CI-full.yml

name: Build and Publish VCell Docker Images

on:
  workflow_dispatch:
    inputs:
      tag:
        description: "Repository tag (e.g., 7.7.0.37)"
        required: true
  release:
    types: [published]

env:
  python-version: "3.10"

jobs:
  setup:
    runs-on: ubuntu-22.04
    outputs:
      vcell_tag: ${{ steps.set-vars.outputs.vcell_tag }}
      vcell_repo_namespace: ${{ steps.set-vars.outputs.vcell_repo_namespace }}
      friendly_tag: ${{ steps.set-vars.outputs.friendly_tag }}
    steps:
    - uses: actions/checkout@v4

    - name: set global environment variables
      id: set-vars
      run: |
        if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
          echo "friendly_tag=${{ github.event.inputs.tag }}" >> $GITHUB_OUTPUT
        else
          echo "friendly_tag=${GITHUB_REF:10}" >> $GITHUB_OUTPUT
        fi
        echo "vcell_tag=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT
        echo "vcell_repo_namespace=ghcr.io/virtualcell" >> $GITHUB_OUTPUT

  maven-build:
    runs-on: ubuntu-22.04
    needs: setup
    steps:
    - name: Free up VM's disk space
      run: |
        sudo rm -rf /usr/local/lib/android
        sudo rm -rf /usr/local/.ghcup
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf /usr/share/swift
        sudo apt-get clean

    - 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 python packages
      run: |
        set -ux
        for POETRY_DIR in vcell-cli-utils docker/swarm/vcell-admin pythonCopasiOpt/vcell-opt pythonVtk python-utils python-restclient pythonData;\
        do pushd $POETRY_DIR;\
          poetry install;\
          poetry run python -m pytest;\
          popd;\
        done

    - name: setup java 17 with maven cache
      uses: actions/setup-java@v4
      with:
        distribution: 'temurin'
        java-version: '17'
        cache: 'maven'

    - name: Maven build
      run: mvn --batch-mode clean install dependency:copy-dependencies -DskipTests=true

    - name: Upload Maven artifacts
      uses: actions/upload-artifact@v4
      with:
        name: maven-build-output
        retention-days: 1
        path: |
          **/target/
          localsolvers/


  docker-build:
    runs-on: ubuntu-22.04
    needs: [setup, maven-build]
    strategy:
      fail-fast: false
      matrix:
        image:
          - name: api
            dockerfile: docker/build/Dockerfile-api-dev
            context: .
            needs_maven: true
            needs_secrets: false
          - name: rest
            dockerfile: vcell-rest/src/main/docker/Dockerfile.jvm
            context: vcell-rest
            needs_maven: true
            needs_secrets: false
            pre_build: "mvn --batch-mode clean install dependency:copy-dependencies -DskipTests -Dvcell.exporter=false"
          - name: exporter
            dockerfile: vcell-rest/src/main/docker/Dockerfile.jvm
            context: vcell-rest
            needs_maven: true
            needs_secrets: false
            pre_build: "mvn --batch-mode clean install dependency:copy-dependencies -DskipTests -Dvcell.exporter=true"
          - name: webapp-dev
            dockerfile: webapp-ng/Dockerfile-webapp
            context: webapp-ng
            needs_maven: false
            needs_secrets: false
            build_args: "BUILD_COMMAND=build_dev"
          - name: webapp-stage
            dockerfile: webapp-ng/Dockerfile-webapp
            context: webapp-ng
            needs_maven: false
            needs_secrets: false
            build_args: "BUILD_COMMAND=build_stage"
          - name: webapp-prod
            dockerfile: webapp-ng/Dockerfile-webapp
            context: webapp-ng
            needs_maven: false
            needs_secrets: false
            build_args: "BUILD_COMMAND=build_prod"
          - name: webapp-island
            dockerfile: webapp-ng/Dockerfile-webapp
            context: webapp-ng
            needs_maven: false
            needs_secrets: false
            build_args: "BUILD_COMMAND=build_island"
          - name: webapp-remote
            dockerfile: webapp-ng/Dockerfile-webapp
            context: webapp-ng
            needs_maven: false
            needs_secrets: false
            build_args: "BUILD_COMMAND=build_remote"
          - name: db
            dockerfile: docker/build/Dockerfile-db-dev
            context: .
            needs_maven: true
            needs_secrets: false
          - name: sched
            dockerfile: docker/build/Dockerfile-sched-dev
            context: .
            needs_maven: true
            needs_secrets: false
          - name: submit
            dockerfile: docker/build/Dockerfile-submit-dev
            context: .
            needs_maven: true
            needs_secrets: false
          - name: data
            dockerfile: docker/build/Dockerfile-data-dev
            context: .
            needs_maven: true
            needs_secrets: false
          - name: mongo
            dockerfile: docker/build/mongo/Dockerfile
            context: docker/build/mongo
            needs_maven: false
            needs_secrets: false
          - name: batch
            dockerfile: docker/build/Dockerfile-batch-dev
            context: .
            needs_maven: true
            needs_secrets: false
          - name: opt
            dockerfile: pythonCopasiOpt/Dockerfile
            context: pythonCopasiOpt
            needs_maven: false
            needs_secrets: false
          - name: clientgen
            dockerfile: docker/build/Dockerfile-clientgen-dev
            context: .
            needs_maven: true
            needs_secrets: false
            needs_installer_secrets: true
          - name: admin
            dockerfile: docker/build/Dockerfile-admin-dev
            context: .
            needs_maven: true
            needs_secrets: false
    steps:
    - name: Free up VM's disk space
      run: |
        sudo rm -rf /usr/local/lib/android
        sudo rm -rf /usr/local/.ghcup
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf /usr/share/swift
        sudo apt-get clean

