test scc+att

benchmark/bench_sd_attractors_scc+att.py

@@ -0,0 +1,37 @@
+import sys
+sys.path.append("..")
+
+import balm
+
+from biodivine_aeon import BooleanNetwork
+from balm.SuccessionDiagram import SuccessionDiagram
+from balm._sd_algorithms.expand_source_SCCs import expand_source_SCCs
+
+# Print progress and succession diagram size.
+balm.SuccessionDiagram.DEBUG = True
+
+NODE_LIMIT = 1_000_000
+DEPTH_LIMIT = 10_000
+
+# This is unfortunately necessary for PyEDA Boolean expression parser (for now).
+sys.setrecursionlimit(150000)
+
+bn = BooleanNetwork.from_file(sys.argv[1])
+bn = bn.infer_regulatory_graph()
+
+# Compute the succession diagram.
+sd = SuccessionDiagram(bn)
+fully_expanded = expand_source_SCCs(sd, SuccessionDiagram.expand_attractor_seeds)
+assert fully_expanded
+
+attractor_count = 0
+motif_avoidant_count = 0
+
+for node in sd.node_ids():
+    attr = sd.node_attractor_seeds(node, compute=True)
+    attractor_count += len(attr)
+    if not sd.node_is_minimal(node):
+        motif_avoidant_count += len(attr)
+
+print("nodes, attractors, motif-avoidant")
+print(f"{len(sd)}, {attractor_count}, {motif_avoidant_count}")

benchmark/bench_sd_attractors_scc.py

@@ -1,14 +1,14 @@
 import sys
-sys.path.append(".")
+sys.path.append("..")
+
+import balm
 
 from biodivine_aeon import BooleanNetwork
-from nfvsmotifs.SuccessionDiagram import SuccessionDiagram
-from nfvsmotifs._sd_algorithms.expand_source_SCCs import expand_source_SCCs
-import sys
-import nfvsmotifs
+from balm.SuccessionDiagram import SuccessionDiagram
+from balm._sd_algorithms.expand_source_SCCs import expand_source_SCCs
 
 # Print progress and succession diagram size.
-nfvsmotifs.SuccessionDiagram.DEBUG = True
+balm.SuccessionDiagram.DEBUG = True
 
 NODE_LIMIT = 1_000_000
 DEPTH_LIMIT = 10_000