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Release v1.3.1

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@github-actions github-actions released this 15 Aug 14:12
· 1022 commits to master since this release
v1.3.1
f4359f1

Backwards-incompatible changes

  • Change the distribution name of the sampled-speciation birth-death model from dnSBBDP to dnSSBDP (#714).

Features

  • Distributions
    • Add a topologically constrained distribution for the state-dependent speciation and extinction process (#693).
    • Allow nonzero rho values in FBD analyses without extant tips (#788).
    • Make dnGLHBDSP faster and allow reporting stochastic mappings (#693).
  • Methods / arguments
    • Add an .nbranches( ) method to Tree (#759).
    • Add a method for calculating the standard error of marginal likelihood estimates (#779).
    • Add a nanoseconds option to time( ) (#796).
  • Interface
    • Nicer printing of member method lists (#800).
  • Misc
    • Biogeography: allow regional features and non-existent regions (#693).

Bug fixes

  • Regression fixes
    • Fix posterior predictive simulations that were broken in 1.3.0 (#778).
    • Fix validation analyses that were broken in 1.3.0 (#814).
  • Member procedures
    • Fix .getTopologyFrequency( ) behavior for tree traces (#750).
    • Fix .resolveMultifurcations( ) behavior in edge cases (#771, #780).
  • Nexus I/O
    • Make sure writeNexus( ) can handle BranchLengthTree vectors (#758).
    • Fix parsing of the STATELABELS block in Nexus files (#760).
    • Allow reading Nexus files with an ASSUMPTIONS block (#764).
  • MPI / MC^3
    • Fix segfault in MPI + MC^3 (#763).
    • Fix logging and progress monitoring for .runOneStone( ) + MPI (#782).
  • Moves
    • Fix argument name mismatch in mvUpDownSlide (#766).
    • Fix mvEllipticalSliceSamplingSimple to not require strict equality of likelihoods (#773).
    • Reject tree moves if there are no nodes for them to operate on (#798, #802).
  • Misc
    • Synchronize dirty flagging for nodes and transition probability matrices (#773).
    • Fix caching to avoid crashes when using dnReversibleJumpMixture (#773).
  • Partial
    • Avoid subscripting by -1 in dnAutocorrelatedEvent (#773).

Documentation improvements

  • Basic data types: Integer, Natural, Probability, Real (#714).
  • Birth-death models: dnCBDSP, dnCDBDP, dnSSBDP (#714).
  • Marginal likelihood estimators: pathSampler, steppingStoneSampler (#779).
  • Expand documentation for TraceTree (#800).

Infrastructure

  • Update DLLs to allow running RevStudio on Windows (#751).
  • Don't print operator summaries in coalescent tests, and only run 1 generation (#770).
  • Enable testing with assertions to detect out-of-bounds indices in std::vector (#773).
  • Don't skip remaining scripts in a test if one fails, and combine error message from multiple failing scripts in a test (#773).
  • Allow specifying a required exit code to allow/require failure (#773).
  • Fix check for missing output files (#773).
  • Make test runner output clearer and more informative (#773).
  • Replace boost::filesystem with std::filesystem (#807).

New contributors

Contributors

prilau
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