; 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