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pyproject.toml
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pyproject.toml
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[project]
name = "cellfinder-core"
description = "Automated 3D cell detection in large microscopy images"
readme = "README.md"
authors = [
{name = "Adam Tyson, Christian Niedworok, Charly Rousseau", email = "[email protected]"},
]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Image Recognition",
]
requires-python = ">=3.8"
dependencies = [
"dask[array]",
"fancylog>=0.0.7",
"brainglobe-utils",
"natsort",
"numba",
"numpy",
"scikit-image",
"scikit-learn",
# See https://github.com/brainglobe/cellfinder-core/issues/103 for < 2.12.0 pin
"tensorflow-macos>=2.5.0,<2.12.0; platform_system=='Darwin' and platform_machine=='arm64'",
"tensorflow>=2.5.0,<2.12.0; platform_system!='Darwin' or platform_machine!='arm64'",
"tifffile",
"tqdm",
]
dynamic = ['version']
[project.urls]
Homepage = "https://brainglobe.info"
"Source Code" = "https://github.com/brainglobe/cellfinder-core"
"Bug Tracker" = "https://github.com/brainglobe/cellfinder-core/issues"
Documentation = "https://brainglobe.info/documentation/cellfinder/index.html"
[project.optional-dependencies]
dev = [
"black",
"gitpython",
"pre-commit",
"pyinstrument",
"pytest",
"pytest-cov",
"pytest-lazy-fixture",
"pytest-mock",
"pytest-timeout",
"tox",
]
[project.scripts]
cellfinder_download = "cellfinder_core.download.cli:main"
cellfinder_train = "cellfinder_core.train.train_yml:cli"
[build-system]
requires = [
"setuptools>=45",
"wheel",
"setuptools_scm[toml]>=6.2",
]
build-backend = 'setuptools.build_meta'
[tool.setuptools]
include-package-data = true
[tool.setuptools_scm]
[tool.cibuildwheel]
build = "cp38-* cp39-* cp310-*"
[tool.cibuildwheel.macos]
archs = ["x86_64", "arm64"]
[tool.pytest.ini_options]
addopts = "--cov=cellfinder_core --cov-report=xml"
filterwarnings = [
"error",
# Raised by tensorflow; should be removed when tensorflow 2.12.0 is released. Fix is:
# https://github.com/tensorflow/tensorflow/commit/b23c5750c9f35a87872793eef7c56e74ec55d4a7
"ignore:`np.bool8` is a deprecated alias for `np.bool_`",
# See https://github.com/numba/numba/issues/8676
"ignore:.*:numba.core.errors.NumbaTypeSafetyWarning"
]
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
"serial",
]
log_level = "WARNING"
[tool.black]
target-version = ['py38', 'py39', 'py310']
skip-string-normalization = false
line-length = 79
[tool.ruff]
line-length = 79
exclude = ["__init__.py","build",".eggs"]
select = ["I", "E", "F"]
fix = true
[tool.ruff.isort]
known-first-party = ["cellfinder_core"]
[tool.mypy]
[[tool.mypy.overrides]]
module = [
"fancylog.*",
"brainglobe_utils.*",
"natsort.*",
"numba.*",
"tensorflow.*",
"tifffile.*",
"pyinstrument.*",
"pytest.*",
"pytest_lazyfixture.*",
"scipy.*",
"skimage.*",
"sklearn.*",
"cellfinder_core.tools.prep.*",
]
ignore_missing_imports = true
[[tool.mypy.overrides]]
module = [
"cellfinder_core.detect.*",
"cellfinder_core.classify.*",
]
disallow_untyped_defs = true
disallow_incomplete_defs = true
disallow_untyped_calls = true