Merge networkx from python-type-stubs

stubs/networkx/networkx/algorithms/approximation/maxcut.pyi

@@ -1,4 +1,5 @@
 from _typeshed import Incomplete
+from collections.abc import Iterable
 
 from networkx.classes.graph import Graph, _Node
 from networkx.utils.backends import _dispatchable
@@ -12,5 +13,8 @@ def randomized_partitioning(
 ) -> tuple[float, tuple[set[Incomplete], set[Incomplete]]]: ...
 @_dispatchable
 def one_exchange(
-    G: Graph[_Node], initial_cut: set[Incomplete] | None = None, seed: int | RandomState | None = None, weight: str | None = None
+    G: Graph[_Node],
+    initial_cut: Iterable[Incomplete] | None = None,
+    seed: int | RandomState | None = None,
+    weight: str | None = None,
 ) -> tuple[float, tuple[set[Incomplete], set[Incomplete]]]: ...

stubs/networkx/networkx/algorithms/assortativity/correlation.pyi

@@ -23,3 +23,4 @@ def degree_pearson_correlation_coefficient(
 def attribute_assortativity_coefficient(G: Graph[_Node], attribute: str, nodes: Iterable[Incomplete] | None = None) -> float: ...
 @_dispatchable
 def numeric_assortativity_coefficient(G: Graph[_Node], attribute: str, nodes: Iterable[Incomplete] | None = None) -> float: ...
+def attribute_ac(M) -> float: ...

stubs/networkx/networkx/algorithms/bipartite/edgelist.pyi

@@ -1,5 +1,5 @@
 from _typeshed import Incomplete, StrPath, SupportsRead, SupportsWrite
-from collections.abc import Collection, Generator, Iterable
+from collections.abc import Callable, Collection, Generator, Iterable
 
 from networkx.classes.graph import Graph, _Node
 from networkx.utils.backends import _dispatchable
@@ -12,28 +12,32 @@ def write_edgelist(
     path: StrPath | SupportsWrite[bytes],
     comments: str = "#",
     delimiter: str = " ",
-    data: bool = True,
+    data: bool | Collection[Incomplete] = True,  # Not Iterable: iterated more than once, one-shot iterables give wrong results
     encoding: str = "utf-8",
 ) -> None: ...
 @_dispatchable
-def generate_edgelist(G: Graph[_Node], delimiter: str = " ", data: bool = True) -> Generator[str]: ...
+def generate_edgelist(
+    G: Graph[_Node],
+    delimiter: str = " ",
+    data: bool | Collection[Incomplete] = True,  # Not Iterable: iterated more than once, one-shot iterables give wrong results
+) -> Generator[str]: ...
 @_dispatchable
 def parse_edgelist(
     lines: Iterable[str],
-    comments: str | None = "#",
+    comments: str = "#",
     delimiter: str | None = None,
     create_using: Graph[_Node] | type[Graph[_Node]] | None = None,
-    nodetype: type[Incomplete] | None = None,
-    data: bool | Collection[tuple[str, type[Incomplete]]] = True,
+    nodetype: Callable[[str], Incomplete] | None = None,
+    data: bool | Collection[tuple[str, Callable[[str], Incomplete]]] = True,
 ) -> Graph[Incomplete]: ...
 @_dispatchable
 def read_edgelist(
     path: StrPath | SupportsRead[bytes],
-    comments: str | None = "#",
+    comments: str = "#",
     delimiter: str | None = None,
     create_using: Graph[Incomplete] | type[Graph[Incomplete]] | None = None,
-    nodetype=None,
-    data: bool | Collection[tuple[str, type[Incomplete]]] = True,
+    nodetype: Callable[[str], Incomplete] | None = None,
+    data: bool | Collection[tuple[str, Callable[[str], Incomplete]]] = True,
     edgetype=None,
-    encoding: str | None = "utf-8",
+    encoding: str = "utf-8",
 ) -> Graph[Incomplete]: ...

stubs/networkx/networkx/algorithms/bipartite/generators.pyi

@@ -1,5 +1,4 @@
-from _typeshed import Incomplete
-from collections.abc import Iterable
+from collections.abc import Sequence
 
