Expansion limits - Githubissues

daemontus commented 3 months ago

This PR adds a few extra options to the expansion methods, but otherwise should not impact performance or correctness.

expand_minimal_spaces now has an optional starting node.
expand_block now has a size limit.
expand_block now has an optimize_source_nodes flag: this is mainly to ensure compatibility in tests. Normal expansion performs source node elimination before percolation, but block expansion does it after percolation, so it might run into source nodes that the full expansion does not see. In such case the two diagrams can be incomparable, even though both are technically correct.

github-actions[bot] commented 3 months ago

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	115	15	87%	11, 31, 46, 54, 59, 62, 86, 98, 141, 167, 176, 209, 219, 225, 234
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	1987	345	83%

Tests	Skipped	Failures	Errors	Time
359	0 :zzz:	0 :x:	0 :fire:	54.428s :stopwatch:

daemontus commented 3 months ago

Again, I am merging this PR since these are well understood changes that don't break any tests and don't introduce anything substantially new.

jcrozum / biobalm