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tox.ini
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# Tox (http://tox.testrun.org/) is a tool for running tests
# in multiple virtualenvs. This configuration file will run the
# test suite on all supported python versions. To use it, "pip install tox"
# and then run "tox" from this directory.
[tox]
isolated_build = true
envlist =
# always keep coverage-clean first
#coverage-clean
# code linters/stylers
manifest
lint
flake8
pyroma
mypy
# documentation linters/checkers
doc8
docstr-coverage
docs
# the actual tests
py-pydantic1
py-pydantic2
doctests
# always keep coverage-report last
#coverage-report
[testenv]
commands =
coverage run -p -m pytest --durations=20 {posargs:tests}
coverage combine
coverage xml
deps =
pydantic1: pydantic<2.0
pydantic2: pydantic>=2.0
passenv =
HOME
extras =
tests
align
export
web
allowlist_externals =
cat
cp
mkdir
git
[testenv:update]
description = Update the Bioregistry
commands =
python -m bioregistry update
usedevelop = true
extras =
align
export
charts
ndex
passenv =
BIOPORTAL_API_KEY
ECOPORTAL_API_KEY
AGROPORTAL_API_KEY
FAIRSHARING_LOGIN
FAIRSHARING_PASSWORD
NDEX_USERNAME
NDEX_PASSWORD
[testenv:coverage-clean]
deps = coverage
skip_install = true
commands = coverage erase
[testenv:manifest]
deps = check-manifest
skip_install = true
commands = check-manifest
[testenv:pre-commit]
skip_install = true
deps =
pre-commit
commands = pre-commit run -a
usedevelop = true
description = Run the pre-commit tool
[testenv:flake8]
skip_install = true
deps =
darglint
flake8>5.0.0
# flake8-bandit
flake8-black
flake8-bugbear
flake8-colors
flake8-docstrings
flake8-isort
flake8-print
pep8-naming
pydocstyle
commands =
flake8 src/bioregistry/ tests/
description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming).
[testenv:lint]
deps =
black[jupyter]
isort
skip_install = true
commands =
black .
isort .
description = Run linters.
[testenv:bioregistry-lint]
usedevelop = true
commands =
python -m bioregistry lint
description = Lint the Bioregistry data
[testenv:mypy]
deps =
mypy
pydantic
types-PyYAML
types-Markdown
types-tabulate
types-requests
types-python-dateutil
skip_install = true
commands = mypy --ignore-missing-imports src/bioregistry/
description = Run the mypy tool to check static typing on the project.
[testenv:pyroma]
deps =
pygments
pyroma
skip_install = true
commands = pyroma --min=10 .
description = Run the pyroma tool to check the package friendliness of the project.
[testenv:doc8]
skip_install = true
deps =
sphinx
doc8
commands =
doc8 docs/source/
description = Run the doc8 tool to check the style of the RST files in the project docs.
[testenv:docs]
extras =
docs
gha
align
export
charts
web
commands =
python -m sphinx -W -b {posargs:html} -d docs/build/doctrees docs/source docs/build/{posargs:html}
[testenv:docs-test]
changedir = docs
extras =
{[testenv:docs]extras}
commands =
mkdir -p {envtmpdir}
cp -r source {envtmpdir}/source
sphinx-build -W -b html -d {envtmpdir}/build/doctrees {envtmpdir}/source {envtmpdir}/build/html
sphinx-build -W -b coverage -d {envtmpdir}/build/doctrees {envtmpdir}/source {envtmpdir}/build/coverage
cat {envtmpdir}/build/coverage/c.txt
cat {envtmpdir}/build/coverage/python.txt
[testenv:docstr-coverage]
skip_install = true
deps =
docstr-coverage
commands =
docstr-coverage src/bioregistry/ tests/ --skip-private --skip-magic
description = Run the docstr-coverage tool to check documentation coverage
[testenv:doctests]
commands =
xdoctest -m src/bioregistry/ --quiet
deps =
xdoctest
pygments
extras =
web
[testenv:coverage-report]
deps = coverage
skip_install = true
commands =
coverage combine
coverage report
[testenv:erdantic]
usedevelop = true
deps =
erdantic
commands =
erdantic bioregistry.Registry bioregistry.Resource -o docs/img/datamodel_umls.svg
erdantic bioregistry.Registry bioregistry.Resource -o docs/img/datamodel_umls.png
[testenv:schema]
usedevelop = true
deps =
pydantic<2.0
commands =
python -m bioregistry.schema.struct
[testenv:send-prefixcc]
usedevelop = true
commands =
python -m bioregistry.export.prefixcc
description = Send a Bioregistry CURIE prefix/URI prefix pair to Prefix.cc via its "create" API endpoint. Note that only one request to this endpoint can be sent per day.
