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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "perturbvi"
dynamic = ["version"]
description = ''
readme = "README.md"
requires-python = ">=3.9"
license = "MIT"
keywords = []
authors = [
{ name = "Dong Yuan", email = "[email protected]" },
{ name = "Nicholas Mancuso", email = "[email protected]" },
]
classifiers = [
"Development Status :: 4 - Beta",
"Programming Language :: Python",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = [
"importlib-metadata; python_version<\"3.8\"",
"jaxlib",
"jax",
"jaxtyping",
"equinox",
"lineax",
"optimistix",
"optax",
"plum-dispatch"
]
[project.urls]
Documentation = "https://mancusolab.github.io/perturbvi"
Issues = "https://github.com/mancusolab/perturbvi/issues"
Source = "https://github.com/mancusolab/perturbvi"
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.hooks.vcs]
version-file = "src/perturbvi/_version.py"
[tool.hatch.build.targets.sdist]
include = ["src/"]
exclude = ["docs/"]
[tool.hatch.envs.test]
dependencies = [
"coverage[toml]",
"pytest",
"pytest-cov",
]
[tool.hatch.envs.test.scripts]
run-coverage = "pytest --cov-config=pyproject.toml --cov=pkg --cov=tests"
run = "run-coverage --no-cov"
[[tool.hatch.envs.all.matrix]]
python = ["3.9", "3.10", "3.11"]
[tool.hatch.envs.lint]
detached = true
dependencies = [
"black>=23.1.0",
"mypy>=1.0.0",
"ruff>=0.0.243",
]
[tool.ruff]
target-version = "py37"
line-length = 120
[tool.ruff.lint]
select = ["E", "F", "I001"]
ignore = [
# Allow non-abstract empty methods in abstract base classes
"B027",
# Allow boolean positional values in function calls, like `dict.get(... True)`
"FBT003",
# Ignore checks for possible passwords
"S105", "S106", "S107",
# Ignore complexity
"C901", "PLR0911", "PLR0912", "PLR0913", "PLR0915",
# Ignore syntax checks on jaxarray shaped typing
"F722",
# Ignore multidispatch false positives
"F811",
]
ignore-init-module-imports = true
[tool.ruff.lint.isort]
known-first-party = ["susieguy"]
combine-as-imports = true
lines-after-imports = 2
lines-between-types = 1
known-local-folder = ["src"]
section-order = ["future", "standard-library", "third-party", "jax-ecosystem", "first-party", "local-folder"]
extra-standard-library = ["typing_extensions"]
order-by-type = false
[tool.ruff.lint.isort.sections]
jax-ecosystem = ["equinox", "jax", "jaxtyping", "lineax", "optimistix", "optax"]
[tool.ruff.lint.per-file-ignores]
# Tests can use magic values, assertions, and relative imports
"tests/**/*" = ["PLR2004", "S101", "TID252"]
[tool.pyright]
reportIncompatibleMethodOverride = true
reportIncompatibleVariableOverride = false # Incompatible with eqx.AbstractVar
include = ["perturbvi", "tests"]
exclude = ["docs"]
[tool.coverage.run]
source_pkgs = ["perturbvi", "tests"]
branch = true
parallel = true
omit = [
"src/susieguy/__about__.py",
]
[tool.coverage.paths]
susieguy = ["src/perturbvi", "*/perturbvi/src/perturbvi"]
tests = ["tests", "*/perturbvi/tests"]
[tool.coverage.report]
exclude_lines = [
"no cov",
"if __name__ == .__main__.:",
"if TYPE_CHECKING:",
]