mirror of
https://github.com/HannesStark/boltzgen.git
synced 2026-06-04 11:54:23 +08:00
130 lines
3.3 KiB
TOML
Executable File
130 lines
3.3 KiB
TOML
Executable File
[build-system]
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requires = ["setuptools>=61"]
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build-backend = "setuptools.build_meta"
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# [build-system]
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# requires = ["setuptools>=68", "setuptools_scm[toml]>=8"]
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# build-backend = "setuptools.build_meta"
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[project]
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name = "boltzgen"
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requires-python = ">=3.11"
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version = "0.1.5"
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readme = { file = "PYPI_DESCRIPTION.md", content-type = "text/markdown" }
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description = "Protein design"
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dependencies = [
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# Add runtime dependencies here
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"numpy==2.0.2",
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"numba==0.61.0",
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"matplotlib",
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"hydride",
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"biotite",
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"pydssp",
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"logomaker",
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"gemmi==0.6.5",
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"torch>=2.4.1",
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"scikit-learn",
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"hydra-core",
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"edit_distance",
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"pytorch-lightning",
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"rdkit",
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"pandas",
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"pdbeccdutils",
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"einx",
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"einops",
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"mashumaro",
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"nvidia-ml-py>=12.535.133",
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"cuequivariance_ops_cu12>=0.5.0",
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"cuequivariance_ops_torch_cu12>=0.5.0",
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"cuequivariance_torch>=0.5.0",
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"huggingface_hub",
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"biopython",
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]
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# Enables the usage of setuptools_scm
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# [tool.setuptools_scm]
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[tool.setuptools]
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package-dir = {"" = "src"}
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include-package-data = true
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[tool.setuptools.packages.find]
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where = ["src"]
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[tool.setuptools.package-data]
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boltzgen = ["resources/config/**/*"]
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[project.scripts]
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boltzgen = "boltzgen.cli.boltzgen:main"
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[project.optional-dependencies]
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lint = ["ruff"]
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test = ["pytest"]
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doc = []
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build = []
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dev = [
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"redis",
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"wandb",
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"requests",
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"types-requests==2.32.4.*",
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"boltzgen[lint]",
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"boltzgen[test]",
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"boltzgen[doc]",
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"boltzgen[build]",
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]
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[tool.ruff]
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src = ["src"]
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extend-exclude = ["conf.py"]
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target-version = "py38"
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lint.select = ["ALL"]
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lint.ignore = [
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"COM812", # Conflicts with the formatter
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"ISC001", # Conflicts with the formatter
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"ANN101", # "missing-type-self"
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"RET504", # Unnecessary assignment to `x` before `return` statementRuff
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"S101", # Use of `assert` detected
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"D100", # Missing docstring in public module
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"D104", # Missing docstring in public package
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"PT001", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
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"PT004", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
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"PT005", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
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"PT023", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
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"FBT001",
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"FBT002",
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"PLR0913", # Too many arguments to init (> 5)
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"TRY003", # Exception messages
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"EM101", # Exception messages
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"FA102", # typing
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"T201", # Print statements
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]
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[tool.ruff.lint.per-file-ignores]
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"tests/**" = [
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"S101", # Use of `assert` detected
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"D103", # Missing docstring in public function
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]
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"**/__init__.py" = [
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"F401", # Imported but unused
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"F403", # Wildcard imports
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]
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"docs/**" = [
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"INP001", # Requires __init__.py but folder is not a package.
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]
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"scripts/**" = [
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"INP001", # Requires __init__.py but folder is not a package.
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]
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[tool.ruff.lint.pyupgrade]
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# Preserve types, even if a file imports `from __future__ import annotations`(https://github.com/astral-sh/ruff/issues/5434)
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keep-runtime-typing = true
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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[tool.mypy]
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# Functions need to be annotated
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disallow_untyped_defs = true
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warn_unused_ignores = true
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exclude = ["configs/", "build/", "dist/", "docs/", "tests/"]
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