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Update test workflow to run lighter testing on draft PRs (#720)
* Update test workflow Updated workflow to run tests only on latest release of MATLAB for draft PRs * Create test.m * Update run_tests.yml Fixed json formatting bug * Update test.m * Update run_tests.yml Cline suggested fix for error on github runner * Update run_tests.yml Cline suggested fix for error on github runner * Update test.m * Update run_tests.yml Added step for caching pip dependencies * Update UnitTimesIOTest.m Minor fix for failing test * Remove EOF sandwich * Add comments in `set-matrix` workflow job * Delete test.m * Revert caching of pip dependencies Does not have significant speedup gains Risk having outdated versions in cache as the cache does not detect if dependencies are updated
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‎+tests/+system/UnitTimesIOTest.m

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@@ -13,7 +13,7 @@ function addContainer(~, file)
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, 'waveform_mean', 5 ...
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);
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% the following is solely for a2a comparison with files.
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file.units.spike_times.description = 'the spike times for each unit';
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file.units.spike_times.description = 'the spike times for each unit in seconds';
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file.units.waveforms.description = ['Individual waveforms for each spike. ' ...
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'If the dataset is three-dimensional, the third dimension shows the response ' ...
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'from different electrodes that all observe this unit simultaneously. ' ...

‎+tests/requirements.txt

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@@ -2,5 +2,5 @@ scipy
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matplotlib
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hdf5plugin
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dataframe_image
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git+https://github.com/NeurodataWithoutBorders/nwbinspector.git@dev
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git+https://github.com/NeurodataWithoutBorders/pynwb.git@dev
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git+https://github.com/NeurodataWithoutBorders/nwbinspector.git@dev

‎.github/workflows/configurations/matlab_release_matrix_strategy.yml

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- matlab-version: R2021a
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '1'
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- matlab-version: R2021b
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '1'
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- matlab-version: R2022a
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2022b
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2023a
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python-version: '3.10'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2023b
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python-version: '3.10'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2024a
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python-version: '3.11'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2024b
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python-version: '3.11'
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skip-pynwb-compatibilty-test-for-tutorial: '0'

‎.github/workflows/run_tests.yml

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@@ -2,6 +2,7 @@
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name: Run tests
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on:
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pull_request:
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types: [opened, synchronize, reopened, ready_for_review]
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branches:
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- main
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paths-ignore:
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- main
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concurrency:
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group: ${{ github.ref }}
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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set_matrix:
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name: Set test matrix
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runs-on: ubuntu-latest
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outputs:
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matrix: ${{ steps.set-matrix.outputs.matrix }}
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latest_matlab_version: ${{ steps.set-matrix.outputs.latest_matlab_version }}
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set matrix
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id: set-matrix
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run: |
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# Load the matrix configuration and extract latest version
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latest_matlab_version=$(yq '.[-1].matlab-version' .github/workflows/configurations/matlab_release_matrix_strategy.yml)
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# Conditionally define the MATLAB test matrix based on the PR type.
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# Draft pull requests are only tested against the latest MATLAB release,
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# while non-draft PRs and push events are tested against all configured releases.
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if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.event.pull_request.draft }}" == "true" ]]; then
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echo "Draft PR detected - using latest MATLAB version only"
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# Create matrix with only the latest entry
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matrix=$(yq -o=json '.[-1:] | {"include": .}' .github/workflows/configurations/matlab_release_matrix_strategy.yml | tr -d '\n')
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else
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echo "Non-draft PR or push event - using full matrix"
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# Create matrix with all entries
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matrix=$(yq -o=json '{"include": .}' .github/workflows/configurations/matlab_release_matrix_strategy.yml | tr -d '\n')
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fi
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# Assign `matrix` and `latest_matlab_version` as outputs of this job
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echo "matrix=$matrix" >> $GITHUB_OUTPUT
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echo "latest_matlab_version=$latest_matlab_version" >> $GITHUB_OUTPUT
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run_tests:
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name: Run MATLAB tests (${{ matrix.matlab-version }})
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needs: set_matrix
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runs-on: ubuntu-latest
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env:
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USE_CACHE: ${{ github.event_name == 'pull_request' && github.event.pull_request.draft == true }}
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strategy:
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fail-fast: false
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matrix:
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include:
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- matlab-version: R2021a
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '1'
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- matlab-version: R2021b
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '1'
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- matlab-version: R2022a
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2022b
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2023a
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python-version: '3.10'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2023b
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python-version: '3.10'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2024a
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python-version: '3.11'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2024b
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python-version: '3.11'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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matrix: ${{ fromJSON(needs.set_matrix.outputs.matrix) }}
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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uses: matlab-actions/setup-matlab@v2
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with:
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release: ${{ matrix.matlab-version }}
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cache: ${{ env.USE_CACHE }}
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- name: Run tests
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uses: matlab-actions/run-command@v2
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retention-days: 1
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- name: Upload coverage results
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if: always()
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if: always() && matrix.matlab-version == needs.set_matrix.outputs.latest_matlab_version
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uses: actions/upload-artifact@v4
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with:
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name: test-coverage-${{ matrix.matlab-version }}
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publish_coverage:
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name: Publish Cobertura test coverage
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runs-on: ubuntu-latest
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needs: [run_tests]
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needs: [run_tests, set_matrix]
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Retrieve code coverage files
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uses: actions/download-artifact@v4
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with:
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name: test-coverage-R2024b
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name: test-coverage-${{ needs.set_matrix.outputs.latest_matlab_version }}
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- name: Publish on coverage results on Codecov
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uses: codecov/codecov-action@v4

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