quicktest.yaml

name: quicktest

on:
  pull_request:
  workflow_dispatch:

jobs:
  # Checkout repo
  checkout:
    runs-on: self-hosted
    steps:
    - uses: actions/checkout@v2

  # Prepare job: Set up Python, Go, Singularity
  prepare-job:
    runs-on: self-hosted
    needs: checkout
    steps:
    - name: Set up Python 3.10
      uses: actions/setup-python@v3
      with:
        python-version: "3.10"
    - name: Set up Go 
      uses: actions/setup-go@v5
      with:
        go-version: '^1.13.1' # The Go version to download (if necessary) and use.
    - name: Set up Singularity
      uses: eWaterCycle/setup-singularity@v7
      with:
        singularity-version: 3.8.3
        
  # Build Docker Image and convert it to Singularity
  build-singularity-image:
    runs-on: self-hosted
    needs: prepare-job
    steps:
    - name: Build Docker Image and convert to Singularity
      run: |
        cd $RUNNER_SINGULARITY_IMGS
        FILE="fastsurfer-gpu.sif"
        if [ ! -f "$FILE" ]; then
        # If the file does not exist, build the file
          echo "SIF File does not exist. Building file."
          PYTHONPATH=$PYTHONPATH
          cd $PYTHONPATH
          python3 Docker/build.py --device cuda --tag fastsurfer_gpu:cuda
          cd $RUNNER_SINGULARITY_IMGS
          singularity build --force fastsurfer-gpu.sif docker-daemon://fastsurfer_gpu:cuda
        else
          echo "File already exists"
          cd $PYTHONPATH
        fi

  # Run FastSurfer on MRI data
  run-fastsurfer:
    runs-on: self-hosted
    needs: build-singularity-image
    steps:
    - name: Run FastSurfer
      run: |
        singularity exec --nv \
                      --no-home \
                      --bind $GITHUB_WORKSPACE:/fastsurfer-dev \
                      --env FASTSURFER_HOME=/fastsurfer-dev \
                      -B $RUNNER_FS_MRI_DATA:/data \
                      -B $RUNNER_FS_OUTPUT:/output \
                      -B $RUNNER_FS_LICENSE:/fs_license \
                      $RUNNER_SINGULARITY_IMGS/fastsurfer-gpu.sif \
                      /fastsurfer/run_fastsurfer.sh \
                      --fs_license /fs_license/.license \
                      --t1 /data/subjectx/orig.mgz \
                      --sid subjectX --sd /output \
                      --parallel --3T

  # Test file existence
  test-file-existence:
    runs-on: self-hosted
    needs: run-fastsurfer
    steps:
    - name: Test File Existence
      run: |
        python3 test/quick_test/test_file_existence.py $RUNNER_FS_OUTPUT_FILES

  # Test for errors in log files
  test-error-messages:
    runs-on: self-hosted
    needs: [run-fastsurfer, test-file-existence]
    steps:
    - name: Test Log Files For Error Messages
      run: |
        python3 test/quick_test/test_errors.py $RUNNER_FS_OUTPUT_LOGS

  # Test seg_stats
  test-seg-stats:
  runs-on: self-hosted
  needs: [run-fastsurfer, test-file-existence, test-error-messages]
  steps:
  - name: Test seg_stats
    run: |
      python3 test/quick_test/test_stats.py $RUNNER_FS_REF_STATS $RUNNER_FS_OUTPUT_STATS