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pyproject.toml
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pyproject.toml
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[project]
name = "segment-embryo"
dynamic = ["version"]
description = "3D Segment ascidian embryos using cellpose. The images are first rescaled to be isotropic and then downscaled, before cellpose is used. The resulting labels are upscaled to match the original data."
readme = "README.md"
license = {file = "LICENSE"}
authors = [
{name = "Volker Baecker"},
{email = "[email protected]"},
]
classifiers = [
"Development Status :: 2 - Pre-Alpha",
"Framework :: napari",
"Intended Audience :: Developers",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Image Processing",
]
requires-python = ">=3.9"
dependencies = [
"numpy",
"magicgui",
"qtpy",
"scikit-image",
"cellpose",
"czifile",
"napari-czifile2",
"set-calibration",
"big-fish",
"napari-bigfish",
"scikit-image"
]
[project.optional-dependencies]
testing = [
"tox",
"pytest", # https://docs.pytest.org/en/latest/contents.html
"pytest-cov", # https://pytest-cov.readthedocs.io/en/latest/
"pytest-qt", # https://pytest-qt.readthedocs.io/en/latest/
"napari",
"pyqt5",
'numpy'
]
[project.entry-points."napari.manifest"]
segment-embryo = "segment_embryo:napari.yaml"
[project.urls]
Homepage = "https://github.com/MontpellierRessourcesImagerie/segment-embryo"
Documentation = "https://github.com/MontpellierRessourcesImagerie/segment-embryo#segment-embryo"
Repository = "https://github.com/MontpellierRessourcesImagerie/segment-embryo.git"
Issues = "https://github.com/MontpellierRessourcesImagerie/segment-embryo/issues"
Changelog = "https://github.com/MontpellierRessourcesImagerie/segment-embryo/releases"
[build-system]
requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
include-package-data = true
[tool.setuptools.packages.find]
where = ["src"]
[tool.setuptools.package-data]
"*" = ["*.yaml"]
[tool.setuptools_scm]
write_to = "src/segment_embryo/_version.py"
[tool.black]
line-length = 79
target-version = ['py38', 'py39', 'py310']
[tool.ruff]
line-length = 79
lint.select = [
"E", "F", "W", #flake8
"UP", # pyupgrade
"I", # isort
"BLE", # flake8-blind-exception
"B", # flake8-bugbear
"A", # flake8-builtins
"C4", # flake8-comprehensions
"ISC", # flake8-implicit-str-concat
"G", # flake8-logging-format
"PIE", # flake8-pie
"SIM", # flake8-simplify
]
lint.ignore = [
"E501", # line too long. let black handle this
"UP006", "UP007", # type annotation. As using magicgui require runtime type annotation then we disable this.
"SIM117", # flake8-simplify - some of merged with statements are not looking great with black, reanble after drop python 3.9
]
exclude = [
".bzr",
".direnv",
".eggs",
".git",
".mypy_cache",
".pants.d",
".ruff_cache",
".svn",
".tox",
".venv",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"node_modules",
"venv",
"*vendored*",
"*_vendor*",
]
target-version = "py38"
fix = true