ci.yml

name: CI
on: [push, pull_request, workflow_dispatch]

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

      - name: Build the Docker container
        run: docker build -t unmicst:test .

      # Cache test data to avoid repeated download
      - uses: actions/cache@v3
        id: cache-data
        with:
          path: |
            ~/data/exemplar-001-cycle6.ome.tif
          key: testdata-2022-04-29

      # Download test data only if no cache is present
      - name: Test data download
        if: steps.cache-data.outputs.cache-hit != 'true'
        run: |
          mkdir ~/data
          cd ~/data
          curl -f -o exemplar-001-cycle6.ome.tif https://mcmicro.s3.amazonaws.com/ci/exemplar-001-cycle6.ome.tif

      - name: Test the container
        run: |
          cd ~/data
          rm -f exemplar-001-cycle6_Probabilities_1.tif
          rm -rf qc/
          docker run -v "$PWD":/data unmicst:test /bin/bash -c "cd /data; \
            python /app/unmicstWrapper.py --stackOutput --outputPath . exemplar-001-cycle6.ome.tif"

      # If the action is successful, the output will be available as a downloadable artifact
      - name: Upload processed result
        uses: actions/upload-artifact@v2
        with:
          name: exemplar-001
          path: |
            ~/data/exemplar-001-cycle6_Probabilities_1.tif
            ~/data/qc/**