TreePPL bridge #374
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TreePPL bridge #374
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That's awesome, let's talk in detail during today's meeting. |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #374 +/- ##
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- Coverage 87.82% 87.14% -0.69%
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Files 107 108 +1
Lines 2654 2675 +21
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Hits 2331 2331
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This should crash on CI, maybe remove new line after?
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No need to redefined it if it's identical to the one in the blang file.
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This PR adds TreePPL support via the
stdiointerface for non-Julian MCMC. TreePPL is a universal probabilistic programming language aimed at phylogeneticists.I've tried to follow the
BlangTargetclosely in implementing this bridge both here and on the TreePPL side, but tried to keep the API as slim as possible. The API gives access to all relevant flags in TreePPL via thetppl_compile_modelfunction. I have however deferred the installation to the TreePPL installation guide since installation of it along with all dependencies is too complicated to maintain here in my opinion.This PR depends on two PRs on the TreePPL side:
Miking CorePPL is a somewhat low level functional PPL that TreePPL compiles to. Both PRs are in the merge pipeline on the TreePPL/Miking side -- I thought I would keep this PR in a draft state until they are merged.
Note on sampling at temperature 0.0
Many models that are familiar in TreePPL contain hard constraints which means that there would be a discontinuity in the tempering path at temperature zero if we were to temper from the prior. Since I believe that this is not desired I have allowed two different options for sampling at temperature 0.0:
These option is controlled via the
use_global::Boolargument intppl_compile_modelfunction. Please let me know if you have any other suggestions for addressing this problem!