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Add time intervals - #325
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Co-authored-by: oruebel <10999845+oruebel@users.noreply.github.com>
- Add SubjectMetadata struct to NWBFile.hpp with optional fields for
species, sex, age, description, subjectId, genotype, strain, weight
- Add subject parameter to NWBFile::initialize() defaulting to an empty
SubjectMetadata{} (creates a Subject group by default); pass
std::nullopt to explicitly opt out
- Implement subject group creation in createFileStructure() with
neurodata_type/namespace attributes for NWB compliance
- Update testNWBFile.cpp to expect Subject in findOwnedTypes results
- Update workflow example to demonstrate Subject usage with actual data
- Remove --ignore=check_subject_exists from tests.yml and
upgrade_schema.yml CI workflows
Co-authored-by: oruebel <10999845+oruebel@users.noreply.github.com>
…thub.com/NeurodataWithoutBorders/aqnwb into copilot/make-subject-required-by-default
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
…s for root groups, e.g, /events and /intervals
…for efficient runtime check for data type matches to safeguard VectorData::appendData and appendBuffer
…d isCompatibleVector()
…e vector for empty cells
typed data facades transient, and document the revised factory behavior.
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Thanks for the helpful comments @rly . I've addressed all remaining threads here. |
rly
approved these changes
Sep 2, 2026
…ject-required-by-default Make Subject required by default in NWBFile::initialize()
This was referenced Sep 3, 2026
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Fix #323
Fix #324
src/nwb/epoch/TimeIntervalfor annotating time intervalssrc/nwb/hdmf/table/VectorIndexfor storing index columnsVectorData::appendDataandVectorIndex::appendDatato simplify appending values to columnsVectorData.hppto the sourceVectorData.cppfileCellValueandRowDatasto `Types to avoid circular dependencyCellValueto support both scalar and vector data for support of ragged array columnsDynamicTable::addRowsetc to support ragged array column writeDynamicTable::toStringto support converting rows to a string representationDynamicTable::getNumberOfRowsto support retrieving the number of rows in aDynamicTable.VectorIndexTimeintervalsDynamicTable::readRowsto support reading of full rows. This also movedCellValueandRowDatatoTypes.hpp. It also addedVectorData::readCellValuesandVectorIndex::readTargetCellValues.intervalstables, e.g.,trials,invalid_time,epochsTimeIntervalstype indocs/pages/userdocs/time_intervals.doxand corresponding newtests/examples/testTimeIntervalsWorkflowExamples.cpplint.ymlworkflow to installclang-formatviapipxto ensure use of the latest version ofclang-formatTypes.hppto use anamespaceinstead ofclassto group types. For more users this change should not require any code changes since the syntax for accessing the types is the same (e.g.,AQNWB::Types::Status), but for users who were usingusingdeclarations to import the type can now useusing namespace AQNWB::Types.Additional changes from #328
Fix #327.
RegisteredType::createto retrieve objects from theRecordingObjectscache of the I/O if they already exist, rather than creating a new instance. This ensures that multiple requests for the same object path return the exact same object instance.BaseRecordingDatacache fromRegisteredTypetoBaseIO, which also ensures that there is only one BaseRecordingObject per Dataset path+io. This makes the caching consistent between objects and datasets by moving all the caches to the I/O and provides stronger consistency in management of objects for users.VectorIndex::setTargetColumnfrom Add time intervals #325. This logic was problematic as it: i) exposed internal logic to avoid duplicate objects to the user and ii) requiredDynamicTableto updated caches inVectorIndex. By centralizing all the object caches this is no longer necessary.Future tasks