CI-full.yml

name: CI-application-containers

on:
  workflow_dispatch:
  release:
    types: [published]
  
env:
  python-version: "3.10"
  
jobs:
  build:
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
    - name: Get the VCell version from tags
      id: version
      run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
    - name: set global environment variables
      run: |
        echo "VCELL_TAG=`git rev-parse --short HEAD`" >> $GITHUB_ENV
        echo "VCELL_REPO_NAMESPACE=ghcr.io/virtualcell" >> $GITHUB_ENV
        echo "VCELL_DEPLOY_REMOTE_DIR=/share/apps/vcell3/deployed_github" >> $GITHUB_ENV
        echo "VCELL_MANAGER_NODE=vcellapi-beta.cam.uchc.edu" >> $GITHUB_ENV
    - name: setup ssh-agent
      uses: webfactory/ssh-agent@v0.8.0
      with:
        ssh-private-key: ${{ secrets.VC_KEY }}
    - name: get installer secrets
      run: |
        ssh-keyscan vcellapi-beta.cam.uchc.edu >> ~/.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_2023_07_30.tar .
        cd ..
        sudo tar -xvf deploy/deploy_dir_2023_07_30.tar
        sudo chmod 777 -R deploy
    - 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: Install Singularity # to make singularity image for cluster
      uses: eWaterCycle/setup-singularity@v6
      with:
        singularity-version: 3.7.1
    - name: build and publish all images
      shell: bash
      run: |
        cd docker/build
        sudo docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
        docker login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} ghcr.io
        ./build.sh all ${{ env.VCELL_REPO_NAMESPACE }} ${{ env.VCELL_TAG }}
        cd singularity-vm
        singularity remote login -u ${{ secrets.ACTION_USER }} -p ${{ secrets.ACTION_TOKEN }} oras://ghcr.io
    - name: tag as latest and push to registry  # (jcs) are explicit singularity push commands redundant? (see ./build.sh)
      shell: bash
      run: |
        for CONTAINER in vcell-api vcell-rest vcell-webapp-prod vcell-webapp-dev vcell-webapp-stage vcell-webapp-island vcell-batch vcell-opt vcell-clientgen vcell-data vcell-db vcell-mongo vcell-sched vcell-submit vcell-admin;\
        do docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:latest;\
        docker tag ${VCELL_REPO_NAMESPACE}/$CONTAINER:${VCELL_TAG} ${VCELL_REPO_NAMESPACE}/$CONTAINER:${{ steps.version.outputs.tag }};\
        docker push --all-tags ${VCELL_REPO_NAMESPACE}/$CONTAINER;\
        done
        cd docker/build/singularity-vm
        singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${VCELL_TAG}
        singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:${{ steps.version.outputs.tag }}
        singularity push -U $(ls *batch*img) oras://${VCELL_REPO_NAMESPACE}/vcell-batch-singularity:latest
        singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${VCELL_TAG}
        singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:${{ steps.version.outputs.tag }}
        singularity push -U $(ls *opt*img) oras://${VCELL_REPO_NAMESPACE}/vcell-opt-singularity:latest

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