jcrozum / biobalm

The biologist's Boolean attractor landscape mapper, building Waddington landscapes from Boolean networks.
https://jcrozum.github.io/biobalm/
MIT License
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Succession diagram exposure #96

Closed jcrozum closed 9 months ago

jcrozum commented 9 months ago

This PR reorganizes things a little bit for three reasons:

  1. To make it so users can write balm.SuccessionDiagram.from_aeon(bn) instead of balm.SuccessionDiagram.SuccessionDiagram.from_aeon(bn).
  2. Reduce ambiguity between the SuccessionDiagram class and module (the module is now called succession_diagram).
  3. To make it easier to auto-generate the API docs later (the auto-doc can get confused when classes and modules share names, especially when we still have a not-quite-fully-resolved cyclic import problem).
github-actions[bot] commented 9 months ago

Coverage

Coverage Report
FileStmtsMissCoverMissing
balm
   control.py1231489%48, 57, 61, 67, 81, 90–106, 329, 332, 345
   interaction_graph_utils.py54591%6–8, 47, 165–166
   motif_avoidant.py152299%24, 120
   petri_net_translation.py1481193%17–21, 57, 93, 206–207, 231–232, 241, 345
   space_utils.py129497%24–26, 251, 277
   succession_diagram.py2471295%6, 163, 177, 185, 188, 205–206, 312, 439, 627, 665, 700
   symbolic_utils.py26388%10–12, 44
   trappist_core.py1833084%10–14, 44, 46, 81, 128, 194, 196, 198, 226–229, 233–235, 255–261, 319, 321, 351, 391, 393, 424, 453
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.py164696%19–21, 91, 101, 143, 287
   expand_to_target.py31390%6, 38, 43
TOTAL147410093% 

Tests Skipped Failures Errors Time
364 0 :zzz: 0 :x: 0 :fire: 49.565s :stopwatch:
jcrozum commented 9 months ago

Merging as per our discussion this morning.