v0.1 release

[vitkl]

This release introduces changes listed below:

Big changes to code:

• Updates for compatibility with scvi-tools>=0.16.0
• Deleting pymc3 code
• Revised tutorial (including per cell type expression prediction
• Amortised NN using AutoGuideMessenger and option to use hierarchical guide

Changes to defaults:

• Changing our default detection_alpha because within-slide tech effects seem to be more prevalent than their absence (detection_alpha=20) and recommend to run both detection_alpha=20 and detection_alpha=200 in the tutorial.

Changes to docs

• Template issue: bug (version, are you following scvi-tools tutorial)
• Template issue: usage question (version, are you following scvi-tools tutorial, which technology was used to generate reference data / spatial data, how many cell types, how many batches, how many genes, how many spatial locations)
• Update tutorial to match scvi-tools tutorial
• Update tutorial according to this feedback Feedback on new user interface and tutorials (pyro & scvi-tools) #65 (comment)
• Delete pymc3 tutorials from documentation website (reorder the rest to make it easier to understand that pymc3 should not be used)
• Fix documentation website for various classes including user-facing Cell2location class (automodule->autoclass)
• Update readme - shorten what's possible
• Update readme - future work
• Update readme - add link to Nat Biotech paper
• Update acknowledgements
• Update copyright date
• Revise colab version of the notebook (less posterior samples)
• Add this line to tutorial: "The values are stored in adata.uns[f"mod_coloc_n_fact{n_fact}"] in a similar output format main cell2location results."

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This discussion was created from the release v0.1 release.