Integrate into scanpy and anndata

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
python
Domain
bioinformatics

Research direction

The issue names no files or tests. Start by locating asarray, sum, and axis_sum, then compare their behavior with the stated scanpy and anndata integration differences; done means the listed compatibility gaps are addressed and verified.

Written by the indexing model from the issue text.

Description

Current differences:

  • asarray uses to_dense internally for cs{cr}_{matrix,array}
  • asarray supports zarr (#2)
  • asarray operates on a protocol OutOfCoreDataset defined by a to_memory method instead of the concrete class BaseCompressedSparseDataset (#4)

sum/axis_sum

  • returns np.ndarrays even when passing in a cs{rc}_matrix
Dominant language
Python
Stars
15
Forks
5
Avg merge
10h 33m
Merged PRs (30d)
9

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