Use `AnnData` as a component rather than a superclass of `DeseqDataSet`
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Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Refactor
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- python
- Domain
- bioinformatics
Research direction
Start by locating the DeseqDataSet implementation and understanding how it currently inherits from AnnData. Review the existing serialization and loading behavior, especially the stated pickle and lazy-loading limitations. Done means the relationship is changed to composition while preserving the class’s existing behavior and supporting externally stored or lazily loaded AnnData.
Written by the indexing model from the issue text.
Description
This would offer more flexibility and robustness wrt future AnnData development.
E.g., as pointed out by @grst, his would also allow storing the anndata if the user has stored that elsewhere, and using lazy loading on the h5ad which is not possible using pickle.
Beside, composition is usually better practice than inheritance.
- Dominant language
- Python
- Stars
- 763
- Forks
- 90
- Avg merge
- 23m
- Merged PRs (30d)
- 11
Getting set up
- No Dockerfile or Docker Compose file
- Has a pull request template
- Read the contributing 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.
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