aa_unittest.yml

# This is a basic workflow to help you get started with Actions

name: Non-Use case tests

# Controls when the workflow will run
on:
  # Triggers the workflow on push or pull request events but only for the master branch
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

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

# Default settings
defaults:
    run:
      shell: bash

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  not_large:
    name: Run all tests that do NOT have the Large tag

    # The type of runner that the job will run on
    runs-on: ubuntu-20.04

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      - name: Free Disk Space (Ubuntu)
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: true
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          swap-storage: true

      - name: Create test space
        run: |
          sudo mkdir /test
          sudo chown runner: /test
          sudo chmod u+w /test
          echo "Free space:"
          df -h
      
      - name: Set git to use LF
        run: |
          git config --global core.autocrlf false
          git config --global core.eol lf

      - name: Check out repository under $GITHUB_WORKSPACE
        uses: actions/checkout@v3

      - name: Set up Python 3.6
        uses: actions/setup-python@v4
        with:
          # Semantic version range syntax or exact version of a Python version
          python-version: '3.6'
          # Optional - x64 or x86 architecture, defaults to x64
          architecture: 'x64'

      - name: Set up MATLAB
        uses: matlab-actions/setup-matlab@v1
        with:
          # MATLAB release to set up R2020a
          release: R2020a

      - name: Install tools and configure aa
        run: |
          python trigger_install.py
        working-directory: ${{github.workspace}}/.github/workflows
        env:
          LOAD_FSL: 0
          LOAD_FREESURFER: 0
          PARAMETER_XML: aap_parameters_defaults_GitHub.xml

      - name: Run script
        uses: matlab-actions/run-command@v1
        with:
          command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('haltonerror', true, 'not_tags', {'Large'}); aa_test_getreport('/test/projects','/test/projects/report')
        env:
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          AWS_EC2_METADATA_DISABLED: true

      - name: Archive data
        uses: actions/upload-artifact@v3
        with:
          name: data_${{github.job}}
          path: |
            /test/projects/report/

      - name: Archive log
        uses: actions/upload-artifact@v3
        with:
          name: testlog_${{github.job}}
          path: |
            ${{github.workspace}}/developer/aa_test.log

  tutorial_minimal:
    # Since aa states that the minimal tools needed are only aa and spm, and at least some of the
    # examples should work correctly with just those installed.
    name: Run all tutorial tests with only a minimal parameter xml / tools install

    # The type of runner that the job will run on
    runs-on: ubuntu-20.04

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
      - name: Free Disk Space (Ubuntu)
        uses: jlumbroso/free-disk-space@main
        with:
          tool-cache: true
          android: true
          dotnet: true
          haskell: true
          large-packages: true
          swap-storage: true

      - name: Create test space
        run: |
          sudo mkdir /test
          sudo chown runner: /test
          sudo chmod u+w /test
          echo "Free space:"
          df -h
      
      - name: Set git to use LF
        run: |
          git config --global core.autocrlf false
          git config --global core.eol lf

      - name: Check out repository under $GITHUB_WORKSPACE
        uses: actions/checkout@v3

      - name: Set up Python 3.6
        uses: actions/setup-python@v4
        with:
          # Semantic version range syntax or exact version of a Python version
          python-version: '3.6'
          # Optional - x64 or x86 architecture, defaults to x64
          architecture: 'x64'

      - name: Set up MATLAB
        uses: matlab-actions/setup-matlab@v1
        with:
          # MATLAB release to set up R2020a
          release: R2020a

      - name: Install tools and configure aa
        run: |
          python trigger_install.py
        working-directory: ${{github.workspace}}/.github/workflows
        env:
          # Do not even install the FSL standards
          LOAD_FSL: 0
          LOAD_FREESURFER: 0
          PARAMETER_XML: aap_parameters_defaults_GitHub_minimal.xml

      - name: Run script
        uses: matlab-actions/run-command@v1
        with:
          command: addpath(getenv('GITHUB_WORKSPACE')); aa_ver5; SPM = spmClass(fullfile('/test','tools','spm12')); SPM.load; aa_test('haltonerror', true, 'tags', {'Minimal_install'}); aa_test_getreport('/test/projects','/test/projects/report')

      - name: Archive data
        uses: actions/upload-artifact@v3
        with:
          name: data_${{github.job}}
          path: |
            /test/projects/report/

      - name: Archive log
        uses: actions/upload-artifact@v3
        with:
          name: testlog_${{github.job}}
          path: |
            ${{github.workspace}}/developer/aa_test.log