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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 = "multimil"
version = "0.2.0"
description = "Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases"
readme = "README.md"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
{name = "Anastasia Litinetskaya"},
]
maintainers = [
{name = "Anastasia Litinetskaya", email = "[email protected]"},
]
urls.Documentation = "https://multimil.readthedocs.io/"
urls.Source = "https://github.com/theislab/multimil"
urls.Home-page = "https://github.com/theislab/multimil"
dependencies = [
"anndata<0.11",
"numpy<2.0",
# for debug logging (referenced from the issue template)
"session-info",
# multimil specific
"scanpy",
"scvi-tools<1.0.0",
"matplotlib",
]
[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",
"setuptools", # Until pybtex >0.23.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
"sphinx-autodoc-typehints",
"sphinxext-opengraph",
# For notebooks
"ipykernel",
"ipython",
"sphinx-copybutton",
"pandas",
]
test = [
"pytest",
"coverage",
]
tutorials = [
"muon",
"jupyterlab",
"ipywidgets",
"leidenalg",
"igraph",
"gdown",
]
[tool.coverage.run]
source = ["multimil"]
omit = [
"**/test_*.py",
]
[tool.pytest.ini_options]
testpaths = ["tests"]
xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
[tool.ruff]
line-length = 120
src = ["src"]
extend-include = ["*.ipynb"]
[tool.ruff.format]
docstring-code-format = true
[tool.ruff.lint]
select = [
"F", # Errors detected by Pyflakes
"E", # Error detected by Pycodestyle
"W", # Warning detected by Pycodestyle
"I", # isort
"D", # pydocstyle
"B", # flake8-bugbear
"TID", # flake8-tidy-imports
"C4", # flake8-comprehensions
"BLE", # flake8-blind-except
"UP", # pyupgrade
"RUF100", # Report unused noqa directives
]
ignore = [
# line too long -> we accept long comment lines; formatter gets rid of long code lines
"E501",
# Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
"E731",
# allow I, O, l as variable names -> I is the identity matrix
"E741",
# Missing docstring in public package
"D104",
# Missing docstring in public module
"D100",
# Missing docstring in __init__
"D107",
# Errors from function calls in argument defaults. These are fine when the result is immutable.
"B008",
# __magic__ methods are often self-explanatory, allow missing docstrings
"D105",
# first line should end with a period [Bug: doesn't work with single-line docstrings]
"D400",
# First line should be in imperative mood; try rephrasing
"D401",
## Disable one in each pair of mutually incompatible rules
# We don’t want a blank line before a class docstring
"D203",
# We want docstrings to start immediately after the opening triple quote
"D213",
]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.per-file-ignores]
"docs/*" = ["I"]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
"src/multimil/module/__init__.py" = ["I"]
[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",
]