pyproject.toml

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

[tool.hatch.version]
source = "vcs"

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

# https://peps.python.org/pep-0621/
[project]
name = "napari-omero"
dynamic = ["version"]
description = "napari/OMERO interoperability"
readme = "README.md"
requires-python = ">=3.9"
license = { text = "GPL-2.0-or-later" }
authors = [
    { name = "Talley Lambert", email = "talley.lambert@gmail.com" },
    { name = "Will Moore", email = "w.moore@dundee.ac.uk" },
    { name = "Johannes Soltwedel", email = "johannes_richard.soltwedel@tu-dresden.de" },
    { name = "Peter Sobolewski" },
]
keywords = ["OMERO.CLI", "plugin", "napari", "napari-plugin"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: X11 Applications :: Qt",
    "Framework :: napari",
    "Intended Audience :: Developers",
    "Intended Audience :: Education",
    "Intended Audience :: End Users/Desktop",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
    "Natural Language :: English",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Information Analysis",
    "Topic :: Scientific/Engineering :: Visualization",
    "Topic :: Scientific/Engineering",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "Topic :: Utilities",
    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
    "Typing :: Typed",
]
# add your package dependencies here
dependencies = [
    "napari>=0.4.13",
    "omero-py",
    "omero-rois",
    # these come with napari ...
    # but are directly imported here as well so are included explicitly
    "qtpy>=1.10.0",
    "dask[array]>=2021.10.0",
    "vispy>=0.14.1,<0.15",
    "superqt>=0.6.7",
]

# https://peps.python.org/pep-0621/#dependencies-optional-dependencies
# "extras" (e.g. for `pip install .[test]`)
[project.optional-dependencies]
all = ["napari[all]"]
test = [
    "pytest",
    "pytest-cov",
    "pytest-qt",
    "pytest-regressions",
    "pywin32; sys_platform == 'win32'",
]
dev = [
    "napari-omero[all, test]",
    "ipython",
    "mypy",
    "pdbpp",
    "pre-commit",
    "rich",
    "ruff",
]

[project.urls]
homepage = "https://github.com/tlambert03/napari-omero"
repository = "https://github.com/tlambert03/napari-omero"

# Entry points
# https://peps.python.org/pep-0621/#entry-points
# same as console_scripts entry point
[project.scripts]
napari-omero = "napari_omero.__main__:main"

[project.entry-points."napari.manifest"]
napari-omero = "napari_omero:napari.yaml"

# https://docs.astral.sh/ruff
[tool.ruff]
line-length = 88
target-version = "py39"
src = ["src"]

# 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
    "TC",   # flake8-type-checking
    "TID",  # flake8-tidy-imports
]
ignore = [
    "D401", # First line should be in imperative mood
    "D100", # Missing docstring in public module
    "D101", # Missing docstring in public class
    "D102", # Missing docstring in public method
    "D103", # Missing docstring in public function
    "D104", # Missing docstring in public package
]

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

# 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 = false
check_untyped_defs = true
ignore_missing_imports = true
disallow_any_generics = false
disallow_subclassing_any = false
show_error_codes = true
pretty = true


# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "7.0"
testpaths = ["tests"]
filterwarnings = [
    "error",
    "ignore:distutils Version classes are deprecated:",
    "ignore:the imp module is deprecated in:",
    "ignore:'U' mode is deprecated",
    "ignore:Please import PackageMetadata from 'npe2'",
    "ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning:skimage",
]


# 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()",
    "pass",
]
[tool.coverage.run]
source = ["src"]

# 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 = [
    ".github_changelog_generator",
    ".pre-commit-config.yaml",
    ".ruff_cache/**/*",
    "setup.py",
    "tests/**/*",
]