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-13]
                matlab: [R2023b]
                include:
        # only run bms on ubuntu because of datalad setup
                -   test_type: system
                    os: ubuntu-latest
                    matlab: R2023b
                    script: bms
                -   test_type: unit
                    os: ubuntu-latest
                    matlab: R2023b
                    mode: fast
                -   test_type: unit
                    os: macos-13
                    matlab: R2023b
                    mode: fast
                -   test_type: unit
                    os: ubuntu-latest
                    matlab: R2023b
                    mode: slow
                -   test_type: unit
                    os: macos-13
                    matlab: R2023b
                    mode: slow
                -   test_type: unit
                    os: macos-13
                    matlab: R2023b
                    mode: fast
            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@v4
            with:
                node-version: 18

        -   name: Install python
            uses: actions/setup-python@v5
            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@v4
            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: 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: Get data for testing QA
            if: matrix.os == 'ubuntu-latest'
            run: |
                cd demos/openneuro/
                make data_ds000114_mriqc
                make data_ds000114_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@v2.2.0
            with:
                release: ${{ matrix.matlab }}

        -   name: Run fast unit tests MATLAB
            if: matrix.test_type == 'unit' && matrix.mode == 'fast'
            uses: matlab-actions/run-command@v2.1.1
            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@v2.1.1
            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@v4
            with:
                file: coverage.xml
                flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }}
                name: codecov-matlab
                fail_ci_if_error: false
                token: ${{ secrets.CODECOV_TOKEN }}

        -   name: Run system tests MATLAB ${{ matrix.script }}
            if: matrix.test_type == 'system'
            uses: matlab-actions/run-command@v2.1.1
            with:
                command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};