Spin off read/write into it's own package?
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- Dominant language
- Python
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Description
As we are refactoring scvi, I'm wondering what the utility would be to spin off the i/o part of scanpy into it's own lightweight package that's more general for reading single cell pipeline outputs into anndata. For example, we'd like to use the scanpy read from 10x/visium functions, but don't necessarily want to have scanpy be a full requirement. It's also a bit confusing why something like read_umi_tools is in anndata but not read_10x_h5. The same goes for loom to some extent. I could imagine either moving such functionality to anndata or a standalone package that could be expanded to include support for other technologies like scATAC-seq.
This overall could be a big benefit to methods developers who would like to build on anndata.
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Research direction
Review scanpy’s read_10x_h5, Visium, read_umi_tools, and loom functionality alongside anndata’s existing readers. Clarify whether the goal is an anndata move or a standalone package, define supported single-cell formats and dependency boundaries, and document a concrete package scope before implementation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100