Linted the package

Author: Joao Felipe Rocha

.gitignore

@@ -53,6 +53,7 @@ Python/doc/build/
 
 # Jupyter
 .ipynb_checkpoints/
+Python/tutorial/cache
 
 # Mac
 .DS_Store

Python/phate/mds.py

@@ -218,6 +218,7 @@ def embed_MDS(
     # which is much faster than scipy's pdist + squareform
     if distance_metric == "euclidean" and X.shape[0] > 1000:
         from sklearn.metrics.pairwise import euclidean_distances
+
         X_dist = euclidean_distances(X, X)
     else:
         X_dist = squareform(pdist(X, distance_metric))
@@ -235,7 +236,7 @@ def embed_MDS(
             n_components=ndim,
             random_state=seed,
             init=Y_classic,
-            verbose=verbose
+            verbose=verbose,
         )
     elif solver == "smacof":
         Y = smacof(

Python/phate/phate.py

@@ -33,6 +33,7 @@
 
 _logger = tasklogger.get_tasklogger("graphtools")
 
+
 # Check graphtools version
 def _graphtools_version_is_at_least_2_0():
     """Check if installed graphtools version is >= 2.0.0.
@@ -132,9 +133,9 @@ class PHATE(BaseEstimator):
         If an integer is given, it fixes the seed
         Defaults to the global `numpy` random number generator
 
-    random_landmarking : bool, optional, default: False   
-        Whether to use random sampling for landmarking. If True, landmarks 
-        are selected randomly. If False, landmarks are selected deterministically 
+    random_landmarking : bool, optional, default: False
+        Whether to use random sampling for landmarking. If True, landmarks
+        are selected randomly. If False, landmarks are selected deterministically
         using spectral clustering.
         Defaults to False.
 
@@ -231,7 +232,7 @@ def __init__(
                 "Landmarking is disabled when n_landmark=None. "
                 "To use random landmarking, please set n_landmark to a positive integer "
                 "(e.g., n_landmark=2000).",
-                UserWarning
+                UserWarning,
             )
             # Disable random_landmarking since it has no effect
             random_landmarking = False
@@ -242,7 +243,7 @@ def __init__(
                 "Please update graphtools to use this feature: "
                 "https://pypi.org/project/graphtools/2.0.0/. "
                 "Falling back to spectral clustering for landmark selection.",
-                UserWarning
+                UserWarning,
             )
             # Disable random_landmarking since it's not supported
             random_landmarking = False
@@ -532,9 +533,9 @@ def set_params(self, **params):
             If an integer is given, it fixes the seed
             Defaults to the global `numpy` random number generator
 
-        random_landmarking : bool, optional, default: False   
-            Whether to use random sampling for landmarking. If True, landmarks 
-            are selected randomly. If False, landmarks are selected deterministically 
+        random_landmarking : bool, optional, default: False
+            Whether to use random sampling for landmarking. If True, landmarks
+            are selected randomly. If False, landmarks are selected deterministically
             using spectral clustering.
             Defaults to False.
 
@@ -819,21 +820,21 @@ def _update_graph(self, X, precomputed, n_pca, n_landmark, random_landmarking):
             try:
                 # Prepare graph params
                 graph_params = {
-                    'decay': self.decay,
-                    'knn': self.knn,
-                    'knn_max': self.knn_max,
-                    'distance': self.knn_dist,
-                    'precomputed': precomputed,
-                    'n_jobs': self.n_jobs,
-                    'verbose': self.verbose,
-                    'n_pca': n_pca,
-                    'n_landmark': n_landmark,
-                    'random_state': self.random_state,
+                    "decay": self.decay,
+                    "knn": self.knn,
+                    "knn_max": self.knn_max,
+                    "distance": self.knn_dist,
+                    "precomputed": precomputed,
+                    "n_jobs": self.n_jobs,
+                    "verbose": self.verbose,
+                    "n_pca": n_pca,
+                    "n_landmark": n_landmark,
+                    "random_state": self.random_state,
                 }
 
                 # Only add random_landmarking if graphtools supports it
                 if _graphtools_version_is_at_least_2_0():
-                    graph_params['random_landmarking'] = random_landmarking
+                    graph_params["random_landmarking"] = random_landmarking
 
                 self.graph.set_params(**graph_params)
                 _logger.log_info("Using precomputed graph and diffusion operator...")
@@ -880,30 +881,32 @@ def fit(self, X):
             n_landmark = self.n_landmark
 
         if self.graph is not None and update_graph:
-            self._update_graph(X, precomputed, n_pca, n_landmark, self.random_landmarking)
+            self._update_graph(
+                X, precomputed, n_pca, n_landmark, self.random_landmarking
+            )
 
         self.X = X
 
         if self.graph is None:
             with _logger.log_task("graph and diffusion operator"):
                 # Prepare graph params
                 graph_params = {
-                    'n_pca': n_pca,
-                    'n_landmark': n_landmark,
-                    'distance': self.knn_dist,
-                    'precomputed': precomputed,
-                    'knn': self.knn,
-                    'knn_max': self.knn_max,
-                    'decay': self.decay,
-                    'thresh': 1e-4,
-                    'n_jobs': self.n_jobs,
-                    'verbose': self.verbose,
-                    'random_state': self.random_state,
+                    "n_pca": n_pca,
+                    "n_landmark": n_landmark,
+                    "distance": self.knn_dist,
+                    "precomputed": precomputed,
+                    "knn": self.knn,
+                    "knn_max": self.knn_max,
+                    "decay": self.decay,
+                    "thresh": 1e-4,
+                    "n_jobs": self.n_jobs,
+                    "verbose": self.verbose,
+                    "random_state": self.random_state,
                 }
 
                 # Only add random_landmarking if graphtools supports it
                 if _graphtools_version_is_at_least_2_0():
-                    graph_params['random_landmarking'] = self.random_landmarking
+                    graph_params["random_landmarking"] = self.random_landmarking
 
                 # Merge with any additional kwargs
                 graph_params.update(self.kwargs)

Python/phate/sgd_mds.py

@@ -159,7 +159,7 @@ def sgd_mds(
         Y = Y - lr * gradients
 
         # Compute stress for convergence checking
-        stress = np.sum(errors ** 2) / len(errors)  # Normalized by number of samples
+        stress = np.sum(errors**2) / len(errors)  # Normalized by number of samples
         stress_history.append(stress)
 
         if verbose > 0 and iteration % 100 == 0:
@@ -189,7 +189,9 @@ def sgd_mds(
         last_10pct = max(1, len(stress_history) // 10)
         recent_stress = stress_history[-last_10pct:]
         if len(recent_stress) > 1:
-            stress_trend = (recent_stress[-1] - recent_stress[0]) / (recent_stress[0] + 1e-10)
+            stress_trend = (recent_stress[-1] - recent_stress[0]) / (
+                recent_stress[0] + 1e-10
+            )
             if abs(stress_trend) > 0.01:  # Still changing by more than 1%
                 _logger.log_warning(
                     f"SGD-MDS may not have converged: stress changed by {stress_trend*100:.1f}% "

Python/test/test_simple.py

@@ -126,7 +126,7 @@ def test_tree():
     np.testing.assert_allclose(
         phate_precomputed_D, phate_precomputed_distance, atol=5e-4
     )
-    
+
     return None