tox.ini

[tox]
env_list =
  py310,
  py311,
  py39,
  coverage,
  docs,
  package_description
  py38,
  fix_lint,
  hypothesis,
  khmer,
  khmer_master
min_version = 3.27
isolated_build = true
skip_missing_interpreters = true

[testenv]
description = run the tests with pytest under {basepython}
package = wheel
wheel_build_env = .pkg
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
pass_env =
    TOXENV
    CURL_CA_BUNDLE
    http_proxy
    https_proxy
    no_proxy
    REQUESTS_CA_BUNDLE
    SSL_CERT_FILE
    PYTEST_*
    PIP_CACHE_DIR
    CI
    PYTHONDEVMODE
    LIBCLANG_PATH
    BINDGEN_EXTRA_CLANG_ARGS
deps =
    pip >= 19.3.1
extras =
    test
    storage
commands = pytest \
           --cov "{envsitepackagesdir}/sourmash" \
           --cov-config "{toxinidir}/tox.ini" \
           --cov-report= \
           --junitxml {toxworkdir}/junit.{envname}.xml \
           {posargs:doc tests}

[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:.}

[testenv:khmer]
basepython = python3.8
deps =
  khmer
commands = pytest \
           --cov "{envsitepackagesdir}/sourmash" \
           --cov-config "{toxinidir}/tox.ini" \
           --cov-report= \
           --junitxml {toxworkdir}/junit.{envname}.xml \
           -k test_nodegraph \
           {posargs:.}

[testenv:khmer_master]
basepython = python3.8
deps =
  -e git+https://github.com/dib-lab/khmer.git\#egg=khmer
commands = pytest \
           --cov "{envsitepackagesdir}/sourmash" \
           --cov-config "{toxinidir}/tox.ini" \
           --cov-report= \
           --junitxml {toxworkdir}/junit.{envname}.xml \
           -k test_nodegraph \
           {posargs:.}

[testenv:asv]
description = run asv for benchmarking (compare current commit with latest)
deps =
  asv==0.5.1
  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
whitelist_externals = pandoc
pass_env = HOME
change_dir = {toxinidir}
#commands = sphinx-build -d "{toxworkdir}/docs_doctree" doc "{toxworkdir}/docs_out" --color -W -bhtml {posargs}
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"))'

[testenv:package_description]
description = check that the long description is valid
basepython = python3.8
deps = twine >= 1.12.1
       # TODO installing readme-renderer[md] should not be necessary
       readme-renderer[md] >= 24.0
       pip >= 19.1
skip_install = true
change_dir = {toxinidir}
extras =
commands = pip wheel -w {envtmpdir}/build --no-deps .
           twine check {envtmpdir}/build/*

[testenv:mypy]
description = run mypy checker
basepython = python3.8
pass_env = {[testenv]pass_env}
          # without PROGRAMDATA cloning using git for Windows will fail with an `error setting certificate verify locations` error
          PROGRAMDATA
deps  = mypy
commands = mypy src/sourmash

[testenv:fix_lint]
description = format the code base to adhere to our styles, and complain about what we cannot do automatically
basepython = python3.8
pass_env = {[testenv]pass_env}
          # without PROGRAMDATA cloning using git for Windows will fail with an `error setting certificate verify locations` error
          PROGRAMDATA
          PRE_COMMIT_HOME
extras = lint
deps = pre-commit>=2
skip_install = True
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"))'

[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)
deps = {[testenv]deps}
       coverage >= 5.0.1
       diff_cover
skip_install = True
pass_env = {[testenv]pass_env}
          DIFF_AGAINST
set_env = COVERAGE_FILE={toxworkdir}/.coverage
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 = py39, py38, py37, pypy3
parallel_show_output = True

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

[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
  3.9: py39, coverage
  3.8: py38, coverage

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

[pep8]
max-line-length = 99

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