pyproject.toml

[build-system]
requires = ["setuptools>=61", "setuptools-scm[toml]>=6.2"]
build-backend = "setuptools.build_meta"

[project]
name = "cellrank"
dynamic = ["version"]
description = "CellRank: dynamics from multi-view single-cell data"
readme = "README.rst"
requires-python = ">=3.9"
license = {file = "LICENSE"}
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Operating System :: Microsoft :: Windows",
    "Typing :: Typed",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Mathematics",
    "Topic :: Scientific/Engineering :: Visualization",
]
keywords = [
    "single-cell",
    "bio-informatics",
    "RNA velocity",
    "Markov chain",
    "GPCCA",
]
authors = [
    {name = "Marius Lange"},
    {name = "Michal Klein"},
    {name = "Philipp Weiler"},
]
maintainers = [
    {name = "Michal Klein", email = "info@cellrank.org"}
]


dependencies = [
    "anndata>=0.9",
    "docrep>=0.3.0",
    "joblib>=0.13.1",
    "matplotlib>=3.5.0",
    "networkx>=2.2",
    "numba>=0.51.0,!=0.57.0",
    "numpy>=1.22.0",
    "pandas>=1.5.0",
    "pygam>=0.8.0",
    "pygpcca>=1.0.4",
    "scanpy>=1.7.2",
    "scikit-learn>=0.24.0",
    "scipy>=1.12.0",
    "scvelo>=0.2.5",
    "seaborn>=0.10.0",
    "wrapt>=1.12.1",
]

[project.optional-dependencies]
dev = [
    "pre-commit>=3.0.0",
    "tox>=4",
]
test = [
    "pytest>=8",
    "pytest-mock>=3.5.0",
    "pytest-cov>=4",
    "pytest-xdist",
    "coverage[toml]>=7",
    "zarr",
    "igraph",
    "leidenalg",
    "Pillow",
    "jax",
]
docs = [
    "sphinx>=5.1.1",
    "furo>=2022.09.29",
    "myst-nb>=0.17.1",
    "sphinx-tippy>=0.4.1",
    "sphinx-autodoc-typehints>=1.10.3",
    "sphinx_copybutton>=0.5.0",
    "sphinx_design>=0.3.0",
    "sphinxcontrib-bibtex>=2.3.0",
    "sphinxcontrib-spelling>=7.6.2",
]

[project.urls]
Homepage = "https://github.com/theislab/cellrank"
Download = "https://cellrank.readthedocs.io/en/latest/installation.html"
"Bug Tracker" = "https://github.com/theislab/cellrank/issues"
Documentation = "https://cellrank.readthedocs.io"
"Source Code" = "https://github.com/theislab/cellrank"

[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = true

[tool.setuptools_scm]

[tool.ruff]
target-version = "py39"
line-length = 120

[tool.ruff.lint]
exclude = [
    ".eggs",
    ".git",
    ".ruff_cache",
    ".tox",
    "__pypackages__",
    "_build",
    "build",
    "dist",
]
ignore = [
    "PT011",  # TODO/
    # Do not implicitly `return None` in function able to return non-`None` value
    "RET502",
    # Missing explicit `return` at the end of function able to return non-`None` value
    "RET503",
    # 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, i, j, k, l is reasonable indexing notation
    "E741",
    # Missing docstring in public package
    "D104",
    # Missing docstring in public module
    "D100",
    # Missing docstring in __init__
    "D107",
    # Missing docstring in magic method
    "D105",
]
select = [
    "D", # flake8-docstrings
    "E", # pycodestyle
    "F", # pyflakes
    "W", # pycodestyle
    "Q", # flake8-quotes
    "SIM", # flake8-simplify
    "NPY",  # NumPy-specific rules
    "PT",  # flake8-pytest-style
    "TID",  # flake8-tidy-imports
    "B", # flake8-bugbear
    "UP", # pyupgrade
    "C4", # flake8-comprehensions
    "BLE", # flake8-blind-except
    "T20",  # flake8-print
    "RET", # flake8-raise
]
unfixable = ["B", "C4", "BLE", "T20", "RET"]
[tool.ruff.lint.per-file-ignores]
"tests/*" = ["D"]
"*/__init__.py" = ["F401"]
"docs/*" = ["D"]
[tool.ruff.lint.pydocstyle]
convention = "numpy"
[tool.ruff.lint.flake8-tidy-imports]
ban-relative-imports = "all"
[tool.ruff.lint.flake8-quotes]
inline-quotes = "double"

