manual merge master -> trait_beauti

beast-dev · Sep 19, 2023 · 872bef4 · 872bef4
2 parents b4b6438 + 185cfc9
commit 872bef4
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Showing 62 changed files with 3,061 additions and 444 deletions.
diff --git a/src/dr/app/beagle/tools/CompleteHistorySimulator.java b/src/dr/app/beagle/tools/CompleteHistorySimulator.java
@@ -114,12 +114,12 @@ public class CompleteHistorySimulator extends SimpleAlignment
      * @param branchRateModel
      * @param nReplications:  nr of samples to generate
      */
-//    public CompleteHistorySimulator(Tree tree, GammaSiteRateModel siteModel, BranchRateModel branchRateModel,
+//    public CompleteHistorySimulator(Tree tree, GammaSiteRateModelParser siteModel, BranchRateModel branchRateModel,
 //                                    int nReplications) {
 //        this(tree, siteModel, branchRateModel, nReplications, false);
 //    }
 //
-//    public CompleteHistorySimulator(Tree tree, GammaSiteRateModel siteModel, BranchRateModel branchRateModel,
+//    public CompleteHistorySimulator(Tree tree, GammaSiteRateModelParser siteModel, BranchRateModel branchRateModel,
 //                                    int nReplications, boolean sumAcrossSites) {
 //        this(tree, siteModel, branchRateModel, nReplications, sumAcrossSites, null, null);
 //

diff --git a/src/dr/app/beast/BeastMain.java b/src/dr/app/beast/BeastMain.java
@@ -356,7 +356,7 @@ public static void main(String[] args) throws java.io.IOException {
                         new Arguments.StringOption("prefix", "PREFIX", "Specify a prefix for all output log filenames"),
                         new Arguments.Option("overwrite", "Allow overwriting of log files"),
                         new Arguments.IntegerOption("errors", "Specify maximum number of numerical errors before stopping"),
-                        new Arguments.IntegerOption("threads", "The number of computational threads to use (default auto)"),
+                        new Arguments.IntegerOption("threads", "The maximum number of computational threads to use (default auto)"),
                         new Arguments.Option("fail_threads", "Exit with error on uncaught exception in thread."),
                         new Arguments.Option("java", "Use Java only, no native implementations"),
                         new Arguments.LongOption("tests", "The number of full evaluation tests to perform (default 1000)"),
@@ -375,8 +375,8 @@ public static void main(String[] args) throws java.io.IOException {
                         new Arguments.Option("beagle_GPU", "BEAGLE: use GPU instance if available"),
                         new Arguments.Option("beagle_SSE", "BEAGLE: use SSE extensions if available"),
                         new Arguments.Option("beagle_SSE_off", "BEAGLE: turn off use of SSE extensions"),
-                        new Arguments.Option("beagle_threading_off", "BEAGLE: turn off auto threading for a CPU instance"),
-                        new Arguments.IntegerOption("beagle_thread_count", 1, Integer.MAX_VALUE, "BEAGLE: manually set number of threads for a CPU instance"),
+                        new Arguments.Option("beagle_threading_off", "BEAGLE: turn off multi-threading for a CPU instance"),
+                        new Arguments.IntegerOption("beagle_threads", 0, Integer.MAX_VALUE, "BEAGLE: manually set number of threads per CPU instance (default auto)"),
                         new Arguments.Option("beagle_cuda", "BEAGLE: use CUDA parallization if available"),
                         new Arguments.Option("beagle_opencl", "BEAGLE: use OpenCL parallization if available"),
                         new Arguments.Option("beagle_single", "BEAGLE: use single precision if available"),
@@ -579,6 +579,9 @@ public static void main(String[] args) throws java.io.IOException {
         if (arguments.hasOption("beagle_thread_count")) {
             System.setProperty("beagle.thread.count", Integer.toString(arguments.getIntegerOption("beagle_thread_count")));
         }
+        if (arguments.hasOption("beagle_threads")) {
+            System.setProperty("beagle.thread.count", Integer.toString(arguments.getIntegerOption("beagle_threads")));
+        }
         if (arguments.hasOption("beagle_threading_off")) {
             System.setProperty("beagle.thread.count", Integer.toString(1));
         }

diff --git a/src/dr/app/beast/development_parsers.properties b/src/dr/app/beast/development_parsers.properties
@@ -122,9 +122,9 @@ dr.inferencexml.distribution.FactorTreeGibbsOperatorParser
 dr.inferencexml.operators.factorAnalysis.LatentFactorLiabilityGibbsOperatorParser
 dr.inferencexml.operators.JointGibbsOperatorParser
 dr.inferencexml.operators.factorAnalysis.LFMSplitMergeOperatorParser
-dr.evomodel.continuous.hmc.IntegratedLoadingsGradient
+#dr.evomodel.continuous.hmc.IntegratedLoadingsGradient ## doesn't seem to exist?
 dr.inferencexml.hmc.LoadingsTransformParser
-dr.evomodel.continuous.hmc.TaskPool
+#dr.evomodel.continuous.hmc.TaskPool ## doesn't seem to exist?
 dr.inference.model.LogOrderedMatrix
 dr.inference.operators.factorAnalysis.LoadingsRotationOperator
 dr.inference.model.SVDStatistic
@@ -182,6 +182,7 @@ dr.inference.regression.SelfControlledCaseSeries
 # SITE PATTERNS
 dr.evomodelxml.operators.PatternWeightIncrementOperatorParser
 
