[ENH] make addConfoundsToDesignMatrix a method of BidsModel
#735
Workflow file for this run
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| --- | |
| name: tests octave | |
| # 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) | |
| # │ │ │ │ │ | |
| # │ │ │ │ │ | |
| # │ │ │ │ │ | |
| # * * * * * | |
| env: | |
| OCTFLAGS: --no-gui --no-window-system --silent | |
| 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: | |
| test: | |
| if: github.repository_owner == 'cpp-lln-lab' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| test_type: [system] | |
| script: [moae, facerep, fmriprep] | |
| include: | |
| - test_type: unit | |
| mode: fast | |
| - test_type: unit | |
| mode: slow | |
| fail-fast: false | |
| steps: | |
| - name: ${{ matrix.test_type }} test | |
| if: matrix.test_type == 'system' | |
| run: echo ${{ matrix.test_type }} test ${{ matrix.script }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get -y -qq update | |
| sudo apt-get -y install unzip wget | |
| - 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: 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: Prepare test data | |
| run: | | |
| cd tests | |
| make data | |
| - 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 octave | |
| run: | | |
| sudo apt-get -y -qq update | |
| sudo apt-get -y install \ | |
| octave \ | |
| liboctave-dev\ | |
| octave-common \ | |
| octave-io \ | |
| octave-image \ | |
| octave-signal \ | |
| octave-statistics | |
| make -C MOxUnit install | |
| make -C MOcov install | |
| - name: Compile SPM | |
| run: | | |
| make -C spm12/src PLATFORM=octave distclean | |
| make -C spm12/src PLATFORM=octave | |
| make -C spm12/src PLATFORM=octave install | |
| octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();" | |
| - name: Run fast unit tests Octave | |
| if: matrix.test_type == 'unit' && matrix.mode == 'fast' | |
| run: | | |
| octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();" | |
| octave $OCTFLAGS --eval "bidspm(); cd demos/MoAE; download_moae_ds(true);" | |
| cd .github/workflows | |
| octave $OCTFLAGS --eval "tests_octave;" | |
| - name: Run slow unit tests Octave | |
| if: matrix.test_type == 'unit' && matrix.mode == 'slow' | |
| run: | | |
| octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();" | |
| octave $OCTFLAGS --eval "bidspm(); cd demos/MoAE; download_moae_ds(true);" | |
| cd .github/workflows | |
| octave $OCTFLAGS --eval " global SLOW; SLOW=true; tests_octave;" | |
| - name: Code coverage | |
| if: matrix.test_type == 'unit' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| file: coverage.xml | |
| flags: octave | |
| name: codecov-octave_${{ matrix.mode }} | |
| fail_ci_if_error: false | |
| # token: ${{ secrets.CODECOV_TOKEN }} # not required but might help API rate limits | |
| - name: Run system tests octave ${{ matrix.script }} | |
| if: matrix.test_type == 'system' | |
| run: | | |
| cd /home/runner/work/bidspm/bidspm/.github/workflows | |
| octave $OCTFLAGS --eval "run system_tests_${{ matrix.script }};" |