Update nx-cugraph metadata, README generation, from_biadjacency_matrix for networkx 3.6.1 compat (#218)

networkx/networkx#8286, introduced in networkx 3.6, changed the documentation URLs.
networkx/networkx#8373, introduced in networkx 3.6.1, reverted this change. Require networkx 3.6.1 to get the reversion.

Authors:
  - Kyle Edwards (https://github.com/KyleFromNVIDIA)
  - Rick Ratzel (https://github.com/rlratzel)

Approvers:
  - Gil Forsyth (https://github.com/gforsyth)
  - Bradley Dice (https://github.com/bdice)
  - Rick Ratzel (https://github.com/rlratzel)

URL: #218

Author: KyleFromNVIDIA

.pre-commit-config.yaml

@@ -99,7 +99,7 @@ repos:
         types: [python]
         language: python
         pass_filenames: false
-        additional_dependencies: ["networkx>=3.6"]
+        additional_dependencies: ["networkx>=3.6.1"]
   - repo: local
     hooks:
       - id: nx-cugraph-readme-update
@@ -109,7 +109,7 @@ repos:
         types_or: [python, markdown]
         language: python
         pass_filenames: false
-        additional_dependencies: ["networkx>=3.6"]
+        additional_dependencies: ["networkx>=3.6.1"]
   - repo: local
     hooks:
       - id: disallow-improper-nxver-comparison
@@ -122,7 +122,7 @@ repos:
         # Use e.g. `_nxver < ...` or `_nxver >= ...` instead
         exclude: .pre-commit-config.yaml
   - repo: https://github.com/rapidsai/pre-commit-hooks
-    rev: v1.2.0
+    rev: v1.2.1
     hooks:
       - id: verify-copyright
         args: [--fix, --spdx]

README.md

@@ -219,35 +219,35 @@ Below is the list of algorithms that are currently supported in nx-cugraph.
 <a href="https://networkx.org/documentation/stable/reference/algorithms/reciprocity.html#module-networkx.algorithms.reciprocity">reciprocity</a>
  ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.reciprocity.overall_reciprocity.html#networkx.algorithms.reciprocity.overall_reciprocity">overall_reciprocity</a>
  └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.reciprocity.reciprocity.html#networkx.algorithms.reciprocity.reciprocity">reciprocity</a>
-<a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/index.html">shortest_paths</a>
- ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/index.html#module-networkx.algorithms.shortest_paths.generic">generic</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.generic.has_path.html#networkx.algorithms.shortest_paths.generic.has_path">has_path</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html#networkx.algorithms.shortest_paths.generic.shortest_path">shortest_path</a>
- │   └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.generic.shortest_path_length.html#networkx.algorithms.shortest_paths.generic.shortest_path_length">shortest_path_length</a>
- ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/index.html#module-networkx.algorithms.shortest_paths.unweighted">unweighted</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path">all_pairs_shortest_path</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path_length.html#networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path_length">all_pairs_shortest_path_length</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.bidirectional_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.bidirectional_shortest_path">bidirectional_shortest_path</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path">single_source_shortest_path</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path_length.html#networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path_length">single_source_shortest_path_length</a>
- │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path">single_target_shortest_path</a>
- │   └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path_length.html#networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path_length">single_target_shortest_path_length</a>
- └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/index.html#module-networkx.algorithms.shortest_paths.weighted">weighted</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path.html#networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path">all_pairs_bellman_ford_path</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path_length">all_pairs_bellman_ford_path_length</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra.html#networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra">all_pairs_dijkstra</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path.html#networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path">all_pairs_dijkstra_path</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path_length.html#networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path_length">all_pairs_dijkstra_path_length</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.bellman_ford_path.html#networkx.algorithms.shortest_paths.weighted.bellman_ford_path">bellman_ford_path</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.bellman_ford_path_length">bellman_ford_path_length</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.dijkstra_path.html#networkx.algorithms.shortest_paths.weighted.dijkstra_path">dijkstra_path</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.dijkstra_path_length.html#networkx.algorithms.shortest_paths.weighted.dijkstra_path_length">dijkstra_path_length</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford.html#networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford">single_source_bellman_ford</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path.html#networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path">single_source_bellman_ford_path</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path_length">single_source_bellman_ford_path_length</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.single_source_dijkstra.html#networkx.algorithms.shortest_paths.weighted.single_source_dijkstra">single_source_dijkstra</a>
-     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path.html#networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path">single_source_dijkstra_path</a>
-     └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths/generated/networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path_length.html#networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path_length">single_source_dijkstra_path_length</a>
+<a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths.html">shortest_paths</a>
+ ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths.html#module-networkx.algorithms.shortest_paths.generic">generic</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.has_path.html#networkx.algorithms.shortest_paths.generic.has_path">has_path</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path.html#networkx.algorithms.shortest_paths.generic.shortest_path">shortest_path</a>
+ │   └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.generic.shortest_path_length.html#networkx.algorithms.shortest_paths.generic.shortest_path_length">shortest_path_length</a>
+ ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths.html#module-networkx.algorithms.shortest_paths.unweighted">unweighted</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path">all_pairs_shortest_path</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path_length.html#networkx.algorithms.shortest_paths.unweighted.all_pairs_shortest_path_length">all_pairs_shortest_path_length</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.bidirectional_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.bidirectional_shortest_path">bidirectional_shortest_path</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path">single_source_shortest_path</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path_length.html#networkx.algorithms.shortest_paths.unweighted.single_source_shortest_path_length">single_source_shortest_path_length</a>
+ │   ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path.html#networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path">single_target_shortest_path</a>
+ │   └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path_length.html#networkx.algorithms.shortest_paths.unweighted.single_target_shortest_path_length">single_target_shortest_path_length</a>
+ └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/shortest_paths.html#module-networkx.algorithms.shortest_paths.weighted">weighted</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path.html#networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path">all_pairs_bellman_ford_path</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.all_pairs_bellman_ford_path_length">all_pairs_bellman_ford_path_length</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra.html#networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra">all_pairs_dijkstra</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path.html#networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path">all_pairs_dijkstra_path</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path_length.html#networkx.algorithms.shortest_paths.weighted.all_pairs_dijkstra_path_length">all_pairs_dijkstra_path_length</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.bellman_ford_path.html#networkx.algorithms.shortest_paths.weighted.bellman_ford_path">bellman_ford_path</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.bellman_ford_path_length">bellman_ford_path_length</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.dijkstra_path.html#networkx.algorithms.shortest_paths.weighted.dijkstra_path">dijkstra_path</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.dijkstra_path_length.html#networkx.algorithms.shortest_paths.weighted.dijkstra_path_length">dijkstra_path_length</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford.html#networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford">single_source_bellman_ford</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path.html#networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path">single_source_bellman_ford_path</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path_length.html#networkx.algorithms.shortest_paths.weighted.single_source_bellman_ford_path_length">single_source_bellman_ford_path_length</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.single_source_dijkstra.html#networkx.algorithms.shortest_paths.weighted.single_source_dijkstra">single_source_dijkstra</a>
+     ├─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path.html#networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path">single_source_dijkstra_path</a>
+     └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path_length.html#networkx.algorithms.shortest_paths.weighted.single_source_dijkstra_path_length">single_source_dijkstra_path_length</a>
 <a href="https://networkx.org/documentation/stable/reference/algorithms/tournament.html#module-networkx.algorithms.tournament">tournament</a>
  └─ <a href="https://networkx.org/documentation/stable/reference/algorithms/generated/networkx.algorithms.tournament.tournament_matrix.html#networkx.algorithms.tournament.tournament_matrix">tournament_matrix</a>
 <a href="https://networkx.org/documentation/stable/reference/algorithms/traversal.html">traversal</a>

