chore(deps): update actions/checkout action to v3 #96

Workflow file for this run

	name: Continuous integration

	on:
	- push

	jobs:
	build:
	name: Lint, test, and compile documentation
	if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'"
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v3
	with:
	fetch-depth: 1
	submodules: recursive
	lfs: true

	########## install package and its requirements
	- name: Install Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9'

	- name: Setup pip cache
	uses: actions/cache@v2
	with:
	path: /opt/hostedtoolcache/Python
	key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install pip and setuptools
	run: \|
	python -m pip install --upgrade pip
	python -m pip install --upgrade setuptools

	- name: Install XPP
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends wget make gcc libx11-dev libc6-dev

	cd /tmp
	wget http://www.math.pitt.edu/~bard/bardware/xppaut_latest.tar.gz
	mkdir xpp
	tar zxvf xppaut_latest.tar.gz --directory xpp
	cd xpp
	make
	sudo make install

	cd /tmp
	rm xppaut_latest.tar.gz
	rm -r xpp

	# install package
	- name: Install the package
	run: python -m pip install .

	########## lint, test, package, compile documentation
	# lint
	- name: Install flake8
	run: python -m pip install flake8

	- name: Lint the package
	run: python -m flake8

	# test and upload coverage report to Codecov
	- name: Install pytest
	run: python -m pip install pytest pytest-cov

	- name: Install the requirements for the tests
	run: python -m pip install .[tests]

	- name: Run the tests
	env:
	ENTREZ_EMAIL: ${{ secrets.ENTREZ_EMAIL }}
	GRB_WLSACCESSID: ${{ secrets.GRB_WLSACCESSID }}
	GRB_WLSSECRET: ${{ secrets.GRB_WLSSECRET }}
	GRB_LICENSEID: ${{ secrets.GRB_LICENSEID }}
	run: python -m pytest tests/ --cov=./biosimulations_modeldb --cov-report=xml

	- name: Upload the coverage report to Codecov
	uses: codecov/codecov-action@v2
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	flags: unittests
	file: ./coverage.xml

	# compile documentation
	- name: Install the requirements for compiling the documentation
	run: python -m pip install -r docs-src/requirements.txt

	- name: Compile the documentation
	run: \|
	sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
	mkdir -p docs-src/_static
	sphinx-build docs-src docs

	release:
	name: Release a new version
	needs: [build]
	if: startsWith(github.ref, 'refs/tags/')
	runs-on: ubuntu-latest
	steps:
	# checkout code
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	fetch-depth: 1
	ref: dev
	submodules: recursive
	lfs: true

	# install Python and Pip
	- name: Install Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.9'

	- name: Setup pip cache
	uses: actions/cache@v2
	with:
	path: /opt/hostedtoolcache/Python
	key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements.optional.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install pip and setuptools
	run: \|
	python -m pip install --upgrade pip
	python -m pip install --upgrade setuptools

	# convert README.md to RST for PyPI
	- name: Install pandoc
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends wget

	wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
	urlPart=`grep "\.deb" /tmp/pandocVersions.html \| head -n 1 \| cut -d'/' -f2-7 \| cut -d'"' -f1`
	wget "https://github.com/$urlPart" -O /tmp/pandoc.deb
	sudo dpkg -i /tmp/pandoc.deb
	rm /tmp/pandocVersions.html
	rm /tmp/pandoc.deb

	- name: Convert README to .rst format
	run: pandoc --from=gfm --output=README.rst --to=rst README.md

	# compile package
	- name: Install twine
	run: \|
	python -m pip install wheel twine

	- name: Create packages to upload to PyPI
	run: \|
	python setup.py sdist
	python setup.py bdist_wheel

	# compile documentation
	- name: Install the requirements for compiling the documentation
	run: python -m pip install -r docs-src/requirements.txt

	- name: Compile the documentation
	run: \|
	sphinx-apidoc . setup.py --output-dir docs-src/source --force --module-first --no-toc
	mkdir -p docs-src/_static
	sphinx-build docs-src docs

	########## Release
	# get version number
	- id: get-version-number
	name: Get version number
	env:
	TAG: ${{ github.ref }}
	run: \|
	version="${TAG/refs\/tags\//}"
	echo "::set-output name=version::$version"

	# Push the compiled documentation
	- id: commit-docs
	name: Commit the compiled documentation
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "biosimulationsdaemon"
	git config pull.rebase false
	git stash
	git pull
	set +e
	git stash pop
	git add docs
	git commit -m "Updating compiled documentation"
	if [[ $? = 0 ]]; then
	docsChanged=1
	else
	docsChanged=0
	fi
	echo "::set-output name=docsChanged::$docsChanged"

	- name: Push the compiled documentation
	if: steps.commit-docs.outputs.docsChanged == '1'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: dev

	# Create PyPI release
	- name: Upload packages to PyPI
	env:
	TWINE_USERNAME: __token__
	TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
	run: \|
	twine upload dist/*

	# Create GitHub release
	- name: Create GitHub release
	uses: actions/create-release@v1
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	with:
	tag_name: ${{ steps.get-version-number.outputs.version }}
	release_name: Release ${{ steps.get-version-number.outputs.version }}

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chore(deps): update actions/checkout action to v3 #96

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chore(deps): update actions/checkout action to v3 #96

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