pyproject.toml

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

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

# read more about configuring hatch at:
# https://hatch.pypa.io/latest/config/build/
[tool.hatch.build.targets.wheel]
only-include = ["src"]
sources = ["src"]

# https://peps.python.org/pep-0621/
[project]
name = "abba-python"
version = "0.25.0"
description = "Aligning Big Brains and Atlases (ABBA), controlled from python."
readme = "README.md"
requires-python = ">=3.10"
license = { text = "BSD-3-Clause" }
authors = [{ name = "Nicolas Chiaruttini", email = "nicolas.chiaruttini@unige.ch" }]
# https://pypi.org/classifiers/
classifiers = [
    "Development Status :: 3 - Alpha",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Typing :: Typed",
]
# add your package dependencies here
dependencies = [
    # >=1.8.0 (scyjava>=1.12.4, jgo>=2.1): fetches Java itself and resolves jars
    # without Maven; 1.7.x needs a pre-installed JDK
    "pyimagej>=1.8.0"
]

# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
# "extras" (e.g. for `pip install .[test]`)
[project.optional-dependencies]
# add dependencies used for testing here
test = ["pytest", "pytest-cov"]
# add anything else you like to have in your dev environment here
dev = [
    "ipython",
    "mypy",
    "pdbpp",  # https://github.com/pdbpp/pdbpp
    "pre-commit",
    "rich",  # https://github.com/Textualize/rich
    "ruff",

]

[project.urls]
homepage = "https://github.com/BIOP/abba_python"
repository = "https://github.com/BIOP/abba_python"

# Entry points
# https://peps.python.org/pep-0621/#entry-points
# same as console_scripts entry point
# [project.scripts]
# abba-python-cli = "abba_python:main_cli"

# [project.entry-points."some.group"]
# tomatoes = "abba_python:main_tomatoes"

# https://docs.astral.sh/ruff
[tool.ruff]
line-length = 120
target-version = "py310"
src = ["src"]
# Generated by scripts/generate_commands.py
extend-exclude = ["src/abba_python/commands.py"]

# https://docs.astral.sh/ruff/rules
[tool.ruff.lint]
pydocstyle = { convention = "numpy" }
select = [
    "E",    # style errors
    "W",    # style warnings
    "F",    # flakes
    "D",    # pydocstyle
    "D417", # Missing argument descriptions in Docstrings
    "I",    # isort
    "UP",   # pyupgrade
    "C4",   # flake8-comprehensions
    "B",    # flake8-bugbear
    "A001", # flake8-builtins
    "RUF",  # ruff-specific rules
    "TCH",  # flake8-type-checking
    "TID",  # flake8-tidy-imports
]
ignore = [
    "D401", # First line should be in imperative mood (remove to opt in)
    "D205", # summary lines may run on: docstrings here are not in numpy style
    "D400", # First line should end with a period
]

[tool.ruff.lint.per-file-ignores]
"tests/*.py" = ["D", "S"]
# Scripts, not API: no docstring required
"examples/*.py" = ["D"]
"scripts/*.py" = ["D"]

# https://docs.astral.sh/ruff/formatter/
[tool.ruff.format]
docstring-code-format = true
skip-magic-trailing-comma = false  # default is false

# 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

# The Java bridge libraries ship no type information
[[tool.mypy.overrides]]
module = ["imagej.*", "jpype.*", "scyjava.*"]
ignore_missing_imports = true

# https://docs.pytest.org/
[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
filterwarnings = ["error"]

# https://coverage.readthedocs.io/
[tool.coverage.report]
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "@overload",
    "except ImportError",
    "\\.\\.\\.",
    "raise NotImplementedError()",
    "pass",
]

[tool.coverage.run]
source = ["abba_python"]

# https://github.com/mgedmin/check-manifest#configuration
# add files that you want check-manifest to explicitly ignore here
# (files that are in the repo but shouldn't go in the package)
[tool.check-manifest]
ignore = [
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "tests/**/*",
]

# https://github.com/crate-ci/typos
[tool.typos.default.extend-words]
ba = "ba"    # the atlas parameter of ABBA's Java commands
ome = "ome"  # OME-TIFF