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"
license = "BSD-3-Clause"
maintainers = [ { name = "scverse team", email = "core-team@scverse.org" } ]
authors = [ { name = "scverse team" } ]
requires-python = ">=3.13"
classifiers = [
  "Private :: Do Not Upload",                    # Prevent uploading to PyPI
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
optional-dependencies.dev = [ "pre-commit" ]
optional-dependencies.docs = [
  # For notebooks
  "ipykernel",
  "ipython",
  "myst-nb>=1.1",
  "sphinx>=9",
  "sphinx-autodoc-typehints",
  "sphinx-book-theme>=1.1",
  "sphinx-copybutton",
  "sphinx-issues>=5.0.1",
  "sphinxcontrib-bibtex>=1",
  "sphinxext-opengraph",
]
optional-dependencies.registry = [ "httpx", "jsonschema", "pillow", "pyyaml" ]
urls.Documentation = "https://scverse.org/scverse-tutorials"
urls.Home-page = "https://github.com/scverse/scverse-tutorials"
urls.Source = "https://github.com/scverse/scverse-tutorials"

[tool.hatch]
build.targets.wheel.bypass-selection = true  # This is not a package
envs.default.installer = "uv"
envs.default.features = [ "dev" ]
envs.docs.features = [ "docs" ]
envs.docs.extra-dependencies = [
  # fix from here: https://github.com/executablebooks/MyST-NB/pull/597
  "myst-nb @ git+https://github.com/flying-sheep/MyST-NB.git@eval-metadata",
]
envs.docs.scripts.build = "sphinx-build -M html docs docs/_build {args}"
envs.docs.scripts.open = "python3 -m webbrowser -t docs/_build/html/index.html"
envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
envs.registry.features = [ "registry" ]
envs.registry.scripts.validate = "python tutorial-registry/validate.py {args}"

[tool.ruff]
line-length = 120
src = [ "src" ]
extend-include = [ "*.ipynb" ]
format.docstring-code-format = true
lint.select = [
  "B",      # flake8-bugbear
  "BLE",    # flake8-blind-except
  "C4",     # flake8-comprehensions
  "D",      # pydocstyle
  "E",      # Error detected by Pycodestyle
  "F",      # Errors detected by Pyflakes
  "I",      # isort
  "RUF100", # Report unused noqa directives
  "TID",    # flake8-tidy-imports
  "UP",     # pyupgrade
  "W",      # Warning detected by Pycodestyle
]
lint.ignore = [
  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
  "C408", # dict() is nice for some use cases
  "D100", # Missing docstring in public module
  "D104", # Missing docstring in public package
  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
  "D107", # Missing docstring in __init__
  # Disable one in each pair of mutually incompatible rules
  "D203", # We don’t want a blank line before a class docstring
  "D213", # <> We want docstrings to start immediately after the opening triple quote
  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
  "D401", # First line should be in imperative mood; try rephrasing
  "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
  "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
  "E741", # allow I, O, l as variable names -> I is the identity matrix
]
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
]
lint.pydocstyle.convention = "numpy"

[tool.cruft]
skip = [
  ".github/ISSUE_TEMPLATE",
  "environment.yml",
  "*.md",
  "src",
  "docs/*.md",
  "docs/notebooks",
  "docs/references.bib",
  "tests",
  "tutorial-registry",
]