Rm deprecated

[PierreBoyeau]

Removals:

Visualization utils

• Remove distance visualization method explore_stratifications. It wrapped scipy.cluster.hierarchy. It also relied on convert_pandas_to_colors, which converted a pandas dataframe of scalars/categoricals into a pandas of hex colors, used to visualize covariates along with heat maps.

Model architectures

• All encoders/decoders that were not attention-based.
• Module classes FactorizedEmbedding and MLP, which were not used in the main flavor of MrVI.

Distance matrices & other

• Normalized distance matrix option in compute_local_statistics and all components that were used for normalizing distance matrices.
• Remove all alternative outlier detections heuristics in get_outlier_cell_sample_pairs except ap.
• compute_cell_scores, which only seemed to be used to visualize some cells statistics (Geary C or nearest-neighbors-based).
• Components to compute Geary C, permutation-based p-values.

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TL;DR Removals in _model.py

• Any option to consider something else than attention-based encoders and decoders
• Any option to remove outliers other than with ball option
• _compute_local_baseline_dists
• compute_cell_scores
• explore_stratifications

[justjhong]

• There is a line of 167 of model.py for a hack to loading old models. We should remove this now.
• on line 907 in model.py we commented out the jax.jit decorator? why? lets make a decision.
• Nit: let's move the property original_donor_key to below the init function in model.py
• Nit: in module.py we have names like EncoderUZ2Attention, etc. Let's make them all the most basic version now like EncoderUZ.

[justjhong]

Looks good! thank you!