pyproject.toml

# https://peps.python.org/pep-0517/
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

# https://peps.python.org/pep-0621/
[project]
name = "membrain-seg"
description = "membrane segmentation in 3D for cryo-ET"
readme = "README.md"
requires-python = ">=3.8"
license = { text = "BSD 3-Clause License" }
authors = [
    { email = "lorenz.lamm@helmholtz-munich.de", name = "Lorenz Lamm" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: BSD License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Typing :: Typed",
]
dynamic = ["version"]
dependencies = [
    "monai",
    "pytorch-lightning",
    "torch",
    "imageio",
    "scipy",
    "typer[all]",
    "scikit-image",
    "simpleitk",
    "pandas",
    "mrcfile",
]


# extras
# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
[project.optional-dependencies]
test = ["pytest>=6.0", "pytest-cov"]
dev = [
    "black",
    "ipython",
    "pdbpp",
    "pre-commit",
    "pytest-cov",
    "pytest",
    "rich",
    "ruff",
    "mkdocs-material",
]

[project.urls]
homepage = "https://github.com/teamtomo/membrain-seg"
repository = "https://github.com/teamtomo/membrain-seg"

# same as console_scripts entry point
# [project.scripts]
# spam-cli = "spam:main_cli"
[project.scripts]
tomo_preprocessing = "membrain_seg.tomo_preprocessing:cli"
membrain = "membrain_seg.segmentation.cli:cli"
patch_corrections = "membrain_seg.annotations:cli"


# Entry points
# https://peps.python.org/pep-0621/#entry-points
# [project.entry-points."spam.magical"]
# tomatoes = "spam:main_tomatoes"

# https://hatch.pypa.io/latest/config/metadata/
[tool.hatch.version]
source = "vcs"

# https://hatch.pypa.io/latest/config/build/#file-selection
# [tool.hatch.build.targets.sdist]
# include = ["/src", "/tests"]

# [tool.hatch.build.targets.wheel]
# only-include = ["src"]
# sources = ["src"]

# https://github.com/charliermarsh/ruff
[tool.ruff]
line-length = 88
target-version = "py38"
# https://beta.ruff.rs/docs/rules/
extend-select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "D",    # pydocstyle
    "I",    # isort
    "U",    # pyupgrade
    # "S",    # bandit
    "C",    # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "RUF",  # ruff-specific rules
]
# I do this to get numpy-style docstrings AND retain
# D417 (Missing argument descriptions in the docstring)
# otherwise, see:
# https://beta.ruff.rs/docs/faq/#does-ruff-support-numpy-or-google-style-docstrings
# https://github.com/charliermarsh/ruff/issues/2606
extend-ignore = [
    "D100", # Missing docstring in public module
    "D107", # Missing docstring in __init__
    "D203", # 1 blank line required before class docstring
    "D212", # Multi-line docstring summary should start at the first line
    "D213", # Multi-line docstring summary should start at the second line
    "D401", # First line should be in imperative mood
    "D413", # Missing blank line after last section
    "D416", # Section name should end with a colon
]

[tool.ruff.per-file-ignores]
"tests/*.py" = ["D", "S"]
"setup.py" = ["D"]

# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
testpaths = ["tests"]
filterwarnings = ["error"]

# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "src/**/"
strict = true
disallow_any_generics = false
disallow_subclassing_any = false
show_error_codes = true
pretty = true

# # module specific overrides
# [[tool.mypy.overrides]]
# module = ["numpy.*",]
# ignore_errors = true


# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "@overload",
    "except ImportError",
    "\\.\\.\\.",
    "raise NotImplementedError()",
]
[tool.coverage.run]
source = ["src"]

# https://github.com/mgedmin/check-manifest#configuration
[tool.check-manifest]
ignore = [
    ".github_changelog_generator",
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "setup.py",
    "tests/**/*",
]

# https://python-semantic-release.readthedocs.io/en/latest/configuration.html
[tool.semantic_release]
version_source = "tag_only"
branch = "main"
changelog_sections = "feature,fix,breaking,documentation,performance,chore,:boom:,:sparkles:,:children_crossing:,:lipstick:,:iphone:,:egg:,:chart_with_upwards_trend:,:ambulance:,:lock:,:bug:,:zap:,:goal_net:,:alien:,:wheelchair:,:speech_balloon:,:mag:,:apple:,:penguin:,:checkered_flag:,:robot:,:green_apple:,Other"
# commit_parser=semantic_release.history.angular_parser
build_command = "pip install build && python -m build"

# # for things that require compilation
# # https://cibuildwheel.readthedocs.io/en/stable/options/
# [tool.cibuildwheel]
# # Skip 32-bit builds & PyPy wheels on all platforms
# skip = ["*-manylinux_i686", "*-musllinux_i686", "*-win32", "pp*"]
# test-extras = ["test"]
# test-command = "pytest {project}/tests -v"
# test-skip = "*-musllinux*"

# [tool.cibuildwheel.environment]
# HATCH_BUILD_HOOKS_ENABLE = "1"