scverse / scverse/spatialdata

CLI for modular creation/edit/concatenation of `SpatialData` objects

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Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

Related to https://github.com/scverse/spatialdata-io/issues/231 and https://github.com/scverse/spatialdata-io/pull/72.

We could enable a way to merge/edit spatialdata stored objects in a modular way without having to use Python code.

a possible example

The first part here assumes the two issues linked above are solved (note, this is a draft syntax, the final one may be different)

python -m spatialdata_io convert xenium path/to/raw/data path/to/output/zarr/store
python -m spatialdata_io convert tiff path/to/tiff/file path/to/output/zarr/store2 --name "my_image"

New proposed CLI (this is one of possible design to discuss):

python -m spatialdata write_element --from path/to/output/zarr/store2/images/my_image --to path/to/output/zarr/store

Equivalent syntax for concatenating SpatialData objects and for removing/renaming elements from an object.

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 reviewing the linked spatialdata-io issue and pull request, then inspect the existing python -m spatialdata_io convert entry point shown in the examples. Clarify the final command syntax and scope for writing, concatenating, removing, and renaming SpatialData elements. Done means the agreed modular operations work from the CLI without Python code.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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