Closed Anaphory closed 5 years ago
Merging #226 into develop will decrease coverage by
1.84%
. The diff coverage is72.54%
.
@@ Coverage Diff @@
## develop #226 +/- ##
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- Coverage 93.49% 91.64% -1.85%
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Files 21 23 +2
Lines 2612 2704 +92
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+ 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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Okay, so it works, but examples for uniform and birth-death tree priors are still missing.
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.