[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
YosefLab · Dec 13, 2024 · ce57fa9 · ce57fa9
1 parent cc83b1a
commit ce57fa9
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Showing 4 changed files with 18 additions and 22 deletions.
diff --git a/popv/algorithms/_celltypist.py b/popv/algorithms/_celltypist.py
@@ -70,9 +70,9 @@ def predict(self, adata):
 
         adata.obs[self.result_key] = predictions.predicted_labels[out_column]
         if adata.uns["_return_probabilities"]:
-            adata.obs[
-                self.result_key + "_probabilities"
-            ] = predictions.probability_matrix.max(axis=1).values
+            adata.obs[self.result_key + "_probabilities"] = (
+                predictions.probability_matrix.max(axis=1).values
+            )
 
     def compute_embedding(self, adata):
         pass
diff --git a/popv/algorithms/_onclass.py b/popv/algorithms/_onclass.py
@@ -109,9 +109,9 @@ def predict(self, adata):
         logging.info(
             f'Computing Onclass. Storing prediction in adata.obs["{self.result_key}"]'
         )
-        adata.obs.loc[
-            adata.obs["_dataset"] == "query", self.cell_ontology_obs_key
-        ] = adata.uns["unknown_celltype_label"]
+        adata.obs.loc[adata.obs["_dataset"] == "query", self.cell_ontology_obs_key] = (
+            adata.uns["unknown_celltype_label"]
+        )
 
         train_idx = adata.obs["_dataset"] == "ref"
 

diff --git a/popv/preprocessing.py b/popv/preprocessing.py
@@ -345,19 +345,17 @@ def _preprocess(self):
             except (
                 ValueError
             ):  # seurat_v3 tends to error with singularities then use Poisson hvg.
-                self.adata.var[
-                    "highly_variable"
-                ] = sc.experimental.pp.highly_variable_genes(
-                    self.adata[self.adata.obs["_dataset"] == "ref"].copy(),
-                    n_top_genes=self.hvg,
-                    subset=False,
-                    layer="scvi_counts",
-                    flavor="pearson_residuals",
-                    inplace=False,
-                    batch_key="_batch_annotation",
-                )[
-                    "highly_variable"
-                ]
+                self.adata.var["highly_variable"] = (
+                    sc.experimental.pp.highly_variable_genes(
+                        self.adata[self.adata.obs["_dataset"] == "ref"].copy(),
+                        n_top_genes=self.hvg,
+                        subset=False,
+                        layer="scvi_counts",
+                        flavor="pearson_residuals",
+                        inplace=False,
+                        batch_key="_batch_annotation",
+                    )["highly_variable"]
+                )
             self.adata = self.adata[:, self.adata.var["highly_variable"]].copy()
 
         sc.pp.normalize_total(self.adata, target_sum=1e4)

diff --git a/popv/reproducibility/_alluvial.py b/popv/reproducibility/_alluvial.py
@@ -246,9 +246,7 @@ def get_color_array(
         lci = len(color_items)
         if rand_seed is not None:
             np.random.seed(rand_seed)
-        cmap = (
-            cmap if cmap is not None else matplotlib.cm.get_cmap("hsv", lci * 10**3)
-        )
+        cmap = cmap if cmap is not None else matplotlib.cm.get_cmap("hsv", lci * 10**3)
         color_array = (
             colors
             if colors is not None