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tox.ini
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tox.ini
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; 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