scverse / scverse/spatialdata

Problems with `chunks`

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Dominant language
Python
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Merged PRs (30d)
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Description

It seems that:

  • the parameter chunks is ignored by SpatialData.write()
  • the parameter chunks is handled by the parser, but not fully correctly (it's not applied to some axis, maybe it's applied to the wrong axes order)

Contributor guide

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the chunks parameter through SpatialData.write() and the parser, checking how it is propagated across axes. Reproduce the reported behavior and compare the requested chunks with the resulting data layout. Done means chunks is applied to every intended axis in the correct order, with tests covering both reported cases.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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