[med-svn] [Git][med-team/beast2-mcmc][master] 12 commits: Removing Priority: optional, which is now defaults

[Pierre Gruet (@pgt)]

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


Commits:
54ba6d89 by Pierre Gruet at 2026-08-06T17:28:00+02:00
Removing Priority: optional, which is now defaults

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9d2531c0 by Pierre Gruet at 2026-08-06T17:28:04+02:00
Removing R-R-R: no, which is now defaults

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999d9c95 by Pierre Gruet at 2026-08-06T17:28:27+02:00
Raising Standards version to 4.7.4

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250fc2d7 by Pierre Gruet at 2026-08-06T17:29:06+02:00
Switching to debhelper-compat 14, removing shlibs and misc substvars

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3b024840 by Pierre Gruet at 2026-08-06T17:32:36+02:00
Raising d/watch version to 5

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9c47944b by Pierre Gruet at 2026-08-06T17:42:23+02:00
New upstream version 2.7.8+dfsg
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4ff923b7 by Pierre Gruet at 2026-08-06T17:42:28+02:00
Update upstream source from tag 'upstream/2.7.8+dfsg'

Update to upstream version '2.7.8+dfsg'
with Debian dir eda9540df6a5300c3d0999e80e014aae99292224
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80b762f9 by Pierre Gruet at 2026-08-06T17:43:30+02:00
Updating the list of files to exclude when repacking

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7a8ffdd5 by Pierre Gruet at 2026-08-06T19:02:54+02:00
Refreshing patches

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f2002a43 by Pierre Gruet at 2026-08-06T19:03:24+02:00
Updating changelog

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a85d043f by Pierre Gruet at 2026-08-06T21:48:12+02:00
Dropping an unnecessary dependency in build.xml

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32f1516f by Pierre Gruet at 2026-08-06T21:48:22+02:00
Upload to unstable

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99 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
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/disable_test_with_gpu.patch
- debian/patches/exclude_tests_using_testfx.patch
- debian/patches/fix_classpath_in_build_xml.patch
- debian/patches/grasp_beast2app_from_component.patch
- debian/patches/location_of_shipped_version_xml.patch
- debian/patches/no_embedding_of_dependencies_in_jars.patch
- debian/patches/remove_appbundler.patch
- debian/patches/remove_jsign_from_build.patch
- debian/watch
- + 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/-/compare/224ceec723b365f2c69acfdfba252584ddfbbebb...32f1516fa24f6c56ae37a6308c452b68386e9f3d

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View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/224ceec723b365f2c69acfdfba252584ddfbbebb...32f1516fa24f6c56ae37a6308c452b68386e9f3d
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