scverse / scverse/annbatch

Improve the shuffling/preprocessing code

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Dominant language
Python
Stars
68
Forks
6
Avg merge
7h 24m
Merged PRs (30d)
6

Description

The current shuffling code is very slow, reportedly. The first step should be profiling the code especially in the wake of https://github.com/scverse/anndata/pull/2005. Other things should be considered in light of profiling

Contributor guide

Open the contributing guide

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 profiling the shuffling and preprocessing code, especially in light of scverse/anndata pull request 2005. Compare the listed options, including zarrs-python for writing, a non-dask X loader, and the tiny-shard approach in arrayloaders/io/store_creation.py. Done means the bottleneck is identified and a measured direction is established.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-engineering, performance
Issue type
Refactor
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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