Refactor SCC expansion

[daemontus]

Should fix the SCC expansion bug, plus perform some other clean up in that Python module.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
biobalm
_pint_reachability.py	61	50	18%	24, 40–54, 69–93, 101–146
control.py	114	14	88%	107, 119, 125, 129, 134, 143–159, 477, 480, 493
interaction_graph_utils.py	52	6	88%	11–13, 151–152, 206–207
petri_net_translation.py	149	11	93%	22–26, 79, 136, 308–309, 333–334, 343, 452
space_utils.py	132	20	85%	26–28, 104–110, 133–139, 347–350, 414, 462
succession_diagram.py	370	65	82%	6, 119, 208–213, 226, 273–280, 384–391, 408–409, 419, 425, 541, 628–634, 750, 753, 871–889, 921, 931, 934, 974, 981, 1032, 1046, 1126, 1278, 1289, 1297, 1325, 1340, 1352, 1357, 1363
symbolic_utils.py	32	5	84%	10, 39–44, 100, 128
trappist_core.py	183	27	85%	14–18, 55, 57, 92, 215, 217, 219, 247–250, 254–256, 276–282, 340, 342, 372, 420, 422
biobalm/_sd_algorithms
expand_attractor_seeds.py	60	7	88%	6, 28, 42, 109–114, 119
expand_bfs.py	28	1	96%	6
expand_dfs.py	30	1	97%	6
expand_minimal_spaces.py	37	2	95%	6, 31
expand_source_SCCs.py	111	16	86%	11–13, 50, 69, 77, 82, 103, 112, 120, 131, 140, 143, 167, 179, 242–243
expand_to_target.py	31	3	90%	6, 38, 43
biobalm/_sd_attractors
attractor_candidates.py	264	90	66%	13–15, 26–27, 93, 101, 107–108, 130, 152, 187, 193–204, 223, 239–320, 325, 329, 335, 341, 352, 376, 381, 385, 391, 393–431, 504, 575–576, 677
attractor_symbolic.py	114	16	86%	6–7, 75, 88–92, 103, 112, 144, 179, 191–193, 202, 230, 236
TOTAL	1853	334	82%

Tests	Skipped	Failures	Errors	Time
356	0 💤	0 ❌	0 🔥	54.006s ⏱️

[jcrozum]

Any reason check_maa isn't optional anymore?

[daemontus]

Ah, I forgot to put it back. I was playing with it when I started using the function recursively because it seemed like the flag wasn't propagating correctly. I'll put it back.

[kyuhyongpark]

Would having no source SCCs make the node a fixed point?

[kyuhyongpark]

I proof-read the code to my best ability. Everything looks very nice.