quicktest #121
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| name: quicktest | |
| # File: quicktest.yaml | |
| # Author: Taha Abdullah | |
| # Created on: 2023-03-04 | |
| # Functionality: This workflow runs some quick integration tests on FastSurfer commits. It checks out the new | |
| # FastSurfer repo, sets up Python, builds a Singularity image, runs FastSurfer on sample MRI data, and | |
| # runs pytest to check if the results are acceptable | |
| # Usage: This workflow is triggered on a push or pull-request to the dev and main branch of DeepMI/FastSurfer. | |
| # It can also be triggered manually with workflow-dispatch | |
| on: | |
| # pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| # Checkout repo | |
| checkout: | |
| runs-on: self-hosted | |
| steps: | |
| - uses: actions/checkout@v2 | |
| # Prepare job: Set up Python, Go, Apptainer | |
| 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: 3.8.7 | |
| - name: Set up Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: 1.3.3 | |
| # Build Docker Image and convert it to Apptainer | |
| build-apptainer-image: | |
| runs-on: self-hosted | |
| needs: prepare-job | |
| steps: | |
| - name: Build Docker Image and convert to Apptainer | |
| run: | | |
| cd $RUNNER_FASTSURFER_IMGS | |
| FILE="fastsurfer-gpu.sif" | |
| if [ ! -f "$FILE" ]; then | |
| # If the file does not exist, build the file | |
| echo "SIF File does not exist. Building file." | |
| cd $FASTSURFER_HOME | |
| python3 Docker/build.py --device cuda --tag fastsurfer_gpu:cuda | |
| cd $RUNNER_FASTSURFER_IMGS | |
| apptainer build --force fastsurfer-gpu.sif docker-daemon://fastsurfer_gpu:cuda | |
| else | |
| echo "File already exists" | |
| cd $FASTSURFER_HOME | |
| fi | |
| # Run FastSurfer on MRI data | |
| run-fastsurfer: | |
| runs-on: self-hosted | |
| needs: build-apptainer-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 | |
| apptainer 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_FASTSURFER_IMGS/fastsurfer-gpu.sif \ | |
| /fastsurfer/brun_fastsurfer.sh \ | |
| --fs_license /fs_license/.license \ | |
| --subject_list /data/subject_list.txt \ | |
| --sd /output \ | |
| --parallel --3T \ | |
| --parallel_subjects surf | |
| # 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 |