build_and_test.yml

name: build containers and run tests

on:
  pull_request:
    branches:
      - 'main'
  workflow_dispatch:
    

jobs:
  Setup_and_build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Setup Mamba
        uses: mamba-org/setup-micromamba@v1
        with:
          cache-environment: true
          post-cleanup: 'all'
          environment-file: env.yml
          init-shell: bash
      
      - name: Install local python package
        run: |
          pip install . --no-deps
        shell: micromamba-shell {0}

      - name: build containers
        run: |
          python containers/build_containers.py
        env:
          TOKEN: ${{ secrets.GITHUB_TOKEN }}
        shell: micromamba-shell {0}
      
      - name: zip built containers
        run: |
          cd ./containers/
          tar -czvf containers.tar.gz builtcontainers.json $(find . -type f -name "*.tar" -printf '%f ')


      - name: Upload container artifacts
        uses: actions/upload-artifact@v4
        with:
          name: built_containers
          path: ./containers/containers.tar.gz
          overwrite: true
  
  Test:
    runs-on: ubuntu-latest
    needs: Setup_and_build
    steps:
      - uses: actions/checkout@v3
      
      - uses: actions/download-artifact@v4
        with:
          name: built_containers

      - name: move artifact
        run: |
          mv ./containers.tar.gz ./containers/containers.tar.gz
      
      - name: unzip built containers
        run: |
          cd ./containers/
          tar -xzvf containers.tar.gz
          cd ..

      - name: Setup Apptainer
        uses: eWaterCycle/setup-apptainer@v2

      - name: Setup Mamba
        uses: mamba-org/setup-micromamba@v1
        with:
          cache-environment: true
          post-cleanup: 'all'
          environment-file: env.yml
          init-shell: bash
      
      - name: Install local python package
        run: |
          pip install . --no-deps
        shell: micromamba-shell {0}

      - name: convert containers
        run: |
          python containers/convert_artifact_containers_for_apptainer.py

      - name: download existing containers
        run: |
          python containers/pull_published_containers.py
        shell: micromamba-shell {0}
      
      ## rest of the testing suite here