/
tox.ini
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/
tox.ini
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[tox]
envlist = isort, black, flake8, safety, py3{6,7,8,9}
[gh-actions]
# We ignore flake8 for the time being because there are tons of things to fix.
python =
3.6: isort, black, safety, py36
3.7: safety, py37
3.8: safety, py38
[testenv]
extras =
array
deps=
pytest
pytest-benchmark
pytest-cov
pytest-mock
pytest-raises
jsonschema
commands =
pytest --cov=cobra --cov-report=term {posargs: --benchmark-skip}
[testenv:isort]
skip_install = True
deps=
isort >=5.0.5,<6
commands=
isort --check-only --diff {toxinidir}/src/cobra {toxinidir}/setup.py
[testenv:black]
skip_install = True
deps=
black
commands=
black --check --diff {toxinidir}/src/cobra {toxinidir}/setup.py
[testenv:flake8]
skip_install = True
deps=
flake8
flake8-docstrings
flake8-bugbear
commands=
flake8 {toxinidir}/src/cobra {toxinidir}/setup.py
[testenv:safety]
deps=
safety
commands=
safety check --full-report
################################################################################
# Testing tools configuration #
################################################################################
[pytest]
testpaths =
src/cobra/test
markers =
raises
[coverage:paths]
source =
src/cobra
*/site-packages/cobra
[coverage:run]
branch = true
parallel = true
omit =
*/cobra/test/*
[coverage:report]
exclude_lines =
# Have to re-enable the standard pragma
pragma: no cover
precision = 2
omit =
*/cobra/test/*
[isort]
skip = __init__.py
line_length = 88
indent = 4
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
lines_after_imports = 2
known_first_party = cobra
known_third_party =
depinfo
future
importlib_resources
libsbml
numpy
optlang
pandas
pytest
ruamel.yaml
scipy
swiglpk
[flake8]
exclude =
__init__.py
max-line-length = 88
# The following conflict with `black` which is the more pedantic.
ignore =
E203
W503
D202