scverse / scverse/scirpy

Split IO into separate package

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#385 2 comments 0 reactions 0 assignees View on GitHub

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Dominant language
Python
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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_xxx and write_xxx functions in scirpy.io
  • AirrCell, to_airr_cells and from_airr_cells functions
  • to/from_dandelion (ideally dandelion adapts the scverse datastructure. Otherwise these functions should live in dandelion itself)

Maybe

  • merge_airr
  • index_chains
  • get.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

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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