mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
fff63051b4
* Harden MMseqs species ID resolution fallback * Reorganize tests for CPU coverage CI * New * Fix function coverage checker def-line false positives * Expand unit coverage for helper and backend manager utilities * New. * New. * Expand unit coverage for template and post-processing helpers * Expand unit coverage for objects.py edge cases * Publish HTML coverage reports via GitHub Pages * Add CPU unit coverage for AlphaFold3 backend helpers * Reorganize tests and expand backend coverage * Reset shared test flags between cases * Expand AF3 prepare_input unit coverage * Cover AF3 and truemultimer feature creation * Test AF3 multimer MSA translation paths * Cover AF3 duplicate-residue multimer fallback * Cover AF2 resume and postprocess edge paths * Cover AF3 template mmCIF preparation * Test small script entry points * Expand workflow and ModelCIF test coverage * Add backend extras and install guide * Clarify AF3 backend installation path * Stabilize cluster GPU test runners * Document AF3 CMake SQLite hints * Simplify backend installation guide * Align AF3 install with working cluster env * Backfill typing dataclass_transform for AF2 * Pin TensorFlow for cluster installs * Fallback AF2 relax when CUDA OpenMM is unavailable * Raise AF3 default minimum bucket size * Simplify backend cluster installation guide * Fix AF3 wrapper JSON output isolation * Fix AF3 JSON wrapper outputs and MMseqs ID parsing * Fix CI entrypoint stub and Python 3.8 typing * Document release readiness test gates
143 lines
3.8 KiB
TOML
143 lines
3.8 KiB
TOML
[build-system]
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requires = ["setuptools<82", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "alphapulldown"
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description = "Pipeline allows massive screening using alphafold"
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readme = { file = "README.md", content-type = "text/markdown" }
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requires-python = ">=3.8"
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license = "MIT"
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license-files = ["LICENSE"]
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authors = [
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{ name = "EMBL Hamburg", email = "alphapulldown@embl-hamburg.de" }
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]
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classifiers = [
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"Programming Language :: Python :: 3",
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"Operating System :: OS Independent",
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]
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dynamic = ["version"]
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dependencies = [
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"absl-py>=0.13.0",
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"alphapulldown-input-parser>=0.4.0",
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"dm-haiku",
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"dm-tree>=0.1.6",
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"h5py>=3.1.0",
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"matplotlib>=3.3.3",
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"ml-collections>=0.1.0",
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"pandas>=1.5.3",
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"tensorflow-cpu==2.20.0",
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"importlib-resources>=6.1.0",
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"importlib-metadata>=4.8.2,<5.0.0",
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"biopython>=1.81,<1.82",
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"nbformat>=5.9.2",
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"py3Dmol==2.0.4",
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"ipython==8.16.1",
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"tqdm>=4.66.1",
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"appdirs>=1.4.4",
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"jupyterlab>=3.0",
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"ipywidgets",
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"ml-dtypes",
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"chex>=0.1.86",
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"immutabledict>=2.0.0",
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"typing-extensions==4.14.0",
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]
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[project.optional-dependencies]
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alphafold2 = [
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"jax==0.5.3",
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"jax[cuda12]==0.5.3; platform_system == 'Linux' and platform_machine == 'x86_64'",
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"modelcif>=1.6",
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"numpy<2",
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"openmm>=8.2",
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"pdbfixer>=1.10",
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]
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alphafold3 = [
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"jaxtyping==0.2.34",
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"jax==0.5.3",
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"jax[cuda12]==0.5.3; platform_system == 'Linux' and platform_machine == 'x86_64'",
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"jax-triton==0.2.0; platform_system == 'Linux' and platform_machine == 'x86_64'",
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"modelcif>=1.6",
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"numpy<2",
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"openmm>=8.2",
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"pdbfixer>=1.10",
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"rdkit==2024.3.5",
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"triton==3.1.0; platform_system == 'Linux' and platform_machine == 'x86_64'",
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"typeguard==2.13.3",
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"zstandard",
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]
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test = [
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"parameterized",
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"pytest>=8.0",
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"pytest-cov>=5.0",
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"pytest-timeout>=2.3",
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"pytest-xdist>=3.6",
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]
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[project.urls]
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Homepage = "https://github.com/KosinskiLab/AlphaPulldown"
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[tool.setuptools]
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include-package-data = true
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packages = [
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"alphapulldown",
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"alphapulldown.utils",
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"alphapulldown.folding_backend",
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"alphapulldown.analysis_pipeline",
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"alphapulldown.scripts",
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"alphafold",
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"alphafold.data",
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"alphafold.data.tools",
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"alphafold.common",
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"alphafold.relax",
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"alphafold.model",
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"alphafold.model.geometry",
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"alphafold.model.tf",
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"alphafold.notebooks",
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"alphafold3",
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"alphafold3.structure",
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"colabfold",
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"analysis_pipeline",
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"af2plots",
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"unifold",
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"unifold.data",
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"unifold.modules",
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"unifold.msa",
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"unifold.losses",
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"unifold.symmetry",
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]
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script-files = [
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"./alphapulldown/scripts/create_individual_features.py",
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"./alphapulldown/scripts/run_multimer_jobs.py",
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"./alphapulldown/analysis_pipeline/create_notebook.py",
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"./alphapulldown/analysis_pipeline/get_good_inter_pae.py",
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"./alphapulldown/scripts/rename_colab_search_a3m.py",
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"./alphapulldown/scripts/prepare_seq_names.py",
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"./alphapulldown/scripts/generate_crosslink_pickle.py",
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"./alphapulldown/scripts/convert_to_modelcif.py",
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"./alphapulldown/scripts/run_structure_prediction.py",
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"./alphapulldown/scripts/truncate_pickles.py",
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"./alphafold/run_alphafold.py",
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]
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[tool.setuptools.package-dir]
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"" = "."
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"alphapulldown" = "./alphapulldown"
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"alphapulldown.folding_backend" = "./alphapulldown/folding_backend"
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"alphafold" = "./alphafold/alphafold"
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"alphafold3" = "./alphafold3/src/alphafold3"
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"alphafold3.structure" = "./alphafold3/src/alphafold3/structure"
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"colabfold" = "./ColabFold/colabfold"
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"analysis_pipeline" = "./alphapulldown/analysis_pipeline"
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"af2plots" = "./alphapulldown/analysis_pipeline/af2plots/af2plots"
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"unifold" = "./AlphaLink2/unifold/"
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"unifold.data" = "./AlphaLink2/unifold/data"
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"unifold.losses" = "./AlphaLink2/unifold/losses"
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"unifold.symmetry" = "./AlphaLink2/unifold/symmetry"
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[tool.setuptools.package-data]
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"alphafold.common" = ["stereo_chemical_props.txt"]
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[tool.setuptools.dynamic]
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version = { attr = "alphapulldown.__version__" }
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