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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[project]
name = "monkeybread"
version = "1.0.3"
description = "Analyze cellular niches in single-cell spatial transcriptomics data"
readme = "README.md"
requires-python = ">=3.8"
license = {file = "LICENSE"}
authors = [
{name = "Immunitas Therapeutics"},
]
maintainers = [
{name = "Immunitas Therapeutics", email = "[email protected]"},
{name = "Immunitas Therapeutics", email = "[email protected]"}
]
urls.Documentation = "https://monkeybread.readthedocs.io/"
urls.Source = "https://github.com/immunitastx/monkeybread"
urls.Home-page = "https://github.com/immunitastx/monkeybread"
dependencies = [
"scanpy>=1.9.0",
"anndata>=0.7.4",
"numpy>=1.17.0",
"matplotlib>=3.4",
"pandas>=1.0",
"seaborn",
"tqdm",
"scikit-learn>=0.22",
"omnipath>=1.0.7",
"zarr>=2.17.2",
"tifffle>=2024.8.30",
"tqdm>=4.64.1",
# for debug logging (referenced from the issue template)
"session-info",
]
[project.optional-dependencies]
dev = [
# CLI for bumping the version number
"bump2version",
"pre-commit"
]
doc = [
"sphinx>=4",
"sphinx-book-theme>=0.3.3",
"myst-nb",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
# For notebooks
"ipykernel",
"ipython==8.4.0",
"sphinx-copybutton",
]
test = [
"pytest",
"pytest-cov",
"pytest_nunit"
]
[tool.coverage.run]
source = ["monkeybread"]
omit = [
"**/test_*.py",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
[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/example.ipynb"
]