Migrating Quicktest to PyTest and adding dockerized self hosted runner #36
Workflow file for this run
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| name: quicktest-runner | |
| # File: quicktest_runner.yaml | |
| # Author: Taha Abdullah | |
| # Created on: 2023-07-10 | |
| # Functionality: This workflow runs FastSurfer on MRI data and runs pytest to check if the results are acceptable. It | |
| # also checks if the FastSurfer environment and output already exist, and if not, it creates them. | |
| # Usage: This workflow is triggered on a pull request to the dev and main branch. It can also be triggered manually | |
| # with workflow-dispatch. | |
| # Expected/Used Environment Variables: | |
| # - MAMBAPATH: Path to the micromamba binary. | |
| # - MAMBAROOT: Root path for micromamba. | |
| # - RUNNER_FS_OUTPUT: Path to the directory where FastSurfer output is stored. | |
| # - RUNNER_FS_MRI_DATA: Path to the directory where MRI data is stored. | |
| # - FREESURFER_HOME: Path to the freesurfer directory. | |
| # - FS_LICENSE: Path to the FreeSurfer license file. | |
| on: | |
| pull_request: | |
| branches: | |
| - dev | |
| - stable | |
| workflow_dispatch: | |
| jobs: | |
| # Checkout repo | |
| checkout: | |
| runs-on: self-hosted | |
| steps: | |
| - uses: actions/checkout@v2 | |
| # Check if fastsurfer output already exists, if so, skip run-fastsurfer and run pytest directly | |
| check-output: | |
| runs-on: self-hosted | |
| needs: checkout | |
| steps: | |
| - name: Check FastSurfer Output Directory | |
| run: | | |
| if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then | |
| echo "FastSurfer output directory for subject1 exists. Finishing job..." | |
| echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT | |
| else | |
| echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..." | |
| echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT | |
| fi | |
| id: check-fastsurfer-output | |
| # Create conda environment, install packages, and run Fastsurfer | |
| run-fastsurfer: | |
| runs-on: self-hosted | |
| if: ${{ always() && contains(join(needs.*.result, ','), 'HAS_FASTSURFER=true') }} | |
| needs: check-output | |
| steps: | |
| # Check if the Environment Variables used in further steps are present | |
| - name: Check Environment Variables | |
| run: | | |
| REQUIRED_ENV_VARS=( | |
| "MAMBAPATH" | |
| "MAMBAROOT" | |
| "RUNNER_FS_OUTPUT" | |
| "RUNNER_FS_MRI_DATA" | |
| "FREESURFER_HOME" | |
| "FS_LICENSE" | |
| ) | |
| for VAR_NAME in "${REQUIRED_ENV_VARS[@]}"; do | |
| if [ -z "${!VAR_NAME}" ]; then | |
| echo "Error: Required environment variable $VAR_NAME is not set" | |
| exit 1 | |
| fi | |
| done | |
| if [ ! -f "$FS_LICENSE" ]; then | |
| echo "Error: FreeSurfer license file does not exist at $FS_LICENSE" | |
| exit 1 | |
| fi | |
| if [ ! -d "$FREESURFER_HOME" ]; then | |
| echo "Error: FreeSurfer installation directory does not exist at $FREESURFER_HOME" | |
| exit 1 | |
| fi | |
| # Set up Python using setup-python@v3 action | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| # Check if FastSurfer environment already exists | |
| - name: Check Environment | |
| run: | | |
| if [ ! -f "$MAMBAPATH" ]; then | |
| echo "FastSurfer environment does not exist. Creating FastSurfer Environment..." | |
| echo "HAS_MAMBA=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "FastSurfer environment exists. Skipping FastSurfer Environment creation..." | |
| echo "HAS_MAMBA=false" >> $GITHUB_OUTPUT | |
| fi | |
| id: check-environment | |
| # Create FastSurfer environment if it does not exist | |
| - name: Create FastSurfer Environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: env/fastsurfer.yml | |
| micromamba-root-path: $MAMBAROOT | |
| micromamba-binary-path: $MAMBAPATH | |
| cache-downloads: true | |
| cache-environment: true | |
| init-shell: none | |
| if: steps.check-environment.outputs.HAS_MAMBA == 'true' | |
| # Set up cache for python packages | |
| - name: Cache Python packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| # Install required python packages | |
| - name: Install package | |
| run: | | |
| python -m pip install --progress-bar off --upgrade pip \ | |
| setuptools wheel | |
| python -m pip install --progress-bar off .[test] | |
| # Run fastsurfer on list of subjects | |
| - name: Run FastSurfer | |
| run: | | |
| echo "Running FastSurfer..." | |
| export FREESURFER_HOME=/freesurfer | |
| source $FREESURFER_HOME/SetUpFreeSurfer.sh | |
| export FASTSURFER_HOME=$(pwd) | |
| ./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \ | |
| --sd $RUNNER_FS_OUTPUT \ | |
| --parallel --threads 4 --3T --parallel_subjects surf | |
| # Test fastsurfer output | |
| run-pytest: | |
| runs-on: self-hosted | |
| if: ${{ always() }} | |
| needs: [check-output, run-fastsurfer] | |
| steps: | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| - name: Cache Python packages | |
| uses: actions/cache@v3 | |
| with: | |
| path: /home/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Run pytest | |
| run: python -m pytest test/quick_test |