This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository beast2-mcmc.
commit 7d77a988a27d9b8a4fadf83bddac0f4876eceba3 Merge: 7975391 37327ec Author: Andreas Tille <[email protected]> Date: Tue Aug 30 08:31:11 2016 +0200 Merge tag 'upstream/2.4.3+dfsg' Upstream version 2.4.3+dfsg build.xml | 4 +- release/common/README.txt | 4 +- release/common/VERSION HISTORY.txt | 27 +- src/beast/app/BEASTVersion.java | 2 +- src/beast/app/BEASTVersion2.java | 2 +- src/beast/app/BeastMCMC.java | 8 +- src/beast/app/DocMaker.java | 3 +- src/beast/app/beastapp/BeastLauncher.java | 2 +- src/beast/app/beastapp/BeastMain.java | 2 + src/beast/app/beauti/AlignmentImporter.java | 54 +++ src/beast/app/beauti/AlignmentListInputEditor.java | 8 +- src/beast/app/beauti/Beauti.java | 12 +- src/beast/app/beauti/BeautiAlignmentProvider.java | 468 ++++++++++++--------- src/beast/app/beauti/BeautiDoc.java | 1 + src/beast/app/beauti/GuessPatternDialog.java | 5 +- src/beast/app/beauti/JPackageDialog.java | 166 +++++++- src/beast/app/beauti/JPackageRepositoryDialog.java | 2 + src/beast/app/beauti/MRCAPriorInputEditor.java | 101 +++++ src/beast/app/beauti/OperatorListInputEditor.java | 3 +- .../beauti/ParametricDistributionInputEditor.java | 19 +- src/beast/app/beauti/PriorInputEditor.java | 4 +- src/beast/app/beauti/PriorListInputEditor.java | 173 +++++--- src/beast/app/beauti/PriorProvider.java | 24 ++ src/beast/app/beauti/TaxonSetDialog.java | 6 +- src/beast/app/beauti/TaxonSetInputEditor.java | 9 +- src/beast/app/beauti/TipDatesInputEditor.java | 159 ------- src/beast/app/draw/BEASTObjectInputEditor.java | 3 +- src/beast/app/draw/DoubleListInputEditor.java | 7 +- src/beast/app/draw/EnumInputEditor.java | 4 + src/beast/app/draw/InputEditor.java | 2 +- src/beast/app/draw/IntegerListInputEditor.java | 3 +- src/beast/app/tools/LogCombiner.java | 8 +- src/beast/app/treeannotator/TreeAnnotator.java | 2 + src/beast/app/util/Utils.java | 2 +- src/beast/core/BEASTInterface.java | 38 +- src/beast/core/Citation.java | 18 +- src/beast/core/Logger.java | 2 +- src/beast/core/parameter/Parameter.java | 2 +- src/beast/core/util/Sum.java | 32 +- src/beast/evolution/alignment/TaxonSet.java | 4 +- src/beast/evolution/datatype/IntegerData.java | 7 + .../likelihood/ThreadedTreeLikelihood.java | 8 +- .../evolution/speciation/CalibratedYuleModel.java | 1 + src/beast/evolution/tree/RandomTree.java | 16 +- src/beast/evolution/tree/TraitSet.java | 3 +- src/beast/evolution/tree/Tree.java | 1 + src/beast/evolution/tree/TreeHeightLogger.java | 7 +- src/beast/evolution/tree/TreeStatLogger.java | 80 ++++ .../tree/coalescent/ExponentialGrowth.java | 5 +- .../evolution/tree/coalescent/TreeIntervals.java | 21 +- src/beast/math/distributions/Gamma.java | 42 +- src/beast/math/distributions/MRCAPrior.java | 2 +- src/beast/util/AddOnManager.java | 89 +++- src/beast/util/Package.java | 16 +- src/beast/util/TreeParser.java | 15 +- src/beast/util/XMLParser.java | 37 +- src/beast/util/XMLParserUtils.java | 19 +- src/beast/util/XMLProducer.java | 26 +- .../beast/app/beauti/BeautiRateTutorialTest.java | 5 +- src/test/beast/core/BEASTInterfaceTest.java | 16 + src/test/beast/core/util/SumTest.java | 63 +++ .../beast/evolution/datatype/IntegerDataTest.java | 32 ++ src/test/beast/evolution/tree/TraitSetTest.java | 78 ++++ src/test/beast/math/distributions/GammaTest.java | 101 +++++ .../beast/math/distributions/InvGammaTest.java | 128 ++++++ .../LogNormalDistributionModelTest.java | 140 +++++- .../beast/math/distributions/MRCAPriorTest.java | 19 + .../math/distributions/NormalDistributionTest.java | 132 ++++++ 68 files changed, 1954 insertions(+), 550 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
