Promote specialized attributes of included typed datasets (e.g. Units.spike_times_resolution)#797
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ehennestad merged 76 commits intomainfrom Apr 7, 2026
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Extend the test helper to treat types.untyped.DataPipe like DataStub by calling load() on actualValue before comparing.
…ject-checks-in-tutorialtests
Replace the old SKIP_PYNWB_COMPATIBILITY_TEST_FOR_TUTORIALS env var with SKIP_PYNWB_TESTS across tests and nwbtest.m, and update +tests/nwbtest.default.env.
Update CI workflow matrix keys and usage in prepare_release.yml, run_tests.yml, and configurations/matlab_release_matrix_strategy.yml to use the new key (matrix.skip-pynwb-tests) and wire the MATLAB setenv accordingly.
Move conditional installation of pynwb into the workflows (install pynwb only when skip-pynwb-tests == '0') and remove the direct git+ dependency from +tests/requirements.txt (update comment to reflect conditional installs).
Also add TestTags = {'UsesPython'} to PyNWBIOTest.
These changes centralize the CI control of pynwb installation and standardize the skip variable name.
…nore-nwbinspector-subject-checks-in-tutorialtests
checking if this class attribute trips up docs build
Move TestTags to methods blocks. Check if that fixes issue with sphinx build of docs
…nore-nwbinspector-subject-checks-in-tutorialtests
Install pynwb and nwbinspector from PyPI stable releases in the main test workflow so CI only fails due to matnwb regressions. Add a separate weekly workflow that tests against the dev branches to catch upstream incompatibilities early without blocking PRs. Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Added more details in comments Removed unused vars NWB_TEST_DEBUG, GITHUB_TOKEN Added PYNWB_REPO_DIR
Replace custom venv/download/GitHub API infrastructure with a simple
approach: read tutorial files from PYNWB_REPO_DIR env var pointing to
a pre-cloned pynwb repo, and run them against the system Python. The
CI workflows are now responsible for cloning the repo and setting the
env var. TestTags = {'UsesPython'} added so the tag selector in the
dev workflow picks up these tests, and SKIP_PYNWB_TESTS correctly
excludes them on older MATLAB releases.
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Covers prerequisites, running tests via nwbtest() and the MATLAB unit testing framework, Python dependency setup, environment variable configuration, and test authoring conventions. Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
actions/checkout requires path to be within the workspace directory. Use path: pynwb-repo (inside workspace) instead of ../pynwb-repo. Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
Suppress output
Suppress warning that happens due to wrong values in the file's version attribute in the source schemas for v 2.2.0 and 2.6.0
Added section about setting up dynamically loaded filters
Move test tags to methods block, as testtags in classdef breaks the sphinx/docs build
Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
resolution property of spike_times VectorData object was previously cleared when spike_times was added to the units object
Improve test diagnostic message
data -> datasetValue info -> datasetInfo fullpath -> datasetPath datadim -> dataDims class_id -> classId
bendichter
approved these changes
Apr 1, 2026
…ributes-of-typed-datasets-to-containing-type
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## main #797 +/- ##
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- Coverage 95.53% 95.49% -0.05%
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Files 192 192
Lines 7011 7097 +86
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…ributes-of-typed-datasets-to-containing-type
ehennestad
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ehennestad
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ehennestad
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Units.spike_times_resolution)
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Unittest failing due to unexpected behaviour in PyNWB: |
…sets-to-containing-type
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Summary
This PR exposes attributes that are added at the inclusion site of a typed dataset on the containing MATLAB class API using the
dataset_attributenaming pattern.Why
The NWB schema allows a typed dataset reused via
neurodata_type_incto gain additional attributes when it is included into another type. matnwb was not surfacing those specialized attributes consistently in the generated API. This showed up most clearly forUnits.spike_times.resolution.What changed
User impact
Users can access specialized included-dataset attributes directly from the containing type, e.g.
spike_times_resolution, without leaking those attributes onto unrelatedVectorDatainstances.Root cause
The generator handled untyped dataset attributes as dependent properties on the containing class, but typed reused datasets did not have an equivalent schema-driven path. A temporary hidden-property-based heuristic also turned out to be too tied to legacy
VectorDatapatching.Validation
2.9.0tests.system.UnitTimesIOTest.testRoundTripUnitsexposesspike_times_resolutionSimultaneousRecordingsTabledoes not exposerecordings_table