Upgrade networkx dependency (#9718)

pyg-team · Oct 21, 2024 · facf0c4 · facf0c4
1 parent 3ac9fda
commit facf0c4
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Showing 5 changed files with 11 additions and 8 deletions.
diff --git a/torch_geometric/config_mixin.py b/torch_geometric/config_mixin.py
@@ -83,7 +83,7 @@ def _recursive_from_config(value: Any) -> Any:
     if is_dataclass(value):
         if getattr(value, '_target_', None):
             try:
-                cls = _locate_cls(value._target_)  # type: ignore[attr-defined]
+                cls = _locate_cls(value._target_)  # type: ignore
             except ImportError:
                 pass  # Keep the dataclass as it is.
         else:

diff --git a/torch_geometric/metrics/link_pred.py b/torch_geometric/metrics/link_pred.py
@@ -78,8 +78,8 @@ def update(
         ) + 1
         arange = torch.arange(
             start=0,
-            end=max_index * pred_index_mat.size(0),
-            step=max_index,
+            end=max_index * pred_index_mat.size(0),  # type: ignore
+            step=max_index,  # type: ignore
             device=pred_index_mat.device,
         ).view(-1, 1)
         flat_pred_index = (pred_index_mat + arange).view(-1)

diff --git a/torch_geometric/transforms/add_positional_encoding.py b/torch_geometric/transforms/add_positional_encoding.py
@@ -92,7 +92,7 @@ def forward(self, data: Data) -> Data:
             from numpy.linalg import eig, eigh
             eig_fn = eig if not self.is_undirected else eigh
 
-            eig_vals, eig_vecs = eig_fn(L.todense())  # type: ignore
+            eig_vals, eig_vecs = eig_fn(L.todense())
         else:
             from scipy.sparse.linalg import eigs, eigsh
             eig_fn = eigs if not self.is_undirected else eigsh

diff --git a/torch_geometric/transforms/mask.py b/torch_geometric/transforms/mask.py
@@ -19,7 +19,11 @@ def get_attrs_with_suffix(
     return [key for key in store.keys() if key.endswith(suffix)]
 
 
-def get_mask_size(attr: str, store: BaseStorage, size: Optional[int]) -> int:
+def get_mask_size(
+    attr: str,
+    store: BaseStorage,
+    size: Optional[int],
+) -> Optional[int]:
     if size is not None:
         return size
     return store.num_edges if store.is_edge_attr(attr) else store.num_nodes

diff --git a/torch_geometric/visualization/graph.py b/torch_geometric/visualization/graph.py
@@ -140,9 +140,8 @@ def _visualize_graph_via_networkx(
             ),
         )
 
-    nodes = nx.draw_networkx_nodes(g, pos, node_size=node_size,
-                                   node_color='white', margins=0.1)
-    nodes.set_edgecolor('black')
+    nx.draw_networkx_nodes(g, pos, node_size=node_size, node_color='white',
+                           margins=0.1, edgecolors='black')
     nx.draw_networkx_labels(g, pos, font_size=10)
 
     if path is not None: