regressiontests.yml

name: Regression tests

on:
  pull_request:
    branches: ['develop']

jobs:

  compute_seg_masks:
    name: Compute results
    runs-on: self-hosted
    defaults:
      run:
        shell: bash -el {0}

    steps:

      - name: Checkout
        uses: actions/checkout@v2

#      - uses: actions/setup-python@v4
#        with:
#          python-version: '3.8.5'
#
#      - name: Install dependencies
#        run: pip install -r requirements.txt

      - name: Setup Miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniconda-version: 'latest'
          channels: conda-forge, bioconda
          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
          auto-update-conda: true
          auto-activate-base: false
          activate-environment: superdsm
          environment-file: superdsm.yml

      - name: Download image data
        run: |
          conda info
          python --version
          cd examples
          python load_data.py

      - name: Run SuperDSM
        run: python -m "superdsm.batch" examples --task-dir "U2OS" --task-dir "NIH3T3" --task-dir "BBBC039" --task-dir "GOWT1-1" --task-dir "GOWT1-2" --run

      - name: Aggregate results
        run: |
          rm -rf examples/fibroblast
          for taskdir in $(cd examples && find . -name 'seg')
          do
            mkdir -p "results/$taskdir"
            mv examples/$taskdir/*.png "results/$taskdir/"
          done

      - name: Upload results artifact
        uses: actions/upload-artifact@v3
        with:
          name: seg_masks
          path: results

  validate_results:
    name: Validate results
    runs-on: ubuntu-latest
    needs: ['compute_seg_masks']
    strategy:
      matrix:
        taskdir:
          - U2OS/default
          - U2OS/default/adapted
          - U2OS/default/adapted/isbi24
    steps:

      - name: Checkout
        uses: actions/checkout@v2

      - uses: actions/setup-python@v5
        with:
          python-version: '3.8.5' 

      - name: Install dependencies
        run: pip install -r tests/regression/requirements.txt

      - name: Download results artifact
        uses: actions/download-artifact@v3

      - name: Run tests
        run: |
          mkdir actual_csv
          python tests/regression/test.py results/${{ matrix.taskdir }}/seg actual_csv tests/regression/expected/${{ matrix.taskdir }}