Closed mattjones315 closed 3 years ago
(@mattjones315 just added a couple comments / questions, not really a review!)
Merging #125 (9dd8fde) into master (9ff60ed) will decrease coverage by
0.00%
. The diff coverage is100.00%
.
@@ Coverage Diff @@
## master #125 +/- ##
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- Coverage 85.31% 85.31% -0.01%
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Files 65 65
Lines 4434 4527 +93
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+ Hits 3783 3862 +79
- Misses 651 665 +14
Impacted Files | Coverage Δ | |
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cassiopeia/data/CassiopeiaTree.py | 92.22% <100.00%> (+0.84%) |
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cassiopeia/mixins/errors.py | 100.00% <100.00%> (ø) |
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cassiopeia/tools/__init__.py | 100.00% <100.00%> (ø) |
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cassiopeia/tools/small_parsimony.py | 98.51% <100.00%> (-1.49%) |
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cassiopeia/solver/HybridSolver.py | 73.94% <0.00%> (-11.77%) |
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cassiopeia/solver/MaxCutGreedySolver.py | 93.47% <0.00%> (-4.35%) |
:arrow_down: |
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Thanks for the help @sprillo & @Lioscro! I believe I've addressed all of your collective comments. @Lioscro -- would you mind taking another look when you have a chance and letting me know if the codebase looks good for merging in or if there's anything else you'd like me to change? Thanks in advance!
This PR implements FitchCount, previously described in Quinn et al, Science 2021. This is implemented as a function in
cassiopeia/tools/small_parsimony.py
, but per a conversation with @sprillo, we are entertaining the idea of eventually moving this over to a separate library with an emphasis on rate-matrix estimation.As I implemented FitchCount, I also implemented functionality for performing a breadth-first-search on the tree, as well as subsetting the tree to get the subtree below a given node.