####################
# Deployment tools #
####################
[testenv:bumpversion]
commands = bump-my-version bump {posargs}
skip_install = true
passenv = HOME
deps =
bump-my-version
[testenv:bumpversion-release]
description = Remove the -dev tag from the version
commands = bump-my-version bump release --tag
skip_install = true
passenv = HOME
deps =
bump-my-version
[testenv:build]
skip_install = true
deps =
uv
setuptools
commands =
uv build --sdist --wheel --no-build-isolation
############
# Releases #
############
# In order to make a release to PyPI, you'll need to take the following steps:
#
# 1. Navigate to https://pypi.org/account/register/ to register for Test PyPI
# 2. Navigate to https://pypi.org/manage/account/ and request to re-send a verification email.
# This is not sent by default, and is required to set up 2-Factor Authentication.
# 3. Get account recovery codes
# 4. Set up 2-Factor Authentication
# 5. Get an API token from https://pypi.org/manage/account/token/
# 6. Create a file called .pypirc in the home directory if it does not already exist.
# 7. Add the following content to the .pypirc file
#
# [distutils]
# index-servers=
# pypi
# testpypi
#
# [pypi]
# username = __token__
# password = <the API token you just got>
#
# If there's already an `index-servers =` list, just make sure you add `pypi` to it.
# More information about .pypirc can be found at https://packaging.python.org/en/latest/specifications/pypirc/
[testenv:release]
description = Release the code to PyPI so users can pip install it
skip_install = true
passenv =
TWINE_USERNAME
TWINE_PASSWORD
deps =
{[testenv:build]deps}
twine >= 1.5.0
commands =
{[testenv:build]commands}
twine upload --skip-existing dist/*
[testenv:finish]
description =
Run a workflow that removes -dev from the version, creates a tagged release on GitHub,
creates a release on PyPI, and bumps the version again.
skip_install = true
passenv =
HOME
TWINE_USERNAME
TWINE_PASSWORD
deps =
{[testenv:release]deps}
bump-my-version
commands =
bump-my-version bump release --tag
{[testenv:release]commands}
git push --tags
bump-my-version bump patch
git push
allowlist_externals =
git
#################
# Test Releases #
#################
# In order to test making a release to Test PyPI, you'll need to take the following steps:
#
# 1. Navigate to https://test.pypi.org/account/register/ to register for Test PyPI
# 2. Navigate to https://test.pypi.org/manage/account/ and request to re-send a verification email.
# This is not sent by default, and is required to set up 2-Factor Authentication.
# 3. Get account recovery codes
# 4. Set up 2-Factor Authentication
# 5. Get an API token from https://test.pypi.org/manage/account/token/
# 6. Create a file called .pypirc in the home directory if it does not already exist.
# 7. Add the following content to the .pypirc file
#
# [distutils]
# index-servers=
# pypi
# testpypi
#
# [testpypi]
# repository = https://test.pypi.org/legacy/
# username = __token__
# password = <the API token you just got>
#
# If there's already an `index-servers =` list, just make sure you add `testpypi` to it.
# More information about .pypirc can be found at https://packaging.python.org/en/latest/specifications/pypirc/
[testenv:testrelease]
description = Release the code to the test PyPI site
skip_install = true
passenv =
TWINE_USERNAME
TWINE_PASSWORD
deps =
{[testenv:build]deps}
twine >= 1.5.0
commands =
{[testenv:build]commands}
twine upload --skip-existing --repository testpypi dist/*
[testenv:testfinish]
description =
Run a workflow that removes -dev from the version, creates a tagged release on GitHub,
creates a release on Test PyPI, and bumps the version again.
skip_install = true
passenv =
HOME
TWINE_USERNAME
TWINE_PASSWORD
deps =
{[testenv:testrelease]deps}
bump-my-version
commands =
bump-my-version bump release --tag
{[testenv:testrelease]commands}
git push --tags
bump-my-version bump patch
git push
allowlist_externals =
git