updaing lock file #552

Workflow file for this run

	name: Continuous integration

	on:
	- push

	jobs:
	getVersionNumber:
	name: Get version number
	if: startsWith(github.ref, 'refs/tags/') && github.actor != 'biosimulators-daemon' && !contains(github.event.head_commit.message, '[skip ci]')
	runs-on: ubuntu-20.04
	outputs:
	version: ${{ steps.get-version-number.outputs.version }}
	steps:
	- id: get-version-number
	name: Get version number
	env:
	TAG: ${{ github.ref }}
	run: \|
	version="${TAG/refs\/tags\//}"
	echo "::set-output name=version::$version"

	build:
	name: Lint, test, and compile documentation
	if: github.actor != 'biosimulators-daemon' && !contains(github.event.head_commit.message, '[skip ci]')
	runs-on: ubuntu-20.04
	steps:
	- name: Checkout repository
	uses: actions/checkout@v2
	with:
	fetch-depth: 1

	- name: Configure Git
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "biosimulatorsdaemon"
	git config pull.rebase false

	- 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 Java # for pyNeuroML
	uses: actions/setup-java@v2
	with:
	distribution: 'adopt'
	java-version: '15'

	- name: Install Perl # for BioNetGen
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends perl

	- 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

	- name: Install Singularity # to validate that the Docker image can be converted into a Singularity image
	uses: eWaterCycle/setup-singularity@v6

	# install package
	- name: Install the package
	run: \|
	python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
	python -m pip install .[all]

	# zip COMBINE/OMEX archives
	- name: Zip COMBINE/OMEX archives
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends zipcmp
	python scripts/zip_examples.py

	- id: commit-archives
	name: Commit zipped COMBINE/OMEX archives
	if: startsWith(github.ref, 'refs/heads/')
	env:
	HEAD: ${{ github.ref }}
	run: \|
	git stash \|\| true
	git pull
	set +e
	git stash pop \|\| true
	git add examples/*/.omex
	git commit -m "chore: Updated COMBINE/OMEX archives [skip ci]"
	if [[ $? = 0 ]]; then
	archivesChanged=1
	else
	archivesChanged=0
	fi
	echo "::set-output name=archivesChanged::$archivesChanged"

	branch="${HEAD/refs\/heads\//}"
	echo "::set-output name=branch::$branch"

	- name: Push the zipped COMBINE/OMEX archives
	if: steps.commit-archives.outputs.archivesChanged == '1' && startsWith(github.ref, 'refs/heads/')
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: ${{ steps.commit-archives.outputs.branch }}

	# 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:
	# BIOSIMULATORS_API_ENDPOINT: https://api.biosimulators.dev/ # uncomment to run tests using the dev deployment
	uses: GabrielBB/xvfb-action@v1
	with:
	run: python -m pytest tests/ --cov=./biosimulators_test_suite --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: [getVersionNumber, build]
	runs-on: ubuntu-20.04
	outputs:
	docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
	steps:
	- name: Checkout code
	uses: actions/checkout@v2
	with:
	fetch-depth: 1
	ref: deploy

	- name: Configure Git
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "biosimulatorsdaemon"
	git config pull.rebase false

	- 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

	# install package
	- name: Install the package
	run: \|
	python -m pip install git+https://github.com/biosimulators/RBApy.git#egg=rbapy
	python -m pip install .[all]

	# compile and push 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

	- id: commit-docs
	name: Commit the compiled documentation
	run: \|
	git stash \|\| true
	git pull
	set +e
	git stash pop \|\| true
	git add docs
	git add docs-src
	git commit -m "chore: Updating compiled documentation [skip ci]"
	git checkout .
	git clean -f -d
	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: deploy

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

	# Create PyPI release
	- 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

	- 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

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

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updaing lock file #552

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updaing lock file #552

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