Patching scanpy for xeus
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- Dominant language
- Python
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Description
What kind of feature would you like to request?
Other?
Please describe your wishes
Hi! I tried running scanpy using JupyterLite for teaching purposes. However, it fails, as only noarch packages are currently supported in xeus. From my error log it seems the only non-noarch dependency is h5py, which is not really needed for teaching.
Would it be possible to make h5py an optional dependency on conda-forge somehow? It would be really helpful for many students to be able to try scanpy without the need to install anything locally.
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 Scanpy's packaging metadata and dependency declarations, then check the xeus and JupyterLite preinstalled-package documentation mentioned in the issue. Reproduce installation without h5py and determine whether Scanpy still runs for the teaching use case; done means a noarch-compatible install works while h5py-dependent functionality remains appropriately handled.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter, python
- Domain
- bioinformatics, build-system
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100