pyproject.toml

[build-system]
# Minimum requirements for the build system to execute.
requires = ["setuptools>=77.0.0", "setuptools_scm[toml]>=8"]  # PEP 508 specifications.
build-backend = "setuptools.build_meta"

[tool.setuptools_scm]
write_to = "package/PartSeg/version.py"
fallback_version = "0.17.0dev0"

[project]
name = "PartSeg"
description = "PartSeg is python GUI and set of napari plugins for bio imaging analysis especially nucleus analysis,"
authors = [
    { name = "Grzegorz Bokota", email = "g.bokota@uw.edu.pl" },
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Framework :: napari",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3"
    ,
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: Python :: Implementation :: CPython",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Image Processing",
    "Topic :: Scientific/Engineering :: Visualization",
]
keywords = [
    "bioimaging",
    "GUI",
]
license = "BSD-3-Clause"
license-files = [
    "License.txt",
]
requires-python = ">=3.10"
dependencies = [
    "IPython>=7.7.0",
    "PartSegCore-compiled-backend>=0.13.11,<0.16.0",
    "PartSegData==0.10.0",
    "QtAwesome!=1.2.0,>=1.0.3",
    "QtPy>=2.3.1",
    "SimpleITK>=2.2.0",
    "platformdirs>=4.3.0",
    "czifile>=2019.5.22",
    "defusedxml>=0.6.0",
    "fonticon-fontawesome6>=6.1.1",
    "h5py>=3.7.0",
    "imagecodecs>=2023.9.18",
    "imageio>=2.20.0",
    "ipykernel>=5.2.0",
    "local-migrator>=0.1.10",
    "magicgui>=0.7.0",
    "mahotas>=1.4.13",
    "napari>=0.6.2 ; python_version < '3.14'",
    "napari >= 0.7.0 ; python_version >= '3.14'",
    "numpy>=1.24.2",
    "oiffile>=2020.1.18",
    "openpyxl>=3.0.7",
    "packaging>=22.0",
    "pandas>=1.4.0",
    "psygnal>=0.10.0",
    "pydantic>=2.2.0",
    "pygments>=2.12.0",
    "qtconsole>=4.7.7",
    "requests>=2.25.0",
    "scipy>=1.10.1",
    "sentry-sdk>=2.4.0",
    "six>=1.11.0",
    "superqt>=0.7.3",
    "sympy>=1.10",
    "tifffile>=2023.9.26",
    "traceback-with-variables>=2.0.4",
    "vispy>=0.15.2",
    "xlrd>=1.1.0",
    "xlsxwriter>=2.0.0",
]
dynamic = [
    "version",
    "readme",
]

[project.urls]
Homepage = "https://partseg.github.io/"
Documentation = "https://partseg.readthedocs.io/en/stable/"
"Source Code" = "https://github.com/4DNucleome/PartSeg"
"User Support" = "https://github.com/4DNucleome/PartSeg/issues"
"Bug Tracker" = "https://github.com/4DNucleome/PartSeg/issues"

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

[project.optional-dependencies]
accelerate = [
#    "PyOpenGL-accelerate>=3.1.5 ; platform_machine != 'arm64'",
]
all = [
    "PartSeg[accelerate,pyqt]"
]
docs = [
    "autodoc-pydantic",
    "sphinx!=3.0.0,!=3.5.0",
    "sphinx-autodoc-typehints",
    "sphinx-qt-documentation",
]
pyinstaller = [
    "PartSeg[pyinstaller_base,pyqt5]",
]
pyinstaller_base = [
    "PartSeg[accelerate]",
    "PyInstaller",
    "pydantic",
    "nme", # for older plugins that still use nme
]
pyqt = [
    "PartSeg[pyqt6]",
]
pyqt5 = [
    "PyQt5!=5.15.0,>=5.12.3",
    "napari[pyqt5]",
]
pyqt6 = [
    "PyQt6",
    "napari[pyqt6]>=0.5.0",
]
pyside = [
    "PartSeg[pyside6]",
]
pyside2 = [
    "PySide2!=5.15.0,>=5.12.3",
    "napari[pyside]<0.7.0",
    "superqt<0.8.0",  # superqt 0.8+ uses type annotations which are not supported in pyside2, so we need to use older version
]
pyside6 = [
    "PySide6",
    "napari[pyside6]>=0.5.0",
]
test = [
    "coverage",
    "lxml[html_clean]",
    "pytest>=7.0.0",
    "pytest-qt",
    "pytest-timeout",
    "scikit-image",
]
testing = [
    "pytest",
    "pytest-qt",
    "lxml",
]

