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 - - - - - 9d2531c0 by Pierre Gruet at 2026-08-06T17:28:04+02:00 Removing R-R-R: no, which is now defaults - - - - - 999d9c95 by Pierre Gruet at 2026-08-06T17:28:27+02:00 Raising Standards version to 4.7.4 - - - - - 250fc2d7 by Pierre Gruet at 2026-08-06T17:29:06+02:00 Switching to debhelper-compat 14, removing shlibs and misc substvars - - - - - 3b024840 by Pierre Gruet at 2026-08-06T17:32:36+02:00 Raising d/watch version to 5 - - - - - 9c47944b by Pierre Gruet at 2026-08-06T17:42:23+02:00 New upstream version 2.7.8+dfsg - - - - - 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 - - - - - 80b762f9 by Pierre Gruet at 2026-08-06T17:43:30+02:00 Updating the list of files to exclude when repacking - - - - - 7a8ffdd5 by Pierre Gruet at 2026-08-06T19:02:54+02:00 Refreshing patches - - - - - f2002a43 by Pierre Gruet at 2026-08-06T19:03:24+02:00 Updating changelog - - - - - a85d043f by Pierre Gruet at 2026-08-06T21:48:12+02:00 Dropping an unnecessary dependency in build.xml - - - - - 32f1516f by Pierre Gruet at 2026-08-06T21:48:22+02:00 Upload to unstable - - - - - 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 -- View it on GitLab: https://salsa.debian.org/med-team/beast2-mcmc/-/compare/224ceec723b365f2c69acfdfba252584ddfbbebb...32f1516fa24f6c56ae37a6308c452b68386e9f3d You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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