/
pyproject.toml
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pyproject.toml
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[project]
name = "cellfinder"
description = "Automated 3D cell detection in large microscopy images"
readme = "README.md"
license = { text = "BSD-3-Clause" }
authors = [
{ name = "Adam Tyson, Christian Niedworok, Charly Rousseau", email = "code@adamltyson.com" },
]
classifiers = [
"Development Status :: 4 - Beta",
"Framework :: napari",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering :: Image Recognition",
]
requires-python = ">=3.9"
dependencies = [
"brainglobe-utils>=0.5.0",
"brainglobe-napari-io>=0.3.4",
"dask[array]",
"fancylog>=0.0.7",
"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.entry-points."napari.manifest"]
cellfinder = "cellfinder.napari:napari.yaml"
[project.optional-dependencies]
dev = [
"black",
"pre-commit",
"pyinstrument",
"pytest-cov",
"pytest-mock",
"pytest-qt",
"pytest-timeout",
"pytest",
"tox",
]
napari = [
"brainglobe-napari-io",
"magicgui",
"napari-ndtiffs",
"napari-plugin-engine >= 0.1.4",
"napari[pyqt5]",
"pooch >= 1",
"qtpy",
]
[project.scripts]
cellfinder_download = "cellfinder.core.download.cli:main"
cellfinder_train = "cellfinder.core.train.train_yml:cli"
cellfinder = "cellfinder.cli_migration_warning:cli_catch"
[project.urls]
Homepage = "https://brainglobe.info/documentation/cellfinder/index.html"
"Source Code" = "https://github.com/brainglobe/cellfinder"
"Bug Tracker" = "https://github.com/brainglobe/cellfinder/issues"
Documentation = "https://brainglobe.info/documentation/cellfinder/index.html"
"User Support" = "https://forum.image.sc/tag/brainglobe"
[build-system]
requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
build-backend = 'setuptools.build_meta'
[tool.black]
target-version = ['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"]
[tool.setuptools]
include-package-data = true
[tool.setuptools.packages.find]
include = ["cellfinder*"]
[tool.setuptools.package-data]
include = ["cellfinder*"]
[tool.setuptools_scm]
[tool.pytest.ini_options]
addopts = "--cov=cellfinder"
markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
[tool.tox]
legacy_tox_ini = """
# For more information about tox, see https://tox.readthedocs.io/en/latest/
[tox]
envlist = py{39,310}
isolated_build = true
[gh-actions]
python =
3.9: py39
3.10: py310
[testenv]
commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml
deps =
pytest
pytest-cov
pytest-mock
pytest-timeout
# Even though napari is a requirement for cellfinder.napari, we have to
# ensure it is installed with the default Qt backend here.
napari[all]
pytest-qt
extras =
napari
passenv =
NUMBA_DISABLE_JIT
CI
GITHUB_ACTIONS
DISPLAY
XAUTHORITY
NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
PYVISTA_OFF_SCREEN
"""