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Allow Codec for compression for use with LINDI #1162

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@magland magland commented Aug 7, 2024

Motivation

While hdf5 does not allow numcodecs.Codec for compression, lindi does. Right now hdmf does type checking for the compression parameter and raises an exception if the type is not in (str, bool, int). This PR simply allows the Codec type to be passed through so that it can be used with lindi.

How to test the behavior?

Here's an example that applies a custom compressor to filtered ephys data

https://github.com/NeurodataWithoutBorders/lindi/blob/lindi-tar/examples/DANDI/preprocess_ephys.py

You need to install the lindi-tar branch of lindi and pip install qfc. See https://github.com/magland/qfc

@oruebel @rly

Checklist

  • Did you update CHANGELOG.md with your changes?
  • Does the PR clearly describe the problem and the solution?
  • Have you reviewed our Contributing Guide?
  • Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

@rly rly self-requested a review August 8, 2024 20:20
@rly rly added category: enhancement improvements of code or code behavior category: proposal proposed enhancements or new features and removed category: enhancement improvements of code or code behavior labels Aug 15, 2024
@magland magland closed this by deleting the head repository Sep 15, 2024
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magland commented Sep 18, 2024

Oops I accidentally deleted my fork and that closed this PR. I created a new fork and I am going to open another PR. Sorry about that.

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