tox.ini

[tox]
isolated_build = true
skip_missing_interpreters = true
env_list =
    py311,
    py312,
    py310,
    coverage,
    docs,
    package_description
    fix_lint,
    hypothesis,
    khmer,
    khmer_master
min_version = 3.27

[testenv]
description = run the tests with pytest under {basepython}
deps =
    pip>=19.3.1
extras =
    storage
    test
commands =
    pytest \
      --cov "{envsitepackagesdir}/sourmash" \
      --cov-config "{toxinidir}/tox.ini" \
      --cov-report= \
      --junitxml {toxworkdir}/junit.{envname}.xml \
      {posargs:doc tests}
package = wheel
pass_env =
    TOXENV
    CURL_CA_BUNDLE
    http_proxy
    https_proxy
    no_proxy
    REQUESTS_CA_BUNDLE
    SSL_CERT_FILE
    PYTEST_*
    PIP_CACHE_DIR
    CI
    PYTHONDEVMODE
    PYTHONTRACEMALLOC
    LIBCLANG_PATH
    BINDGEN_EXTRA_CLANG_ARGS
    NIX_LD
set_env =
    PIP_DISABLE_VERSION_CHECK = 1
    COVERAGE_FILE = {env:COVERAGE_FILE:{toxworkdir}/.coverage.{envname}}
    VIRTUALENV_NO_DOWNLOAD = 1
    PIP_EXTRA_INDEX_URL = https://antocuni.github.io/pypy-wheels/manylinux2010
wheel_build_env = .pkg

[testenv:.pkg]
pass_env =
    LIBCLANG_PATH
    BINDGEN_EXTRA_CLANG_ARGS
    NIX_*

[testenv:pypy3]
deps =
    pip>=19.3.1
    psutil<=5.6.7

[testenv:hypothesis]
commands =
    pytest \
      --cov "{envsitepackagesdir}/sourmash" \
      --cov-config "{toxinidir}/tox.ini" \
      --cov-report= \
      --junitxml {toxworkdir}/junit.{envname}.xml \
      --run-hypothesis \
      --hypothesis-show-statistics \
      --hypothesis-profile ci \
      {posargs:doc tests}

[testenv:khmer]
basepython = python3.10
deps =
    khmer
commands =
    pytest \
      --cov "{envsitepackagesdir}/sourmash" \
      --cov-config "{toxinidir}/tox.ini" \
      --cov-report= \
      --junitxml {toxworkdir}/junit.{envname}.xml \
      -k test_nodegraph \
      {posargs:doc tests}

[testenv:khmer_master]
basepython = python3.10
deps =
    git+https://github.com/dib-lab/khmer.git\#egg
commands =
    pytest \
      --cov "{envsitepackagesdir}/sourmash" \
      --cov-config "{toxinidir}/tox.ini" \
      --cov-report= \
      --junitxml {toxworkdir}/junit.{envname}.xml \
      -k test_nodegraph \
      {posargs:doc tests}

[testenv:asv]
description = run asv for benchmarking (compare current commit with latest)
deps =
    asv==0.6.2
    virtualenv
changedir = {toxinidir}
commands =
    asv machine --yes
    asv continuous latest HEAD {posargs}

[testenv:docs]
description = invoke sphinx-build to build the HTML docs
basepython = python3.10
extras =
    doc
commands =
    sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_out" --color -bhtml {posargs}
    python -c 'import pathlib; print("documentation available under file://\{0\}".format(pathlib.Path(r"{toxworkdir}") / "docs_out" / "index.html"))'
allowlist_externals = pandoc
change_dir = {toxinidir}
pass_env =
    HOME
    LC_ALL
    LOCALE_*

[testenv:package_description]
description = check that the long description is valid
basepython = python3.10
skip_install = true
deps =
    pip>=19.1
    readme-renderer[md]>=24
    twine>=1.12.1
extras =
commands =
    pip wheel -w {envtmpdir}/build --no-deps .
    twine check {envtmpdir}/build/*
change_dir = {toxinidir}

[testenv:mypy]
description = run mypy checker
basepython = python3.10
deps =
    mypy
commands =
    mypy src/sourmash
pass_env = {[testenv]pass_env}
    PROGRAMDATA

[testenv:fix_lint]
description = format the code base to adhere to our styles, and complain about what we cannot do automatically
basepython = python3.10
skip_install = true
deps =
    pre-commit>=2
extras =
    lint
commands =
    pre-commit run --all-files --show-diff-on-failure {posargs}
    python -c 'import pathlib; print("hint: run \{\} install to add checks as pre-commit hook".format(pathlib.Path(r"{envdir}") / "bin" / "pre-commit"))'
pass_env = {[testenv]pass_env}
    PROGRAMDATA
    PRE_COMMIT_HOME

[testenv:coverage]
description = [run locally after tests]: combine coverage data and create report;
    generates a diff coverage against origin/latest (can be changed by setting DIFF_AGAINST env var)
skip_install = true
deps =
    {[testenv]deps}
    coverage>=5.0.1
    diff_cover
parallel_show_output = true
commands =
    coverage combine
    coverage report -i -m
    coverage xml -i -o {toxworkdir}/coverage.xml
    coverage html -i -d {toxworkdir}/htmlcov
    diff-cover --compare-branch {env:DIFF_AGAINST:origin/latest} {toxworkdir}/coverage.xml
depends = py312, py311, py310, pypy3
pass_env = {[testenv]pass_env}
    DIFF_AGAINST
set_env = COVERAGE_FILE={toxworkdir}/.coverage

[testenv:X]
description = print the positional arguments passed in with echo
commands =
    echo {posargs}

[testenv:dev]
description = dev environment with all deps at {envdir}
usedevelop = true
deps =
    {[testenv]deps}
extras =
    doc
    storage
    test
commands =
    python -m pip list --format=columns
    python -c "print(r'{envpython}')"

[coverage:run]
branch = true
parallel = true

[coverage:report]
skip_covered = True
show_missing = True
exclude_lines =
    \#\s*pragma: no cover
    ^\s*raise AssertionError\b
    ^\s*raise NotImplementedError\b
    ^\s*return NotImplemented\b
    ^\s*raise$
    ^if __name__ == ['"]__main__['"]:$

[coverage:paths]
source = src/sourmash/
    tests/
    */.tox/*/lib/python*/site-packages/sourmash
    */.tox/pypy*/site-packages/sourmash
    */.tox\*\Lib\site-packages\sourmash
    */src/sourmash
    *\src\sourmash
    */tests
    *\tests

[gh-actions]
python =
    3.10: py310, docs, package_description, coverage
    3.11: py311, coverage
    3.12: py312, coverage

[flake8]
max-complexity = 22
max-line-length = 99
ignore = E203, W503, C901, E402, B011

[pep8]
max-line-length = 99