scverse / scverse/scanpy

Performance: Investigate `pp.scale` with sparse matrices

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Area – Performance 🐌
Dominant language
Python
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Merged PRs (30d)
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Description

With the new numba kernel for sparse scaling, we need to figure out how and when the numba code becomes faster than the array code. This might lead to numba completly replaceing the array operations for sparse matrices.

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at the pp.scale implementation and inspect the new numba kernel for sparse scaling alongside the existing array operations. Benchmark both paths across representative sparse-matrix sizes and identify when numba becomes faster. Done means documenting the performance crossover and whether numba should replace the array operations.

Written by the indexing model from the issue text.

Assessment

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

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