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vitessce / vitessce-python

Python API and Jupyter widget for Vitessce
https://python-docs.vitessce.io
MIT License
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(chore): Clean up `AnnDataWrapper` API #341

Open ilan-gold opened 6 months ago

ilan-gold commented 6 months ago

Open to other options here, but basically I did two things.

  1. adata_XXX -> base_XXX since the semantics are a bit more general and I think adata is redundant anyway
  2. path -> elem since I think elem is a bit nicer and path can refer to a sub-URL which is kind of a path, but also not really.

This is definitely a breaking change, so I'm going to try to finish up other PRs that are also breaking at the same time, like our python support.

keller-mark commented 6 months ago

While I agree it may not be the nicest API, without more context/motivation, I don't think there is enough to justify this breaking change, as it will break existing docs/reference materials, Vitessce config generation code in portal-visualization package, and notebooks that are being used in HuBMAP workspaces that rely on the VitessceConfig.to_python function

ilan-gold commented 6 months ago

@keller-mark This is motivated by https://github.com/vitessce/vitessce-python/pull/333. We could just keep the non-outward-facing changes so that when the SpatialDataWrapper calls "private" attributes, they have better names.