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[Documentation]: Invalid(?) dtype in general/extensions.py tutorial #1952

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ehennestad opened this issue Aug 29, 2024 · 2 comments
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category: bug errors in the code or code behavior priority: low alternative solution already working and/or relevant to only specific user(s) topic: docs issues related to documentation

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@ehennestad
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What would you like changed or added to the documentation and why?

in the general/extensions.py tutorial, one of the dtype values is set to uint
https://github.com/NeurodataWithoutBorders/pynwb/blob/2d00afe30b3116c714e53a39522488e97c9160c5/docs/gallery/general/extensions.py#L404C13-L404C18

However, I don't find 'uint' as a valid type in the documentation for the schema language:
https://schema-language.readthedocs.io/en/latest/description.html#dtype

Do you have any interest in helping write or edit the documentation?

No.

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@oruebel
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oruebel commented Aug 29, 2024

Thanks for reporting this issue. It looks like in the HDF5 backend, uint is being mapped to uint32 (similar to how int is mapped to int32) here:

https://github.com/hdmf-dev/hdmf/blob/d378dec53c3be69cbd03695960e2478cd1f1f455/src/hdmf/backends/hdf5/h5tools.py#L904

However, looking at hdmf-zarr it seems it is missing the mapping for uint:

https://github.com/hdmf-dev/hdmf-zarr/blob/82c993c5177c31480210c7d0982700760dea8cbf/src/hdmf_zarr/backend.py#L1135-L1164

I think there are two options:

  1. Update the schema language docs to include uint as uint32 and also update hdfm-zarr to define it
  2. Change the extension tutorial to using uint32 instead of uint
  3. Do both 1 and 2

Personally, I'm leaning towards option 1 because it seems more consistent with how int is defined. Option 3 is fine too. @rly toughts?

@oruebel oruebel added category: bug errors in the code or code behavior topic: docs issues related to documentation priority: low alternative solution already working and/or relevant to only specific user(s) labels Aug 29, 2024
@bendichter
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@oruebel MatNWB does not know how to handle "uint", so this is blocking any extensions that use that data type to be readable in MatNWB

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category: bug errors in the code or code behavior priority: low alternative solution already working and/or relevant to only specific user(s) topic: docs issues related to documentation
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