scverse / scverse/spatialdata-io
Use `scanpy` for reading matrixes
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 103
- Forks
- 65
- Avg merge
- 1h 8m
- Merged PRs (30d)
- 3
Description
We currently have a the custom implementation for reading matrices (copied from scanpy) in https://github.com/scverse/spatialdata-io/blob/main/src/spatialdata_io/readers/_utils/_read_10x_h5.py.
I would remove that code and use directly scanpy, which is already a dependency. I think initially the code was copied to minimize the number of dependencies (@giovp what this the case?) but then we chose to add scanpy anyway.
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
Start with src/spatialdata_io/readers/_utils/_read_10x_h5.py and compare its custom matrix-reading implementation with the corresponding scanpy functionality. Replace the copied implementation with direct use of the existing scanpy dependency; done means the custom code is removed and matrix reading still works as before.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Refactor
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 55/100