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Remi-GauRemi-Gau
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[MAINT] split system and unit tests for matlab linux and mac os (#1309)
* split system and unit tests for matlab linux and mac os * move into a single workflow
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‎.github/workflows/tests.yml‎

Lines changed: 165 additions & 43 deletions
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@@ -27,57 +27,25 @@ on:
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schedule:
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- cron: 0 0 1,15 * *
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# Allows you to run this workflow manually from the Actions tab
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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tests:
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fast_tests:
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if: github.repository_owner == 'cpp-lln-lab'
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strategy:
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matrix:
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test_type: [system]
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script: [moae, facerep, fmriprep]
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os: [ubuntu-latest, macos-13]
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matlab: [R2023b]
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include:
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# only run bms on ubuntu because of datalad setup
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- test_type: system
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os: ubuntu-latest
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matlab: R2023b
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script: bms
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- test_type: unit
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os: ubuntu-latest
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matlab: R2023b
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mode: fast
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- test_type: unit
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os: macos-13
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matlab: R2023b
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mode: fast
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- test_type: unit
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os: ubuntu-latest
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matlab: R2023b
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mode: slow
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- test_type: unit
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os: macos-13
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matlab: R2023b
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mode: slow
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- test_type: unit
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os: macos-13
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matlab: R2023b
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mode: fast
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: ${{ matrix.test_type }} test
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if: matrix.test_type == 'system'
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run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
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- name: Install Node
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uses: actions/setup-node@v4
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with:
@@ -129,10 +97,6 @@ jobs:
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cd tests
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make data
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- name: Get data for BMS
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if: matrix.script == 'bms'
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run: make -C demos/bayes data_ds000114
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- name: Install Moxunit and MOcov
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run: |
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git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
@@ -144,29 +108,187 @@ jobs:
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release: ${{ matrix.matlab }}
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- name: Run fast unit tests MATLAB
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if: matrix.test_type == 'unit' && matrix.mode == 'fast'
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uses: matlab-actions/[email protected]
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with:
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command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
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- name: Code coverage matlab
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uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_fast
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name: codecov-matlab
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fail_ci_if_error: false
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token: ${{ secrets.CODECOV_TOKEN }}
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slow_tests:
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needs: [fast_tests]
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if: github.repository_owner == 'cpp-lln-lab'
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strategy:
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matrix:
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os: [ubuntu-latest, macos-13]
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matlab: [R2023b]
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: Install Node
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uses: actions/setup-node@v4
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with:
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node-version: 18
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- name: Install python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install dependencies
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if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install unzip wget git-annex
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python -m pip install --upgrade pip setuptools
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pip install datalad
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- name: Clone bidspm
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uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Install validators
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run: make install
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- name: Install SPM
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run: |
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git clone https://github.com/spm/spm12.git --depth 1
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- name: Get moae fmriprep data from OSF
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run: |
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mkdir -p demos/MoAE/inputs/
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cd demos/MoAE/inputs/
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wget https://osf.io/vufjs/download
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unzip download
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mv moae_fmriprep fmriprep
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- name: Get data for testing QA
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if: matrix.os == 'ubuntu-latest'
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run: |
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cd demos/openneuro/
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make data_ds000114_mriqc
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make data_ds000114_fmriprep
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- name: Prepare test data unix
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run: |
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cd tests
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make data
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- name: Install Moxunit and MOcov
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run: |
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git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
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git clone https://github.com/MOcov/MOcov.git --depth 1
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- name: Install MATLAB
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uses: matlab-actions/[email protected]
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with:
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release: ${{ matrix.matlab }}
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- name: Run slow unit tests MATLAB
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if: matrix.test_type == 'unit' && matrix.mode == 'slow'
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uses: matlab-actions/[email protected]
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with:
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command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab;
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- name: Code coverage matlab
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if: matrix.test_type == 'unit'
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uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }}
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flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_slow
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name: codecov-matlab
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fail_ci_if_error: false
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token: ${{ secrets.CODECOV_TOKEN }}
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system_tests:
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needs: [fast_tests]
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if: github.repository_owner == 'cpp-lln-lab'
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strategy:
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matrix:
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script: [moae, facerep, fmriprep]
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os: [ubuntu-latest, macos-13]
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matlab: [R2023b]
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include:
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# only run bms on ubuntu because of datalad setup
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- os: ubuntu-latest
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matlab: R2023b
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script: bms
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: test ${{ matrix.script }}
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run: test ${{ matrix.script }}
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- name: Install Node
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uses: actions/setup-node@v4
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with:
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node-version: 18
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- name: Install python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install dependencies
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if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get -y -qq update
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sudo apt-get -y install unzip wget git-annex
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python -m pip install --upgrade pip setuptools
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pip install datalad
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- name: Clone bidspm
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uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Install validators
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run: make install
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- name: Install SPM
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run: |
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git clone https://github.com/spm/spm12.git --depth 1
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- name: Get moae fmriprep data from OSF
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run: |
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mkdir -p demos/MoAE/inputs/
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cd demos/MoAE/inputs/
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wget https://osf.io/vufjs/download
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unzip download
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mv moae_fmriprep fmriprep
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- name: Prepare test data unix
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run: |
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cd tests
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make data
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- name: Get data for BMS
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if: matrix.script == 'bms'
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run: make -C demos/bayes data_ds000114
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- name: Install MATLAB
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uses: matlab-actions/[email protected]
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with:
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release: ${{ matrix.matlab }}
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- name: Run system tests MATLAB ${{ matrix.script }}
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if: matrix.test_type == 'system'
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uses: matlab-actions/[email protected]
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with:
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command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};

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