pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = [ "hatch-vcs", "hatchling" ]

[project]
name = "cell-annotator"
description = "Automated cell annotation from scRNA-seq data using LLMs"
readme = "README.md"
license = { file = "LICENSE" }
maintainers = [
  { name = "Marius Lange", email = "mlange@ethz.ch" },
]
authors = [
  { name = "Marius Lange" },
]
requires-python = ">=3.11"
classifiers = [
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python :: 3.13",
  "Programming Language :: Python :: 3.14",
]
dynamic = [ "version" ]
dependencies = [
  "docrep",
  "packaging",
  "pydantic>=2",
  "python-dotenv",
  "rich",
  "scanpy>=1.11.5",
  # for debug logging (referenced from the issue template)
  "session-info2",
]
# Convenience groups combining providers
optional-dependencies.all-providers = [
  "cell-annotator[anthropic]",
  "cell-annotator[gemini]",
  "cell-annotator[openai]",
]
optional-dependencies.anthropic = [
  "anthropic>=0.75",
]
# Other optional functionality
optional-dependencies.colors = [
  "colorspacious>=1.1.2",
]
optional-dependencies.gemini = [
  "google-genai>=1.57",
]
optional-dependencies.gpu = [
  "rapids-singlecell>=0.13",
]
# Core provider dependencies - one of these is required to use the package
optional-dependencies.openai = [
  "openai>=2",
]
# Thin pointer so `pip install cell-annotator[test]` pulls in the provider extras
# that the test suite exercises. Python test dependencies live in
# [dependency-groups] test below and are pulled in by hatch / `uv sync --group test`.
optional-dependencies.test = [
  "cell-annotator[all-providers]",
  "cell-annotator[colors]",
]
optional-dependencies.tutorials = [
  "squidpy>=1.7",
]
# https://docs.pypi.org/project_metadata/#project-urls
urls.Documentation = "https://cell-annotator.readthedocs.io/"
urls.Homepage = "https://cell-annotator.readthedocs.io/"
urls.Source = "https://github.com/quadbio/cell-annotator"

[dependency-groups]
dev = [
  "pre-commit",
  "twine>=4.0.2",
]
test = [
  "coverage>=7.10",
  "flaky",
  "pytest",
  "pytest-cov",     # For VS Code's coverage functionality
]
doc = [
  "docutils>=0.8,!=0.18.*,!=0.19.*",
  "ipykernel",
  "ipython",
  "ipywidgets",                      # for tqdm/notebook progress bars in Jupyter
  "myst-nb>=1.1",
  "pandas",
  # Until pybtex >0.24.0 releases: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
  "setuptools",
  "sphinx>=8.1",
  "sphinx-autodoc-typehints",
  "sphinx-book-theme>=1",
  "sphinx-copybutton",
  "sphinx-tabs",
  "sphinxcontrib-bibtex>=1",
  "sphinxext-opengraph",
]

[tool.hatch]
version.source = "vcs"
envs.default.installer = "uv"
envs.default.dependency-groups = [ "dev" ]
envs.docs.dev-mode = true
envs.docs.scripts.build = "sphinx-build -M html docs docs/_build {args}"
envs.docs.scripts.clean = "git clean -fdX -- {args:docs}"
envs.docs.scripts.open = "python -m webbrowser -t docs/_build/html/index.html"
envs.docs.dependency-groups = [ "doc" ]
envs.hatch-test.features = [ "test" ]
envs.hatch-test.matrix = [
  # Test the lowest and highest supported Python versions with normal deps
  { deps = [ "stable" ], python = [ "3.11", "3.14" ] },
  # Test the newest supported Python version also with pre-release deps
  { deps = [ "pre" ], python = [ "3.14" ] },
]
# If the matrix variable `deps` is set to "pre",
# set the environment variable `UV_PRERELEASE` to "allow".
envs.hatch-test.overrides.matrix.deps.env-vars = [
  { value = "allow", key = "UV_PRERELEASE", if = [ "pre" ] },
]
# hatch-test needs both:
#   - dependency-groups: Python test packages (pytest, coverage, flaky, ...)
#   - features: provider extras via optional-dependencies.test thin pointer
envs.hatch-test.dependency-groups = [ "dev", "test" ]

[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.
  "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."*/__init__.py" = [ "F401" ]
lint.per-file-ignores."docs/*" = [ "I" ]
lint.per-file-ignores."tests/*" = [ "D" ]
lint.pydocstyle.convention = "numpy"

[tool.pytest]
ini_options.testpaths = [ "tests" ]
ini_options.addopts = [
  "--import-mode=importlib", # allow using test files with same name
]
ini_options.markers = [
  "real_llm_query: mark a test that sends data to an actual LLM provider.",
]
ini_options.xfail_strict = true

[tool.coverage]
run.omit = [
  "**/test_*.py",
]
run.patch = [ "subprocess" ]
run.source = [ "cell_annotator" ]

[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",
]