Upgrade networkx to 3.1, igraph/python_igraph to 0.10.4

build/pkgs/igraph/checksums.ini

@@ -1,5 +1,5 @@
 tarball=igraph-VERSION.tar.gz
-sha1=20587332f0f36d6d7eb3cca248e2dab76e1e58ad
-md5=af41eb9c614946c4a92a51834e9cab4a
-cksum=4011381306
+sha1=fc3c6627f889b13581b2b468e1b16aceff453cfc
+md5=10a3f325425970c75a7ba8359376e208
+cksum=3103730646
 upstream_url=https://github.com/igraph/igraph/releases/download/VERSION/igraph-VERSION.tar.gz

build/pkgs/igraph/package-version.txt

@@ -1 +1 @@
-0.10.2
+0.10.4

build/pkgs/networkx/checksums.ini

@@ -1,5 +1,5 @@
 tarball=networkx-VERSION.tar.gz
-sha1=40e981041664856ba473c9079006367ed0d0e71b
-md5=22139ab5a47818fa00cbaa91eb126381
-cksum=4201985987
+sha1=d4b1d6117b7c54db61f6cbec8f0ccfb0f7d47293
+md5=1a9baa93b7fd4470c80e29a7a6d93ccf
+cksum=1675580484
 upstream_url=https://pypi.io/packages/source/n/networkx/networkx-VERSION.tar.gz

build/pkgs/networkx/install-requires.txt

@@ -1,2 +1 @@
-# features removed in 3.0 listed in https://networkx.org/documentation/stable/developer/deprecations.html#version-3-0
-networkx >=2.4, <3.0
+networkx >=2.4, <3.2

build/pkgs/networkx/package-version.txt

@@ -1 +1 @@
-2.8.8
+3.1

build/pkgs/python_igraph/checksums.ini

@@ -1,5 +1,5 @@
 tarball=python-igraph-VERSION.tar.gz
-sha1=6a6bca77737ff501e97f808aa18a9045e86b3e3e
-md5=6951cc2e803118b74209ae21d54de38a
-cksum=650236223
+sha1=807a95ad4080d8eb500e7797325d6f11a5c46892
+md5=2ac3561dda7e7321789041261a29aba4
+cksum=754615899
 upstream_url=https://pypi.io/packages/source/i/igraph/igraph-VERSION.tar.gz

build/pkgs/python_igraph/package-version.txt

@@ -1 +1 @@
-0.10.2
+0.10.4

src/sage/graphs/graph.py

@@ -6799,13 +6799,26 @@ def cliques_number_of(self, vertices=None, cliques=None):
             {(0, 0): 2, (0, 1): 3, (0, 2): 2, (1, 0): 2, (1, 1): 3, (1, 2): 2}
             sage: F.cliques_number_of(vertices=[(0, 1), (1, 2)])
             {(0, 1): 3, (1, 2): 2}
+            sage: F.cliques_number_of(vertices=(0, 1))
+            3
             sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
             sage: G.show(figsize=[2,2])
             sage: G.cliques_number_of()
             {0: 2, 1: 2, 2: 1, 3: 1}
         """
-        import networkx
-        return networkx.number_of_cliques(self.networkx_graph(), vertices, cliques)
+        if cliques is None:
+            cliques = self.cliques_maximal()
+
+        if vertices in self:  # single vertex
+            return sum(1 for c in cliques if vertices in c)
+
+        from collections import Counter
+        count = Counter()
+
+        for c in cliques:
+            count.update(c)
+
+        return {v : count[v] for v in vertices or self}
 
     @doc_index("Clique-related methods")
     def cliques_get_max_clique_graph(self):
@@ -7506,17 +7519,32 @@ def cliques_containing_vertex(self, vertices=None, cliques=None):
 
             sage: C = Graph('DJ{')
             sage: C.cliques_containing_vertex()
-            {0: [[4, 0]], 1: [[4, 1, 2, 3]], 2: [[4, 1, 2, 3]], 3: [[4, 1, 2, 3]], 4: [[4, 0], [4, 1, 2, 3]]}
+            {0: [[0, 4]],
+             1: [[1, 2, 3, 4]],
+             2: [[1, 2, 3, 4]],
+             3: [[1, 2, 3, 4]],
+             4: [[0, 4], [1, 2, 3, 4]]}
+            sage: C.cliques_containing_vertex(4)
+            [[0, 4], [1, 2, 3, 4]]
+            sage: C.cliques_containing_vertex([0, 1])
+            {0: [[0, 4]], 1: [[1, 2, 3, 4]]}
             sage: E = C.cliques_maximal()
             sage: E
             [[0, 4], [1, 2, 3, 4]]
             sage: C.cliques_containing_vertex(cliques=E)
-            {0: [[0, 4]], 1: [[1, 2, 3, 4]], 2: [[1, 2, 3, 4]], 3: [[1, 2, 3, 4]], 4: [[0, 4], [1, 2, 3, 4]]}
+            {0: [[0, 4]],
+             1: [[1, 2, 3, 4]],
+             2: [[1, 2, 3, 4]],
+             3: [[1, 2, 3, 4]],
+             4: [[0, 4], [1, 2, 3, 4]]}
 
             sage: G = Graph({0:[1,2,3], 1:[2], 3:[0,1]})
             sage: G.show(figsize=[2,2])
             sage: G.cliques_containing_vertex()
-            {0: [[0, 1, 2], [0, 1, 3]], 1: [[0, 1, 2], [0, 1, 3]], 2: [[0, 1, 2]], 3: [[0, 1, 3]]}
+            {0: [[0, 1, 2], [0, 1, 3]],
+             1: [[0, 1, 2], [0, 1, 3]],
+             2: [[0, 1, 2]],
+             3: [[0, 1, 3]]}
 
         Since each clique of a 2 dimensional grid corresponds to an edge, the
         number of cliques in which a vertex is involved equals its degree::
@@ -7531,8 +7559,20 @@ def cliques_containing_vertex(self, vertices=None, cliques=None):
             sage: sorted(sorted(x for x in L) for L in d[(0, 1)])
             [[(0, 0), (0, 1)], [(0, 1), (0, 2)], [(0, 1), (1, 1)]]
         """
-        import networkx
-        return networkx.cliques_containing_node(self.networkx_graph(), vertices, cliques)
+        if cliques is None:
+            cliques = self.cliques_maximal()
+
+        if vertices in self:  # single vertex
+            return [c for c in cliques if vertices in c]
+
+        from collections import defaultdict
+        d = defaultdict(list)
+
+        for c in cliques:
+            for v in c:
+                d[v].append(c)
+
+        return {v : d[v] for v in vertices or self}
 
     @doc_index("Clique-related methods")
     def clique_complex(self):