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

  # 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
          exit 0
        else
          echo "FastSurfer output directory for subject1 does not exist. Running FastSurfer..."
          echo "HAS_FASTSURFER=true" >> $GITHUB_OUTPUT
          exit 1
        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, ','), 'failure') }}
    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() && contains(join(needs.*.result, ','), 'success') }}
    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