Swapped out actions #547

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
	forceRelease:
	description: Type "true" (case sensitive) to ensure a release will happen (use carefully!)
	required: true
	schedule:
	- cron: "0 0 * * *"

	jobs:
	continuousIntegration:
	name: Update simulator version, lint, test, compile documentation, and release
	runs-on: ubuntu-latest
	outputs:
	version: ${{ steps.get-tagged-version.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 }}
	docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
	defaults:
	run:
	shell: bash
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4
	with:
	fetch-depth: 1

	#############################################
	## If tagged, set the `_version.py` file to reflect it
	#############################################
	- name: Align Version with tag
	id: get-tagged-version
	if: startsWith(github.ref, 'refs/tags/')
	run: \|
	taggedVersion = $(echo $(echo "refs/tags/22.2" \| cut -d '/' -f 3))
	echo "processing `$taggedVersion`"
	echo "__version__ = ${taggedVersion}" > biosimulators_copasi/_version.py
	echo "version=${taggedVersion}" >> $GITHUB_OUTPUT

	#############################################
	## Install package and its dependencies
	#############################################
	# install package
	- name: Set up the environment
	uses: ./.github/actions/setup-poetry-env
	with:
	python-version: "3.10"

	#############################################
	## Lint and Test
	#############################################
	- name: Lint the package
	run: poetry run python -m flake8

	- name: Run the tests
	run: poetry run python -m pytest tests/ --cov=./biosimulators_copasi/ --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: poetry install --with docs

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

	#############################################
	## Apply the version of the simulator to `biosimulators.json`
	#############################################
	- name: Gets latest created release info
	id: latest_release_info
	uses: fangqiuming/[email protected]

	- id: update-simulator-version
	name: Update the version of the simulator
	run: \|
	# We version the containers with the `biosimulators_copasi` version, but list the version as the
	# COPASI version inside.
	copasiVersion = $(poetry -q run python -c "import COPASI; print(COPASI.__version__)")
	bioSimVersion = $(poetry -q run python -c "import biosimulators_copasi as bsc; print(bsc.__version__)")
	oldBioSimVersion = ${{ steps.latest_release_info.outputs.tag_name }}

	if [ $oldBioSimVersion < $bioSimVersion]; then
	echo "needDeploy=true" >> "$GITHUB_OUTPUT"
	else
	echo "needDeploy=false" >> "$GITHUB_OUTPUT"
	fi

	sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json

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

	sed -i -E \
	"s/ARG VERSION=([^ \n]+\|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" \
	Dockerfile

	echo "::set-output name=biosimulatorsVersion::$bioSimVersion"
	echo "::set-output name=simulatorVersion::$copasiVersion"
	echo

	#############################################
	## Check for Deploy, Stop if not Deploying
	#############################################
	- name: Cancel build if the specifications already have the latest version of COPASI
	uses: andymckay/[email protected]
	if: github.event_name == 'schedule' && steps.update-simulator-version.outputs.needDeploy != 'true'

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

	#############################################
	## Build Docker image
	#############################################
	- 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 "::set-output name=simulatorId::${SIMULATOR_ID}"
	echo "::set-output name=simulatorVersion::${SIMULATOR_VERSION}"
	echo "::set-output name=simulatorName::${SIMULATOR_NAME}"
	echo "::set-output name=dockerImageBaseUrl::${IMAGE_BASE_URL}"
	echo "::set-output name=dockerRegistry::${DOCKER_REGISTRY}"

	- 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-tagged-version.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 \
	.

	#############################################
	## Apply the digest of the container to `biosimulators.json`
	#############################################
	- name: Update the version of the simulator
	run: \|
	containerLabel=${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:${{ steps.get-docker-image-tag.outputs.simulatorVersion }}
	docker pull $containerLabel
	imageId=docker image ls \| grep ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }} \
	grep ${{ steps.get-docker-image-tag.outputs.simulatorVersion }} \| awk '{ print $3; ]'
	dockerDigest=docker inspect --format='{{index .RepoDigests 0}}' $imageId \| cut -d '@' -f 2
	sed -i -e 's/__CONTAINER_DIGEST__/${dockerDigest}/g' biosimulators.json

	#############################################
	## 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: steps.update-simulator-version.outputs.simulatorVersion && steps.update-simulator-version.outputs.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: steps.update-simulator-version.outputs.simulatorVersion && steps.update-simulator-version.outputs.simulatorVersionLatest == 'true'
	uses: ad-m/github-push-action@master
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	branch: ${{ github.ref }}

	# If new tag, commit and push documentation
	- id: commit-docs
	name: Commit the compiled documentation
	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 [[ $? = 0 ]]; then
	docsChanged=1
	else
	docsChanged=0
	fi
	echo "::set-output name=docsChanged::$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: ${{ steps.get-main-branch.outputs.mainBranch }}

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

	# Create PyPI release
	- name: Create PyPI release
	env:
	POETRY_PYPI_TOKEN_PYPI: ${{ secrets.PYPI_TOKEN }}
	run: \|
	# 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
	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 [[ "${{ github.ref }}" =~ ^refs/tags/ ]] \|\| [ "${{ steps.update-simulator-version.outputs.simulatorVersionLatest }}" == "true" ]; then
	docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
	fi

	# Submit to BioSimulators registry
	- name: Submit to BioSimulators registry
	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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Swapped out actions #547

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Swapped out actions #547

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