scverse / scverse/spatialdata-tutorials
Refactor Xenium + Visium paths and use better names
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- Dominant language
- Jupyter Notebook
- Stars
- 67
- Forks
- 26
- Avg merge
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- Merged PRs (30d)
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Description
- all the paths used in notebooks
00_xenium_and_visium.ipynb,01_xenium_and_visium.ipynband02_xenium_and_visium.ipynbshould be placed in aconfig.pyfile -
sandbox.zarrwas a poorly chosen name, rename it tomanual_annotations.zarr. I have already made a copy in the S3 bucket of that file (so that now bothsandbox.zarr.zipandmanual_annotations.zarr.zipare present), so one needs just to adjust the notebooks.
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First steps
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- Fork the repository and make your change on a branch.
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Research direction
Start with the paths in 00_xenium_and_visium.ipynb, 01_xenium_and_visium.ipynb, and 02_xenium_and_visium.ipynb, then review how config.py should hold them. Update the notebooks to use manual_annotations.zarr instead of sandbox.zarr and verify that all paths are centralized and the renamed S3 copy is referenced.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- documentation
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 45/100