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 = "blik"
description = "Python tool for visualising and interacting with cryo-ET and subtomogram averaging data."
readme = "README.md"
requires-python = ">=3.10"
license = { text = "GPLv3" }
authors = [
    { email = "brisvag@gmail.com", name = "Lorenzo Gaifas" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Typing :: Typed",
    "Topic :: Scientific/Engineering :: Visualization",
    "Framework :: napari",
]
dynamic = ["version"]
dependencies = [
    "numpy",
    "dask",
    "pandas",
    "scipy",
    "magicgui>=0.4.0",
    "cryohub>=0.6.4",
    "cryotypes>=0.2.0",
    "einops",
    "morphosamplers[segment]>=0.0.10",
    "pydantic<2",  # migration will take a while for napari
    "packaging",
]

# extras
# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
[project.optional-dependencies]
all = [
    "napari[all]>=0.5.0",
    "napari-properties-plotter",
    "napari-properties-viewer",
    "napari-label-interpolator>=0.1.1",
]
test = [
    "pytest>=6.0",
    "pytest-cov",
    "pytest-qt",
    "napari[all]>=0.5.0",
]
dev = [
    "blik[test]",
    "black",
    "ipython",
    "mypy",
    "pdbpp",
    "pre-commit",
    "rich",
    "ruff",
]

[project.urls]
homepage = "https://github.com/brisvag/blik"
repository = "https://github.com/brisvag/blik"

# same as console_scripts entry point
# [project.scripts]
# spam-cli = "spam:main_cli"

# Entry points
# https://peps.python.org/pep-0621/#entry-points
[project.entry-points."napari.manifest"]
blik = "blik:napari.yaml"

# 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 = 120
target-version = "py39"
src = ["src"]
# https://beta.ruff.rs/docs/rules/
select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "I",    # isort
    "UP",   # pyupgrade
    "C4",   # 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
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"]

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

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

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