
+      - jsonschema==4.25.1
+      - jsonschema-specifications==2025.4.1
+      - jupyter-client==8.6.3
+      - jupyter-core==5.8.1
+      - jupyter-events==0.12.0
+      - jupyter-lsp==2.2.6
+      - jupyter-server==2.16.0
+      - jupyter-server-mathjax==0.2.6
+      - jupyter-server-proxy==4.4.0
+      - jupyter-server-terminals==0.5.3
+      - jupyterlab==4.4.6
+      - jupyterlab-code-formatter==3.0.2
+      - jupyterlab-git==0.51.2
+      - jupyterlab-lsp==5.2.0
+      - jupyterlab-pygments==0.3.0
+      - jupyterlab-search-replace==1.1.0
+      - jupyterlab-server==2.27.3
+      - jupyterlab-spreadsheet-editor==0.7.2
+      - keras==3.12.0
+      - kiwisolver==1.4.9
+      - lark==1.2.2
+      - lazy-loader==0.4
+      - lckr-jupyterlab-variableinspector==3.2.4
+      - legacy-api-wrap==1.5
+      - leidenalg==0.11.0
+      - libclang==18.1.1
+      - libcudf-cu12==25.12.0
+      - libcugraph-cu12==25.12.2
+      - libcuml-cu12==25.12.0
+      - libcuvs-cu12==25.12.0
+      - libkvikio-cu12==25.12.0
+      - libraft-cu12==25.12.0
+      - librmm-cu12==25.12.0
+      - libucx-cu12==1.19.0
+      - libucxx-cu12==0.47.0
+      - lightning==2.5.5
+      - lightning-utilities==0.15.2
+      - linearboost==0.1.4
+      - linkify-it-py==2.0.3
+      - llvmlite==0.44.0
+      - locket==1.0.0
+      - loguru==0.7.3
+      - mako==1.3.10
+      - markdown==3.9
+      - markdown-it-py==4.0.0
+      - markupsafe==2.1.5
+      - matplotlib==3.10.6
+      - matplotlib-inline==0.1.7
+      - mccabe==0.7.0
+      - mdit-py-plugins==0.5.0
+      - mdshare==0.4.2
+      - mdtraj==1.10.3
+      - mdurl==0.1.2
+      - mistune==3.1.3
+      - ml-dtypes==0.5.3
+      - mpmath==1.3.0
+      - msgpack==1.1.2
+      - msgpack-numpy==0.4.8
+      - multidict==6.6.4
+      - multipledispatch==1.0.0
+      - multiprocess==0.70.16
+      - mypy-extensions==1.1.0
+      - namex==0.1.0
+      - natsort==8.4.0
+      - nbclient==0.10.2
+      - nbconvert==7.16.6
+      - nbdime==4.0.2
+      - nbformat==5.10.4
+      - nest-asyncio==1.6.0
+      - netcdf4==1.7.2
+      - networkx==3.4.2
+      - notebook==7.4.5
+      - notebook-shim==0.2.4
+      - numba==0.61.2
+      - numba-cuda==0.19.1
+      - numpy==1.26.4
+      - nvidia-cublas-cu12==12.8.4.1
+      - nvidia-cuda-cccl-cu12==12.9.27
+      - nvidia-cuda-cupti-cu12==12.8.90
+      - nvidia-cuda-nvcc-cu12==12.9.86
+      - nvidia-cuda-nvrtc-cu12==12.8.93
+      - nvidia-cuda-runtime-cu12==12.8.90
+      - nvidia-cudnn-cu12==9.10.2.21
+      - nvidia-cufft-cu12==11.3.3.83
+      - nvidia-cufile-cu12==1.13.1.3
+      - nvidia-curand-cu12==10.3.9.90
+      - nvidia-cusolver-cu12==11.7.3.90
+      - nvidia-cusparse-cu12==12.5.8.93
+      - nvidia-cusparselt-cu12==0.7.1
+      - nvidia-ml-py==13.590.44
+      - nvidia-nccl-cu12==2.27.3
+      - nvidia-nvimgcodec-cu12==0.6.1.37
+      - nvidia-nvjitlink-cu12==12.8.93
+      - nvidia-nvtx-cu12==12.8.90
+      - nvtx==0.2.14
+      - nx-cugraph-cu12==25.12.0
+      - omegaconf==2.3.0
+      - opt-einsum==3.4.0
+      - optree==0.17.0
+      - optuna==4.6.0
+      - orjson==3.11.4
+      - overrides==7.7.0
+      - p2smi==1.1.1
+      - packaging==25.0
+      - pandas==2.3.2
+      - pandocfilters==1.5.1
+      - panel==1.7.5
+      - param==2.3.1
+      - paretoflow==0.1.5
+      - parso==0.8.4
+      - partd==1.4.2
+      - pathos==0.3.2
+      - pathspec==0.12.1
+      - patsy==1.0.2
+      - peft==0.17.1
+      - pexpect==4.9.0
+      - pfzy==0.3.4
+      - pillow==11.3.0
+      - platformdirs==4.3.8
+      - pluggy==1.6.0
+      - pox==0.3.6
+      - ppft==1.7.7
+      - prdc==0.2
+      - prometheus-client==0.22.1
+      - prompt-toolkit==3.0.51
+      - propcache==0.3.2
+      - protobuf==6.32.0
+      - psutil==7.0.0
+      - ptyprocess==0.7.0
+      - pure-eval==0.2.3
+      - pyarrow==21.0.0
