scverse / scverse/napari-spatialdata
Extend CLI
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- Dominant language
- Python
- Stars
- 90
- Forks
- 25
- Avg merge
- 22m
- Merged PRs (30d)
- 1
Description
The napari CLI has support for loading one or more plugins. Supporting this fully is beneficial as this is what new users with napari experience will expect.
When combining CLI options, we would expect being able to open a dataset and also open the View or Scatter plugin. The following now opens two separate windows instead of one, because a new viewer instead of the current one is used.
napari -w napari-spatialdata View --plugin napari-spatialdata '/Users/benjaminr/Documents/GitHub/napari-spatialdata/data/cosmx/data.zarr'
- bug for
-wand--plugin
Right now, python -m napari-spatialdata view <path> and napari --plugin napari-spatialdata <path> have the same behavior. But the first case could in the future support more advanced behavior (combining multiple datasets, filtering...).
- Support CLI for multiple datasets
- Support filtering SpatialData elements
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 tracing the CLI entry points used by python -m napari-spatialdata view <path> and napari --plugin napari-spatialdata <path>. Reproduce the combined -w and --plugin command, then compare it with the multiple-dataset behavior. Done means the dataset and requested View or Scatter plugin open in one window, with filtering treated as a separate scope.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100