Merge branch 'dev' of https://github.com/biosimulators/Biosimulators_… #155
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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-latest | |
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" >> $GITHUB_OUTPUT | |
echo "mainBranchRef=$mainBranchRef" >> $GITHUB_OUTPUT | |
echo "mainBranchHeadRevision=$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: Install Python | |
uses: actions/setup-python@v3 | |
with: | |
python-version: '3.11' | |
- name: Setup pip cache | |
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 --upgrade pip==23.0.0 | |
python -m pip install --upgrade pip==23.0.0 | |
- name: Install system dependencies | |
run: | | |
sudo apt-get update -y | |
sudo apt-get install -y --no-install-recommends \ | |
g++ \ | |
libatlas-base-dev \ | |
swig | |
# 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" >> $GITHUB_OUTPUT | |
- id: get-docker-image-tag | |
name: Determine Docker image tag | |
run: | | |
sudo apt-get update -y | |
sudo apt-get install -y --no-install-recommends jq | |
simulatorId=$(jq -r '.id' biosimulators.json) | |
simulatorVersion=$(jq -r '.version' biosimulators.json) | |
simulatorName=$(jq -r '.name' biosimulators.json) | |
dockerImageBaseUrl=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1) | |
dockerRegistry=$(echo $dockerImageBaseUrl | cut -d / -f 1) | |
echo "simulatorId=$simulatorId" >> $GITHUB_OUTPUT | |
echo "simulatorVersion=$simulatorVersion" >> $GITHUB_OUTPUT | |
echo "simulatorName=$simulatorName" >> $GITHUB_OUTPUT | |
echo "dockerImageBaseUrl=$dockerImageBaseUrl" >> $GITHUB_OUTPUT | |
echo "dockerRegistry=$dockerRegistry" >> $GITHUB_OUTPUT | |
- name: Build Docker image | |
run: | | |
REVISION=$(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_amici/ --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 | |
echo "Not dash-z." | |
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 }}") | |
echo "tag hash: $tag_hash" | |
if [ "$tag_hash" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then | |
release="1" | |
fi | |
fi | |
echo "release=$release" >> $GITHUB_OUTPUT | |
# 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: | |
TWINE_USERNAME: __token__ | |
TWINE_PASSWORD: ${{ 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/download/3.1.3/pandoc-3.1.3-1-amd64.deb" -O /tmp/pandoc.deb | |
sudo dpkg -i /tmp/pandoc.deb | |
rm /tmp/pandoc.deb | |
# Convert README to .rst format | |
pandoc --from=gfm --output=README.rst --to=rst README.md | |
# Install twine | |
python -m pip install wheel twine | |
# Create packages to upload to PyPI | |
python setup.py sdist | |
python setup.py bdist_wheel | |
# Upload packages to PyPI | |
twine upload dist/* | |
# 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---\"}" |