    - uses: actions/checkout@v4

    - name: setup java 17 with maven cache
      if: ${{ matrix.image.pre_build }}
      uses: actions/setup-java@v4
      with:
        distribution: 'temurin'
        java-version: '17'
        cache: 'maven'

    - name: Download Maven artifacts
      if: ${{ matrix.image.needs_maven }}
      uses: actions/download-artifact@v4
      with:
        name: maven-build-output
        path: .

    - name: setup ssh-agent for installer secrets
      if: ${{ matrix.image.needs_installer_secrets }}
      uses: webfactory/ssh-agent@v0.8.0
      with:
        ssh-private-key: ${{ secrets.VC_KEY }}

    - name: get installer secrets
      if: ${{ matrix.image.needs_installer_secrets }}
      env:
        VCELL_MANAGER_NODE: vcellapi.cam.uchc.edu
        VCELL_DEPLOY_REMOTE_DIR: /share/apps/vcell3/deployed_github
      run: |
        ssh-keyscan ${VCELL_MANAGER_NODE} >> ~/.ssh/known_hosts
        sudo mkdir /usr/local/deploy
        sudo chmod 777 /usr/local/deploy
        cd /usr/local/deploy
        scp ${{ secrets.CD_FULL_USER }}@${VCELL_MANAGER_NODE}:${VCELL_DEPLOY_REMOTE_DIR}/deploy_dir_2025_03_18.tar .
        cd ..
        sudo tar -xvf deploy/deploy_dir_2025_03_18.tar
        sudo chmod 777 -R deploy

    - name: Pre-build step
      if: ${{ matrix.image.pre_build }}
      run: ${{ matrix.image.pre_build }}

    - name: Log in to GHCR
      run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin

    - name: Build and push Docker image
      run: |
        IMAGE_NAME="vcell-${{ matrix.image.name }}"
        FULL_TAG="${{ needs.setup.outputs.vcell_repo_namespace }}/${IMAGE_NAME}:${{ needs.setup.outputs.vcell_tag }}"
        BUILD_ARGS=""
        if [ -n "${{ matrix.image.build_args || '' }}" ]; then
          BUILD_ARGS="--build-arg ${{ matrix.image.build_args }}"
        fi
        echo "Building ${FULL_TAG}"
        docker buildx build --platform=linux/amd64 \
          ${BUILD_ARGS} \
          -f ${{ matrix.image.dockerfile }} \
          --tag ${FULL_TAG} \
          ${{ matrix.image.context }}
        docker push ${FULL_TAG}

  tag-and-push:
    runs-on: ubuntu-22.04
    needs: [setup, docker-build]
    steps:
    - name: Log in to GHCR
      run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin

    - name: Tag and push all images
      run: |
        REPO="${{ needs.setup.outputs.vcell_repo_namespace }}"
        TAG="${{ needs.setup.outputs.vcell_tag }}"
        FRIENDLY="${{ needs.setup.outputs.friendly_tag }}"
        CONTAINERS="vcell-exporter vcell-api vcell-rest vcell-webapp-prod vcell-webapp-dev vcell-webapp-stage vcell-webapp-island vcell-webapp-remote vcell-batch vcell-opt vcell-clientgen vcell-data vcell-db vcell-mongo vcell-sched vcell-submit vcell-admin"
        for CONTAINER in ${CONTAINERS}; do
          docker pull ${REPO}/${CONTAINER}:${TAG}
          docker tag ${REPO}/${CONTAINER}:${TAG} ${REPO}/${CONTAINER}:latest
          docker tag ${REPO}/${CONTAINER}:${TAG} ${REPO}/${CONTAINER}:${FRIENDLY}
          docker push --all-tags ${REPO}/${CONTAINER}
        done

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

  build-and-publish-sif:
    name: Build and publish Apptainer SIF images
    runs-on: ubuntu-22.04
    needs: [setup, tag-and-push]
    steps:
    - name: Install Apptainer
      uses: eWaterCycle/setup-apptainer@v2

    - name: Log in to GHCR (for pull and push)
      run: apptainer registry login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io

    - name: Build, validate, and publish SIF images
      run: |
        set -eux
        REPO="${{ needs.setup.outputs.vcell_repo_namespace }}"
        TAG="${{ needs.setup.outputs.friendly_tag }}"
        for IMG in vcell-opt vcell-batch; do
          SIF_NAME="$(echo "${REPO}/${IMG}_singularity:${TAG}" | tr '/:' '__').img"
          echo "Building SIF for ${REPO}/${IMG}:${TAG} -> ${SIF_NAME}"
          apptainer build "${SIF_NAME}" "docker://${REPO}/${IMG}:${TAG}"
          apptainer inspect "${SIF_NAME}" > /dev/null
          echo "Publishing ${SIF_NAME} to oras://${REPO}/${IMG}_singularity:${TAG}"
          apptainer push "${SIF_NAME}" "oras://${REPO}/${IMG}_singularity:${TAG}"
        done

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