scverse / scverse/spatialdata-tutorials
Check reproducibility of Steinbock and NanoString notebooks on Windows
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- Dominant language
- Jupyter Notebook
- Stars
- 67
- Forks
- 26
- Avg merge
- 4m
- Merged PRs (30d)
- 1
Description
As reported here for Steinbock (https://github.com/scverse/spatialdata-io/issues/129) and here for NanoString (https://github.com/scverse/spatialdata/issues/637), it looks like that / in paths (I guess inside one of the AnnData objects), create reproducibility issues on Windows machine.
Contributor guide
No contributing guide indexed for this repository
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 running the Steinbock and NanoString notebooks on Windows and review the linked spatialdata-io and spatialdata issues for the reported path behavior. Compare the resulting AnnData paths and notebook outputs with the expected results; done means the reproducibility problem is confirmed and the affected notebook steps or paths are identified.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- operating-systems, testing
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100