fix register_fields bug in tuner and add dependencies#55
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chelseabright96 wants to merge 1 commit intomainfrom
Open
fix register_fields bug in tuner and add dependencies#55chelseabright96 wants to merge 1 commit intomainfrom
chelseabright96 wants to merge 1 commit intomainfrom
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ArianAmani
requested changes
Jun 26, 2024
Comment on lines
+598
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| # getattr(experiment.model_cls, experiment.setup_method_name)( | ||
| # experiment.data, | ||
| # # **experiment.setup_method_args, | ||
| # ) | ||
| experiment.model_cls.setup_anndata(experiment.data, **setup_anndata_kwargs) | ||
|
|
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| 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) |
Collaborator
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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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Fixed register_fields bug in tuner:
Added dependencies and fixed compatibility issue with scipy