Anaphory commented 5 years ago

At some point I would like to get towards supporting speciesnetwork and possibly other methods for reticuate phylogenies, effectively adding new classes of phylogeny priors.

Currently, handling of trees and tree priors is done very ad-hoc inside beastxml.py. The first step to greater prior flexibility is therefore to separate tree handling out to separate classes/modules, as is the case already for models and clocks.

This pull request presents a start of that process. The TreePrior object still contains functionality that should be moved to the base classes, and the communication between configuration object and tree prior still relies heavily on the BeastXML object, but I think this provides a good basis from which to work further.

codecov-io commented 5 years ago

Codecov Report

Merging #226 into develop will decrease coverage by 1.84%. The diff coverage is 72.54%.

@@             Coverage Diff             @@
##           develop     #226      +/-   ##
===========================================
- Coverage    93.49%   91.64%   -1.85%     
===========================================
  Files           21       23       +2     
  Lines         2612     2704      +92     
===========================================
+ Hits          2442     2478      +36     
- Misses         170      226      +56

Impacted Files	Coverage Δ
beastling/treepriors/coalescent.py	`100% <100%> (ø)`
beastling/beastxml.py	`94.73% <100%> (+0.84%)`	:arrow_up:
beastling/configuration.py	`92.03% <100%> (+0.03%)`	:arrow_up:
beastling/treepriors/base.py	`69.4% <69.4%> (ø)`

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Anaphory commented 5 years ago

Okay, so it works, but examples for uniform and birth-death tree priors are still missing.

lmaurits / BEASTling

Separate tree handling out to a separate module #226

Codecov Report