+      - pycodestyle==2.12.1
+      - pycparser==2.22
+      - pyct==0.6.0
+      - pydantic==2.11.9
+      - pydantic-core==2.33.2
+      - pydocstyle==6.3.0
+      - pydub==0.25.1
+      - pyemma==2.5.12
+      - pyflakes==3.2.0
+      - pygments==2.19.2
+      - pylibcudf-cu12==25.12.0
+      - pylibcugraph-cu12==25.12.2
+      - pylibraft-cu12==25.12.0
+      - pylint==3.3.8
+      - pymoo==0.6.1.5
+      - pynndescent==0.5.13
+      - pyogrio==0.12.1
+      - pyparsing==3.2.5
+      - pyproj==3.7.1
+      - python-dateutil==2.9.0.post0
+      - python-json-logger==3.3.0
+      - python-lsp-jsonrpc==1.1.2
+      - python-lsp-server==1.13.0
+      - python-multipart==0.0.20
+      - pytoolconfig==1.3.1
+      - pytorch-lightning==2.5.5
+      - pytorch-lightning-bolts==0.3.2.post1
+      - pytorch-metric-learning==2.9.0
+      - pytz==2025.2
+      - pyviz-comms==3.0.6
+      - pyyaml==6.0.2
+      - pyzmq==27.0.1
+      - raft-dask-cu12==25.12.0
+      - rapids-dask-dependency==25.12.0
+      - rapids-logger==0.2.3
+      - rdkit==2025.9.1
+      - referencing==0.36.2
+      - regex==2025.7.34
+      - requests==2.32.5
+      - requests-toolbelt==1.0.0
+      - rfc3339-validator==0.1.4
+      - rfc3986-validator==0.1.1
+      - rfc3987-syntax==1.1.0
+      - rich==14.1.0
+      - rmm-cu12==25.12.0
+      - rope==1.14.0
+      - rpds-py==0.27.0
+      - ruff==0.14.3
+      - safehttpx==0.1.7
+      - safetensors==0.6.2
+      - scanpy==1.11.5
+      - schedulefree==1.4.1
+      - scikit-image==0.25.2
+      - scikit-learn==1.7.1
+      - scipy==1.15.3
+      - seaborn==0.13.2
+      - semantic-version==2.10.0
+      - send2trash==1.8.3
+      - sentry-sdk==2.35.0
+      - session-info2==0.2.3
+      - setuptools==80.9.0
+      - shapely==2.0.7
+      - shellingham==1.5.4
+      - simpervisor==1.0.0
+      - six==1.17.0
+      - smart-open==7.4.3
+      - smilespe==0.0.3
+      - smmap==5.0.2
+      - sniffio==1.3.1
+      - snowballstemmer==3.0.1
+      - sortedcontainers==2.4.0
+      - soupsieve==2.7
+      - sqlalchemy==2.0.45
+      - stack-data==0.6.3
+      - starlette==0.49.3
+      - statsmodels==0.14.5
+      - sympy==1.14.0
+      - tblib==3.2.2
+      - tenacity==9.1.2
+      - tensorboard==2.20.0
+      - tensorboard-data-server==0.7.2
+      - tensorflow==2.20.0
+      - termcolor==3.2.0
+      - terminado==0.18.1
+      - texttable==1.7.0
+      - threadpoolctl==3.6.0
+      - tifffile==2025.5.10
+      - timm==1.0.22
+      - tinycss2==1.4.0
+      - tokenizers==0.20.3
+      - tomli==2.2.1
+      - tomlkit==0.13.3
+      - toolz==1.1.0
+      - torch==2.8.0
+      - torch-geometric==2.6.1
+      - torchaudio==2.8.0+cu128
+      - torchmetrics==1.8.2
+      - torchtext==0.18.0
+      - torchvision==0.23.0+cu128
+      - tornado==6.5.2
+      - tqdm==4.67.1
+      - traitlets==5.14.3
+      - transformers==4.46.0
+      - treelite==4.6.1
+      - triton==3.4.0
+      - typer==0.20.0
+      - types-python-dateutil==2.9.0.20250809
+      - typing-extensions==4.15.0
+      - typing-inspection==0.4.1
+      - tzdata==2025.2
+      - uc-micro-py==1.0.3
+      - ucxx-cu12==0.47.0
+      - ujson==5.11.0
+      - umap-learn==0.5.9.post2
+      - uri-template==1.3.0
+      - urllib3==2.5.0
+      - uvicorn==0.38.0
+      - vampnet==0.1.4.dev16+gc88ed3f0f.d20251028
+      - wandb==0.21.1
+      - wcwidth==0.2.13
+      - webcolors==24.11.1
+      - webencodings==0.5.1
+      - websocket-client==1.8.0
+      - websockets==15.0.1
+      - werkzeug==3.1.3
+      - whatthepatch==1.0.7
+      - wrapt==1.17.3
+      - xarray==2025.6.1
+      - xgboost==3.0.4
+      - xxhash==3.5.0
+      - xyzservices==2025.11.0
+      - yapf==0.43.0
+      - yarl==1.20.1
+      - zict==3.0.0
+      - zipp==3.23.0
+      - zstd==1.5.7.2
 prefix: /vast/projects/pranam/lab/yz927/envs/metal