MAGeTbrain/.github/workflows/test_latest.yml at master · bids-apps/MAGeTbrain · GitHub

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---
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:

    strategy:
      matrix:
        participant: ['01', '02']
        masking: ['', --label-masking]
      fail-fast: false

    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/magetbrain:latest

    - name: print version
      run: |
        docker run -t --rm \
              bids/magetbrain:latest -v
        docker run -t --rm \
              bids/magetbrain: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 ds003_downsampled

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

    - name: template level run for downsampled dataset ${{ matrix.masking }}
      run: |
        docker run -t --rm \
        -v ${HOME}/data/ds003_downsampled:/bids_dataset \
        -v ${HOME}/outputs:/outputs \
          bids/magetbrain:latest \
            --n_cpus 2 --segmentation_type colin27-subcortical ${{ matrix.masking }} \
            /bids_dataset /outputs participant1 --participant_label ${{ matrix.participant }}

    - name: participant level tests for a longitudinal dataset ${{ matrix.masking }}
      run: |
        docker run -t --rm  \
        -v ${HOME}/data/ds003_downsampled:/bids_dataset \
        -v ${HOME}/outputs:/outputs \
          bids/magetbrain:latest \
            --n_cpus 2 --segmentation_type colin27-subcortical ${{ matrix.masking }} \
            /bids_dataset /outputs participant2 --participant_label ${{ matrix.participant }}

    - name: check output
      run: |
        tree ${HOME}/outputs
        tree ${HOME}/outputs-labelmask