New uted

[BadPrograms]

Reimagined calculating tree distancces
We have 4 new files:
Approximations: The way to approximate a tree
deltas: the delta to compare trees, serves as a parameter for the approximator
distances: How to compare trees
Comparator: a new object to compare trees, where all previous parts are inserted as parameters ( can be referred to as El Comparator)

• Also added a new hashing system for LineageTrees

Approximations, deltas and distances contain template classes up for modification.
Also now it is streamlined to do parallel comparisons and plot a clustermap with ease.
important commands:

from lineagetree import LineageTree
from lineagetree.distance.comparator import TreeComparator
from lineagetree.distance.distance_calculator import UnorderedTreeEditDistance
from lineagetree.distance.approximations import ReducedTreeTimed,DownsampledTree, ResampledTree
from lineagetree.distance.delta import delta_binary,delta_normalized_difference
lT = ...

model = TreeComparator(UnorderedTreeEditDistance, ReducedTreeTimed(delta_normalized_difference))

model.compare((lT,6729, None), (lT, 10696, None))

trees = [(lT, root, None) for root in lT.roots if len(lT.get_subtree_nodes(root))>1000 ]

model.p_compare(*trees,n_proccessors=22)

model.plot_clustermap(*trees,norm= "sum")

model.compare_all_trees_that_start_at_t(lT,40)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.19%. Comparing base (8263d4d) to head (5bea21e).

Additional details and impacted files

@@            Coverage Diff             @@
##             v3.x     #112      +/-   ##
==========================================
+ Coverage   87.16%   87.19%   +0.02%     
==========================================
  Files          20       20              
  Lines        1932     1936       +4     
==========================================
+ Hits         1684     1688       +4     
  Misses        248      248              

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