Merge remote-tracking branch 'origin/master' into health-sim-status #4626
Workflow file for this run
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name: CI/CD | |
on: | |
push: | |
branches: | |
- '*' | |
- '*/*' | |
- '**' | |
release: | |
types: [published, edited] | |
env: | |
python-version: "3.9" | |
jobs: | |
CI-Build: | |
name: CI-build | |
runs-on: ubuntu-22.04 | |
if: ${{ github.event_name == 'push' }} | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ env.python-version }} | |
cache: "pip" | |
- name: Install Dependencies | |
run: pip install -r requirements.txt | |
- name: build vcell-cli-utils package | |
run: | | |
cd vcell-cli-utils | |
poetry install | |
poetry run python -m pytest | |
- name: build vcell-admin package | |
run: | | |
cd docker/swarm/vcell-admin | |
poetry install | |
poetry run python -m pytest | |
- name: build pythonCopasiOpt package | |
run: | | |
cd pythonCopasiOpt/vcell-opt | |
poetry install | |
poetry run python -m pytest | |
- name: build pythonVtk package | |
run: | | |
cd pythonVtk | |
poetry install | |
poetry run python -m pytest | |
- name: build vcutils package | |
run: | | |
cd python-utils | |
poetry install | |
poetry run python -m pytest | |
- name: build python-restclient package | |
run: | | |
cd python-restclient | |
poetry install | |
poetry run python -m pytest | |
- name: build vcelldata package | |
run: | | |
cd pythonData | |
poetry install | |
poetry run python -m pytest | |
- name: setup java 17 with maven cache | |
uses: actions/setup-java@v3 | |
with: | |
distribution: 'temurin' | |
java-version: '17' | |
cache: 'maven' | |
- name: Add Linux dependencies | |
shell: bash | |
run: | | |
mvn -version | |
java -version | |
mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true | |
- name: Test building of docker image | |
run: | | |
docker build \ | |
--file Dockerfile \ | |
. | |
- name: Setup tmate session | |
uses: mxschmitt/action-tmate@v3 | |
if: ${{ failure() }} | |
CI-Test: | |
runs-on: ubuntu-22.04 | |
strategy: | |
matrix: | |
test-group: [Fast, MathGen_IT, SBML_IT, SEDML_SBML_IT, SEDML_VCML_IT, BSTS_IT, Quarkus] | |
fail-fast: false | |
if: ${{ github.event_name == 'push' }} | |
name: CI-Test-group-${{ matrix.test-group }} | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Install hdf5 tools needed for testing | |
run: sudo apt-get -y update && sudo apt-get -y install hdf5-tools | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ env.python-version }} | |
cache: "pip" | |
- name: Install Dependencies | |
run: pip install -r requirements.txt | |
- name: build vcell-cli-utils package | |
run: | | |
cd vcell-cli-utils | |
poetry install | |
poetry run python -m pytest | |
- name: build vcell-admin package | |
run: | | |
cd docker/swarm/vcell-admin | |
poetry install | |
poetry run python -m pytest | |
- name: build pythonCopasiOpt package | |
run: | | |
cd pythonCopasiOpt/vcell-opt | |
poetry install | |
poetry run python -m pytest | |
- name: build pythonVtk package | |
run: | | |
cd pythonVtk | |
poetry install | |
poetry run python -m pytest | |
- name: build vcutils package | |
run: | | |
cd python-utils | |
poetry install | |
poetry run python -m pytest | |
- name: build python-restclient package | |
run: | | |
cd python-restclient | |
poetry install | |
poetry run python -m pytest | |
- name: build vcelldata package | |
run: | | |
cd pythonData | |
poetry install | |
poetry run python -m pytest | |
- name: setup java 17 with maven cache | |
uses: actions/setup-java@v3 | |
with: | |
distribution: 'temurin' | |
