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Separate reading/writing keys in HDF5AnnData #392

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Separate reading/writing keys in HDF5AnnData #392

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@lazappi lazappi commented Dec 3, 2025

Related to: Fixes #334

Description

Allow reading/writing of keys in HDF5AnnData separately from the whole element (i.e. read the names of a list without reading the whole list):

  • Add helper functions to read keys from H5AD files
  • Add helper functions to write a data frame index to a H5AD file
  • Use new helpers in HDF5AnnData
  • Add new *_keys() methods to HDF5AnnData

Checklist

Before review

  • Update and regenerate man pages
  • Add/update tests
  • Add/update examples in vignettes
  • Pass CI checks

Before merge

  • Update NEWS
  • Bump devel version

@lazappi lazappi requested review from LouiseDck and rcannood December 3, 2025 15:20
@lazappi
Merge remote-tracking branch 'origin/devel' into feature/issue-334/im…
9f72d79 
…prove-keys

* origin/devel:
  Update GitHub actions based on those used by {rhdf5} (#378)
@lazappi lazappi marked this pull request as ready for review December 4, 2025 09:23
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@rcannood rcannood Awaiting requested review from rcannood

@LouiseDck LouiseDck Awaiting requested review from LouiseDck

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Successfully merging this pull request may close these issues.

Avoid reading/writing all of obs/var when only names are needed

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