jcrozum / biobalm

The biologist's Boolean attractor landscape mapper, building Waddington landscapes from Boolean networks.
https://jcrozum.github.io/biobalm/
MIT License
2 stars 0 forks source link

Organize SCC expansion module #112

Closed jcrozum closed 8 months ago

jcrozum commented 8 months ago

@daemontus I forgot that I had never made a PR for this branch. We'll need to do some more work to make the expansion methods intuitive for the end-user still, but I think this is a necessary first step.

Moves some of the source scc logic to the SuccessionDiagram class (adds component_subdiagrams method) and to the interaction_graph_utils module (adds source_SCCs function). This finally gives a proper resolution to our cyclic import issues.

Also, functionality from the custom percolation function in expand_source_SCCs.py was integrated into space_utils.percolate_network as an option.

github-actions[bot] commented 8 months ago

Coverage

Coverage Report
FileStmtsMissCoverMissing
balm
   control.py1141488%107, 119, 125, 129, 134, 143–159, 477, 480, 493
   interaction_graph_utils.py38489%11–13, 151–152
   motif_avoidant.py148299%26, 181
   petri_net_translation.py1491193%22–26, 79, 136, 305–306, 330–331, 340, 449
   space_utils.py132497%26–28, 414, 462
   succession_diagram.py2801794%6, 188–193, 201, 261–262, 272, 278, 394, 584, 660, 851, 889, 926
   symbolic_utils.py26388%10–12, 102
   trappist_core.py1833084%14–18, 55, 57, 92, 168, 215, 217, 219, 247–250, 254–256, 276–282, 340, 342, 372, 420, 422, 453, 506
balm/_sd_algorithms
   compute_attractor_seeds.py30197%8
   expand_attractor_seeds.py51590%6, 42, 97–102
   expand_bfs.py28196%6
   expand_dfs.py30197%6
   expand_minimal_spaces.py37295%6, 31
   expand_source_SCCs.py122497%14–16, 86, 131
   expand_to_target.py31390%6, 38, 43
TOTAL146010293% 

Tests Skipped Failures Errors Time
361 0 :zzz: 0 :x: 0 :fire: 36.863s :stopwatch: