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: Install package
#      run: |
#        python -m pip install --progress-bar off --upgrade pip setuptools wheel
#        python -m pip install --progress-bar off .[test]
    - 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: |
        cd $RUNNER_FS_OUTPUT
        # DIRECTORY="subjectX"
        echo "pwd: $(pwd)"
        # if [ -d "$DIRECTORY" ]; then
        #   # if output already exists, delete it and run again
        #   echo "Output already exists. Deleting output directory and running FastSurfer again."
        #   rm -rf $DIRECTORY
        fi
        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/brun_fastsurfer.sh \
                      --fs_license /fs_license/.license \
                      --subject_list subject_list.txt \
                      --sd /output \
                      --parallel --3T
                      --parallel_subjects

  # Run pytest
  run-pytest:
      runs-on: self-hosted
      needs: run-fastsurfer
      steps:
      - name: Set up Python 3.10
        uses: actions/setup-python@v3
        with:
          python-version: "3.10"
      - name: Install package
        run: |
          python -m pip install --progress-bar off --upgrade pip setuptools wheel
          python -m pip install --progress-bar off .[test]
      - name : Run pytest
        run: pytest test/quick_test