removed redundat functions in code base

scverse · Oct 13, 2024 · f94f7fa · f94f7fa
1 parent 47376ca
commit f94f7fa
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Showing 3 changed files with 4 additions and 31 deletions.
diff --git a/src/scvi/model/_scvi.py b/src/scvi/model/_scvi.py
@@ -7,7 +7,7 @@
 
 import scvi
 from scvi import REGISTRY_KEYS
-from scvi.data import AnnDataManager, _constants
+from scvi.data import AnnDataManager
 from scvi.data._constants import _ADATA_MINIFY_TYPE_UNS_KEY, ADATA_MINIFY_TYPE
 from scvi.data._utils import _get_adata_minify_type
 from scvi.data.fields import (
@@ -23,7 +23,7 @@
 from scvi.model.base import EmbeddingMixin, UnsupervisedTrainingMixin
 from scvi.model.utils import get_minified_adata_scrna
 from scvi.module import VAE
-from scvi.utils import attrdict, setup_anndata_dsp
+from scvi.utils import setup_anndata_dsp
 
 from .base import ArchesMixin, BaseMinifiedModeModelClass, RNASeqMixin, VAEMixin
 
@@ -229,19 +229,11 @@ def setup_anndata(
         adata_manager.register_fields(adata, **kwargs)
         cls.register_manager(adata_manager)
 
-    @staticmethod
-    def _get_summary_stats_from_registry(registry: dict) -> attrdict:
-        summary_stats = {}
-        for field_registry in registry[_constants._FIELD_REGISTRIES_KEY].values():
-            field_summary_stats = field_registry[_constants._SUMMARY_STATS_KEY]
-            summary_stats.update(field_summary_stats)
-        return attrdict(summary_stats)
-
     @classmethod
     @setup_anndata_dsp.dedent
     def setup_datamodule(
         cls,
-        datamodule,  # TODO: what to put here?
+        datamodule,
         source_registry=None,
         layer: str | None = None,
         batch_key: list[str] | None = None,
@@ -263,7 +255,6 @@ def setup_datamodule(
         %(param_cat_cov_keys)s
         %(param_cont_cov_keys)s
         """
-        # TODO: from adata (czi)?
         if datamodule.__class__.__name__ == "CensusSCVIDataModule":
             # CZI
             categorical_mapping = datamodule.datapipe.obs_encoders["batch"].classes_
@@ -300,7 +291,7 @@ def setup_datamodule(
                     "state_registry": {
                         "n_obs": datamodule.n_obs,
                         "n_vars": datamodule.n_vars,
-                        "column_names": [str(i) for i in column_names],  # TODO: from adata (czi)?
+                        "column_names": [str(i) for i in column_names],
                     },
                     "summary_stats": {"n_vars": datamodule.n_vars, "n_cells": datamodule.n_obs},
                 },

diff --git a/src/scvi/model/base/_base_model.py b/src/scvi/model/base/_base_model.py
@@ -299,23 +299,6 @@ def data_registry(self, registry_key: str) -> np.ndarray | pd.DataFrame:
         else:
             return self._adata_manager.get_from_registry(registry_key)
 
-    # def get_from_registry(self, registry_key: str) -> np.ndarray | pd.DataFrame:
-    #     """Returns the object in AnnData associated with the key in the data registry.
-    #
-    #     Parameters
-    #     ----------
-    #     registry_key
-    #         key of object to get from ``self.data_registry``
-    #
-    #     Returns
-    #     -------
-    #     The requested data.
-    #     """
-    #     if not self.adata:
-    #         raise ValueError("self.adata is None. Please registry AnnData object.")
-    #     else:
-    #         return self._adata_manager.get_from_registry(registry_key)
-
     def deregister_manager(self, adata: AnnData | None = None):
         """Deregisters the :class:`~scvi.data.AnnDataManager` instance associated with `adata`.
 

diff --git a/tests/dataloaders/test_custom_dataloader.py b/tests/dataloaders/test_custom_dataloader.py
@@ -81,7 +81,6 @@ def test_czi_custom_dataloader(save_path):
     model = scvi.model.SCVI(adata_orig, n_latent=10)
     model.train(max_epochs=1)
 
-    # TODO: do we need to apply those functions to any census model as is?
     dataloader = model._make_data_loader(adata_orig)
     _ = model.get_elbo(dataloader=dataloader)
     _ = model.get_marginal_ll(dataloader=dataloader)