pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]

[project]
name = "scverse-tutorials"
version = "0.0.1"
description = "Tutorials for single-cell analysis with scverse packages"
readme = "README.md"
requires-python = ">=3.10"
license = {file = "LICENSE"}
authors = [
    {name = "scverse team"},
]
maintainers = [
    {name = "scverse team", email = "core-team@scverse.org"},
]
urls.Documentation = "https://scverse.org/scverse-tutorials"
urls.Source = "https://github.com/scverse/scverse-tutorials"
urls.Home-page = "https://github.com/scverse/scverse-tutorials"
classifiers = [
    "Private :: Do Not Upload",  # Prevent uploading to PyPI
]

[project.optional-dependencies]
dev = ["pre-commit"]
registry = [
    "jsonschema",
    "pillow",
    "httpx",
    "pyyaml",
]
docs = [
    "sphinx>=7",
    "sphinx-book-theme>=1.1.0",
    "myst-nb>=1.1.0",
    "sphinxcontrib-bibtex>=1.0.0",
    "sphinx-autodoc-typehints",
    "sphinxext-opengraph",
    # For notebooks
    "ipykernel",
    "ipython",
    "sphinx-copybutton",
]

[tool.hatch.envs.default]
installer = "uv"

[tool.hatch.envs.registry]
features = ["registry"]
[tool.hatch.envs.registry.scripts]
validate = "python tutorial-registry/validate.py {args}"

[tool.hatch.envs.docs]
features = ["docs"]
extra-dependencies = [
    "setuptools",  # undeclared dependency in pybtex
    # fix from here: https://github.com/executablebooks/MyST-NB/pull/597
    "myst-nb @ git+https://github.com/flying-sheep/MyST-NB.git@eval-metadata",
]
[tool.hatch.envs.docs.scripts]
build = "sphinx-build -M html docs docs/_build {args}"

[tool.hatch.build.targets.wheel]
bypass-selection = true  # This is not a package

[tool.black]
line-length = 120

[tool.ruff]
line-length = 120
src = ["src"]
extend-include = ["*.ipynb"]

[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/*" = [
    "B018", # Trailing expressions in notebooks are not “useless”
    "D103", # No need for docstrings in functions, we use literate programming
    "E402", # Imports in non-top cells are fine
]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]

[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",
]