pruned redundant paths in control succession search

[jcrozum]

This improves the control algorithm and better aligns it with pystablemotifs.

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
biobalm
_pint_reachability.py	61	50	18%	24, 40–54, 69–93, 101–146
control.py	149	28	81%	108, 120, 126, 130, 135, 144–160, 173, 417–436, 558, 561, 574
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	449	93	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, 1104, 1220, 1411–1439, 1457, 1490, 1521, 1532, 1540, 1583, 1595, 1600
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	2254	421	81%

Tests	Skipped	Failures	Errors	Time
361	0 :zzz:	0 :x:	0 :fire:	1m 0s :stopwatch:

[jcrozum]

Just realized that some more pruning might be possible and might be necessary to get things perfectly matched up with pystablemotifs. Please hold off on merging until I've had a chance to give it more thought (tomorrow--it's late here and I'm not anywhere near 100% brainpower).

[jcrozum]

@daemontus I think this should resolve the main issues we discussed this morning (afternoon for you, I guess). I made the path skipping you implemented is optional, and the option isn't used anywhere (defaults to not use it). I think with your new method to merge the intervention outputs and the improved descendant checking I just added, we should resolve inconsistencies with pystablemotifs (except in cases where pystablemotifs messes up due to worse percolation, as we discussed).

[daemontus]

Thank you!

Your latest changes with the skip_feedforward_successions did indeed help quite a bit. We still need to prune the control strategies in the benchmark script because there are sometimes duplicates across different intervention objects. But overall, the new situation is much better.

I believe there might be another problem in pystablemotifs (I'll send more in an email), but there's probably nothing we can do with that.

[daemontus]

I've added the fix for "lost" stable motifs. I think we can merge this now.