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pyproject.toml
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pyproject.toml
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[project]
name = "brainglobe-atlasapi"
description = "A lightweight python module to interact with and generate atlases for systems neuroscience."
readme = "README.md"
license = { file = "LICENSE" }
authors = [
{ name = "Luigi Petrucco, Federico Claudi, Adam Tyson", 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",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
requires-python = ">=3.10"
dependencies = [
"brainglobe-space >= 1.0.0",
"click",
"meshio",
"numpy",
"pandas",
"pyarrow",
"requests",
"rich >= 9.0.0",
"tifffile",
"treelib",
]
dynamic = ["version"]
[project.urls]
"Homepage" = "https://brainglobe.info/documentation/brainglobe-atlasapi/index.html"
"Source Code" = "https://github.com/brainglobe/brainglobe-atlasapi"
"Bug Tracker" = "https://github.com/brainglobe/brainglobe-atlasapi/issues"
"Documentation" = "https://brainglobe.info/documentation/brainglobe-atlasapi/index.html"
[project.optional-dependencies]
dev = [
"black",
"check-manifest",
"coverage",
"mypy",
"pre-commit",
"pytest-cov",
"pytest-mock",
"pytest",
"ruff",
"setuptools_scm",
"tox",
]
allenmouse = ["allensdk"]
allenmouse_barrels = [
"allensdk",
"voxcell"]
atlasgen = [
"loguru",
"PyMCubes",
"SimpleITK",
"tqdm>=4.46.1",
"vedo",
"xmltodict",
]
[project.scripts]
brainglobe = "brainglobe_atlasapi.cli:bg_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.packages.find]
include = ["brainglobe_atlasapi*"]
exclude = ["tests*"]
[tool.pytest.ini_options]
addopts = "--cov=brainglobe_atlasapi"
filterwarnings = [
"error",
"ignore::UserWarning",
# note the use of single quote below to denote "raw" strings in TOML
'ignore: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior',
]
markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
[tool.black]
target-version = ['py310', 'py311', 'py312']
skip-string-normalization = false
line-length = 79
[tool.setuptools_scm]
[tool.ruff]
line-length = 79
exclude = ["__init__.py", "build", ".eggs"]
fix = true
[tool.ruff.lint]
select = ["I", "E", "F"]
[tool.ruff.lint.per-file-ignores]
"*.ipynb" = ["E501"]
[tool.tox]
legacy_tox_ini = """
[tox]
envlist = py{310,311,312}
[gh-actions]
python =
3.10: py310
3.11: py311
3.12: py312
[testenv]
extras =
dev
atlasgen
commands = pytest -v --color=yes --cov=brainglobe_atlasapi --cov-report=xml
"""