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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[tool.hatch.build]
exclude = [
"docs*",
"tests*",
]
[project]
name = "cellcharter"
version = "0.3.2"
description = "A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data."
readme = "README.md"
requires-python = ">=3.8,<3.13"
license = {file = "LICENSE"}
authors = [
{name = "CSO group"},
]
maintainers = [
{name = "Marco Varrone", email = "[email protected]"},
]
urls.Documentation = "https://cellcharter.readthedocs.io/"
urls.Source = "https://github.com/CSOgroup/cellcharter"
urls.Home-page = "https://github.com/CSOgroup/cellcharter"
dependencies = [
"anndata < 0.11.0",
"scikit-learn",
"squidpy",
"torchgmm",
# for debug logging (referenced from the issue template)
"session-info",
"spatialdata",
"spatialdata-plot >= 0.1.0",
"rasterio",
"sknw",
"matplotlib < 3.9.0",
]
[project.optional-dependencies]
dev = [
"pre-commit",
"twine>=4.0.2"
]
doc = [
"docutils>=0.8,!=0.18.*,!=0.19.*",
"sphinx>=4",
"sphinx-book-theme>=1.0.0",
"myst-nb>=1.1.0",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
"sphinxext-opengraph",
# For notebooks
"ipykernel",
"ipython",
"sphinx-copybutton",
"sphinx-design"
]
test = [
"pytest",
"pytest-cov",
]
transcriptomics = [
"scvi-tools",
]
proteomics = [
"scarches",
]
[tool.coverage.run]
source = ["cellcharter"]
omit = [
"**/test_*.py",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
filterwarnings = [
"ignore::anndata.OldFormatWarning",
"ignore:.*this fit will run with no optimizer.*",
"ignore:.*Consider increasing the value of the `num_workers` argument.*",
]
[tool.isort]
include_trailing_comma = true
multi_line_output = 3
profile = "black"
skip_glob = ["docs/*"]
[tool.black]
line-length = 120
target-version = ['py38']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
)
'''
[tool.jupytext]
formats = "ipynb,md"
[tool.cruft]
skip = [
"tests",
"src/**/__init__.py",
"src/**/basic.py",
"docs/api.md",
"docs/changelog.md",
"docs/references.bib",
"docs/references.md",
"docs/notebooks"
]