Merge branch 'analysis-first-major-run' of https://github.com/jcrozum…

…/nfvs-motifs into basic_analysis
jcrozum · Sep 14, 2023 · c6495a7 · c6495a7 · github-actions · Sep 14, 2023
2 parents e0fb2db + ed14a18
commit c6495a7
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diff --git a/analysis/SD_analysis.py b/analysis/SD_analysis.py
@@ -1,17 +1,19 @@
 import sys
+
 sys.path.append("..")
 
 from biodivine_aeon import BooleanNetwork
-from nfvsmotifs.SuccessionDiagram import SuccessionDiagram
+
 import nfvsmotifs
+from nfvsmotifs.SuccessionDiagram import SuccessionDiagram
 
-LOG_LOCATION = 'SD_analysis_'+sys.argv[1].split('/')[-2]+'.csv'
+LOG_LOCATION = "SD_analysis_" + sys.argv[1].split("/")[-2] + ".csv"
 
 # Print progress and succession diagram size.
 nfvsmotifs.SuccessionDiagram.DEBUG = True
 
-NODE_LIMIT = 1_000_000
-DEPTH_LIMIT = 10_000
+NODE_LIMIT = 1_000
+DEPTH_LIMIT = 100
 
 # This is unfortunately necessary for PyEDA Boolean expression parser (for now).
 sys.setrecursionlimit(150000)
@@ -40,12 +42,11 @@
 print(f"motif avoidant attactors, {motif_avoidant_count}")
 print(f"minimal trapspaces, {len(sd.minimal_trap_spaces())}")
 
-log = open(LOG_LOCATION, 'a')
-log.write(sys.argv[1].split('/')[-1] + ',')             # model name
-log.write(str(bn.num_vars()) + ',')                     # network size
-log.write(str(len(sd)) + ',')                           # SD size
-log.write(str(sd.depth()) + ',')                        # SD depth
-log.write(str(attractor_count) + ',')                   # number of attractors
-log.write(str(motif_avoidant_count) + ',')              # number of motif avoidant attractors
-log.write(str(len(sd.minimal_trap_spaces())) + '\n')    # number of minimal trapspaces
-
+log = open(LOG_LOCATION, "a")
+log.write(sys.argv[1].split("/")[-1] + ",")  # model name
+log.write(str(bn.num_vars()) + ",")  # network size
+log.write(str(len(sd)) + ",")  # SD size
+log.write(str(sd.depth()) + ",")  # SD depth
+log.write(str(attractor_count) + ",")  # number of attractors
+log.write(str(motif_avoidant_count) + ",")  # number of motif avoidant attractors
+log.write(str(len(sd.minimal_trap_spaces())) + "\n")  # number of minimal trapspaces
diff --git a/analysis/SD_analysis_bbm-bnet-inputs-true.csv b/analysis/SD_analysis_bbm-bnet-inputs-true.csv
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File	Stmts	Miss	Cover	Missing
nfvsmotifs
SuccessionDiagram.py	154	4	97%	6–7, 208, 452
control.py	120	13	89%	47, 56, 60, 66, 80, 89–105, 319, 334
interaction_graph_utils.py	142	8	94%	6–9, 57, 70, 95–96
motif_avoidant.py	163	6	96%	23–24, 130, 147, 184, 309
petri_net_translation.py	84	6	93%	23–24, 52, 63–64, 94
pyeda_utils.py	95	34	64%	12, 56–66, 90, 95, 98–112, 140–144
space_utils.py	118	5	96%	15–16, 198, 213, 270
state_utils.py	68	12	82%	15, 55–66, 98, 105, 114
terminal_restriction_space.py	44	3	93%	6–7, 80
trappist_core.py	186	20	89%	10–11, 39, 41, 81, 127, 192, 194, 196, 231–233, 259, 317, 319, 349, 389, 391, 422, 451
nfvsmotifs/FVSpython3
FVS.py	48	10	79%	90–91, 97, 133, 183–189
FVS_localsearch_10_python.py	90	1	99%	179
nfvsmotifs/_sd_algorithms
compute_attractor_seeds.py	29	1	97%	6
expand_attractor_seeds.py	51	4	92%	6, 95–100
expand_bfs.py	28	1	96%	6
expand_dfs.py	30	1	97%	6
expand_minimal_spaces.py	37	1	97%	6
expand_to_target.py	30	3	90%	6, 37, 42
TOTAL	1614	133	92%