pyproject.toml

[build-system]
requires = ["setuptools>=64", "setuptools_scm[toml]>=8"]
build-backend = "setuptools.build_meta"

[project]
name = "cellxgene-census"
dynamic = ["version"]
description = "API to facilitate the use of the CZ CELLxGENE Discover Census. For more information about the API and the project visit https://github.com/chanzuckerberg/cellxgene-census/"
authors = [
    { name = "Chan Zuckerberg Initiative Foundation", email = "soma@chanzuckerberg.com" }
]
license = { text = "MIT" }
readme = "README.md"
requires-python = ">= 3.8, < 3.12"
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "Intended Audience :: Information Technology",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
]
dependencies= [
    # NOTE: the tiledbsoma version must be >= to the version used in the Census builder, to
    # ensure that the assets are readable (tiledbsoma supports backward compatible reading).
    # Make sure this version does not fall behind the builder's tiledbsoma version.
    "tiledbsoma~=1.11.4",
    "anndata",
    "numpy>=1.21,<2.0",
    "requests",
    "typing_extensions",
    "s3fs>=2021.06.1",
]

[project.optional-dependencies]
experimental = [
    "torch",
    "torchdata~=0.7",
    "scikit-learn~=1.0",
    "scikit-misc>=0.2,<0.4",  # scikit-misc 0.3 dropped Python 3.8 support, and 0.4 doesn't have MacOS/ARM wheels
    "psutil~=5.0",
    "datasets~=2.0",
    "tdigest~=0.5",
    # Not expressible in pyproject.toml:
    #"git+https://huggingface.co/ctheodoris/Geneformer",
    # instead, experimental/ml/geneformer_tokenizer.py catches ImportError to ask user to install that.
]
doc = [
    "nbsphinx",
    "myst-parser",
    "sphinx-rtd-theme",
    "gitpython",
    "sphinx<7.0.0",
]

[project.urls]
homepage = "https://github.com/chanzuckerberg/cellxgene-census"
repository = "https://github.com/chanzuckerberg/cellxgene-census"

[tool.setuptools.packages.find]
where = ["src"]
include = ["cellxgene_census*"]  # package names should match these glob patterns (["*"] by default)
exclude = ["tests*"]  # exclude packages matching these glob patterns (empty by default)

[tool.setuptools.package-data]
"cellxgene_census" = ["py.typed"]

[tool.setuptools_scm]
root = "../../.."

[tool.ruff]
line-length = 120
src = ["api/python/cellxgene_census/src"]
target-version = "py38"

[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 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",
    # Missing argument description in the docstring TODO: enable
    "D417",
    # Blank line required between summary line and description TODO: enable
    "D205",
    # Prefer absolute imports over relative imports from parent modules TODO: enable
    "TID252",
]

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"*/tests/*" = ["D"]
"*/__init__.py" = ["F401"]

[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"
# Like Black, indent with spaces, rather than tabs.
indent-style = "space"
# Like Black, respect magic trailing commas.
skip-magic-trailing-comma = false
# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

[tool.mypy]
show_error_codes = true
ignore_missing_imports = true
warn_unreachable = true
strict = true
plugins = "numpy.typing.mypy_plugin"

[tool.pytest.ini_options]
markers = [
    "live_corpus: runs on the live CELLxGENE Census data corpus and small enough to run in CI",
    "expensive: too expensive to run regularly or in CI",
    "experimental: tests for the `experimental` package",
    "lts_compat_check: check for compatibility with an LTS build",
]