Style Python files

src/data_processors/process_dataset/script.py

@@ -1,8 +1,8 @@
 import sys
 
 import anndata as ad
-import openproblems as op
 import numpy as np
+import openproblems as op
 from sklearn.metrics import pairwise_distances
 
 ## VIASH START
@@ -43,7 +43,7 @@
     adata.layers["normalized"],
     adata.layers["normalized"][adata.obs["is_waypoint"].values, :],
     metric="euclidean",
-    n_jobs = -2
+    n_jobs=-2,
 )
 np.fill_diagonal(adata.obsm["waypoint_distances"], 0)
 
@@ -52,7 +52,7 @@
     adata.layers["normalized"][adata.obs["is_waypoint"].values, :],
     adata.layers["normalized"][adata.obs["is_waypoint"].values, :],
     metric="euclidean",
-    n_jobs = -2
+    n_jobs=-2,
 )
 np.fill_diagonal(adata.uns["between_waypoint_distances"], 0)
 
@@ -68,19 +68,13 @@
 
 print("\n>>> Calculating distances to centroids...", flush=True)
 adata.obsm["centroid_distances"] = pairwise_distances(
-    adata.layers["normalized"],
-    centroids,
-    metric="euclidean",
-    n_jobs = -2
+    adata.layers["normalized"], centroids, metric="euclidean", n_jobs=-2
 )
 np.fill_diagonal(adata.obsm["centroid_distances"], 0)
 
 print("\n>>> Calculating distances between centroids...", flush=True)
 adata.uns["between_centroid_distances"] = pairwise_distances(
-    centroids,
-    centroids,
-    metric="euclidean",
-    n_jobs = -2
+    centroids, centroids, metric="euclidean", n_jobs=-2
 )
 np.fill_diagonal(adata.uns["between_centroid_distances"], 0)
 

src/metrics/distance_correlation/script.py

@@ -9,7 +9,10 @@
 }
 ## VIASH END
 
-print(f"====== Distance correlation metrics (scipy v{scipy.__version__}) ======", flush=True)
+print(
+    f"====== Distance correlation metrics (scipy v{scipy.__version__}) ======",
+    flush=True,
+)
 
 print("\n>>> Reading solution...", flush=True)
 solution = ad.read_h5ad(par["input_solution"])
@@ -43,7 +46,11 @@
         "dataset_id": solution.uns["dataset_id"],
         "normalization_id": solution.uns["normalization_id"],
         "method_id": embedding.uns["method_id"],
-        "metric_ids": ["waypoint_distance_correlation", "centroid_distance_correlation", "label_distance_correlation"],
+        "metric_ids": [
+            "waypoint_distance_correlation",
+            "centroid_distance_correlation",
+            "label_distance_correlation",
+        ],
         "metric_values": [waypoint_corr, centroid_corr, label_corr],
     }
 )