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add known failures for BMDB 800-1080, enable tests 0000-1080 #5214

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add known failures for BMDB 800-1080, enable tests 0000-1080

add known failures for BMDB 800-1080, enable tests 0000-1080 #5214

Workflow file for this run

.github/workflows/ci_cd.yml at 66d3918
name: CI/CD
on:
push:
branches:
- '*'
- '*/*'
- '**'
release:
types: [published, edited]
env:
python-version: "3.10"
jobs:
CI-Build:
name: CI-build
runs-on: ubuntu-22.04
if: ${{ github.event_name == 'push' }}
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
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@v4
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@v4
- name: Install hdf5 tools needed for testing
run: sudo apt -y update && sudo apt -y install hdf5-tools
- name: Set up Python
uses: actions/setup-python@v5
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@v4
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@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ env.python-version }}
cache: "pip"
- name: Install Dependencies
run: pip install -r requirements.txt
- name: build vcell-cli-utils package
run: |
cd vcell-cli-utils
poetry install
poetry run python -m pytest
- name: build vcell-admin package
run: |
cd docker/swarm/vcell-admin
poetry install
poetry run python -m pytest
- name: build pythonCopasiOpt package
run: |
cd pythonCopasiOpt/vcell-opt
poetry install
poetry run python -m pytest
- name: build pythonVtk package
run: |
cd pythonVtk
poetry install
poetry run python -m pytest
- name: build vcutils package
run: |
cd python-utils
poetry install
poetry run python -m pytest
- name: build python-restclient package
run: |
cd python-restclient
poetry install
poetry run python -m pytest
- name: build vcelldata package
run: |
cd pythonData
poetry install
poetry run python -m pytest
- name: setup java 17 with maven cache
uses: actions/setup-java@v4
with:
distribution: 'temurin'
java-version: '17'
cache: 'maven'
- name: Get the VCell version from tags
id: version
run: echo ::set-output name=tag::$(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.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
docker build \
--no-cache \
--file Dockerfile \
--build-arg SIMULATOR_VERSION=${{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() }}