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Overhauled CI/CD, now uses poetry
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@CodeByDrescher
CodeByDrescher committed Sep 22, 2024
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190 changes: 79 additions & 111 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,16 +18,12 @@ jobs:
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 }}
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 }}
release: ${{ steps.determine-if-release-needed.outputs.release }}
docsChanged: ${{ steps.commit-docs.outputs.docsChanged }}
defaults:
run:
Expand All @@ -38,6 +34,18 @@ jobs:
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
#############################################
Expand All @@ -48,85 +56,83 @@ jobs:
python-version: "3.10"

#############################################
## Update the version of the simulator
## 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: jossef/[email protected]

- 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
simulatorVersion=$(poetry -q run python -c "import COPASI; print(COPASI.__version__)")
fi
# 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 = ${{ steps.latest_release_info.outputs.tag_name }}
simulatorSpecVersion=$(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"
if [ $oldBioSimVersion < $bioSimVersion]; then
echo "needDeploy=true" >> "$GITHUB_OUTPUT"
else
simulatorVersionNewer="false"
echo "needDeploy=false" >> "$GITHUB_OUTPUT"
fi
set -e
sudo apt-get update -y
sudo apt-get install -y --no-install-recommends jq moreutils
sed -i -e 's/__COPASI_VERSION__/${copasiVersion}/g' biosimulators.json
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/ARG SIMULATOR_VERSION=([^ \n]+|\".*?\")/ARG SIMULATOR_VERSION=\"${copasiVersion}\"/" \
Dockerfile
sed -i -E \
"s/SIMULATOR_VERSION=([^ \n]+|\".*?\")/SIMULATOR_VERSION=\"${simulatorVersion}\"/" \
"s/ARG VERSION=([^ \n]+|\".*?\")/ARG VERSION=\"${bioSimVersion}\"/" \
Dockerfile
echo "::set-output name=simulatorVersion::$simulatorVersion"
echo "::set-output name=simulatorVersionLatest::$simulatorVersionLatest"
echo "::set-output name=simulatorVersionNewer::$simulatorVersionNewer"
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.simulatorVersionNewer != 'true'
if: github.event_name == 'schedule' && steps.update-simulator-version.outputs.needDeploy != 'true'

#############################################
## Lint and Test
## Release
#############################################
- 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

#############################################
## Build Docker image
#############################################
- id: get-version-number
name: Get version number
env:
TAG: ${{ github.ref }}
run: |
if [[ "${TAG}" =~ ^refs/tags/ ]]; then
version="${TAG/refs\/tags\//}"
else
version=$(poetry run 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::$version"
- id: get-docker-image-tag
name: Determine Docker image tag
run: |
Expand All @@ -153,24 +159,23 @@ jobs:
--label org.opencontainers.image.source=https://github.com/${{ github.repository }} \
--label org.opencontainers.image.revision=${REVISION} \
--label org.opencontainers.image.created=${CREATED} \
--build-arg VERSION=${{ steps.get-version-number.outputs.version }} \
--build-arg VERSION=${{ 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 \
.
#############################################
## Compile documentation
## Apply the digest of the container to `biosimulators.json`
#############################################
- name: Install the requirements for compiling the documentation
run: poetry install --with docs

- name: Compile the documentation
- name: Update the version of the simulator
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
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
Expand All @@ -197,42 +202,9 @@ jobs:
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"
echo "Simulator Version: `${{ github.event.inputs.simulatorVersion }}`"
echo "Input Version: `${{ steps.update-simulator-version.outputs.simulatorVersion }}`"
echo "Simulator Version: `${{ github.event.inputs.simulatorVersion }}`"3
if [ "true" == "${{ github.event.inputs.simulatorVersion }}" ]; then
release="1"
fi
if [ ! -z "${{ steps.update-simulator-version.outputs.simulatorVersion }}" ]; then
if [ "${{ github.ref }}" == "dev" ]; 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"
Expand All @@ -254,25 +226,23 @@ jobs:
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'
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
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 }}
tag_name: ${{ steps.get-tagged-version.outputs.version }}
release_name: Release ${{ steps.get-tagged-version.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: |
Expand All @@ -295,7 +265,6 @@ jobs:
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 ${{ secrets.DOCKER_REGISTRY_USERNAME }} \
Expand All @@ -308,7 +277,6 @@ jobs:
# Submit to BioSimulators registry
- name: Submit to BioSimulators registry
if: steps.determine-if-release-needed.outputs.release == '1'
run: |
REVISION=$(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-)
Expand Down
6 changes: 3 additions & 3 deletions biosimulators.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"id": "copasi",
"name": "COPASI",
"version": "4.44.295",
"version": "__COPASI_VERSION__",
"description": "COPASI is a C++-based software application for the simulation and analysis of biochemical networks and their dynamics.",
"urls": [
{
Expand All @@ -10,8 +10,8 @@
}
],
"image": {
"url": "ghcr.io/biosimulators/biosimulators_copasi/copasi:4.44.295",
"digest": "sha256:d32d7a427b8aeec14acab3ade77f01223082c65d1978d3a150ba863eca8d5b64",
"url": "ghcr.io/biosimulators/biosimulators_copasi/basico:__COPASI_VERSION__",
"digest": "__CONTAINER_DIGEST__",
"format": {
"namespace": "EDAM",
"id": "format_3973",
Expand Down

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