First changes

[aarmey]

• Provides a custom differencing function for performance.
• Uses the sorting of cells in the lineage to simplify loop iteration.
• Fixes some typos in the tests (!)
• Simplifies some of the censoring code.

[aarmey]

@Farnazmdi please go through this carefully. If this all looks reasonable, I will go through it once more and then merge.

[codecov[bot]]

Codecov Report

Merging #979 (63d0702) into master (1a407c1) will decrease coverage by 0.54%. The diff coverage is 96.46%.

:exclamation: Current head 63d0702 differs from pull request most recent head 7ba151c. Consider uploading reports for the commit 7ba151c to get more accurate results

@@            Coverage Diff             @@
##           master     #979      +/-   ##
==========================================
- Coverage   74.74%   74.21%   -0.54%     
==========================================
  Files          26       26              
  Lines        2138     2094      -44     
==========================================
- Hits         1598     1554      -44     
  Misses        540      540              

Flag	Coverage Δ
unittests	74.21% <96.46%> (-0.54%)	:arrow_down:

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Impacted Files	Coverage Δ
lineage/Analyze.py	92.78% <ø> (ø)
lineage/tests/test_CrossVal.py	100.00% <ø> (ø)
lineage/LineageTree.py	97.81% <92.10%> (-2.19%)	:arrow_down:
lineage/Viterbi.py	98.50% <92.85%> (-1.50%)	:arrow_down:
lineage/states/StateDistributionGaPhs.py	100.00% <100.00%> (+3.66%)	:arrow_up:
lineage/states/StateDistributionGamma.py	93.96% <100.00%> (-1.18%)	:arrow_down:
lineage/states/stateCommon.py	100.00% <100.00%> (ø)
lineage/tHMM.py	96.66% <100.00%> (-0.08%)	:arrow_down:
lineage/tests/test_BaumWelch.py	100.00% <100.00%> (ø)
lineage/crossval.py	82.05% <0.00%> (ø)

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[aarmey]

Yes, we need to look into the tests. Those arguments were misspelled, so they were essentially only running for the uncensored case. However, I have gone through this again and am confident in the changes. Merging.