Skip nodes

[daemontus]

This PR introduces "skip nodes". These are nodes that are not expanded, but instead "skip" the rest of the succession diagram and lead to some of the child spaces further down in the succession diagram (by default, these are minimal trap spaces). To preserve the correctness of other methods, it is required that each skip node still has successors that cover every minimal trap space relevant for that skip node (this is mainly to ensure that we don't detect the attractors in minimal trap spaces multiple times).

This makes it possible to stop the expansion at a particular SD size and run attractor detection that uses all available information, even if the SD is incomplete.

[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, 222–223
petri_net_translation.py	149	12	92%	22–26, 79, 136, 234, 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	439	92	79%	6, 128, 218–223, 236, 283–290, 394–401, 418–419, 429, 435, 551, 638–644, 760, 763, 858–872, 903–921, 953, 963, 1006, 1013, 1064, 1082, 1204, 1395–1423, 1441, 1474, 1505, 1516, 1524, 1567, 1579, 1584
symbolic_utils.py	32	5	84%	10, 39–44, 100, 128
trappist_core.py	184	23	88%	14–18, 55, 57, 92, 215, 217, 219, 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	68	6	91%	6, 36, 49, 64, 101, 116
expand_source_SCCs.py	111	16	86%	11–13, 50, 69, 77, 82, 103, 112, 120, 131, 140, 143, 167, 179, 242–243
expand_source_blocks.py	123	19	85%	10, 31, 43–46, 68, 75, 83, 142, 168, 177, 208, 216–217, 221, 231, 237, 246
expand_to_target.py	31	3	90%	6, 38, 43
biobalm/_sd_attractors
attractor_candidates.py	280	91	68%	13–15, 27–28, 94, 102, 108–109, 153, 162, 184, 219, 225–236, 255, 271–352, 357, 361, 367, 373, 388, 415, 420, 424, 430, 432–470, 543, 614–615, 716
attractor_symbolic.py	224	40	82%	6–7, 39–40, 54–68, 77, 95, 102, 107, 112, 193, 206–210, 221, 230, 262, 298, 328–330, 349, 359–361, 371, 380, 422, 442, 449
TOTAL	2209	406	82%

Tests	Skipped	Failures	Errors	Time
359	0 💤	0 ❌	0 🔥	1m 0s ⏱️