integration.yml

name: integration test
on: push
jobs:
  build:
    runs-on: ubuntu-20.04

    strategy:
      matrix:
        python-version: ["3.8", "3.9", "3.10"]
    steps:
    - using: node20
    - uses: actions/checkout@v3
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
          python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
          python -m pip install --upgrade pip
          pip install openpyxl
          pip install flake8 wheel
          pip install .
    - name: instalation test
      run: |
        cd
        bidsme --help
    - name: lint with flake8
      run: |
        flake8 .
    - name: unittests
      run: |
        python -m unittest
    - name: getting Test DS
      run: |
        cd
        git clone https://github.com/CyclotronResearchCentre/bidsme_examples.git
        cd bidsme_examples/example1
    - name: preparation
      run: |
        cd ~/bidsme_examples/example1
        bidsme prepare source/ renamed/ -r nii=MRI --part-template resources/participants.json --plugin resources/plugins/rename_plugin.py
    - name: mapping
      run:  |
        cd ~/bidsme_examples/example1
        bidsme map renamed/ bids/ --plugin resources/plugins/bidsify_plugin.py -b resources/map/bidsmap.yaml
    - name: process
      run:  |
        cd ~/bidsme_examples/example1
        bidsme process renamed/ bids/ --plugin resources/plugins/process_plugin.py -b resources/map/bidsmap.yaml
    - name: bidsfify 
      run: |
        cd ~/bidsme_examples/example1
        bidsme bidsify renamed/ bids/ --plugin resources/plugins/bidsify_plugin.py -b resources/map/bidsmap.yaml