quicktest #123
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: quicktest-runner | |
| # File: quicktest.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 $FREESURFER_HOME" | |
| exit 1 | |
| fi | |
| # Run FastSurfer on test subjects | |
| - name: Run FastSurfer | |
| run: | | |
| echo "Running FastSurfer..." | |
| echo "Output will be saved in data/${GITHUB_SHA:0:7}" | |
| export FASTSURFER_HOME=$(pwd) | |
| export THIS_RUN_OUTDIR=${GITHUB_SHA:0:7} | |
| mkdir -p $SUBJECTS_DIR/$THIS_RUN_OUTDIR | |
| export TEST_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 | |
| # 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 |