Apple Silicon: Accelerate or openBLAS for Numpy
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- Dominant language
- Python
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Description
What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
Please describe your wishes
After naively updated my apple OS to tahoe, my UMAPs and leiden clustering result in slightly different outputs. I learned from chatGPT that this is probably due to an update of the accelerate BLAS that my Numpy accesses. I could use OpenBLAS which would be independent from Apple updates, but performs even more distinct.
What is the general recommendation for scanpy usage?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue names no files, tests, or entry points. Start by determining whether Scanpy or NumPy controls the Apple Silicon BLAS choice and what recommendation is expected for UMAP and Leiden results; done would require a clearly scoped recommendation or change.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- bioinformatics, performance
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100