; a generative tox configuration, see: https://testrun.org/tox/latest/config.html#generative-envlist

[tox]
envlist =
    clean,
    check,
    {py36},
    report,
    docs,
    tf2

[testenv:tf2]
basepython =
    {tf2}: {env:TOXPYTHON:python3.7}
setenv =
    PYTHONPATH={toxinidir}/tests
    PYTHONUNBUFFERED=yes
passenv =
    *
usedevelop = false
install_command = pip install --no-cache-dir {packages}
list_depencencies_command =
    setuptools
deps =
    cython
    pytest
    pytest-travis-fold
    pytest-cov
    numpy
    progress
    pandas
    Biopython==1.77
    keras==2.4.3
    tensorflow==2.2.0
    h5py<3.0.0
    pyBigWig
    pybedtools
    pysam<0.16,!=0.15.3
    urllib3
    matplotlib
    seaborn
    scikit-learn
    pydot
commands =
    {posargs:py.test --cov --cov-report=term-missing -vv tests -p no:warnings}

[testenv]
basepython =
    pypy: {env:TOXPYTHON:pypy}
    {docs,spell}: {env:TOXPYTHON:python3.6}
    {py36}: {env:TOXPYTHON:python3.6}
    {bootstrap,clean,check,report,coveralls,codecov}: {env:TOXPYTHON:python3}
setenv =
    PYTHONPATH={toxinidir}/tests
    PYTHONUNBUFFERED=yes
passenv =
    *
usedevelop = false
install_command = pip install --no-cache-dir {packages}
list_depencencies_command =
    setuptools
deps =
    cython
    pytest
    pytest-travis-fold
    pytest-cov
    numpy
    progress
    pandas
    Biopython==1.77
    keras==2.2.4
    tensorflow==1.14.0
    h5py<3.0.0
    pyBigWig
    pybedtools
    pysam<0.16,!=0.15.3
    urllib3
    matplotlib
    seaborn
    scikit-learn
    pydot
commands =
    {posargs:py.test --cov --cov-report=term-missing -vv tests -p no:warnings}

[testenv:bootstrap]
deps =
    jinja2
    matrix
skip_install = true
commands =
    python ci/bootstrap.py
[testenv:spell]
setenv =
    SPELLCHECK=1
commands =
    - sphinx-build -b spelling docs dist/docs
skip_install = true
recreate = true
deps =
    -r{toxinidir}/docs/requirements.txt
    sphinxcontrib-spelling
    pyenchant

[testenv:docs]
deps =
    -r{toxinidir}/docs/requirements.txt
commands =
    - sphinx-build {posargs:-E} -b html docs dist/docs
    - sphinx-build -b linkcheck docs dist/docs

[testenv:check]
deps =
    docutils
    check-manifest
    bleach>=2.0
    pylama
    pylint
    progress
    readme-renderer
    pygments
    isort
    numpy
    pybedtools
    keras
    pandas
    Biopython==1.77
skip_install = true
ignore_errors = true
commands =
    python setup.py check --metadata --restructuredtext
    check-manifest {toxinidir}
    - isort -q --check-only --diff --recursive src tests setup.py -s tests/test_coverage.py
    - pylint --rcfile .pylintrc -r y setup.py
    - pylint --rcfile .pylintrc -r y src/janggu


[testenv:coveralls]
deps =
    coveralls
skip_install = true
commands =
    coveralls []

[testenv:codecov]
deps =
    codecov
skip_install = true
commands =
    coverage xml --ignore-errors
    codecov []


[testenv:report]
deps = coverage
skip_install = true
commands =
    - coverage combine --append || true
    coverage report
    coverage html

[testenv:clean]
commands = coverage erase
skip_install = true
deps = coverage