Migrating Quicktest to PyTest and adding dockerized self hosted runner #6
Workflow file for this run
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| name: quicktest-docker | ||
| """ | ||
| 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 | ||
| # Create conda environment, install packages, and run Fastsurfer | ||
| run-fastsurfer: | ||
| runs-on: self-hosted | ||
| needs: checkout | ||
| 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 | ||
| log-level: debug | ||
| 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: | | ||
| ${{ runner.os }}-pip- | ||
| # Install required python packages | ||
| - name: Install package | ||
| run: | | ||
| python -m pip install --progress-bar off --upgrade pip \ | ||
| setuptools wheel | ||
| python -m pip install --progress-bar off .[test] | ||
| # Check if FastSurfer output already exists | ||
| - name: Check FastSurfer Output Directory | ||
| run: | | ||
| if [ -d "$RUNNER_FS_OUTPUT/subject1" ]; then | ||
| echo "FastSurfer output directory for subject1 exists. Finishing job..." | ||
| echo "HAS_FASTSURFER=false" >> $GITHUB_OUTPUT | ||
| exit 0 | ||
| else | ||
| echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..." | ||
| echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT | ||
| fi | ||
| id: check-fastsurfer-output | ||
| # Run FastSurfer | ||
| - name: Run FastSurfer | ||
| run: | | ||
| echo "Running FastSurfer..." | ||
| export FREESURFER_HOME=/freesurfer | ||
| source $FREESURFER_HOME/SetUpFreeSurfer.sh | ||
| git config --global --add safe.directory \ | ||
| . | ||
| ./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \ | ||
| --sd $RUNNER_FS_OUTPUT \ | ||
| --parallel --threads 4 --3T --parallel_subjects surf | ||
| if: steps.check-fastsurfer-output.outputs.HAS_FASTSURFER == 'true' | ||
| # 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: 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/quicktest | ||
