mirror of
https://github.com/RosettaCommons/foundry.git
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5a492032d5
* Initial commit of chiral changes Initial checkin of chiral feature code Add chiral metric * Update the way chiral features are incorporated into the model Move initialization to new func use default pytorch reset parameters fix initialization for chirals config rename argument of confidence head fix initialization for chirals * refactor: src nest, rename rf2aa to modelhub * refactor: initial commit without projects * Initial commit of chiral changes * Initial checkin of chiral feature code * Add chiral metric * Remove option for double residual connection. Add kq_norm oiptions to base (20250125) config. * Restoring flag * config * rename argument of confidence head * Update the way chiral features are incorporated into the model * config * rename argument of confidence head * Update the way chiral features are incorporated into the model * Initial commit of chiral changes Initial checkin of chiral feature code Add chiral metric * Update the way chiral features are incorporated into the model Move initialization to new func use default pytorch reset parameters fix initialization for chirals config rename argument of confidence head fix initialization for chirals * refactor: new modelhub --------- Co-authored-by: fdimaio <dimaio@uw.edu> Co-authored-by: HaotianZhangAI4Science <haotianzhang@zju.edu.cn>
86 lines
3.6 KiB
YAML
86 lines
3.6 KiB
YAML
name: modelhub
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channels:
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- nvidia/label/cuda-12.4.0
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- pytorch
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- pyg
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- conda-forge
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- defaults
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dependencies:
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# Core dependencies
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- pip
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- python=3.11
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- cuda
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- pytorch=2.4
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- pytorch-cuda=12.4
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- pytorch-scatter>=2.1.0,<3
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- lightning>=2.4.0,<2.5
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# Small molecule libraries
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- rdkit>=2024.3.5
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- openbabel=3.1.1
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- pip:
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# Project-related dependencies
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# ... generic tools
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- GitPython>=3.0.0,<4 # GitPython is a Python library used to interact with Git repositories
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- cython>=3.0.0,<4 # Cython compiler for C extensions
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- cytoolz>=0.12.3,<1 # Cython-optimized tools for itertools and functional programming
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- assertpy>=1.1.0,<2 # Assertions library
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- tqdm>=4.65.0,<5 # Fast, extensible progress bar for loops and more
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- rootutils>=1.0.7,<1.1 # Setting up the project root paths
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- dm-tree>=0.1.6,<1 # Tree data structure from DeepMind
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- deepdiff>=8.0.0,<9 # Deep difference and search of any Python object
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# ... configuration & CLI
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- fire>=0.6.0,<1 # Better argument parsing than argparse
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- hydra-core>=1.3.0,<1.4 # Config management framework
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- environs>=11.0.0,<12
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# ... linear algebra, maths & ml
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- numpy>=1.25.0,<2
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- scipy>=1.13.1,<2
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- einops>=0.8.0,<1
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- einx>=0.1.0,<1
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- opt_einsum>=3.4.0,<4
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- deepspeed>=0.15.1 # will be uninstalled by the apptainer's `spec` file, if pre-compiling
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# ... data tools
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- pandas>=2.2,<2.3 # Data manipulation and analysis
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- pyarrow==17.0.0 # Columnar data format for efficient data storage and processing
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- fastparquet==2024.5.0 # Fast Parquet file format implementation
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- seaborn>=0.13.0,<1
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# ... bioinformatics
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- biopython>=1.83,<2 # Collection of Python modules for bioinformatics
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- py3Dmol>=2.2.1,<3 # Python wrapper for 3Dmol.js
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- pymol-remote>=0.0.5 # Remote access to PyMOL from Python (has no dependencies)
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- git+https://github.com/biotite-dev/biotite.git@fab175e7ba4608d9613f092ad4e080661c6cc816
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- hydride==1.2.3 #biotite supported hydrogen addition
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# ... logging
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- wandb>=0.15.10,<1
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- rich>=13.9.4,<14
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# Formatting & linting (only needed for development)
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- ruff==0.8.3 # python linter & formatter
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- pre-commit==3.7.1 # pre-commit hooks for formatting & linting
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# Debugger & interactive tools (only needed for development)
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- debugpy>=1.8.5,<2 # debugger for python
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- ipykernel>=6.29.4,<7 # ipython kernel for jupyter
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- icecream>=2.0.0,<3 # print debugging
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- pymol-remote>=0.1.0 # Remote access to PyMOL from Python (has no dependencies)
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- ipdb>=0.13.9 # IPython debugger
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# Pytest plugins (only needed for development)
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- pytest>=8.2.0,<9 # testing framework
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- pytest-testmon>=2.1.1,<3 # run only tests related to changed code
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- pytest-xdist>=3.6.1,<4 # run tests in parallel
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- pytest-dotenv>=0.5.2,<1 # load environment variables from .env file
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- pytest-cov>=4.1.0,<5 # generate coverage report
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- pytest-benchmark>=5.0.0,<6 # benchmark tests for speed
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# Typing & documentation (only needed for development)
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- jaxtyping>=0.2.17,<1
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- beartype>=0.18.0,<1
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# NOTE: After navigating to the datahub / cifutils / modelhub directories, you can install the local package in editable mode with:
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# pip install -e .
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# NOTE: By default, DeepSpeed just-in-time compiles, which may take 3-4 minutes when first running the code on a new machine.
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# It may be possible to pre-compile DeepSpeed within a `conda` environment; see: https://www.deepspeed.ai/tutorials/advanced-install/
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# By default, the apptainers will have DeepSpeed pre-compiled, so when performance is a concern, it is recommended to use the apptainers.
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