test_latest.yml

---
name: test latest image

on:
  pull_request:
    branches: ['*']
  schedule:
  - cron: 0 0 1 * *
  workflow_dispatch:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

defaults:
  run:
    shell: bash -l {0}

jobs:

  test_latest_image:

    runs-on: ubuntu-latest

    steps:
    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y tree

    - name: Clone repo
      uses: actions/checkout@v3

    - name: pull docker image
      run: docker pull bids/mindboggle:latest

    - name: print version
      run: |
        docker run -t --rm \
              bids/mindboggle:latest -v
        docker run -t --rm \
              bids/mindboggle:latest -h

    - name: get data
      run: |
        wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
        bash get_data_from_osf.sh ds114_test1

    - name: prepare output dir
      run: mkdir -p ${HOME}/outputs

    - name: participant level test
      run: |
        docker run -t --rm \
          -v ${HOME}/data/ds114_test1:/home/jovyan/work/bids_dataset \
          -v ${HOME}/outputs1:/home/jovyan/work/outputs \
            bids/mindboggle \
              /home/jovyan/work/bids_dataset \
              /home/jovyan/work/outputs \
              participant \
              --participant_label 01


    - name: check output
      run: tree ${HOME}/data/ds114_test1_with_freesurfer/derivatives