quicktest #75
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| 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 .[quicktest] | |
| - name: Display system information | |
| run: brainprint-sys_info --developer | |
| - name : Run pytest | |
| run: pytest quicktest | |
| # - 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/run_fastsurfer.sh \ | |
| # --fs_license /fs_license/.license \ | |
| # --t1 /data/subjectx/orig.mgz \ | |
| # --sid subjectX --sd /output \ | |
| # --parallel --3T | |
| # Run pytest | |
| # run-pytest: | |
| # runs-on: self-hosted | |
| # needs: prepare-job | |
| # steps: | |
| # - name : Run pytest | |
| # run: pytest quicktest |