Percolation optimizations

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
nfvsmotifs
SuccessionDiagram.py	156	4	97%	6–7, 208, 468
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	5	97%	23–24, 130, 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	145	6	96%	15–16, 189, 218, 233, 290
state_utils.py	68	12	82%	15, 55–66, 98, 105, 114
terminal_restriction_space.py	44	4	91%	6–7, 80, 97
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_source_SCCs.py	184	7	96%	84, 94, 137, 160–161, 166, 281
expand_to_target.py	30	3	90%	6, 37, 42
TOTAL	1827	141	92%

Tests	Skipped	Failures	Errors	Time
366	0 :zzz:	0 :x:	0 :fire:	4m 11s :stopwatch:

[jcrozum]

@kyuhyongpark @daemontus Here is the PR I promised this morning. Feel free to look over it, but be warned that the GitHub website isn't handling all the moved model files very gracefully :)

@giang-trinh for context, this PR has the SCC expansion optimizations @kyuhyongpark was working on (#79), and also a fix for #84. We agreed to merge these into main as soon as possible because the branch structure was getting a bit out of hand.

Edit: forgot to add that there are some analysis scripts in here. We might want to reorganize these later, but for now I think we should just merge them in.

[daemontus]

I also looked at the relevant code and I§m fine with merging this :)