BoltzGen / conf /upstream /pyproject.toml

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[build-system]
requires = ["setuptools>=61"]
build-backend = "setuptools.build_meta"

# [build-system]
# requires = ["setuptools>=68", "setuptools_scm[toml]>=8"]
# build-backend = "setuptools.build_meta"

[project]
name = "boltzgen"
requires-python = ">=3.11"
version = "0.3.2"
readme = { file = "PYPI_DESCRIPTION.md", content-type = "text/markdown" }
description = "Protein design"
dependencies = [
    # Add runtime dependencies here
    "numpy==2.0.2",
    "numba==0.61.0",
    "matplotlib",
    "hydride",
    "biotite",
    "pydssp",
    "logomaker",
    "gemmi>=0.6.5",  # Supports both 0.6.x and 0.7.x (see mmcif.py for compatibility layer)
    "torch>=2.4.1",
    "scikit-learn",
    "hydra-core",
    "edit_distance",
    "pytorch-lightning",
    "rdkit",
    "pandas",
    "pdbeccdutils",
    "einx",
    "einops",
    "mashumaro",
    "nvidia-ml-py>=12.535.133",
    "cuequivariance_ops_cu12>=0.5.0",
    "cuequivariance_ops_torch_cu12>=0.5.0",
    "cuequivariance_torch>=0.5.0",
    "huggingface_hub",
    "biopython", 
]

# Enables the usage of setuptools_scm
# [tool.setuptools_scm]

[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = true

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
boltzgen = ["resources/config/**/*"]

[project.scripts]
boltzgen = "boltzgen.cli.boltzgen:main"

[project.optional-dependencies]
lint = ["ruff"]
test = ["pytest"]
doc = []
build = []
dev = [
    "redis",
    "wandb",
    "requests",
    "types-requests==2.32.4.*",
    "boltzgen[lint]",
    "boltzgen[test]",
    "boltzgen[doc]",
    "boltzgen[build]",
]

[tool.ruff]
src = ["src"]
extend-exclude = ["conf.py"]
target-version = "py38"
lint.select = ["ALL"]
lint.ignore = [
    "COM812",  # Conflicts with the formatter
    "ISC001",  # Conflicts with the formatter
    "ANN101",  # "missing-type-self"
    "RET504",  # Unnecessary assignment to `x` before `return` statementRuff
    "S101",    # Use of `assert` detected
    "D100",    # Missing docstring in public module
    "D104",    # Missing docstring in public package
    "PT001",   # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
    "PT004",   # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
    "PT005",   # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
    "PT023",   # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
    "FBT001",
    "FBT002",
    "PLR0913", # Too many arguments to init (> 5)
    "TRY003",  # Exception messages
    "EM101",   # Exception messages
    "FA102",   # typing
    "T201",    # Print statements
]

[tool.ruff.lint.per-file-ignores]
"tests/**" = [
    "S101", # Use of `assert` detected
    "D103", # Missing docstring in public function
]
"**/__init__.py" = [
    "F401", # Imported but unused
    "F403", # Wildcard imports
]
"docs/**" = [
    "INP001", # Requires __init__.py but folder is not a package.
]
"scripts/**" = [
    "INP001", # Requires __init__.py but folder is not a package.
]

[tool.ruff.lint.pyupgrade]
# Preserve types, even if a file imports `from __future__ import annotations`(https://github.com/astral-sh/ruff/issues/5434)
keep-runtime-typing = true

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.mypy]
# Functions need to be annotated
disallow_untyped_defs = true
warn_unused_ignores = true
exclude = ["configs/", "build/", "dist/", "docs/", "tests/"]

	[build-system]
	requires = ["setuptools>=61"]
	build-backend = "setuptools.build_meta"

	# [build-system]
	# requires = ["setuptools>=68", "setuptools_scm[toml]>=8"]
	# build-backend = "setuptools.build_meta"

	[project]
	name = "boltzgen"
	requires-python = ">=3.11"
	version = "0.3.2"
	readme = { file = "PYPI_DESCRIPTION.md", content-type = "text/markdown" }
	description = "Protein design"
	dependencies = [
	# Add runtime dependencies here
	"numpy==2.0.2",
	"numba==0.61.0",
	"matplotlib",
	"hydride",
	"biotite",
	"pydssp",
	"logomaker",
	"gemmi>=0.6.5", # Supports both 0.6.x and 0.7.x (see mmcif.py for compatibility layer)
	"torch>=2.4.1",
	"scikit-learn",
	"hydra-core",
	"edit_distance",
	"pytorch-lightning",
	"rdkit",
	"pandas",
	"pdbeccdutils",
	"einx",
	"einops",
	"mashumaro",
	"nvidia-ml-py>=12.535.133",
	"cuequivariance_ops_cu12>=0.5.0",
	"cuequivariance_ops_torch_cu12>=0.5.0",
	"cuequivariance_torch>=0.5.0",
	"huggingface_hub",
	"biopython",
	]

	# Enables the usage of setuptools_scm
	# [tool.setuptools_scm]

	[tool.setuptools]
	package-dir = {"" = "src"}
	include-package-data = true

	[tool.setuptools.packages.find]
	where = ["src"]

	[tool.setuptools.package-data]
	boltzgen = ["resources/config/*/"]

	[project.scripts]
	boltzgen = "boltzgen.cli.boltzgen:main"

	[project.optional-dependencies]
	lint = ["ruff"]
	test = ["pytest"]
	doc = []
	build = []
	dev = [
	"redis",
	"wandb",
	"requests",
	"types-requests==2.32.4.*",
	"boltzgen[lint]",
	"boltzgen[test]",
	"boltzgen[doc]",
	"boltzgen[build]",
	]

	[tool.ruff]
	src = ["src"]
	extend-exclude = ["conf.py"]
	target-version = "py38"
	lint.select = ["ALL"]
	lint.ignore = [
	"COM812", # Conflicts with the formatter
	"ISC001", # Conflicts with the formatter
	"ANN101", # "missing-type-self"
	"RET504", # Unnecessary assignment to `x` before `return` statementRuff
	"S101", # Use of `assert` detected
	"D100", # Missing docstring in public module
	"D104", # Missing docstring in public package
	"PT001", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
	"PT004", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
	"PT005", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
	"PT023", # https://github.com/astral-sh/ruff/issues/8796#issuecomment-1825907715
	"FBT001",
	"FBT002",
	"PLR0913", # Too many arguments to init (> 5)
	"TRY003", # Exception messages
	"EM101", # Exception messages
	"FA102", # typing
	"T201", # Print statements
	]

	[tool.ruff.lint.per-file-ignores]
	"tests/**" = [
	"S101", # Use of `assert` detected
	"D103", # Missing docstring in public function
	]
	"**/__init__.py" = [
	"F401", # Imported but unused
	"F403", # Wildcard imports
	]
	"docs/**" = [
	"INP001", # Requires __init__.py but folder is not a package.
	]
	"scripts/**" = [
	"INP001", # Requires __init__.py but folder is not a package.
	]

	[tool.ruff.lint.pyupgrade]
	# Preserve types, even if a file imports `from __future__ import annotations`(https://github.com/astral-sh/ruff/issues/5434)
	keep-runtime-typing = true

	[tool.ruff.lint.pydocstyle]
	convention = "numpy"

	[tool.mypy]
	# Functions need to be annotated
	disallow_untyped_defs = true
	warn_unused_ignores = true
	exclude = ["configs/", "build/", "dist/", "docs/", "tests/"]