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 = "cs2star"
description = "A simple utility to convert cryosparc particle positions to relion star format."
readme = "README.md"
requires-python = ">=3.8"
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 :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]
dynamic = ["version"]
dependencies = [
    "pandas",
    "click",
    "numpy",
    "rich",
]

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

[project.urls]
homepage = "https://github.com/brisvag/cs2star"
repository = "https://github.com/brisvag/cs2star"

# same as console_scripts entry point
[project.scripts]
cs2star = "cs2star.cs2star:main"

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

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

# https://github.com/charliermarsh/ruff
[tool.ruff]
line-length = 120
target-version = "py38"
src = ["src"]
# https://beta.ruff.rs/docs/rules/
select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "D",    # pydocstyle
    "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
]

# 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 = ["cs2star"]

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