tests.yml

---
name: tests matlab

# Uses the cron schedule for github actions
#
# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
#
# ┌───────────── minute (0 - 59)
# │ ┌───────────── hour (0 - 23)
# │ │ ┌───────────── day of the month (1 - 31)
# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
# │ │ │ │ │
# │ │ │ │ │
# │ │ │ │ │
# * * * * *

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

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  schedule:
  - cron: 0 0 1,15 * *

  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

jobs:

  tests:

    if: github.repository_owner == 'cpp-lln-lab'

    strategy:
      matrix:
        test_type: [system]
        script: [moae, facerep, fmriprep]
        os: [ubuntu-latest, macos-latest]
        matlab: [R2022b]
        include:
        # only run bms on ubuntu because of datalad setup
        - test_type: system
          os: ubuntu-latest
          matlab: R2022b
          script: bms
        - test_type: unit
          os: ubuntu-latest
          matlab: R2022b
          mode: fast
        - test_type: unit
          os: macos-latest
          matlab: R2022b
          mode: fast
        - test_type: unit
          os: ubuntu-latest
          matlab: R2022b
          mode: slow
        - test_type: unit
          os: macos-latest
          matlab: R2022b
          mode: slow
      fail-fast: false

    runs-on: ${{ matrix.os }}

    steps:

    - name: ${{ matrix.test_type }} test
      if: matrix.test_type == 'system'
      run: echo ${{ matrix.test_type }} test ${{ matrix.script }}

    - name: Install Node
      uses: actions/setup-node@v3
      with:
        node-version: 18

    - name: Install python
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'

    - name: Install dependencies
      if: matrix.os == 'ubuntu-latest'
      run: |
        sudo apt-get -y -qq update
        sudo apt-get -y install unzip wget git-annex
        python -m pip install --upgrade pip setuptools
        pip install datalad

    - name: Clone bidspm
      uses: actions/checkout@v3
      with:
        submodules: recursive
        fetch-depth: 0

    - name: Install validators
      run: make install

    - name: Install SPM
      run: |
        git clone https://github.com/spm/spm12.git --depth 1

    - name: Copy Macs toolbox to SPM inputs_folder
      run: cp -rv lib/MACS spm12/toolbox/MACS

    - name: Get moae fmriprep data from OSF
      run: |
        mkdir -p demos/MoAE/inputs/
        cd demos/MoAE/inputs/
        wget https://osf.io/vufjs/download
        unzip download
        mv moae_fmriprep fmriprep

    - name: Prepare test data unix
      run: |
        cd tests
        make data

    - name: Get data for BMS
      if: matrix.script == 'bms'
      run: make -C demos/bayes data_ds000114

    - name: Install Moxunit and MOcov
      run: |
        git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
        git clone https://github.com/MOcov/MOcov.git --depth 1

    - name: Install MATLAB
      uses: matlab-actions/setup-matlab@v1.2.4
      with:
        release: ${{ matrix.matlab }}

    - name: Run fast unit tests MATLAB
      if: matrix.test_type == 'unit' && matrix.mode == 'fast'
      uses: matlab-actions/run-command@v1.2.1
      with:
        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;

    - name: Run slow unit tests MATLAB
      if: matrix.test_type == 'unit' && matrix.mode == 'slow'
      uses: matlab-actions/run-command@v1.2.1
      with:
        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab;

    - name: Code coverage matlab
      if: matrix.test_type == 'unit'
      uses: codecov/codecov-action@v3
      with:
        file: coverage.xml
        flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }}
        name: codecov-matlab
        fail_ci_if_error: false
      # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits

    - name: Run system tests MATLAB ${{ matrix.script }}
      if: matrix.test_type == 'system'
      uses: matlab-actions/run-command@v1.2.1
      with:
        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};