Update geneformer/perturber_utils.py

fix overexpression with anchor genes and add perturbation batch with special tokens

add isp for perturb all with cls

define ncells for clearing memory

update isp for cls perturb set

Update geneformer/in_silico_perturber.py

update with isp changes to account for cls from prior PR

account for more than 1 gene being overexpressed

Update geneformer/perturber_utils.py

update to account for set of perturbed genes with aggregate_data

update to enable cls emb

update tokenizer to include eos token

Update geneformer/emb_extractor.py (#350)

Upload in_silico_perturber_stats.py (#313)

fix cell state gene embeddings bug (#345)

patch datasets save_to_disk

update kwargs for pretrainer

refer to token dictionary in self

Update for gene classification (#330)

Update with gene classifier, custom token dict, and str validate options (#329)

add option for hyperparameter tuning to cc.validate

correct typo

update examples for predict_eval and handle roc for 2 cell classes

Update readthedocs for classifier

Get the gene keys and gene list keys from the token dictionary instead of medians (#304)

Prevent ruff/isort on init

Add classifier module and examples

Update geneformer/emb_extractor.py (#303)

Fix typo (#301)

Add option for variable input_size and to add CLS/SEP Tokens (#299)

add load model for train and fix validate anchor gene error

Handle case of single gene del for isp modeling of gene embs

edit docstring format to highlight options

edit docstring codeblock highlighting

update type of null_dict_list in docstring

add readthedocs link to model card

update doc css

change doc formatting

update readthedocs.yaml

add readthedocs yaml and req

add sphinx docs

update dependencies, reinstate compatibility with python<3.9 with typing for List

Add option for modified batch size for loom tokenizer

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

Add option for modifying chunk size for anndata tokenizer

Add pre-commit config

tokenizer-uncropped-input_ids (#275)

fix: incorrect condition control flow (#261)

Update model card to emphasize need to install git-lfs and suggest https method

Add option to output embs as tensor