Split IO into separate package
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 265
- Forks
- 50
- Avg merge
- 9d 9h
- Merged PRs (30d)
- 4
Description
In the scverse core team the consensus was reached that IO should not be part of the analysis packages (e.g. scanpy, scirpy, muon), but rather in an independent package with minimal dependencies and have the analysis packages depend on it. The hope is that this leads to a wider adoption of scverse datastructures, since the "dependency cost" of depending on a lightweight IO packages is lower than depending on an entire framework.
This issue is to track the goal of creating such a package for scirpy.
Name (?)
A couple of ideas
- scirpy-io
- scverse-airr
- airr-io
Scope
- All
read_xxxandwrite_xxxfunctions inscirpy.io AirrCell,to_airr_cellsandfrom_airr_cellsfunctions(ideally dandelion adapts the scverse datastructure. Otherwise these functions should live in dandelion itself)to/from_dandelion
Maybe
merge_airrindex_chainsget.airr
The latter two go beyond just storing AIRR data as an awkward array, but implement the scirpy receptor model. But they are likely useful for some other packages. But then again if a method needs this, they could just depend on the full scirpy.
In case of doubt, err on the side of including less in the package, as it could be added later if required.
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 by inventorying the functions listed under the scope in scirpy.io, including the read_xxx and write_xxx functions, AirrCell, and the conversion helpers. Review the optional merge_airr, index_chains, and get.airr items separately, then determine the smallest independent package boundary and candidate name. Done means the scoped IO functionality is separated with minimal dependencies and scirpy can depend on it.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100