Fix numeric slicing for compound dtype datasets

[Copilot]

LindiH5pyDataset with compound dtypes raised TypeError on numeric slicing (e.g., dataset[:], dataset[0]), breaking PyNWB DynamicTable HTML rendering.

Changes

• Modified LindiH5pyDataset._get_item_for_zarr() to handle numeric indexing on compound dtypes
  • Converts zarr's object array representation (lists) to numpy structured arrays
  • Single element access returns numpy.void, multi-element returns structured array
  • Maintains existing field selection behavior (e.g., dataset['fieldname'])

Example

# Previously raised TypeError, now works
compound_dtype = np.dtype([('x', np.int32), ('y', np.float64)])
dataset = lindi_file.create_dataset('dset', data=[(1, 2.2), (3, 4.4)], dtype=compound_dtype)

dataset[:]      # [(1, 2.2) (3, 4.4)]  - now works
dataset[0]      # (1, 2.2)             - now works
dataset['x'][:] # [1 3]                - still works

Warning

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  • Triggering command: /usr/bin/python python -m pytest tests/test_lindi_h5py_file.py -v (dns block)

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>Error slicing LindiH5pyDataset with compound dtype</issue_title>
<issue_description>I get a TypeError: Compound dataset /processing/optotagging/optogenetic_stimulation/timeseries does not support selection with slice(None, None, None) when attempting to get the html representation of a DynamicTable with a compound dtype when using Lindi. Using the local NWB file or streaming with remfile causes no error.

I think an additional case may need to be added for indexing into a LindiH5pyDataset with compound dtype using None values.

Code to reproduce:

import pynwb
import lindi
import remfile
import h5py

# load from remote nwb file
file = remfile.File("https://dandiarchive.s3.amazonaws.com/blobs/d5f/747/d5f74779-e41e-43af-b32c-1310e996a623")
f = h5py.File(file, 'r')
nwbfile = pynwb.NWBHDF5IO(file=f, mode='r').read()

stim_table = nwbfile.processing["optotagging"]["optogenetic_stimulation"]
stim_table._repr_html_()  # this works

# load from lindi file (same file as above, though any ogen nwbfile in dandiset 000253 should reproduce)
f = lindi.LindiH5pyFile.from_lindi_file("https://lindi.neurosift.org/dandi/dandisets/000253/assets/b305ccec-fa84-445e-aea5-0126d6eff558/nwb.lindi.json")
nwbfile = pynwb.NWBHDF5IO(file=f, mode='r').read()

stim_table = nwbfile.processing["optotagging"]["optogenetic_stimulation"]
stim_table._repr_html_()  # this errors

Traceback:

  File "/Users/smprince/Documents/code/Hippie/scratch.py", line 16, in <module>
    stim_table._repr_html_()
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 1279, in _repr_html_
    html_repr += self.generate_html_repr()
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 1289, in generate_html_repr
    inside = f"{self[:min(nrows, len(self))].to_html()}"
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 1011, in __getitem__
    ret = self.get(key)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 1069, in get
    sel = self.__get_selection_as_dict(key, df, index, **kwargs)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 1107, in __get_selection_as_dict
    ret[name] = col.get(arg, df=df, index=index, **kwargs)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 211, in get
    data = self.target.get(slice(None),  **kwargs)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/pynwb/base.py", line 797, in get
    vals = super().get(key)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/common/table.py", line 61, in get
    return super().get(key)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/container.py", line 982, in get
    return self.data[args]
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/backends/hdf5/h5_utils.py", line 231, in __getitem__
    rows = copy(super().__getitem__(arg))
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/hdmf/query.py", line 20, in __getitem__
    return self.dataset[idx]
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/lindi/LindiH5pyFile/LindiH5pyDataset.py", line 180, in __getitem__
    return self._get_item_for_zarr(self._zarr_array, args)
  File "/Users/smprince/anaconda3/envs/hippie/lib/python3.10/site-packages/lindi/LindiH5pyFile/LindiH5pyDataset.py", line 217, in _get_item_for_zarr
    raise TypeError(
TypeError: Compound dataset /processing/optotagging/optogenetic_stimulation/timeseries does not support selection with slice(None, None, None)
```</issue_description>

## Comments on the Issue (you are @copilot in this section)

<comments>
</comments>

• Fixes Error slicing LindiH5pyDataset with compound dtype #112

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Codecov Report

❌ Patch coverage is 85.71429% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 81.43%. Comparing base (d2296a4) to head (1b04ba3).

Files with missing lines	Patch %	Lines
lindi/LindiH5pyFile/LindiH5pyDataset.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #116   +/-   ##
=======================================
  Coverage   81.43%   81.43%           
=======================================
  Files          30       30           
  Lines        2790     2790           
=======================================
  Hits         2272     2272           
  Misses        518      518           

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