Revert to earlier roadrunner, which in context is faster. #77

Workflow file for this run

	name: Continuous integration

	on:
	push:
	workflow_dispatch:
	inputs:
	simulatorVersion:
	description: New version of the underlying simulation tool (e.g., '1.5.6')
	required: true
	simulatorVersionLatest:
	description: Is this version the latest version of the underlying simulation tool ("true" or "false")?
	required: false

	jobs:
	continuousIntegration:
	name: Update simulator version, lint, test, compile documentation, and release
	runs-on: ubuntu-22.04
	outputs:
	mainBranch: ${{ steps.get-main-branch.outputs.mainBranch }}
	mainBranchRef: ${{ steps.get-main-branch.outputs.mainBranchRef }}
	mainBranchHeadRevision: ${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}
	version: ${{ steps.get-version-number.outputs.version }}
	simulatorId: ${{ steps.get-docker-image-tag.outputs.simulatorId }}
	simulatorVersion: ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
	simulatorName: ${{ steps.get-docker-image-tag.outputs.simulatorName }}
	dockerImageBaseUrl: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}
	dockerRegistry: ${{ steps.get-docker-image-tag.outputs.dockerRegistry }}
	release: ${{ steps.determine-if-release-needed.outputs.release }}
	docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
	steps:
	- name: Clone repository
	run: \|
	git clone https://${{ github.actor }}:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }} .

	- id: get-main-branch
	name: Determine main branch
	run: \|
	mainBranch=$(git symbolic-ref refs/remotes/origin/HEAD \| cut -d '/' -f 4)
	mainBranchHeadRevision=$(git rev-parse refs/remotes/origin/${mainBranch})
	echo "mainBranch=$mainBranch" >> $GITHUB_OUTPUT
	echo "mainBranchRef=refs/heads/$mainBranch" >> $GITHUB_OUTPUT
	echo "mainBranchHeadRevision=$mainBranchHeadRevision" >> $GITHUB_OUTPUT

	- name: Checkout ref
	run: \|
	if [[ "${{ github.ref }}" =~ ^refs/heads/ ]]; then
	branch=$(echo "${{ github.ref }}" \| cut -d'/' -f 3-)
	git checkout ${branch}
	else
	git checkout ${{ github.ref }}
	fi

	#############################################
	## Update the version of the simulator
	#############################################
	- name: Update the version of the simulator
	if: github.event.inputs.simulatorVersion
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends jq moreutils

	IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json \| cut -d : -f 1)
	jq ".version = \"${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json \| sponge biosimulators.json
	jq ".image.url = \"${IMAGE_BASE_URL}:${{ github.event.inputs.simulatorVersion }}\"" biosimulators.json \| sponge biosimulators.json

	sed -i -E \
	"s/SIMULATOR_VERSION=([^ \n]+\|\".*?\")/SIMULATOR_VERSION=\"${{ github.event.inputs.simulatorVersion }}\"/" \
	Dockerfile

	#############################################
	## Install package and its dependencies
	#############################################
	- name: Set up the python environment
	uses: ./.github/actions/setup-poetry-env
	with:
	python-version: "3.9"

	- name: Setup caching for Python packages
	uses: actions/cache@v3
	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 pip==23.0.0
	python -m pip install pip==23.0.0

	# install requirements for MASSpy
	- name: Install libXML2, libncurses5 required for tellurium, which is required for MASSpy
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends libxml2 libncurses5

	- name: Install MASSpy
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends \
	git \
	gcc \
	build-essential \
	libfreetype6-dev \
	pkg-config

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

	#############################################
	## Lint
	#############################################
	- name: Install flake8
	run: python -m pip install flake8

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

	#############################################
	## Build Docker image
	#############################################
	- id: get-version-number
	name: Get version number
	env:
	TAG: ${{ github.ref }}
	run: \|
	if [[ "${TAG}" =~ ^refs/tags/ ]]; then
	version="${TAG/refs\/tags\//}"
	else
	version=$(python -c "import glob; import importlib.util; version_filename = glob.glob('**/_version.py', recursive=True)[0]; spec = importlib.util.spec_from_file_location('module.name', version_filename); module = importlib.util.module_from_spec(spec); spec.loader.exec_module(module); print(module.__version__)")
	fi

	echo "version=$version" >> $GITHUB_OUTPUT
	echo "version=$version"

	- id: get-docker-image-tag
	name: Determine Docker image tag
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y --no-install-recommends jq

	SIMULATOR_ID=$(jq -r '.id' biosimulators.json)
	SIMULATOR_VERSION=$(jq -r '.version' biosimulators.json)
	SIMULATOR_NAME=$(jq -r '.name' biosimulators.json)
	IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json \| cut -d : -f 1)
	DOCKER_REGISTRY=$(echo $IMAGE_BASE_URL \| cut -d / -f 1)

	echo "simulatorId=${SIMULATOR_ID}" >> $GITHUB_OUTPUT
	echo "simulatorVersion=${SIMULATOR_VERSION}" >> $GITHUB_OUTPUT
	echo "simulatorName=${SIMULATOR_NAME}" >> $GITHUB_OUTPUT
	echo "dockerImageBaseUrl=${IMAGE_BASE_URL}" >> $GITHUB_OUTPUT
	echo "dockerRegistry=${DOCKER_REGISTRY}" >> $GITHUB_OUTPUT

	- name: Build Docker image
	run: \|
	REVISION=$(git rev-parse HEAD)
	CREATED=$(date --rfc-3339=seconds \| sed 's/ /T/')
	docker build \
	--label org.opencontainers.image.source=https://github.com/${{ github.repository }} \
	--label org.opencontainers.image.revision=${REVISION} \
	--label org.opencontainers.image.created=${CREATED} \
	--build-arg VERSION=${{ steps.get-version-number.outputs.version }} \
	--build-arg SIMULATOR_VERSION=${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
	--tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \
	--tag ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest \
	.

