Generations and parents by index array

[codecov[bot]]

Codecov Report

Merging #964 (1edc369) into master (1a407c1) will decrease coverage by 0.90%. The diff coverage is 97.66%.

@@            Coverage Diff             @@
##           master     #964      +/-   ##
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- Coverage   74.74%   73.84%   -0.90%     
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  Files          26       26              
  Lines        2138     2065      -73     
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- Hits         1598     1525      -73     
  Misses        540      540              

Flag	Coverage Δ
unittests	73.84% <97.66%> (-0.90%)	:arrow_down:

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Impacted Files	Coverage Δ
lineage/Analyze.py	92.78% <ø> (ø)
lineage/CellVar.py	100.00% <ø> (ø)
lineage/tests/test_CrossVal.py	100.00% <ø> (ø)
lineage/LineageTree.py	97.91% <94.64%> (-2.09%)	:arrow_down:
lineage/Viterbi.py	98.11% <97.05%> (-1.89%)	: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	96.62% <100.00%> (-0.11%)	:arrow_down:
lineage/tests/test_BaumWelch.py	100.00% <100.00%> (ø)
... and 1 more

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[aarmey]

This one's quite a bit of work to follow. It removes many of the list.index() operations for speed. Potentially some of these functions could now be wrapped with numba to speed them up later, too.

[aarmey]

Sure. Let me merge this, then we can put new docstrings on a new branch.

The next step more generally should be allowing rand_init to take a random number generator as an option. This then has to be passed along to all the random substeps, such as randomly generating the emissions, transitions, etc.

https://numpy.org/doc/stable/reference/random/index.html