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Add support for nullable-string-array - #480

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feature/nullable-string-array
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Add support for nullable-string-array#480
lazappi wants to merge 15 commits into
develfrom
feature/nullable-string-array

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@lazappi

@lazappi lazappi commented Jul 15, 2026 •
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Description

Add support for the nullable-string-array encoding, see https://anndata.scverse.org/en/stable/fileformat-prose.html#nullable-string-specifications-v0-1-0.

Fixes #463

  • Read H5AD
  • Write H5AD
  • Read Zarr
  • Write Zarr

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 commented Jul 15, 2026

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There are some open implementation questions:

  • Do we always write nullable string arrays, or have an option to write the old format?
  • How de we handle the na-value attribute?

@github-actions

github-actions Bot commented Jul 15, 2026 •
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🐰 Bencher Report

ProjectanndataR
Branchfeature/nullable-string-array
Testbedubuntu-latest

⚠️ WARNING: Truncated view!

The full continuous benchmarking report exceeds the maximum length allowed on this platform.

🚨 9 Alerts

🐰 View full continuous benchmarking report in Bencher

@lazappi

lazappi commented Jul 22, 2026

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@rcannood FYI I have done some more work on this, will try to finish it off soon. Just so you don't spend time on it.

lazappi added 8 commits July 23, 2026 08:29
@lazappi
Add write_h5ad_nullable_string()
c05e120
@lazappi
Add write_zarr_nullable_string()
b552ae9
@lazappi
Merge remote-tracking branch 'origin/devel' into feature/nullable-str…
60cfa66 
…ing-array

* origin/devel:
  Update NEWS (#488)
  Simplify roxygen docs (#479)
  Require Python `anndata<0.13.0` in tests (#481)
  Fix `create_zarr()` so that Zarr stores can be created at relative paths (#478)
  Fix conditional expression (#487)
  Update multiple actions simultaneously (#486)
@lazappi
Merge remote-tracking branch 'origin/feature/nullable-string-array' i…
69baffd 
…nto feature/nullable-string-array

* origin/feature/nullable-string-array:
@lazappi
Update example files
8d33351
@lazappi
Update example data files
85ecce2
@lazappi
Add tests for nullable strings
531de38
@lazappi
Merge remote-tracking branch 'origin/devel' into feature/nullable-str…
ac534da 
…ing-array

* origin/devel:
  Bump bencherdev/bencher from 0.6.10 to 0.6.11 (#491)
  Write support for anndata-zarr v3 (#455)
@lazappi
lazappi marked this pull request as ready for review July 30, 2026 17:32
@lazappi
lazappi requested a review from rcannood July 30, 2026 17:32
rcannood
rcannood requested changes Jul 30, 2026
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@rcannood rcannood left a comment •
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Great pr!

Things left to do (assuming that CI tests succeed)

  • CI seems to be failing
  • Add entry to the changelog
  • Bump the version number
  • Run the linter once
  • Create an issue in dummy_anndata that nullable arrays need to be added?

@lazappi
lazappi requested a review from rcannood August 3, 2026 12:50
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Add support for nullable string arrays

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@lazappi @rcannood