Try optimizing remap with Cython
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
The next release of Kive will support a docker image for each method, so try converting some of remap's hot spots to compiled code with Cython. Remap is currently the slowest method, so it's a good place to start.
Contributor guide
No contributing guide indexed for this repository
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
Begin with remap, identified as the slowest method, and profile its hot spots before reviewing the Cython documentation. Done means the selected hot spots have been converted to Cython and remap shows a measurable speed improvement.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, performance
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100