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OmicsML · Feb 4, 2024 · 8ea881b · 8ea881b
1 parent b1a7034
commit 8ea881b
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Showing 7 changed files with 78 additions and 17 deletions.
diff --git a/dance/modules/single_modality/imputation/deepimpute.py b/dance/modules/single_modality/imputation/deepimpute.py
@@ -25,8 +25,16 @@
 from torch.utils.data import DataLoader, TensorDataset
 
 from dance.modules.base import BaseRegressionMethod
-from dance.transforms import (AnnDataTransform, CellwiseMaskData, Compose, FilterCellsScanpy, FilterGenesScanpy,
-                              GeneHoldout, SaveRaw, SetConfig)
+from dance.transforms import (
+    AnnDataTransform,
+    CellwiseMaskData,
+    Compose,
+    FilterCellsScanpy,
+    FilterGenesScanpy,
+    GeneHoldout,
+    SaveRaw,
+    SetConfig,
+)
 from dance.typing import Any, List, LogLevel, Optional, Tuple
 
 

diff --git a/dance/modules/single_modality/imputation/graphsci.py b/dance/modules/single_modality/imputation/graphsci.py
@@ -19,8 +19,15 @@
 import torch.nn.functional as F
 
 from dance.modules.base import BaseRegressionMethod
-from dance.transforms import (AnnDataTransform, CellwiseMaskData, Compose, FilterCellsScanpy, FilterGenesScanpy,
-                              SaveRaw, SetConfig)
+from dance.transforms import (
+    AnnDataTransform,
+    CellwiseMaskData,
+    Compose,
+    FilterCellsScanpy,
+    FilterGenesScanpy,
+    SaveRaw,
+    SetConfig,
+)
 from dance.transforms.graph import FeatureFeatureGraph
 from dance.typing import LogLevel
 

diff --git a/dance/modules/spatial/cell_type_deconvo/card.py b/dance/modules/spatial/cell_type_deconvo/card.py
@@ -13,8 +13,15 @@
 
 from dance import logger
 from dance.modules.base import BaseRegressionMethod
-from dance.transforms import (CellTopicProfile, Compose, FilterGenesCommon, FilterGenesMarker, FilterGenesMatch,
-                              FilterGenesPercentile, SetConfig)
+from dance.transforms import (
+    CellTopicProfile,
+    Compose,
+    FilterGenesCommon,
+    FilterGenesMarker,
+    FilterGenesMatch,
+    FilterGenesPercentile,
+    SetConfig,
+)
 from dance.typing import Any, LogLevel, Optional, Tuple
 from dance.utils.matrix import normalize, pairwise_distance
 

diff --git a/dance/modules/spatial/cell_type_deconvo/dstg.py b/dance/modules/spatial/cell_type_deconvo/dstg.py
@@ -20,8 +20,15 @@
 
 from dance import logger
 from dance.modules.base import BaseRegressionMethod
-from dance.transforms import (AnnDataTransform, Compose, FilterGenesCommon, PseudoMixture, RemoveSplit, ScaleFeature,
-                              SetConfig)
+from dance.transforms import (
+    AnnDataTransform,
+    Compose,
+    FilterGenesCommon,
+    PseudoMixture,
+    RemoveSplit,
+    ScaleFeature,
+    SetConfig,
+)
 from dance.transforms.graph import DSTGraph
 from dance.typing import Any, LogLevel, Optional, Tuple
 from dance.utils import get_device

diff --git a/dance/transforms/__init__.py b/dance/transforms/__init__.py
@@ -1,10 +1,22 @@
 from dance.transforms import graph
 from dance.transforms.cell_feature import BatchFeature, CellPCA, CellSVD, WeightedFeaturePCA
-from dance.transforms.filter import (FilterCellsScanpy, FilterCellsScanpyOrder, FilterGenesCommon, FilterGenesMarker,
-                                     FilterGenesMarkerGini, FilterGenesMatch, FilterGenesPercentile,
-                                     FilterGenesRegression, FilterGenesScanpy, FilterGenesScanpyOrder, FilterGenesTopK,
-                                     FilterScanpy, HighlyVariableGenesLogarithmizedByMeanAndDisp,
-                                     HighlyVariableGenesLogarithmizedByTopGenes, HighlyVariableGenesRawCount)
+from dance.transforms.filter import (
+    FilterCellsScanpy,
+    FilterCellsScanpyOrder,
+    FilterGenesCommon,
+    FilterGenesMarker,
+    FilterGenesMarkerGini,
+    FilterGenesMatch,
+    FilterGenesPercentile,
+    FilterGenesRegression,
+    FilterGenesScanpy,
+    FilterGenesScanpyOrder,
+    FilterGenesTopK,
+    FilterScanpy,
+    HighlyVariableGenesLogarithmizedByMeanAndDisp,
+    HighlyVariableGenesLogarithmizedByTopGenes,
+    HighlyVariableGenesRawCount,
+)
 from dance.transforms.gene_holdout import GeneHoldout
 from dance.transforms.interface import AnnDataTransform
 from dance.transforms.mask import CellwiseMaskData, MaskData

diff --git a/dance/typing.py b/dance/typing.py
@@ -2,8 +2,22 @@
 
 import os
 from logging import Logger
-from typing import (TYPE_CHECKING, Any, Callable, Dict, Iterator, List, Literal, Mapping, Optional, Sequence, Set,
-                    Tuple, Type, Union)
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Callable,
+    Dict,
+    Iterator,
+    List,
+    Literal,
+    Mapping,
+    Optional,
+    Sequence,
+    Set,
+    Tuple,
+    Type,
+    Union,
+)
 
 import numpy as np
 from anndata import AnnData

diff --git a/examples/single_modality/imputation/scgnn2.py b/examples/single_modality/imputation/scgnn2.py
@@ -7,8 +7,14 @@
 from dance import logger
 from dance.datasets.singlemodality import ImputationDataset
 from dance.modules.single_modality.imputation.scgnn2 import ScGNN2
-from dance.transforms import (AnnDataTransform, CellwiseMaskData, Compose, FilterCellsScanpy, FilterGenesScanpy,
-                              FilterGenesTopK)
+from dance.transforms import (
+    AnnDataTransform,
+    CellwiseMaskData,
+    Compose,
+    FilterCellsScanpy,
+    FilterGenesScanpy,
+    FilterGenesTopK,
+)
 from dance.utils import set_seed
 
 if __name__ == "__main__":