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pyproject.toml
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pyproject.toml
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[project]
name = "brainglobe-workflows"
authors = [
{ name = "Adam Tyson", email = "[email protected]" },
{ name = "BrainGlobe developers", email = "[email protected]" },
{ name = "Christian Niedworok" },
{ name = "Charly Rousseau" },
]
description = "A collection of end-to-end data analysis workflows executed using BrainGlobe tools."
readme = "README.md"
license = { file = "LICENSE" }
requires-python = ">=3.10"
dynamic = ["version"]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python",
"Topic :: Scientific/Engineering :: Image Recognition",
]
# Below the dependencies for brainmapper (the cellfinder CLI tool) only
# (i.e., only what users will need for brainmapper)
dependencies = [
"brainglobe>=1.3.0",
"configobj",
"fancylog>=0.4.2",
"multiprocessing-logging>=0.3.4",
"natsort",
"numpy",
"pandas",
"packaging",
"pooch",
"scikit-image",
"tifffile",
"tqdm",
]
[project.optional-dependencies]
# Below, everything developers need to contribute
# to the workflows (i.e., run tests, run benchmarks, etc)
dev = [
"black",
"pytest-cov",
"pytest",
"gitpython",
"coverage>=5.0.3",
"pre-commit",
"setuptools_scm",
"asv",
]
napari = ["napari[pyqt5]", "brainglobe-napari-io", "cellfinder[napari]>=1.0.0"]
[project.urls]
"Bug Tracker" = "https://github.com/brainglobe/brainglobe-workflows/issues"
"Documentation" = "https://brainglobe.info/documentation/brainglobe-workflows"
"Homepage" = "https://brainglobe.info"
"Source Code" = "https://github.com/brainglobe/brainglobe-workflows"
[project.scripts]
brainmapper = "brainglobe_workflows.brainmapper.main:main"
[build-system]
requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"
[tool.setuptools]
include-package-data = true
zip-safe = false
[tool.setuptools.packages.find]
include = ["brainglobe_workflows"]
exclude = ["tests", "resources", "benchmarks"]
[tool.black]
target-version = ["py310", "py311", 'py312']
skip-string-normalization = false
line-length = 79
ignore = ["*.yaml"]
[tool.check-manifest]
[tool.pytest.ini_options]
addopts = "--cov=brainglobe-workflows"
markers = [
"slow: marks tests as slow (deselect with '-m \"not slow\"')",
"serial",
]
[tool.coverage.run]
source = ["./*"]
omit = ["benchmarks/*"]
[tool.ruff]
line-length = 79
exclude = ["__init__.py", "build", ".eggs"]
select = ["I", "E", "F"]
fix = true
[tool.setuptools_scm]
[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py{310,311,312}-{coredev}
isolated_build = True
[gh-actions]
python =
3.10: py310
3.11: py311
3.12: py312
[gh-actions:env]
# This runs the coredev environment if the "coredev" github actions input
# is set to "true"
INPUT_COREDEV =
true: coredev
[coverage:run]
source = ./*
omit = benchmarks/*
[testenv]
extras =
dev
deps =
coredev: git+https://github.com/brainglobe/cellfinder.git
commands =
pytest {toxinidir} -v --color=yes --cov=./ --cov-report=xml
description =
Run tests
coredev: Run tests with the development version of cellfinder
passenv =
CI
GITHUB_*
"""