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Fixed register_fields bug in tuner:

  • fixed error where registry was being transferred without existing source registry
    Added dependencies and fixed compatibility issue with scipy

Comment on lines +598 to 610
# getattr(experiment.model_cls, experiment.setup_method_name)(
# experiment.data,
# # **experiment.setup_method_args,
# )
experiment.model_cls.setup_anndata(experiment.data, **setup_anndata_kwargs)

model = experiment.model_cls(experiment.data, **model_args)
model.train(max_epochs=train_args.pop("max_epochs",2000),
use_gpu=train_args.pop("use_gpu",True),
early_stopping_patience=train_args.pop("early_stopping_patience",10),
check_val_every_n_epoch=train_args.pop("check_val_every_n_epoch",5),
plan_kwargs=plan_kwargs,
**train_args)
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Can we have this section similar to the part above it?
Eventually, something like this I think:

Suggested change
# getattr(experiment.model_cls, experiment.setup_method_name)(
# experiment.data,
# # **experiment.setup_method_args,
# )
experiment.model_cls.setup_anndata(experiment.data, **setup_anndata_kwargs)
model = experiment.model_cls(experiment.data, **model_args)
model.train(max_epochs=train_args.pop("max_epochs",2000),
use_gpu=train_args.pop("use_gpu",True),
early_stopping_patience=train_args.pop("early_stopping_patience",10),
check_val_every_n_epoch=train_args.pop("check_val_every_n_epoch",5),
plan_kwargs=plan_kwargs,
**train_args)
adata = experiment.data.copy()
if sub_sample is not None:
sc.pp.subsample(adata, fraction=sub_sample)
experiment.model_cls.setup_anndata(adata, **setup_anndata_kwargs)
model = experiment.model_cls(adata, **model_args)
model.train(plan_kwargs=plan_kwargs, **train_args)
del adata
import gc
gc.collect()

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3 participants