quicktest #54
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: Install package | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip setuptools wheel | |
| python -m pip install --progress-bar off .[quicktest] | |
| - 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 | |
| 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: [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: [test-error-messages] | |
| steps: | |
| - name: Test seg_stats | |
| run: | | |
| python3 test/quick_test/test_stats.py $RUNNER_FS_REF_STATS $RUNNER_FS_OUTPUT_STATS |