	#############################################
	## 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
	run: python -m pytest tests/ --cov=./biosimulators_masspy/ --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

	#############################################
	## Commit and push new version of simulator
	#############################################
	# If new version of simulator, commit and push the new version
	- name: Commit the revised version of the simulator
	if: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true'
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "biosimulatorsdaemon"
	git config pull.rebase false
	git stash -- biosimulators.json Dockerfile
	git clean -f -d
	git checkout .
	git pull
	git stash pop
	git add biosimulators.json Dockerfile
	git commit -m "Updating version of simulator"

	- name: Push the revised version of the simulator
	if: github.event.inputs.simulatorVersion && github.event.inputs.simulatorVersionLatest == 'true'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: ${{ github.ref }}

	#############################################
	## Release
	#############################################

	- id: determine-if-release-needed
	name: Determine if a release should be made
	run: \|
	release="0"

	if [ ! -z "${{ github.event.inputs.simulatorVersion }}" ]; then
	if [ "${{ github.ref }}" == "${{ steps.get-main-branch.outputs.mainBranchRef }}" ]; then
	release="1"
	fi
	fi

	if [[ "${{ github.ref }}" =~ ^refs/tags/ ]]; then
	tag_hash=$(git rev-parse "${{ github.ref }}")
	if [ "$tag_hash" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then
	release="1"
	fi
	fi

	echo "release=$release" >> $GITHUB_OUTPUT
	echo "release=$release"

	# If new tag, commit and push documentation
	- id: commit-docs
	name: Commit the compiled documentation
	if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
	run: \|
	git config --local user.email "[email protected]"
	git config --local user.name "biosimulatorsdaemon"
	git config pull.rebase false
	git stash
	git checkout ${{ steps.get-main-branch.outputs.mainBranch }}
	git pull
	set +e
	git stash pop
	git add docs
	git commit -m "Updating compiled documentation"
	git checkout .
	git clean -f -d
	if [[ $? = 0 ]]; then
	docsChanged=1
	else
	docsChanged=0
	fi
	echo "docsChanged=$docsChanged" >> $GITHUB_OUTPUT

	- name: Push the compiled documentation
	if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1' && steps.commit-docs.outputs.docsChanged == '1'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: ${{ steps.get-main-branch.outputs.mainBranch }}

	# Create GitHub release
	- name: Create GitHub release
	if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
	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 }}

	#############################################
	# Create PyPI release
	#############################################
	- name: Create PyPI release
	if: startsWith(github.ref, 'refs/tags/') && steps.determine-if-release-needed.outputs.release == '1'
	env:
	POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
	run: \|
	echo''
	# Install pandoc
	# 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

	# Convert README to .rst format
	# pandoc --from=gfm --output=README.rst --to=rst README.md

	# Build and Publish
	poetry build
	poetry publish --no-interaction --username __token__ --password $POETRY_PYPI_TOKEN_PYPI

	# build Docker image and push to GitHub Container Registry
	- name: Push Docker image
	if: steps.determine-if-release-needed.outputs.release == '1'
	run: \|
	docker login ${{ steps.get-docker-image-tag.outputs.dockerRegistry }} \
	--username ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
	--password ${{ secrets.DOCKER_REGISTRY_TOKEN }}
	docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}

	if [[ "${{ github.ref }}" =~ ^refs/tags/ ]] \|\| [ "${{ github.event.inputs.simulatorVersionLatest }}" == "true" ]; then
	docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
	fi

	# Submit to BioSimulators registry
	- name: Submit to BioSimulators registry
	if: steps.determine-if-release-needed.outputs.release == '1'
	run: \|
	REVISION=$(git rev-parse HEAD)
	IMAGE_DIGEST=$(docker image inspect ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \| jq -r '.[0].RepoDigests[0]' \| cut -d "@" -f 2-)
	curl \
	-X POST \
	-u ${{ secrets.GH_ISSUE_USERNAME }}:${{ secrets.GH_ISSUE_TOKEN }} \
	-H "Accept: application/vnd.github.v3+json" \
	https://api.github.com/repos/biosimulators/Biosimulators/issues \
	-d "{\"labels\": [\"Validate/submit simulator\"], \"title\": \"Submit ${{ steps.get-docker-image-tag.outputs.simulatorName }} ${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\", \"body\": \"---\nid: ${{ steps.get-docker-image-tag.outputs.simulatorId }}\nversion: \\\"${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\\\"\nspecificationsUrl: https://raw.githubusercontent.com/${{ github.repository }}/${REVISION}/biosimulators.json\nspecificationsPatch:\n version: \\\"${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\\\"\n image:\n url: ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}\n digest: \\\"${IMAGE_DIGEST}\\\"\nvalidateImage: true\ncommitSimulator: true\n\n---\"}"

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Revert to earlier roadrunner, which in context is faster. #77

Workflow file

Revert to earlier roadrunner, which in context is faster. #77

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Workflow file for this run