search

YosefLab / Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
https://cassiopeia-lineage.readthedocs.io/en/latest/
MIT License
77 stars 24 forks source link

SNJ Solver Implementation #161

Closed kevinan1 closed 2 years ago

kevinan1 commented 2 years ago

Updated Spectral Neighbor Joining algorithm implementation

Fixed formatting issues, including some typos, line lengths, and other styling. Also updated (ivan) the algorithm itself to not recalculate second singular values, resulting in performance improvements.

codecov[bot] commented 2 years ago

Codecov Report

Merging #161 (da80d89) into master (034f65c) will increase coverage by 0.10%. The diff coverage is 92.50%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #161      +/-   ##
==========================================
+ Coverage   87.03%   87.13%   +0.10%     
==========================================
  Files          75       76       +1     
  Lines        5521     5637     +116     
==========================================
+ Hits         4805     4912     +107     
- Misses        716      725       +9
Impacted Files Coverage Δ
cassiopeia/solver/dissimilarity_functions.py 84.95% <61.90%> (-5.27%) :arrow_down:
cassiopeia/solver/SpectralNeighborJoiningSolver.py 98.91% <98.91%> (ø)
cassiopeia/solver/DistanceSolver.py 93.33% <100.00%> (+0.22%) :arrow_up:
cassiopeia/solver/__init__.py 100.00% <100.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 034f65c...da80d89. Read the comment docs.