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Commits on Mar 17, 2025

• restore frequencies warning statement #1185

  jordandouglas

  committedMar 17, 2025
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• request frequencies update fixes #1185

  jordandouglas

  committedMar 17, 2025
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Commits on Mar 4, 2025

• make BactrianOperatorSchedule ignore Uniform operators if parameter is not a RealParameter #1183

  rbouckaert

  committedMar 4, 2025
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Commits on Feb 27, 2025

• add public method to GeneralSubstitutionModel fixes #1181

  jordandouglas

  committedFeb 27, 2025
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Commits on Jan 15, 2025

• robustify tree likelihoods for possibility data is not Alignment #1174

  rbouckaert

  committedJan 15, 2025
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• start Alignment refactoring, add TreeTipData #1174

  rbouckaert

  committedJan 15, 2025
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Commits on Jan 5, 2025

• make TreeWithMetaDataLogger produce correct nr of commas. fixes #1177

  rbouckaert

  committedJan 5, 2025
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Commits on Oct 31, 2024

• fix compile error #1172

  rbouckaert

  committedOct 31, 2024
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• add benchmark interface to BeagelTreeLikelihood #1172

  rbouckaert

  committedOct 31, 2024
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Commits on Sep 29, 2024

• towards renaming scaleFactor to windowSize in BactrianRandomWalkOperator #1169

  rbouckaert

  committedSep 29, 2024
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Commits on Sep 24, 2024

• correction to #1168

  jordandouglas

  committedSep 24, 2024
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Commits on Sep 23, 2024

• fix indexing error in beagle tree likellihood fixes #1168

  jordandouglas

  committedSep 23, 2024
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Commits on Sep 16, 2024

• set ids of trees parsed from NEXUS file. fixes CompEvol/BeastFX#87

  rbouckaert

  committedSep 16, 2024
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Commits on Sep 9, 2024

• facilitate beast "-validate" option CompEvol/BeastFX#86

  rbouckaert

  committedSep 9, 2024
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Commits on Sep 1, 2024

• Merge pull request #1164 from tgvaughan/packagemanager-patch

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  rbouckaert

  authoredSep 1, 2024
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Commits on Aug 30, 2024

• Adds CL packagemanager option to add repositories. Closes #1163

  tgvaughan

  committedAug 30, 2024
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Commits on Aug 5, 2024

• update parameter dimension on -resume #fixes 1159

  jordandouglas

  committedAug 5, 2024
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Commits on Jul 19, 2024

• improve error message for XML where the spec attribute is missing #28

  rbouckaert

  committedJul 19, 2024
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Commits on Jun 27, 2024

• deal with spaces in quoted attribute values #30

  rbouckaert

  committedJun 27, 2024
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Commits on Jun 10, 2024

• make alignments non-clonable for BEAUti link/unlink support #1150

  rbouckaert

  committedJun 10, 2024
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• Prerelease v2.7.7 #1152

  rbouckaert

  committedJun 10, 2024
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Commits on May 23, 2024

• allow beast to launch via java -jar launcher.jar fixes #1151

  rbouckaert

  committedMay 23, 2024
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Commits on May 16, 2024

• make Alignment a StateNode -- needs testing #1150

  rbouckaert

  committedMay 16, 2024
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Commits on May 3, 2024

• remove junit test from default ant target -- can still be accessed through ant junit #1149

  rbouckaert

  committedMay 3, 2024
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Commits on Mar 19, 2024

• make Randomizer thread aware, which makes it deterministic even when running with threads. #1141

  rbouckaert

  committedMar 19, 2024
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• fix build.xml to make junit-integration target pass. This introduces a dependency to BeastFX, but there are already other places in the build.xml file that depend on BeastFX, so this is something t…

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  rbouckaert

  committedMar 19, 2024
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Commits on Jan 1, 2024

• make the AdaptableOperatorSampler ignore zero weight operators. fixes #1136

  rbouckaert

  committedJan 1, 2024
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Commits on Nov 19, 2023

• update version history #1131

  rbouckaert

  committedNov 19, 2023
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Commits on Nov 7, 2023

• improve error message when forgetting @ in XML #28

  rbouckaert

  committedNov 7, 2023
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Commits on Oct 8, 2023

• bump version number #1131

  rbouckaert

  committedOct 8, 2023
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Commits on Oct 2, 2023

• ensure restore of Parameter works after dimension change. fixes #1130

  rbouckaert

  committedOct 2, 2023
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Commits on Oct 1, 2023

• make sure TipDatesRandomWalker picks up correct taxon set when used in BEAuti. CompEvol/BeastFX#45

  rbouckaert

  committedOct 1, 2023
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Commits on Sep 14, 2023

• Merge branch 'master' of https://github.com/CompEvol/beast2

  jordandouglas

  committedSep 14, 2023
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• add try catch around tree metric solves #1129

  jordandouglas

  committedSep 14, 2023
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Commits on Sep 12, 2023

• replace RealParameter with Function for clock.rate input of ClusterTree. #932 fixes #1124 as side effect

  rbouckaert

  committedSep 12, 2023
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