nx_cugraph/algorithms/bipartite/matrix.py

@@ -4,12 +4,27 @@
 import networkx as nx
 import numpy as np
 
+from nx_cugraph import _nxver
 from nx_cugraph.convert import _to_graph
 from nx_cugraph.generators._utils import _create_using_class
 from nx_cugraph.utils import index_dtype, networkx_algorithm
 
 __all__ = ["biadjacency_matrix", "from_biadjacency_matrix"]
 
+# row_order and column_order were added in networkx 3.6.1, treat them as extra params
+# for function signature checks when using networkx < 3.6.1.
+if _nxver < (3, 6, 1):
+    _row_col_order_extra_params = {
+        "row_order : list, optional": (
+            "unused, for compatibility with networkx >= 3.6.1"
+        ),
+        "column_order : list, optional": (
+            "unused, for compatibility with networkx >= 3.6.1"
+        ),
+    }
+else:
+    _row_col_order_extra_params = {}
+
 
 @networkx_algorithm(version_added="25.06")
 def biadjacency_matrix(
@@ -76,8 +91,20 @@ def biadjacency_matrix(
         raise nx.NetworkXError(f"Unknown sparse matrix format: {format}") from exc
 
 
-@networkx_algorithm(version_added="25.06", fallback=True, create_using_arg=1)
-def from_biadjacency_matrix(A, create_using=None, edge_attribute="weight"):
+@networkx_algorithm(
+    extra_params={**_row_col_order_extra_params},
+    fallback=True,
+    create_using_arg=1,
+    version_added="25.06",
+)
+def from_biadjacency_matrix(
+    A, create_using=None, edge_attribute="weight", *, row_order=None, column_order=None
+):
+    if row_order is not None or column_order is not None:
+        raise NotImplementedError(
+            f"row_order={row_order} and column_order={column_order} not supported;"
+            " only row_order=None and column_order=None are currently supported"
+        )
     graph_class, inplace = _create_using_class(create_using)
     nrows, ncols = A.shape
     if A.format != "coo":
@@ -115,3 +142,20 @@ def from_biadjacency_matrix(A, create_using=None, edge_attribute="weight"):
     if inplace:
         return create_using._become(G)
     return G
+
+
+@from_biadjacency_matrix._can_run
+def _(
+    A,
+    create_using=None,
+    edge_attribute="weight",
+    *,
+    row_order=None,
+    column_order=None,
+):
+    if row_order is not None or column_order is not None:
+        return (
+            f"row_order={row_order} and column_order={column_order} not supported; "
+            "only row_order=None and column_order=None are currently supported"
+        )
+    return True