Ryan Ly

Write dimension labels to DatasetBuilder on build

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## Motivation Fix #1077 ## How to test the behavior? ``` pytest ``` ## Checklist - [x] Did you update `CHANGELOG.md` with your changes? - [x] Does the PR clearly...

Include `data_types` key in cached schema

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## Description See https://github.com/NeurodataWithoutBorders/matnwb/issues/351 If an extension includes a list of data types from another namespace, the cached extension does not specify that list of data types (and so includes...

Validating links across extensions can fail

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## Description An IndexSeries type links to an ImageSeries. If an extension defines a new type ExtImageSeries that extends ImageSeries, then it should be valid for the IndexSeries to link...

[Feature]: Support annotation of substrings with HERD or another system

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### What would you like to see added to HDMF? Use case 1: HED tags are strings that can contain multiple keys, separated by commas, in any order. A DynamicTable...

[Feature]: Refactor to reduce code complexity

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### What would you like to see added to HDMF? Some functions have high cyclomatic complexity and are therefore more challenging to understand and maintain. See https://github.com/NeurodataWithoutBorders/pynwb/issues/191 We currently use...

[Bug]: Compound dtype attributes are not supported

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### What happened? Compound dtype attributes are not supported, but the schema language says they should be: https://hdmf-schema-language.readthedocs.io/en/latest/description.html#attribute-specification-keys ### Steps to Reproduce ```python NWBAttributeSpec( name="insertion_position_in_mm", doc=("Stereotactic coordinates (AP, ML, DV)...

[Bug]: Custom class generator does not account for fields refined from parent type

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### What happened? In PyNWB, the `TimeSeries` spec has a dataset spec with name "data", dtype "numeric", many possible shapes, and a docstring. If an extension type `ExtracellularSeries` extends `TimeSeries`...

[Bug]: Support writing multidimensional string datasets and attributes

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### What happened? In trying to resolve https://github.com/NeurodataWithoutBorders/pynwb/pull/1886/ in HDMF, I discovered that on build, a multidimensional list or array that maps to a multidimensional dataset/attribute spec is converted to...

[Bug]: Tests with optional requirements failing

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### What happened? See https://github.com/hdmf-dev/hdmf/actions/runs/8415368500 @mavaylon1 can you look into this? Seems to be an issue with pydantic versioning from updating pydantic in the last release ### Steps to Reproduce...

Support modifications of a read file in an external overlay

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In neurophysiology, metadata is often not static. Sometimes, the experiment description, related publications, or data annotations need to be changed after the file is written. Currently, users can open the...