fgcz_python_project_template/pyproject.toml at main · fgcz/fgcz_python_project_template · GitHub

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[project]
name = "fgcz-python-project-reference"
version = "0.1.0"
description = "Minimal reference project for typed, tested, and documented FGCZ Python packages."
readme = "README.md"
requires-python = ">=3.12"
license = "Apache-2.0"
authors = [
    { name = "Functional Genomics Center Zurich" },
]
dependencies = [
    "cyclopts>=5.2,<6",
    "loguru>=0.7.3,<0.8",
]

[project.scripts]
fgcz-reference = "fgcz_reference_project.cli:main"

[build-system]
requires = ["uv_build>=0.12.0,<0.13"]
build-backend = "uv_build"

[dependency-groups]
dev = [
    "deptry>=0.25.1,<0.26",
    "diff-cover>=10.4.1,<11",
    "pip-audit>=2.10,<3",
    "pre-commit>=4.5,<5",
    "pyright>=1.1.408,<2",
    "pytest>=9,<10",
    "pytest-cov>=7,<8",
    "ruff==0.16.7",
]
docs = [
    "mkdocs-material>=9.7,<10",
]

[tool.uv.build-backend]
module-name = "fgcz_reference_project"

[tool.pytest.ini_options]
addopts = "-ra --strict-config --strict-markers"
testpaths = ["tests"]

[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ruff.lint]
select = [
    "F",   # pyflakes
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "I",   # isort
    "N",   # pep8-naming
    "UP",  # pyupgrade
    "B",   # flake8-bugbear
    "A",   # flake8-builtins
    "C4",  # flake8-comprehensions
    "RUF", # ruff-specific
    "C90", # mccabe complexity
    "PL",  # pylint (convention/error/warning/refactor)
    "SIM", # flake8-simplify
    "RET", # flake8-return
    "PTH", # flake8-use-pathlib
    "PT",  # flake8-pytest-style
    "TID", # flake8-tidy-imports
    "TC",  # flake8-type-checking
    "ARG", # flake8-unused-arguments
    "EM",  # flake8-errmsg
    "D",   # pydocstyle
    "ANN", # flake8-annotations
    "S",   # flake8-bandit (security)
]
ignore = ["ANN401"]

[tool.ruff.lint.mccabe]
max-complexity = 10

[tool.ruff.lint.pylint]
max-args = 7

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

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["S101", "D", "ANN", "PLR2004", "ARG"]
"scripts/**" = ["S603", "S607", "D", "PLR2004", "EM"]
# Vendored third-party hook: linted and formatted, but not held to this project's
# docstring, annotation, and typing rules. See .ci/check-tests-structure/README.md.
".ci/**" = ["S101", "D", "ANN", "EM", "PLR2004", "ARG", "TC"]

[tool.ruff.format]
quote-style = "double"

[tool.pyright]
pythonVersion = "3.12"
include = ["src", "tests", "scripts"]
typeCheckingMode = "strict"

[tool.coverage.run]
branch = true
relative_files = true
source = ["fgcz_reference_project"]

[tool.coverage.report]
fail_under = 100
show_missing = true

[tool.deptry]
known_first_party = ["fgcz_reference_project"]
# The vendored hook in .ci/ is a separate distribution with its own dependencies;
# deptry would otherwise report them against this project.
extend_exclude = ["\\.ci"]

[tool.check-tests-structure]
sources_path = "src/fgcz_reference_project"
tests_path = "tests"