Migrating Quicktest to PyTest and adding dockerized self hosted runner #47
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 | |
| # 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 $FREESURFER_HOME" | |
| exit 1 | |
| fi | |
| # - name: create env | |
| # run: | | |
| # if [[ "$(md5sum /fastsurfer/fastsurfer-pytest.yml)" != "$(md5sum env/fastsurfer.yml)" ]] ; then | |
| # mamba env create -n "fastsurfer_$GITHUB_SHA" -f env/fastsurfer.yml | |
| # mamba activate "fastsurfer_$GITHUB_SHA" | |
| # fi | |
| - name: Run FastSurfer | |
| run: | | |
| echo "Running FastSurfer..." | |
| echo "Output will be saved in data/${GITHUB_SHA:0:7}" | |
| export FASTSURFER_HOME=$(pwd) | |
| export THIS_RUN_OUTDIR=${GITHUB_SHA:0:7} | |
| mkdir -p $SUBJECTS_DIR/$THIS_RUN_OUTDIR | |
| ./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \ | |
| --sd $SUBJECTS_DIR/$THIS_RUN_OUTDIR \ | |
| --parallel --threads 4 --3T --parallel_subjects surf | |
| export TEST_DIR=$THIS_RUN_OUTDIR | |
| # - name: cleanup | |
| # run: | | |
| # if [[ "$(md5sum /fastsurfer/fastsurfer.yml)" != "$(md5sum env/fastsurfer.yml)" ]] ; then | |
| # mamba env remove -n "fastsurfer_$GITHUB_SHA" | |
| # fi | |
| # Test fastsurfer output | |
| run-pytest: | |
| runs-on: self-hosted | |
| if: always() | |
| needs: run-fastsurfer | |
| steps: | |
| - name: Run pytest | |
| run: | | |
| source /venv-pytest/bin/activate | |
| python -m pytest test/quick_test |