diff --git a/.github/workflows/quicktest.yaml b/.github/workflows/quicktest.yaml index 1cbd8948..38f9794b 100644 --- a/.github/workflows/quicktest.yaml +++ b/.github/workflows/quicktest.yaml @@ -1,5 +1,16 @@ 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: @@ -28,10 +39,14 @@ jobs: # 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: 1.3.0 + apptainer-version: 1.3.3 # Build Docker Image and convert it to Apptainer build-apptainer-image: @@ -45,14 +60,13 @@ jobs: 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 + 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 $PYTHONPATH + cd $FASTSURFER_HOME fi # Run FastSurfer on MRI data