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

Control and drivers docs #101

Closed jcrozum closed 7 months ago

jcrozum commented 7 months ago

Documentation for the control module. Also some updates to the doc generation to fix small errors and clean up the docs website.

Finally, I changed the way Intervention objects are compared. Previously, we drew a very confusing distinction between equivalence and equality that no one is going to care about. I removed the is_equivalent function and made the equality function a bit more clear.

Note that this branch was derived from #100, so I will close that PR in favor of this one.

jcrozum commented 7 months ago

Forgot to mention I added short doc strings for type aliases because they are heavily used in the control module.

github-actions[bot] commented 7 months ago

Coverage

Coverage Report
FileStmtsMissCoverMissing
balm
   control.py1141488%102, 114, 120, 124, 129, 138–154, 472, 475, 488
   interaction_graph_utils.py54591%6–8, 47, 165–166
   motif_avoidant.py152299%25, 121
   petri_net_translation.py1481193%18–22, 58, 94, 207–208, 232–233, 242, 346
   space_utils.py129497%25–27, 252, 278
   succession_diagram.py2471295%6, 163, 177, 185, 188, 205–206, 312, 439, 627, 665, 700
   symbolic_utils.py26388%10–12, 44
   trappist_core.py1833084%11–15, 45, 47, 82, 129, 195, 197, 199, 227–230, 234–236, 256–262, 320, 322, 352, 392, 394, 425, 454
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
TOTAL146910093% 

Tests Skipped Failures Errors Time
363 0 :zzz: 0 :x: 0 :fire: 1m 2s :stopwatch:
jcrozum commented 7 months ago

We've already discussed most of the changes and the rest should be inoffensive. The tests are passing, so I'm just going to merge this.