[monsterlag]

Note

AI-generated, not reviewed by a human. This pull request was written by an AI coding agent and then checked by a separate AI review agent, which re-ran the tests described below. No human has reviewed the code. It is submitted by @monsterlag, who runs these agents. If that does not fit how you want to receive contributions, please feel free to close it.

Motivation

Fix #1223

Reading a file that was written from a shallow copy (NWBFile.copy()) of a file with a Units table fails. In the copy, the Units group is new but its columns (spike_times, waveform_mean, ...) are links back to the original file, so the builders that UnitsMap gets for them are LinkBuilders. UnitsMap.resolution_carg and UnitsMap._get_waveform_stat read .attributes directly from those builders and fail with:

AttributeError: 'LinkBuilder' object has no attribute 'attributes'

The script in #1223 still reproduces this on current dev (with HDMF 6.2.0).

This PR adds a small UnitsMap._get_column_builder helper that follows the link to the target builder when a column is a LinkBuilder, the same way TimeIntervalsMap.columns_carg already handles a linked timeseries column (#1863), and uses it in both places. resolution, waveform_rate, waveform_unit, and waveform_time_before_peak_in_ms are now read from the linked columns.

How to test the behavior?

tests/integration/hdf5/test_file_copy.py::TestFileCopy::test_copy_file_link_units_columns writes a file with a Units table that has resolution, waveform_rate, and waveform_unit set, writes a shallow copy of it, reads the copy, and checks those values and the spike times.

python -m pytest tests/integration/hdf5/test_file_copy.py

Without the fix, the new test fails with AttributeError: 'LinkBuilder' object has no attribute 'attributes' raised from src/pynwb/io/misc.py. With the fix:

• python -m pytest tests/integration/hdf5/test_file_copy.py tests/integration/hdf5/test_misc.py tests/unit/test_misc.py: 75 passed
• python -m pytest tests/unit tests/integration: 835 passed, 19 skipped
• the reproduction script from Cannot read file after nwbfile.copy() with Units #1223 now reads the copy and prints the spike times
• ruff check . and codespell: clean

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