Vitessce python on remote jupyter servers do not work

vitessce / vitessce-python

Python API and Jupyter widget for Vitessce

https://python-docs.vitessce.io

MIT License

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Vitessce python on remote jupyter servers do not work #358

Closed edwin5588 closed 2 months ago

edwin5588 commented 3 months ago

Vitessce visualizer on remote servers do not work, it outputs a semi-functional visualization with 0 cells detected. It seems to not be able to find the files hosted on the remote Jupyter server
The bug can be replicated using vitessce's Binder example: https://mybinder.org/v2/gh/vitessce/vitessce-python/main?filepath=docs/notebooks/widget_pbmc.ipynb
If you execute all cells until the end, you'll see the visualizer pop out but with 0 cells detected.

edwin5588 commented 2 months ago

@keller-mark Just tagging one of the devs to hopefully get some eyes on this issue. Thanks!

keller-mark commented 2 months ago

Hi @edwin5588 it seems like binder may have updated such that the proxy=True no longer works to allow remote access to the served files (https://python-docs.vitessce.io/data_options.html for background).

As a workaround, I have made a pull request at https://github.com/vitessce/vitessce-python/pull/363 that uses the adata_store functionality to allow access to AnnData objects via Zarr bypassing the need for a web server, allowing it to run in Binder.

edwin5588 commented 2 months ago

Thanks! I'll try it out. Is this going to be merged into main?