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ci.yml
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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
schedule:
- cron: "0 0 * * *"
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/${mainBranch})
echo "::set-output name=mainBranch::$mainBranch"
echo "::set-output name=mainBranchRef::refs/heads/$mainBranch"
echo "::set-output name=mainBranchHeadRevision::$mainBranchHeadRevision"
- 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
#############################################
## Install package and its dependencies
#############################################
- name: Install Python
uses: actions/setup-python@v2
with:
python-version: '3.9'
cache: "pip"
# - 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: |
# ${{ runner.os }}-pip-
- name: Install pip and setuptools
run: |
python -m pip install pip==22.3.1
python -m pip install --upgrade setuptools
# install package
- name: Install the package
run: python -m pip install .[all]
#############################################
## Update the version of the simulator
#############################################
- id: update-simulator-version
name: Update the version of the simulator
if: github.event_name == 'workflow_dispatch' || github.event_name == 'schedule'
run: |
if [ "${{ github.event_name }}" == "workflow_dispatch" ]; then
simulatorVersion="${{ github.event.inputs.simulatorVersion }}"
else
python -m pip install -U python-copasi
simulatorVersion=$(python -m pip show python-copasi | grep "Version: " | cut -d " " -f 2)
fi
simulatorSpecVersion=$(jq -r '.version' biosimulators.json)
set +e
dpkg --compare-versions "$simulatorVersion" ge "$simulatorSpecVersion"
if [[ $? = 0 ]]; then
simulatorVersionLatest="true"
else
simulatorVersionLatest="false"
fi
dpkg --compare-versions "$simulatorVersion" gt "$simulatorSpecVersion"
if [[ $? = 0 ]]; then
simulatorVersionNewer="true"
else
simulatorVersionNewer="false"
fi
set -e
sudo apt-get update -y
sudo apt-get install -y --no-install-recommends jq moreutils
IMAGE_BASE_URL=$(jq -r '.image.url' biosimulators.json | cut -d : -f 1)
jq ".version = \"${simulatorVersion}\"" biosimulators.json | sponge biosimulators.json
jq ".image.url = \"${IMAGE_BASE_URL}:${simulatorVersion}\"" biosimulators.json | sponge biosimulators.json
sed -i -E \
"s/SIMULATOR_VERSION=([^ \n]+|\".*?\")/SIMULATOR_VERSION=\"${simulatorVersion}\"/" \
Dockerfile
echo "::set-output name=simulatorVersion::$simulatorVersion"
echo "::set-output name=simulatorVersionLatest::$simulatorVersionLatest"
echo "::set-output name=simulatorVersionNewer::$simulatorVersionNewer"
- 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.simulatorVersionNewer != 'true'
#############################################
## 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 "::set-output name=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 $IMAGE_BASE_URL | cut -d / -f 1)
echo "::set-output name=simulatorId::${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-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_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: 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: 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: ${{ github.ref }}
#############################################
## Release
#############################################
- id: determine-if-release-needed
name: Determine if a release should be made
run: |
release="0"
if [ ! -z "${{ steps.update-simulator-version.outputs.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" == "${{ steps.get-main-branch.outputs.mainBranchHeadRevision }}" ]; then
release="1"
fi
fi
echo "::set-output name=release::$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 [[ $? = 0 ]]; then
docsChanged=1
else
docsChanged=0
fi
echo "::set-output name=docsChanged::$docsChanged"
- 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: ${{ secrets.PYPI_TOKEN }}
run: |
# Install pandoc
sudo apt-get update -y
sudo apt-get install -y --no-install-recommends wget
wget https://github.com/jgm/pandoc/releases -O /tmp/pandocVersions.html
urlPart=`grep "\.deb" /tmp/pandocVersions.html | head -n 1 | cut -d'/' -f2-7 | cut -d'"' -f1`
wget "https://github.com/$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
# 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 [[ "${{ github.ref }}" =~ ^refs/tags/ ]] || [ "${{ steps.update-simulator-version.outputs.simulatorVersionLatest }}" == "true" ]; then
docker push ${{ steps.get-docker-image-tag.outputs.dockerImageBaseUrl }}:latest
fi
# Submit to BioSimulators registry
- name: Submit to BioSimulators registry
if: steps.determine-if-release-needed.outputs.release == '1'
run: |
REVISION=$(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---\"}"