CLI for modular creation/edit/concatenation of `SpatialData` objects
Nobody has claimed this yet.
- 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
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 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