This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository beast2-mcmc.
commit 18a207f766f1e627b482badde79ac8cdd7d8234a Merge: b9a83f4 e8824d3 Author: Andreas Tille <[email protected]> Date: Tue Mar 8 16:08:54 2016 +0100 Merge tag 'upstream/2.4.0pre+dfsg' Upstream version 2.4.0pre+dfsg build.xml | 25 +- doc/tutorials/EBSP/Makefile | 16 + doc/tutorials/EBSP/ebsp2-tut.bib | 51 + doc/tutorials/EBSP/ebsp2-tut.tex | 376 ++++ doc/tutorials/EBSP/figures/clock_model.png | Bin 0 -> 16792 bytes doc/tutorials/EBSP/figures/clock_model2.png | Bin 0 -> 12830 bytes doc/tutorials/EBSP/figures/clock_model3.png | Bin 0 -> 12619 bytes doc/tutorials/EBSP/figures/clock_model4.png | Bin 0 -> 12816 bytes doc/tutorials/EBSP/figures/clockrate_prior.png | Bin 0 -> 32789 bytes doc/tutorials/EBSP/figures/import_alignment.png | Bin 0 -> 18962 bytes doc/tutorials/EBSP/figures/import_alignment2.png | Bin 0 -> 28831 bytes doc/tutorials/EBSP/figures/mcmc_panel.png | Bin 0 -> 24809 bytes doc/tutorials/EBSP/figures/mystery1.pdf | Bin 0 -> 6323 bytes doc/tutorials/EBSP/figures/mystery2.pdf | 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src/org/json/zip/PostMortem.java | 47 - src/org/json/zip/README | 2 - src/org/json/zip/TrieKeep.java | 396 ---- src/test/beast/BEASTTestCase.java | 3 +- src/test/beast/app/BeautiSubTemplateTest.java | 184 +- src/test/beast/app/BeautiTest.java | 32 +- src/test/beast/app/beauti/BeautiBase.java | 22 +- .../app/beauti/BeautiDivergenceDatingTest.java | 43 +- .../beast/app/beauti/BeautiRateTutorialTest.java | 22 +- src/test/beast/app/beauti/BeautiSimpleTest.java | 16 +- src/test/beast/app/beauti/BeautiStarBeastTest.java | 5 +- src/test/beast/app/beauti/CloneTest.java | 1 - src/test/beast/app/beauti/FixedMeanRateTest.java | 24 +- src/test/beast/app/beauti/LinkUnlinkTest.java | 2 +- src/test/beast/beast2vs1/ClockModelTest.java | 3 +- src/test/beast/beast2vs1/StarBEASTTest.java | 3 +- .../beast/beast2vs1/SubstitutionModelTest.java | 3 +- src/test/beast/beast2vs1/TaxonOrderTest.java | 3 +- src/test/beast/beast2vs1/TestFramework.java | 26 +- src/test/beast/beast2vs1/TipTimeTest.java | 3 +- src/test/beast/beast2vs1/TreePriorTest.java | 3 +- src/test/beast/beast2vs1/TreeTest.java | 3 +- .../beast/beast2vs1/trace/DiscreteStatistics.java | 13 +- src/test/beast/beast2vs1/trace/Expectation.java | 13 +- src/test/beast/beast2vs1/trace/LogAnalyser.java | 25 +- src/test/beast/beast2vs1/trace/LogFileTraces.java | 4 + .../beast/beast2vs1/trace/NumberFormatter.java | 2 +- src/test/beast/beast2vs1/trace/TraceException.java | 4 +- .../beast/beast2vs1/trace/TraceStatistics.java | 4 +- src/test/beast/beast2vs1/trace/TraceType.java | 9 +- src/test/beast/beast2vs1/trace/TrimLineReader.java | 3 +- src/test/beast/core/BEASTInterfaceTest.java | 36 +- src/test/beast/core/StateNodeInitialiserTest.java | 5 +- .../core/parameter/BooleanParameterListTest.java | 18 +- .../core/parameter/IntegerParameterListTest.java | 18 +- src/test/beast/core/parameter/ParameterTest.java | 2 - .../core/parameter/RealParameterListTest.java | 18 +- .../evolution/alignment/FilteredAlignmentTest.java | 17 +- .../alignment/UncertainAlignmentTest.java | 8 +- .../alignment/UnorderedAlignmentsTest.java | 13 +- .../evolution/likelihood/TreeLikelihoodTest.java | 159 +- .../evolution/operator/ExchangeOperatorTest.java | 2 - .../operator/IntRandomWalkOperatorTest.java | 4 +- .../operator/UniformIntegerOperatorTest.java | 4 +- .../speciation/BirthDeathGernhard08ModelTest.java | 24 +- src/test/beast/evolution/substmodel/GTRTest.java | 60 +- src/test/beast/evolution/substmodel/HKYTest.java | 37 +- src/test/beast/evolution/tree/RandomTreeTest.java | 8 +- .../beast/evolution/tree/TreeAnnotatorTest.java | 13 +- .../tree/coalescent/BayesianSkylineTest.java | 2 +- src/test/beast/integration/DocumentationTest.java | 63 +- .../beast/integration/ExampleJSONParsingTest.java | 46 +- .../beast/integration/ExampleXmlParsingTest.java | 46 +- src/test/beast/integration/InputTypeTest.java | 172 +- src/test/beast/integration/ResumeTest.java | 7 +- src/test/beast/integration/XMLElementNameTest.java | 81 +- src/test/beast/integration/XMLProducerTest.java | 33 +- .../LogNormalDistributionModelTest.java | 7 +- .../beast/math/distributions/MRCAPriorTest.java | 35 +- .../MeanOfParametricDistributionTest.java | 11 +- .../beast/util/AnnotatedRunnableTestClass.java | 97 + src/test/beast/util/JSONTest.java | 109 +- src/test/beast/util/NexusParserTest.java | 54 +- src/test/beast/util/TreeParserTest.java | 43 +- src/test/beast/util/XMLTest.java | 43 + templates/Standard.xml | 4 +- templates/StarBeast.xml | 7 +- templates/TreePriors.xml | 2 +- version.xml | 1 + 455 files changed, 21656 insertions(+), 21730 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