[tool.black]
line-length = 120
target-version = ['py39']
include = '\.pyi?$'

[tool.isort]
profile = "black"
include_trailing_comma = true
sections = ["FUTURE", "STDLIB", "THIRDPARTY", "GENERIC", "NUMERIC", "PLOTTING", "BIO", "FIRSTPARTY", "LOCALFOLDER"]
# also contains what we import in notebooks
known_generic = ["wrapt", "joblib"]
known_numeric = ["numpy", "numba", "scipy", "jax", "pandas", "sklearn", "networkx", "statsmodels"]
known_bio = ["anndata", "scanpy"]
known_plotting = ["IPython", "matplotlib", "mpl_toolkits", "seaborn"]

[tool.pytest.ini_options]
testpaths = "tests"
xfail_strict = true

[tool.coverage.run]
branch = true
parallel = true
source = ["src/"]
omit = [
    "*/__init__.py",
]

[tool.coverage.report]
exclude_lines = [
    '\#.*pragma:\s*no.?cover',
    "^if __name__ == .__main__.:$",
    '^\s*raise AssertionError\b',
    '^\s*raise NotImplementedError\b',
    '^\s*return NotImplemented\b',
]
precision = 2
show_missing = true
skip_empty = true
sort = "Miss"

[tool.rstcheck]
ignore_directives = [
    "toctree",
    "currentmodule",
    "autosummary",
    "module",
    "automodule",
    "autoclass",
    "bibliography",
    "grid",
]
ignore_roles = [
    "mod",
    "class",
    "attr",
    "func",
    "meth",
    "doc",
    "cite",
]

[tool.doc8]
max_line_length = 120
ignore-path = "docs/release/**.rst"

[tool.tox]
legacy_tox_ini = """
[tox]
# TODO(michalk8): upgrade to `tox>=4.0` once `tox-conda` supports it
requires = tox-conda
isolated_build = true
envlist = lint-code,py{3.9,3.10,3.11,3.12,3.13}-{slepc,noslepc}
skip_missing_interpreters = true

[testenv]
conda_deps =
    py: r-mgcv
    py: rpy2
    slepc: mpi4py
    slepc: petsc4py
    slepc: slepc4py
conda_channels=
    conda-forge
extras = test
passenv = PYTEST_* CI
commands =
    python -m pytest {tty:--color=yes} {posargs: \
        --cov={envsitepackagesdir}{/}cellrank --cov-config={toxinidir}{/}pyproject.toml \
        --no-cov-on-fail --cov-report=xml --cov-report=term-missing:skip-covered}

[testenv:lint-code]
description = Lint the code.
deps = pre-commit>=3.0.0
skip_install = true
commands =
    pre-commit run --all-files --show-diff-on-failure

[testenv:lint-docs]
description = Lint the documentation.
deps =
extras = docs
ignore_errors = true
allowlist_externals = make
passenv = PYENCHANT_LIBRARY_PATH
setenv = SPHINXOPTS = -W -q --keep-going
changedir = {toxinidir}{/}docs
commands =
    # make linkcheck {posargs}
    # make spelling {posargs}

[testenv:clean-docs]
description = Remove the documentation.
deps =
skip_install = true
changedir = {toxinidir}{/}docs
allowlist_externals = make
commands =
    make clean

[testenv:build-docs]
description = Build the documentation.
deps =
extras = docs
allowlist_externals = make
changedir = {toxinidir}{/}docs
commands =
    make html {posargs}
commands_post =
    python -c 'import pathlib; print("Documentation is under:", pathlib.Path("{toxinidir}") / "docs" / "_build" / "html" / "index.html")'

[testenv:build-package]
description = Build the package.
deps =
    build
    twine
allowlist_externals = rm
commands =
    rm -rf {toxinidir}{/}dist
    python -m build --sdist --wheel --outdir {toxinidir}{/}dist{/} {posargs:}
    python -m twine check {toxinidir}{/}dist{/}*
commands_post =
    python -c 'import pathlib; print(f"Package is under:", pathlib.Path("{toxinidir}") / "dist")'

[testenv:format-references]
description = Format references.bib.
deps =
skip_install = true
allowlist_externals = biber
commands = biber --tool --output_file={toxinidir}{/}docs{/}references.bib --nolog \
    --output_align --output_indent=2 --output_fieldcase=lower \
    --output_legacy_dates --output-field-replace=journaltitle:journal,thesis:phdthesis,institution:school \
    {toxinidir}{/}docs{/}references.bib
"""