AllenInstitute / AllenInstitute/spatial_compare
dependency diet and upgrades
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- Dominant language
- Jupyter Notebook
- Stars
- 7
- Forks
- 8
- Avg merge
- 2h 24m
- Merged PRs (30d)
- 1
Description
we have a few heavy dependencies that have minimal usage:
plotlyused for the sankey diagram in segmentation comparisonseabornused for regplot and boxplot, both of which can be (neatly?) implemented with matplotlib. unfortunately it's also a dependency in ...scanpywhich we use for de novo clustering. we could makescanpyoptional and delayed import only for de novo clustering. this would also clear outstatsmodelsjupyterthis is sort of a matter of taste, but it's nicer to have it as an extra duringpip install.
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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
Review the dependency declarations and the segmentation-comparison, plotting, and de novo-clustering entry points mentioned in the issue, including how Jupyter is installed. Confirm which dependencies can be removed or made optional while preserving the Sankey, regplot, boxplot, and clustering workflows.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter, matplotlib, plotly
- Domain
- data, tooling
- Issue type
- Refactor
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100