quicktest_runner.yaml

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_$GITHUB_SHA"
#        fi
    - name: Run FastSurfer
      run: |
        echo "Running FastSurfer..."
        export FASTSURFER_HOME=$(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
    needs: run-fastsurfer
    steps:
    - name: Run pytest
      run: |
        source /venv-pytest/bin/activate
        python -m pytest test/quick_test