Fast-forward source node expansion anywhere in the succession diagram

[daemontus]

This is a slightly more controversial update:

During the block expansion, allow to "fast-forward" the expansion of source nodes anywhere in the succession diagram. That is, if the percolation of a stable motif results in the creation of a bunch of source nodes, we automatically create 2**n successors for these without further analysis (they can't contain motif-avoidant attractors anyway). However, this only happens with block expansion and can be turned off using the recently added optimize_source_nodes flag.

This eliminates 88 978 SD nodes and almost 9 minutes of compute time for the BBM "easy" models alone. I haven't retested all the hard models yet, but this overall seems like a win. It does sometimes increase the ratio of expanded nodes vs. the non-expanded ones, but is mostly not an issue, because the ones where we expand the source nodes cost us very little compute.

[daemontus]

Performance data for the "easy" BBM models:

biobalm-source-fast-forward.xlsx

[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	380	64	83%	6, 120, 210–215, 228, 275–282, 386–393, 410–411, 421, 427, 543, 630–636, 752, 755, 873–891, 923, 933, 936, 976, 983, 1034, 1052, 1174, 1360, 1371, 1379, 1422, 1434, 1439, 1445
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	40	2	95%	6, 37
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	113	15	87%	10, 30, 42, 54, 64, 71, 76, 79, 138, 164, 173, 206, 216, 222, 231
expand_to_target.py	31	3	90%	6, 38, 43
biobalm/_sd_attractors
attractor_candidates.py	265	90	66%	13–15, 26–27, 93, 101, 107–108, 130, 152, 187, 193–204, 223, 239–320, 325, 329, 335, 341, 356, 383, 388, 392, 398, 400–438, 511, 582–583, 684
attractor_symbolic.py	114	16	86%	6–7, 75, 88–92, 103, 112, 144, 179, 191–193, 202, 230, 236
TOTAL	1985	345	83%

Tests	Skipped	Failures	Errors	Time
359	0 💤	0 ❌	0 🔥	55.206s ⏱️

[daemontus]

Merging since the tests passed and this does not have any affect on the structure produced during the full expansion, so it will not interfere with any other analysis tasks except for attractor detection (where it should be faster).