[med-svn] [Git][med-team/beast2-mcmc][upstream] New upstream version 2.7.8+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / beast2-mcmc


Commits:
9c47944b by Pierre Gruet at 2026-08-06T17:42:23+02:00
New upstream version 2.7.8+dfsg
- - - - -


87 changed files:

- + beastfx/.gitignore
- beastfx/Dockerfile
- beastfx/build.xml
- beastfx/src/beastfx/app/beast/BeastMCMC.java
- beastfx/src/beastfx/app/beast/BeastMain.java
- beastfx/src/beastfx/app/beauti/JPackageDialog.java
- beastfx/src/beastfx/app/inputeditor/AlignmentListInputEditor.java
- beastfx/src/beastfx/app/inputeditor/BeautiAlignmentProvider.java
- beastfx/src/beastfx/app/inputeditor/BeautiDoc.java
- beastfx/src/beastfx/app/inputeditor/BeautiSubTemplate.java
- beastfx/src/beastfx/app/inputeditor/DoubleListInputEditor.java
- beastfx/src/beastfx/app/inputeditor/FastaImporter.java
- beastfx/src/beastfx/app/inputeditor/InputEditor.java
- beastfx/src/beastfx/app/inputeditor/IntegerListInputEditor.java
- beastfx/src/beastfx/app/inputeditor/NexusImporter.java
- beastfx/src/beastfx/app/inputeditor/ParameterInputEditor.java
- beastfx/src/beastfx/app/seqgen/SimulatedAlignment.java
- beastfx/src/beastfx/app/tools/AppLauncher.java
- beastfx/src/beastfx/app/tools/Application.java
- beastfx/src/beastfx/app/tools/LogAnalyser.java
- beastfx/src/beastfx/app/tools/LogCombiner.java
- beastfx/src/beastfx/app/tools/LogCombinerController.java
- beastfx/src/beastfx/app/tools/LogCombinerDialog.java
- beastfx/src/beastfx/app/tools/logcombiner.fxml
- beastfx/src/beastfx/app/treeannotator/Controller.java
- beastfx/src/beastfx/app/treeannotator/TAGui.java
- beastfx/src/beastfx/app/treeannotator/TreeAnnotator.java
- beastfx/src/beastfx/app/treeannotator/services/CommonAncestorNodeHeigtService.java
- beastfx/src/beastfx/app/treeannotator/services/MCCTopologyService.java
- beastfx/src/beastfx/app/treeannotator/services/NodeHeightSettingService.java
- beastfx/src/beastfx/app/treeannotator/services/TopologySettingService.java
- beastfx/src/beastfx/app/util/Alert.java
- beastfx/src/beastfx/app/util/FXUtils.java
- beastfx/version.xml
- build.xml
- + examples/testDirichlet/plotResults.R
- + examples/testDirichlet/testDirichlet.xml
- + examples/testDirichlet/testDirichlet2.xml
- + examples/testDirichlet/testDirichletBact.xml
- + examples/testDirichlet/testDirichletMarginalDensity2.pdf
- + examples/testDirichlet/testDirichletNoPrior.xml
- release/common/README.txt
- release/common/VERSION HISTORY.txt
- src/beast/base/core/BEASTInterface.java
- src/beast/base/core/BEASTVersion2.java
- + src/beast/base/core/Citable.java
- src/beast/base/evolution/TreeWithMetaDataLogger.java
- src/beast/base/evolution/alignment/Alignment.java
- src/beast/base/evolution/alignment/FilteredAlignment.java
- + src/beast/base/evolution/alignment/TreeTipData.java
- src/beast/base/evolution/likelihood/BeagleTreeLikelihood.java
- src/beast/base/evolution/likelihood/ThreadedTreeLikelihood.java
- src/beast/base/evolution/likelihood/TreeLikelihood.java
- src/beast/base/evolution/operator/AdaptableOperatorSampler.java
- src/beast/base/evolution/operator/EpochFlexOperator.java
- src/beast/base/evolution/operator/kernel/BactrianOperatorSchedule.java
- src/beast/base/evolution/sitemodel/SiteModel.java
- src/beast/base/evolution/substitutionmodel/BinaryCovarion.java
- src/beast/base/evolution/substitutionmodel/Frequencies.java
- src/beast/base/evolution/substitutionmodel/GeneralSubstitutionModel.java
- src/beast/base/evolution/substitutionmodel/MutationDeathModel.java
- src/beast/base/evolution/substitutionmodel/TIM.java
- src/beast/base/evolution/substitutionmodel/TVM.java
- src/beast/base/evolution/tree/Tree.java
- src/beast/base/evolution/tree/coalescent/Coalescent.java
- src/beast/base/inference/MCMC.java
- src/beast/base/inference/Runnable.java
- src/beast/base/inference/StateNode.java
- src/beast/base/inference/distribution/Dirichlet.java
- + src/beast/base/inference/distribution/DirichletSimulator.java
- + src/beast/base/inference/distribution/LogNormal.java
- src/beast/base/inference/operator/DeltaExchangeOperator.java
- src/beast/base/inference/operator/kernel/BactrianDeltaExchangeOperator.java
- src/beast/base/inference/operator/kernel/BactrianRandomWalkOperator.java
- src/beast/base/inference/parameter/Map.java
- src/beast/base/inference/parameter/Parameter.java
- src/beast/base/parser/NexusParser.java
- src/beast/base/parser/XMLParser.java
- src/beast/base/util/MersenneTwisterFast.java
- src/beast/base/util/Randomizer.java
- src/beast/pkgmgmt/BEASTClassLoader.java
- src/beast/pkgmgmt/BEASTVersion.java
- src/beast/pkgmgmt/PackageManager.java
- src/org/apache/commons/math/distribution/AbstractIntegerDistribution.java
- + test/test/beast/evolution/inference/DirichletTest.java
- test/test/beast/evolution/operator/DeltaExchangeOperatorTest.java
- version.xml


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/commit/9c47944b8d1b1816624d7075878db751954c644c

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