ci_cd.yml

name: CI/CD

on:
  push:
    branches:
      - '*'
      - '*/*'
      - '**'
  release:
    types: [published, edited]

env:
  python-version: "3.9"

jobs:
  CI-Build:
    name: CI-build
    runs-on: ubuntu-20.04
    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: 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-20.04
    strategy:
      matrix:
        test-group: [Fast, MathGen_IT, SBML_IT, SEDML_SBML_IT, SEDML_VCML_IT, BSTS_IT]
      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: 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 -Dgroups="org.vcell.test.${{ matrix.test-group }}"

#      - name: Setup tmate session
#        uses: mxschmitt/action-tmate@v3
#        if: ${{ failure() }}

  CD:
    name: CD
    runs-on: ubuntu-20.04
    if: ${{ github.event_name == 'release' }}

    steps:
      - uses: actions/checkout@v2

      - 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: 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="org.vcell.test.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/release-tag-to-upload-url-action@v1.0.1
        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() }}