[project.scripts]
PartSeg = "PartSeg.launcher_main:main"

[tool.setuptools]
include-package-data = true
platforms = [
    "Linux",
    "Windows",
    "MacOs",
]


[tool.setuptools.package-dir]
"" = "package"

[tool.setuptools.packages.find]
where = [
    "package",
]
namespaces = false

[tool.setuptools.package-data]
partsegcore = [
    "napari.yaml",
]

[tool.pytest.ini_options]
addopts = "--maxfail=5 --durations=5"
testpaths = [
    "package/tests",
]
junit_family = "legacy"
timeout = 900
filterwarnings = [
    "error:::PartSeg", # turn warnings from napari into errors
    "error:::test_.*", # turn warnings in our own tests into errors
    "ignore:invalid value encountered",
    "ignore:The 'junit_family' encountered",
    "ignore:numpy.ufunc size changed, may indicate",
    "ignore:tostring.*is deprecated",
    "ignore:emitter camera is deprecated,",
    "ignore:`np.float` is a deprecated alias",
    "ignore:divide by zero encountered in true_divide",
    "ignore:the imp module is deprecated in favour of importlib",
    "ignore:distutils Version classes are deprecated.",
    "ignore:Please import PackageMetadata from 'npe2' or from 'npe2.manifest'",
    "ignore:Please use `zoom` from the `scipy.ndimage` namespace",
    "ignore:Converting `np.character` to a dtype",
    "ignore:Public access to Window.qt_viewer",
    "ignore:Pydantic V1 style `@validator`",
    "ignore:Support for class-based `config` is deprecated",
    "ignore:`__get_validators__` is deprecated",
    "ignore:Using extra keyword arguments on `Field` is deprecated",
    "ignore:The `update_forward_refs` method is deprecated;",
    "ignore:The `copy` method is deprecated; use",
    "ignore:The private method `_iter` will be removed and should no longer be used",
    "ignore:The `validate` method is deprecated; use `model_validate` instead.",
    "ignore:The `schema_json` method is deprecated; use `model_json_schema` and json.dumps instead.",
    "ignore:The `dict` method is deprecated; use `model_dump`",
    "ignore:The `__fields__` attribute is deprecated",
#    "ignore::pydantic.warnings.PydanticDeprecatedSince20",
    "ignore:Jupyter is migrating its paths to use standard platformdirs",
    "ignore:ipykernel\\.:DeprecationWarning", # connected with min requirements, check after bump
    "ignore:Please import `zoom`::czifile:193",
    "ignore:__array__ implementation doesn't accept a copy keyword" # hp5y==3.11 warning, need update
]
markers = [
    "enablethread: Allow to use thread in test",
    "enabledialog: Allow to use dialog in test",
    "no_patch_add_layer: Do not patch napari viewer",
    "windows_ci_skip: Skip test when running on windows CI",
    "pyside_skip: Skip test when using pyside2 qt backend",
    "pyside6_skip: Skip test when using pyside6 qt backend"
]

[tool.coverage.paths]
source = [
    "package",
    "*/site-packages",
]

[tool.coverage.run]
source = [
    "PartSeg",
    "PartSegCore",
    "PartSegImage",
    "package/tests",
]
omit = [
    ".tox/*",
    "**/changelog.py",
    "**/version.py",
    "**/PartSegCore/class_generator.py",
]
parallel = true

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "raise NotImplementedError",
    "raise RuntimeError()",
    "pass",
]
exclude_also = [
    "if __name__ == .__main__.:",
    "if TYPE_CHECKING:",
    "if typing.TYPE_CHECKING:",
]