java-version: '17' | |
cache: 'maven' | |
- name: Maven Build and run Test group ${{ matrix.test-group }} | |
shell: bash | |
run: | | |
mvn -version | |
java -version | |
if [ "${{ matrix.test-group }}" == "Quarkus" ]; then | |
mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true | |
cd vcell-rest | |
mvn test | |
else | |
mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="${{ matrix.test-group }}" | |
fi | |
# - name: Setup tmate session | |
# uses: mxschmitt/action-tmate@v3 | |
# if: ${{ failure() }} | |
CD: | |
name: CD | |
runs-on: ubuntu-22.04 | |
if: ${{ github.event_name == 'release' }} | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ env.python-version }} | |
cache: "pip" | |
- name: Install Dependencies | |
run: pip install -r requirements.txt | |
- name: build vcell-cli-utils package | |
run: | | |
cd vcell-cli-utils | |
poetry install | |
poetry run python -m pytest | |
- name: build vcell-admin package | |
run: | | |
cd docker/swarm/vcell-admin | |
poetry install | |
poetry run python -m pytest | |
- name: build pythonCopasiOpt package | |
run: | | |
cd pythonCopasiOpt/vcell-opt | |
poetry install | |
poetry run python -m pytest | |
- name: build pythonVtk package | |
run: | | |
cd pythonVtk | |
poetry install | |
poetry run python -m pytest | |
- name: build vcutils package | |
run: | | |
cd python-utils | |
poetry install | |
poetry run python -m pytest | |
- name: build python-restclient package | |
run: | | |
cd python-restclient | |
poetry install | |
poetry run python -m pytest | |
- name: build vcelldata package | |
run: | | |
cd pythonData | |
poetry install | |
poetry run python -m pytest | |
- name: setup java 17 with maven cache | |
uses: actions/setup-java@v3 | |
with: | |
distribution: 'temurin' | |
java-version: '17' | |
cache: 'maven' | |
- name: Get the VCell version from tags | |
id: version | |
run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10}) | |
- name: Add Linux dependencies | |
shell: bash | |
run: | | |
mvn -version | |
java -version | |
mvn --batch-mode clean install dependency:copy-dependencies -Dgroups="Fast" | |
- name: Build Docker image and push with latest tag | |
run: | | |
set -ux | |
REVISION=$(git rev-parse HEAD) | |
CREATED=$(date --rfc-3339=seconds | sed 's/ /T/') | |
sed -i 's/_VC_VERSION_TAG_/${{steps.version.outputs.tag}}/g' biosimulators.json | |
echo ${{ secrets.ACTION_TOKEN }} | docker login ghcr.io -u ${{ secrets.ACTION_USER }} --password-stdin | |
docker build \ | |
--no-cache \ | |
--file Dockerfile \ | |
--build-arg SIMULATOR_VERSION=${{steps.version.outputs.tag}} \ | |
--tag ghcr.io/virtualcell/biosimulators_vcell:latest \ | |
--label org.opencontainers.image.revision=${REVISION} \ | |
--label org.opencontainers.image.created=${CREATED} \ | |
--label org.opencontainers.image.version=${{steps.version.outputs.tag}} \ | |
--label org.opencontainers.image.license=MIT \ | |
. | |
docker tag ghcr.io/virtualcell/biosimulators_vcell:latest ghcr.io/virtualcell/biosimulators_vcell:${{steps.version.outputs.tag}} | |
docker push --all-tags ghcr.io/virtualcell/biosimulators_vcell | |
- name: Get release upload URL | |
id: get_url | |
uses: pdamianik/[email protected] | |
with: | |
tag: ${{ steps.version.outputs.tag }} | |
token: ${{ github.token }} | |
- name: Upload edited specifications file | |
uses: shogo82148/actions-upload-release-asset@v1 | |
with: | |
upload_url: ${{ steps.get_url.outputs.uploadUrl }} | |
asset_path: biosimulators.json | |
- name: Setup tmate session | |
uses: mxschmitt/action-tmate@v3 | |
if: ${{ failure() }} |