test: added clique percolation benchmark

Author: ntamas

benchmarks/bench_clique_percolation.py

@@ -0,0 +1,61 @@
+from itertools import combinations
+from random import seed
+
+from igraph import Graph as LegacyGraph
+
+from igraph_ctypes.constructors import (
+    create_graph_from_edge_list,
+    create_geometric_random_graph,
+)
+from igraph_ctypes.conversion import get_edge_list
+from igraph_ctypes.paths import components
+from igraph_ctypes._internal.functions import maximal_cliques
+
+seed(42)
+
+n, r, k = 1600, 0.0625, 4
+
+new_g = create_geometric_random_graph(n, r)
+old_g = LegacyGraph(get_edge_list(new_g).tolist())
+
+
+def _gen_pairs(sets, threshold: int):
+    return (
+        (u, v)
+        for u, v in combinations(range(len(sets)), 2)
+        if u != v and len(sets[u] & sets[v]) >= threshold
+    )
+
+
+def _find_edgelist_pairs(sets, threshold: int):
+    return list(_gen_pairs(sets, threshold))
+
+
+def _find_edgelist(sets, threshold: int):
+    result = []
+    for pair in _gen_pairs(sets, threshold):
+        result.extend(pair)
+    return result
+
+
+def clique_percolation_with_old_igraph():
+    cliques = [set(cl) for cl in old_g.maximal_cliques(min=k)]
+    el = _find_edgelist_pairs(cliques, k - 1)
+    clique_g = LegacyGraph(el, directed=False)
+    clique_g.components()
+
+
+def clique_percolation_with_new_igraph():
+    cliques = [set(cl) for cl in maximal_cliques(new_g, min_size=4)]
+    el = _find_edgelist(cliques, k - 1)
+    clique_g = create_graph_from_edge_list(el, directed=False)
+    components(clique_g)
+
+
+__benchmarks__ = [
+    (
+        clique_percolation_with_old_igraph,
+        clique_percolation_with_new_igraph,
+        "Clique percolation method",
+    )
+]

benchmarks/bench_shortest_path.py

@@ -17,16 +17,20 @@
 new_g = create_square_lattice([n, n], directed=False, periodic=False)
 
 
-def with_old_igraph():
+def shortest_path_with_old_igraph():
     for u, v in pairs:
         old_g.get_shortest_paths(u, v)
 
 
-def with_new_igraph():
+def shortest_path_with_new_igraph():
     for u, v in pairs:
         get_shortest_path(new_g, u, v)
 
 
 __benchmarks__ = [
-    (with_old_igraph, with_new_igraph, "Finding shortest path in grid graph")
+    (
+        shortest_path_with_old_igraph,
+        shortest_path_with_new_igraph,
+        "Finding shortest path in grid graph",
+    )
 ]