[tool.ruff]
line-length = 120
exclude = [
    "examples/call_simple_threshold.py",
    ".eggs",
    ".git",
    ".hg",
    ".mypy_cache",
    ".tox",
    ".venv",
    "_build",
    "buck-out",
    "build",
    "dist",
    "foo.py",
    "package/PartSeg/version.py",
]
fix = true

[tool.ruff.lint]
select = [
    "F", # Pyflakes
    "E", "W", # pycodestyle
    "C90", # mccabe
    "I", # isort
    "UP", # pyupgrade
    "A", # flake8-builtins
    "YTT", # flake8-2020
#    "ANN", # flake8-annotations
    "S", # flake8-bandit
#    "BLE", # flake8-blind-except
    "B", # lake8-bugbear
    "A", #flake8-builtins
    "C4", # flake8-comprehensions
    "ISC", # flake8-implicit-str-concat
    "ICN", # flake8-import-conventions
    "G", # flake8-logging-format
    "PIE", # flake8-pie
    "T20", # flake8-print
    "PYI",
    "PT", # flake8-pytest-style
    "Q", # flake8-quotes
    "RSE", # flake8-raise
    "RET", # flake8-return
    "SIM", # flake8-simplify
    "TID", # flake8-tidy-imports
    "TCH", # flake8-type-checking
    "ARG", # flake8-unused-arguments
#    "PTH", # flake8-use-pathlib
    "ERA", # eradicate
    "PGH", # pygrep-hooks
    "PLC", "PLE", "PLR", "PLW", # pylint
    "NPY", # NumPy-specific rules
    "PERF", # perflint
    "RUF", # Ruff-specific rules
]
ignore = ["A003", "SIM108", "ARG002", "ARG003", "ARG004", "PLR2004",
    "PLR0913", # should be re-enabled in a future version
    "PLW1641", # Complain about lack of hash in mutable objects"
    "PLR0917", # migrate more functions to named only arguments
]

[tool.ruff.lint.isort]
known-first-party=['PartSeg', 'PartSegData','PartSegCore','PartSegImage', 'PartSegCore_compiled_backend']

[tool.ruff.lint.flake8-tidy-imports]
# Disallow all relative imports.
ban-relative-imports = "all"

[tool.ruff.lint.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 15

[tool.ruff.lint.per-file-ignores]
"docs/conf.py" = ["A001"]
"package/tests/**" = ["ARG", "PLC1901", "S101", "RUF012", "ANN", "FBT", "PLR0917"]
"package/PartSegCore/sphinx/*" = ["ARG"]
"package/tests/**.py" = ["PLR2004"]
"package/PartSegCore/_old_json_hooks.py" = ["PLR0912", "PLR0911", "PLC0415"]
"package/PartSegCore/class_generator.py" = ["PLR0912", "T20"]
"build_utils/**.py" = ["S603", "S607", "T20"]
"examples/**.py" = ["T20", "PLC0415"]
"package/PartSeg/common_gui/show_directory_dialog.py" = ["S603", "S606", "S607"]
"package/PartSeg/launcher_main.py" = ["T20", "PLC0415"]
"*.ipynb" = ["T20", "ERA001", "E501"]
"setup.py" = ["PLC0415"]
"**/conftest.py" = ["PLC0415"]
"package/PartSeg/common_gui/except_hook.py" = ["PLC0415"]
"package/PartSeg/common_gui/error_report.py" = ["PLC0415"]

[tool.check-manifest]
ignore = [".travis.yml", "package/PartSeg/changelog.py", "package/PartSeg/version.py"]

[tool.mypy]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "tifffile.*"
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "defusedxml"
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "czifile.*"
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = "oiffile"
ignore_missing_imports = true

[tool.check-wheel-contents]
toplevel = ["PartSeg", "PartSegCore", "PartSegImage"]

[tool.codespell]
skip = "package/tests/test_data/ome.xsd.xml,launcher.spec,publications,dist,_build"
ignore-words-list = "setted"


[tool.bandit]
exclude_dirs = ["tests", ".venv"]