Ryan Ly

[Bug]: DTR validation assumes table is set and raises warning aggressively

5

### What happened? See https://github.com/catalystneuro/ndx-photometry/issues/8 Using HDMF 3.7.0, when a table T1 containing a `DynamicTableRegion` R is added to another container T2, HDMF checks whether `DynamicTableRegion` R references a table...

### What happened? These lines convert each element of a list/tuple in a for loop. This could be more performant. Observed in Frank Lab conversions. https://github.com/hdmf-dev/hdmf/blob/dev/src/hdmf/build/objectmapper.py#L234-L236 ### Steps to Reproduce...

### What would you like to see added to HDMF? cc @oruebel as discussed in a zoom meeting https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/src/pynwb/__init__.py has many of the same functions as https://github.com/hdmf-dev/hdmf/blob/dev/src/hdmf/common/__init__.py but specific to...

### What would you like to see added to HDMF? `AbstractContainer.reset_parent` and `LabelledDict.pop` allow users to remove objects from a `MultiContainerInterface`, which is useful during modification and export of an...

Ref: https://github.com/hdmf-dev/hdmf/pull/492#pullrequestreview-547539302 > raise a warning in the spec object when a users tries to create an untyped object with a quantity other than ?, zero_or_one, or 1. There may...

Cached spec is sometimes not the same as the schema

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## Description Related to #501. If an extension data type, e.g., `data_type_def: FRETSeries` extends an existing type `data_type_inc: ImageSeries` that has attributes, then the extension spec that is cached within...

## Description Error: ``` hdmf.build.errors.ConstructError: (root/tvt_mask DatasetBuilder {'attributes': {'data_type': 'TrainValidationTestMask', 'description': 'tvt mask', 'elements': root/tvt_mask_elements DatasetBuilder {'attributes': {'data_type': 'VectorData', 'description': 'fixed set of elements referenced by tvt_mask', 'namespace': 'hdmf-experimental', 'object_id':...

## Description `tvt_mask` is a column of type `EnumData` ``` > table[:, 'tvt_mask'] array(['train', 'train'], dtype='

Overridden dataset dtype and shape are not passed from parent to child

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If a schema has two groups, e.g., `PatchClampSeries` and `CurrentClampSeries` defined as such: ```yaml groups: - neurodata_type_def: PatchClampSeries neurodata_type_inc: TimeSeries doc: ... datasets: - name: data dtype: numeric dims: -...

## Description The code in `DynamicTable.__build_columns` which is called by `DynamicTable.__init__` with `columns=` and by `DynamicTable.from_dataframe` with `columns=` does not support an integer index value in the column spec dictionary....