singularity_container-install.yml

name: Test Singularity Build
on:
  # push:
  #   branches:
  #     - master
  # Do the builds on all pull requests (to test them)
  pull_request:
    branches:
      - "*"

jobs:
  changes:
    name: Checking changed files
    runs-on: ubuntu-latest
    outputs:
      keepgoing: ${{ steps.changed-files.outputs.any_changed }}
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Get changed files
        id: changed-files
        uses: tj-actions/changed-files@v41
        with:
          files: |
            **/*.{yml,yaml,py}
            requirements.txt
            container/database
            container/tests
            container/scripts/*.{sh,py}
            container/*.{yml,yaml,py,def}
            tests
      - name: List all changed files
        run: |
          for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
            echo "$file was changed"
          done
          echo ${{ steps.changed-files.outputs.any_changed }}
  container:
    needs:
      - changes
    if: needs.changes.outputs.keepgoing == 'true'
    runs-on: ubuntu-latest
    steps:
      - name: Check out code for the container build
        uses: actions/checkout@v3
      - name: Setup Singularity
        uses: singularityhub/install-singularity@main
      - name: Extract repository location
        shell: bash
        run: |
          echo "location=$(echo "      - git+https://www.github.com/${GITHUB_REPOSITORY}@${GITHUB_REF#refs/heads/}")" >> $GITHUB_OUTPUT
        id: extract_location
      - name: Build Container
        run: |
          cd container
          echo '${{ steps.extract_location.outputs.location }}' >> environment_test.yml
          sudo -E singularity build --notest sc-dandelion.sif sc-dandelion_test.def
      - name: Test Container
        run: |
          cd container
          sudo singularity test --writable-tmpfs sc-dandelion.sif
          singularity run -B $PWD sc-dandelion.sif dandelion-preprocess --help