tox.ini

[flake8]
per-file-ignores =
    */__init__.py: D104, F401
    tests/*: D
    docs/*: D,B
    squidpy/pl/_ligrec.py: D,B
    squidpy/_constants/_pkg_constants.py: D101,D102,D106
    squidpy/_constants/_constants.py: D101
    squidpy/pl/_interactive/_widgets.py: D
    .scripts/ci/download_data.py: D,B
    squidpy/*.py: RST303
# D104 Missing docstring in public package
# F401 ... imported but unused
# RST303 Unknown directive type

# D100 D100 Missing docstring in public module
# D107 Missing docstring in __init__
# B008 Do not perform function calls in argument defaults.
# W503 line break before binary operator
# D105 Missing docstring in magic method
# E203 whitespace before ':'
# P101 format string does contain unindexed parameters

# docrep interferences:
# RST201 Block quote ends without a blank line; unexpected unindent.
# RST301 Unexpected indentation.
# RST306 Unknown target name:
# RST203 Definition list ends without a blank line; unexpected unindent.
ignore = D100,D107,B008,W503,D105,E203,P101,RST201,RST301,RST306,RST203,B024
exclude =
    .git
    .tox
    build
    dist
    __pycache__
    setup.py
max_line_length = 120
filename = *.py
ban-relative-imports = true
rst-roles =
    mod
    class
    meth
    func
    attr
    paramref
    ref
    cite
rst-directives =
    envvar
    exception

[doc8]
max-line-length = 120
ignore-path = .tox,docs/source/api,squidpy.egg-info,dist,build
quiet = 1

[pytest]
python_files = test_*.py
testpaths = tests/
xfail_strict = true
qt_api=pyqt5
; addopts = -n auto

filterwarnings =
    ignore::UserWarning
    ignore:Using or importing the ABCs from 'collections':DeprecationWarning
    ignore:Converting `np.inexact`:DeprecationWarning
    ignore:the matrix subclass is:PendingDeprecationWarning
    ignore:Please use:DeprecationWarning:dask_image.*
    ignore:Auto-removal of grids by:DeprecationWarning:
    ignore:Support for passing numbers through unit converters:DeprecationWarning
    ignore:distutils Version classes are deprecated:DeprecationWarning
    ignore::anndata.OldFormatWarning

[coverage:run]
branch = true
parallel = true
source = squidpy
omit =
    */__init__.py
    */_version.py
    squidpy/pl/_interactive/*

[coverage:paths]
source =
    squidpy
    */site-packages/squidpy

[coverage:report]
exclude_lines =
    \#.*pragma:\s*no.?cover

    ^if __name__ == .__main__.:$

    ^\s*raise AssertionError\b
    ^\s*raise NotImplementedError\b
    ^\s*return NotImplemented\b
show_missing = true
precision = 2
skip_empty = True
sort = Miss

[gh-actions]
python =
    3.8: py38
    3.9: py39
    3.10: py310

[gh-actions:env]
PLATFORM =
    ubuntu-latest: linux
    macos-latest: macos

[tox]
isolated_build = True
envlist =
    covclean
    lint
    py{3.8,3.9,3.10}-{linux,macos}
    coverage
    readme
    check-docs
    docs
skip_missing_interpreters = true

[testenv]
platform =
    linux: linux
    macos: (osx|darwin)
deps =
    pytest
    pytest-xdist
    pytest-cov
    pytest-qt
    pytest-mock
    pytest-timeout
# see: https://github.com/numba/llvmlite/issues/669
extras = interactive
setenv = linux: PYTEST_FLAGS=--test-napari
passenv = TOXENV,CI,CODECOV_*,GITHUB_ACTIONS,PYTEST_FLAGS,DISPLAY,XAUTHORITY,MPLBACKEND
usedevelop = true
commands =
    python -m pytest --cov --cov-append --cov-report=xml --cov-config={toxinidir}/tox.ini --ignore docs/ {posargs:-vv} {env:PYTEST_FLAGS:}

[testenv:covclean]
description = Clean coverage files.
deps = coverage
skip_install = True
commands = coverage erase

[testenv:coverage]
description = Report the coverage difference.
deps =
    coverage
    diff_cover
skip_install = true
depends = py{38,39,310}-{linux,macos}
parallel_show_output = True
commands =
    coverage report --omit="tox/*"
    coverage xml --omit="tox/*" -o {toxinidir}/coverage.xml
    diff-cover --compare-branch origin/main {toxinidir}/coverage.xml

[testenv:lint]
description = Perform linting.
basepython = python3.9
deps = pre-commit>=3.0.4
skip_install = true
commands = pre-commit run --all-files --show-diff-on-failure {posargs:}

[testenv:clean-docs]
description = Clean the documentation artifacts.
basepython = python3.9
deps =
skip_install = true
changedir = {toxinidir}/docs
allowlist_externals = make
commands = make clean

[testenv:check-docs]
description = Check whether the links in the documentation are valid.
basepython = python3.9
deps = -r{toxinidir}/docs/requirements.txt
skip_install = true
allowlist_externals = sphinx-build
passenv = SQUIDPY_DOWNLOAD_NOTEBOOKS,PYENCHANT_LIBRARY_PATH
commands =
    sphinx-build -W --keep-going -b spelling {toxinidir}/docs/source {toxinidir}/docs/build/spellcheck
    sphinx-build -q -W --keep-going -b linkcheck {toxinidir}/docs/source {toxinidir}/docs/build/linkcheck

[testenv:docs]
description = Build the documentation.
basepython = python3.9
skip_install = true
deps = -r{toxinidir}/docs/requirements.txt
allowlist_externals = sphinx-build
commands =
    sphinx-build --color -b html {toxinidir}/docs/source {toxinidir}/docs/build/html
    python -c 'import pathlib; print(f"Documentation is available under:", pathlib.Path(f"{toxinidir}") / "docs" / "build" / "html" / "index.html")'

[testenv:build-release-notes]
description = Build release notes. Used when a new release happens.
basepython = python3.9
deps =
    towncrier
usedevelop = true
allowlist_externals = rm
commands =
    towncrier build --yes {posargs:} --version="dev"
    rm -f {toxinidir}/docs/source/release/notes-dev.rst
    towncrier build --yes --version="dev"

[testenv:readme]
description = Check if README renders on PyPI.
basepython = python3.9
deps = twine >= 1.12.1
skip_install = true
commands = pip wheel -q -w {envtmpdir}/build --no-deps .
           twine check {envtmpdir}/build/*

[testenv:download-data]
description = Download and cache data.
; basepython = python3.9
skip_install = false
deps = -r{toxinidir}/requirements.txt
commands = python ./.scripts/ci/download_data.py {posargs}