 from networkx.classes.graph import Graph, _Node
 from networkx.utils.backends import _dispatchable
@@ -20,26 +19,26 @@ __all__ = [
 def complete_bipartite_graph(n1, n2, create_using: Graph[_Node] | type[Graph[_Node]] | None = None): ...
 @_dispatchable
 def configuration_model(
-    aseq: Iterable[Incomplete],
-    bseq: Iterable[Incomplete],
+    aseq: Sequence[int],
+    bseq: Sequence[int],
     create_using: Graph[_Node] | type[Graph[_Node]] | None = None,
     seed: int | RandomState | None = None,
 ): ...
 @_dispatchable
 def havel_hakimi_graph(
-    aseq: Iterable[Incomplete], bseq: Iterable[Incomplete], create_using: Graph[_Node] | type[Graph[_Node]] | None = None
+    aseq: Sequence[int], bseq: Sequence[int], create_using: Graph[_Node] | type[Graph[_Node]] | None = None
 ): ...
 @_dispatchable
 def reverse_havel_hakimi_graph(
-    aseq: Iterable[Incomplete], bseq: Iterable[Incomplete], create_using: Graph[_Node] | type[Graph[_Node]] | None = None
+    aseq: Sequence[int], bseq: Sequence[int], create_using: Graph[_Node] | type[Graph[_Node]] | None = None
 ): ...
 @_dispatchable
 def alternating_havel_hakimi_graph(
-    aseq: Iterable[Incomplete], bseq: Iterable[Incomplete], create_using: Graph[_Node] | type[Graph[_Node]] | None = None
+    aseq: Sequence[int], bseq: Sequence[int], create_using: Graph[_Node] | type[Graph[_Node]] | None = None
 ): ...
 @_dispatchable
 def preferential_attachment_graph(
-    aseq: Iterable[Incomplete],
+    aseq: Sequence[int],
     p: float,
     create_using: Graph[_Node] | type[Graph[_Node]] | None = None,
     seed: int | RandomState | None = None,

stubs/networkx/networkx/algorithms/bipartite/matrix.pyi

@@ -1,5 +1,5 @@
 from _typeshed import Incomplete
-from collections.abc import Iterable
+from collections.abc import Collection
 
 import numpy as np
 from networkx.classes.graph import Graph, _Node
@@ -10,8 +10,8 @@ __all__ = ["biadjacency_matrix", "from_biadjacency_matrix"]
 @_dispatchable
 def biadjacency_matrix(
     G: Graph[_Node],
-    row_order: Iterable[_Node],
-    column_order: Iterable[Incomplete] | None = None,
+    row_order: Collection[_Node],
+    column_order: Collection[Incomplete] | None = None,
     dtype: np.dtype[Incomplete] | None = None,
     weight: str | None = "weight",
     format: str = "csr",
@@ -22,6 +22,6 @@ def from_biadjacency_matrix(
     create_using: Graph[_Node] | type[Graph[_Node]] | None = None,
     edge_attribute: str = "weight",
     *,
-    row_order: Iterable[Incomplete] | None = None,
-    column_order: Iterable[Incomplete] | None = None,
+    row_order: Collection[Incomplete] | None = None,
+    column_order: Collection[Incomplete] | None = None,
 ) -> Graph[Incomplete]: ...

stubs/networkx/networkx/algorithms/bipartite/projection.pyi

@@ -1,5 +1,5 @@
 from _typeshed import Incomplete
-from collections.abc import Callable, Iterable
+from collections.abc import Callable, Collection
 
 from networkx.classes.graph import Graph, _Node
 from networkx.utils.backends import _dispatchable
@@ -13,14 +13,26 @@ __all__ = [
 ]
 
 @_dispatchable
-def projected_graph(B: Graph[_Node], nodes: Iterable[Incomplete], multigraph: bool = False) -> Graph[Incomplete]: ...
+def projected_graph(
+    B: Graph[_Node],
+    nodes: Collection[Incomplete],  # Not Iterable: iterated more than once, one-shot iterables give wrong results
+    multigraph: bool = False,
+) -> Graph[Incomplete]: ...
 @_dispatchable
-def weighted_projected_graph(B: Graph[_Node], nodes: Iterable[Incomplete], ratio: bool = False) -> Graph[Incomplete]: ...
+def weighted_projected_graph(B: Graph[_Node], nodes: Collection[Incomplete], ratio: bool = False) -> Graph[Incomplete]: ...
 @_dispatchable
-def collaboration_weighted_projected_graph(B: Graph[_Node], nodes: Iterable[Incomplete]) -> Graph[Incomplete]: ...
+def collaboration_weighted_projected_graph(
+    B: Graph[_Node], nodes: Collection[Incomplete]  # Not Iterable: iterated more than once, one-shot iterables give wrong results
+) -> Graph[Incomplete]: ...
 @_dispatchable
-def overlap_weighted_projected_graph(B: Graph[_Node], nodes: Iterable[Incomplete], jaccard: bool = True) -> Graph[Incomplete]: ...
+def overlap_weighted_projected_graph(
+    B: Graph[_Node],
+    nodes: Collection[Incomplete],  # Not Iterable: iterated more than once, one-shot iterables give wrong results
+    jaccard: bool = True,
+) -> Graph[Incomplete]: ...
 @_dispatchable
 def generic_weighted_projected_graph(
-    B: Graph[_Node], nodes: Iterable[Incomplete], weight_function: Callable[..., Incomplete] | None = None
+    B: Graph[_Node],
+    nodes: Collection[Incomplete],  # Not Iterable: iterated more than once, one-shot iterables give wrong results
+    weight_function: Callable[..., Incomplete] | None = None,
 ) -> Graph[Incomplete]: ...

