Migrating Quicktest to PyTest and adding dockerized self hosted runner #10
Workflow file for this run
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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 | ||
