move dicts to init

add random state to umap

update refs to get_model_emb_dims

embs_df with all model embeddings (#363)

clone embs_i to resolve memory leak in cls embs

update perturber stats to reflect cos sim and emb_extractor to suppress warnings for non-cls

update to enable cls emb

Update geneformer/emb_extractor.py (#350)

Add classifier module and examples

Update geneformer/emb_extractor.py (#303)

edit docstring codeblock highlighting

change doc formatting

add sphinx docs

Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp

Add option to output embs as tensor

Add memory-efficient method for computing emb summary statistics

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146)

Add error message for "gene" embedding extraction under development.

Rename heatmap legend to be correct label

Add function to extract and plot cell embeddings