stubs/networkx/networkx/algorithms/boundary.pyi

@@ -13,7 +13,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node]]: ...
@@ -22,7 +22,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node, dict[str, Incomplete]]]: ...
@@ -31,7 +31,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node, dict[str, Incomplete]]]: ...
@@ -40,7 +40,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default: _U | None = None,
 ) -> Generator[tuple[_Node, _Node, dict[str, _U]]]: ...
@@ -49,7 +49,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default: _U | None = None,
 ) -> Generator[tuple[_Node, _Node, dict[str, _U]]]: ...
@@ -58,7 +58,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node, int]]: ...
@@ -67,7 +67,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node, int]]: ...
@@ -76,7 +76,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node, int, dict[str, Incomplete]]]: ...
@@ -85,7 +85,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default=None,
 ) -> Generator[tuple[_Node, _Node, int, dict[str, Incomplete]]]: ...
@@ -94,7 +94,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default: _U | None = None,
 ) -> Generator[tuple[_Node, _Node, int, dict[str, _U]]]: ...
@@ -103,7 +103,7 @@ def edge_boundary(
     G: Graph[_Node],
     nbunch1: Iterable[Incomplete],
     nbunch2: Iterable[Incomplete] | None = None,
-    data=False,
+    data: bool | str = False,
     keys: bool = False,
     default: _U | None = None,
 ) -> Generator[tuple[_Node, _Node, int, dict[str, _U]]]: ...

stubs/networkx/networkx/algorithms/clique.pyi

@@ -35,11 +35,13 @@ def make_clique_bipartite(
 ) -> Graph[_Node]: ...
 
 @overload
-def node_clique_number(
-    G: Graph[_Node], nodes=None, cliques: Iterable[Incomplete] | None = None, separate_nodes=False
+def node_clique_number(  # type: ignore[overload-overlap]
+    G: Graph[_Node], nodes: Iterable[_Node] | None = None, cliques: Iterable[Incomplete] | None = None, separate_nodes=False
 ) -> dict[_Node, int]: ...
 @overload
-def node_clique_number(G: Graph[_Node], nodes=None, cliques: Iterable[Incomplete] | None = None, separate_nodes=False) -> int: ...
+def node_clique_number(
+    G: Graph[_Node], nodes: _Node, cliques: Iterable[Incomplete] | None = None, separate_nodes=False
+) -> int: ...
 
 def number_of_cliques(
     G: Graph[_Node], nodes: list[_Node] | _Node | None = None, cliques: Iterable[Incomplete] | None = None

stubs/networkx/networkx/algorithms/isomorphism/ismags.pyi

@@ -2,6 +2,8 @@ from _typeshed import Incomplete
 from collections.abc import Callable, Generator, Hashable, Iterable
 from typing import Any
 
+from ...classes.graph import Graph
+
 __all__ = ["ISMAGS"]
 
 def are_all_equal(iterable: Iterable[Any]) -> bool: ...
@@ -21,7 +23,15 @@ class ISMAGS:
     graph: Incomplete
     subgraph: Incomplete
 
-    def __init__(self, graph, subgraph, node_match=None, edge_match=None, cache=None) -> None: ...
+    def __init__(
+        self,
+        # Any: graph and subgraph can have unrelated node and data types
+        graph: Graph[Any, Any, Any],
+        subgraph: Graph[Any, Any, Any],
+        node_match=None,
+        edge_match=None,
+        cache=None,
+    ) -> None: ...
     def create_aligned_partitions(self, thing_matcher, sg_things, g_things): ...
     def find_isomorphisms(self, symmetry: bool = True) -> Generator[Incomplete, Incomplete, Incomplete]: ...
     def largest_common_subgraph(self, symmetry: bool = True) -> Generator[Incomplete, Incomplete]: ...

stubs/networkx/networkx/algorithms/isomorphism/isomorphvf2.pyi

@@ -1,5 +1,9 @@
 from _typeshed import Incomplete
 from collections.abc import Generator
+from typing import Any
+
+from ...classes.digraph import DiGraph
+from ...classes.graph import Graph
 
 __all__ = ["GraphMatcher", "DiGraphMatcher"]
 
@@ -12,7 +16,12 @@ class GraphMatcher:
     old_recursion_limit: Incomplete
     test: str
 
-    def __init__(self, G1, G2) -> None: ...
+    def __init__(
+        self,
+        # Any: G1 and G2 can have unrelated node and data types
+        G1: Graph[Any, Any, Any],
+        G2: Graph[Any, Any, Any],
+    ) -> None: ...
     def reset_recursion_limit(self) -> None: ...
     def candidate_pairs_iter(self) -> Generator[Incomplete]: ...
     core_1: Incomplete
@@ -34,7 +43,12 @@ class GraphMatcher:
     def syntactic_feasibility(self, G1_node, G2_node): ...
 
 class DiGraphMatcher(GraphMatcher):
-    def __init__(self, G1, G2) -> None: ...
+    def __init__(
+        self,
+        # Any: G1 and G2 can have unrelated node and data types
+        G1: DiGraph[Any, Any, Any],
+        G2: DiGraph[Any, Any, Any],
+    ) -> None: ...
     def candidate_pairs_iter(self) -> Generator[Incomplete]: ...
     core_1: Incomplete
     core_2: Incomplete