meyer-lab / tHMM

A general Python framework for using hidden Markov models on binary trees or cell lineage trees.
https://asmlab.org
MIT License
10 stars 1 forks source link

Yet more cleanup #962

Closed aarmey closed 2 years ago

aarmey commented 2 years ago

Getting rid of some unused material, moving lineage-specific functions into the lineage class.

codecov[bot] commented 2 years ago

Codecov Report

Merging #962 (7dab69e) into master (ff27f4d) will decrease coverage by 7.17%. The diff coverage is 99.66%.

@@            Coverage Diff             @@
##           master     #962      +/-   ##
==========================================
- Coverage   82.00%   74.83%   -7.18%     
==========================================
  Files          28       26       -2     
  Lines        2251     2154      -97     
==========================================
- Hits         1846     1612     -234     
- Misses        405      542     +137     
Flag Coverage Δ
unittests 74.83% <99.66%> (-7.18%) :arrow_down:

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Impacted Files Coverage Δ
lineage/BaumWelch.py 88.63% <96.00%> (+1.96%) :arrow_up:
lineage/Analyze.py 93.81% <100.00%> (+7.64%) :arrow_up:
lineage/CellVar.py 98.79% <100.00%> (+1.35%) :arrow_up:
lineage/LineageInputOutput.py 74.00% <100.00%> (-18.00%) :arrow_down:
lineage/LineageTree.py 100.00% <100.00%> (ø)
lineage/Viterbi.py 100.00% <100.00%> (ø)
lineage/import_lineage.py 97.08% <100.00%> (-0.09%) :arrow_down:
lineage/states/stateCommon.py 80.00% <100.00%> (+9.72%) :arrow_up:
lineage/tHMM.py 96.73% <100.00%> (-0.27%) :arrow_down:
lineage/tests/test_BaumWelch.py 100.00% <100.00%> (ø)
... and 8 more

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