+
 # BRANCH SPECIFIC STUFF
 dr.evomodel.branchmodel.lineagespecific.CountableRealizationsParameterParser
 dr.evomodel.branchmodel.lineagespecific.DirichletProcessPriorParser
@@ -316,6 +317,8 @@ dr.inferencexml.distribution.shrinkage.JointBayesianBridgeStatisticsParser
 dr.inferencexml.hmc.CompoundPriorPreconditionerParser
 dr.inferencexml.hmc.NumericalGradientParser
 
+# SIMPLEX TRANSFORM
+dr.util.RealDifferencesToSimplexTransform
 
 # SMOOTH SKYGRID
 dr.evomodelxml.coalescent.smooth.SmoothSkygridLikelihoodParser
@@ -324,3 +327,6 @@ dr.evomodelxml.coalescent.smooth.SmoothSkygridLikelihoodParser
 dr.evomodelxml.substmodel.AminoAcidMixtureParser
 dr.evomodelxml.treedatalikelihood.SequenceDistanceStatisticParser
 dr.evomodelxml.tree.TreeReportParser
+
+# Misc
+dr.inferencexml.loggers.TimeLoggerXMLParser
diff --git a/src/dr/app/beast/release_parsers.properties b/src/dr/app/beast/release_parsers.properties
@@ -74,7 +74,10 @@ dr.evomodelxml.substmodel.InfinitesimalRatesLoggerParser
 dr.evomodelxml.substmodel.LewisMkSubstitutionModelParser
 
 # SITE RATE MODELS
-dr.evomodelxml.siteratemodel.GammaSiteModelParser
+#dr.evomodelxml.siteratemodel.SiteModelParser
+dr.evomodelxml.siteratemodel.OldGammaSiteModelParser
+dr.evomodelxml.siteratemodel.GammaSiteRateModelParser
+dr.evomodelxml.siteratemodel.FreeRateSiteRateModelParser
 dr.evomodelxml.siteratemodel.PdfSiteModelParser
 
 # BRANCH MODELS
@@ -287,6 +290,7 @@ dr.evomodelxml.tree.TreeLengthStatisticParser
 dr.evomodelxml.tree.NodeHeightsStatisticParser
 dr.evomodelxml.tree.TreeShapeStatisticParser
 dr.evomodelxml.tree.TMRCAStatisticParser
+dr.evomodelxml.tree.BranchLengthStatisticParser
 dr.evomodelxml.tree.AgeStatisticParser
 dr.evomodelxml.tree.MRCATraitStatisticParser
 dr.evomodelxml.tree.AncestralTraitParser
@@ -457,13 +461,12 @@ dr.inferencexml.trace.ArithmeticMeanAnalysisParser
 #GMRF
 dr.evomodelxml.coalescent.operators.GMRFSkyrideFixedEffectsGibbsOperatorParser
 dr.evomodelxml.coalescent.operators.GMRFSkyrideBlockUpdateOperatorParser
-dr.evomodelxml.coalescent.operators.GMRFSkygridBlockUpdateOperatorParser
 dr.evomodelxml.coalescent.GMRFSkyrideLikelihoodParser
 dr.evomodelxml.coalescent.GMRFSkyrideGradientParser
 dr.evomodelxml.coalescent.BayesianSkylineGradientParser
 dr.evomodelxml.coalescent.CoalescentGradientParser
 dr.evomodelxml.coalescent.GMRFIntervalHeightsStatisticParser
-dr.evomodelxml.coalescent.GMRFTestLikelihoodParser
+#dr.evomodelxml.coalescent.GMRFTestLikelihoodParser
 dr.evomodelxml.coalescent.GMRFPopSizeStatisticParser
 dr.evomodelxml.coalescent.GMRFBivariateCurveAnalysisParser
 
@@ -604,9 +607,9 @@ dr.evomodel.arg.ARGLogger
 dr.evoxml.MicrosatellitePatternStatisticParser
 
 # N & S counting
-dr.inference.trace.DnDsPerSiteAnalysis
-dr.inference.trace.CnCsPerSiteAnalysis
-dr.inference.trace.CnCsToDnDsPerSiteAnalysis
+dr.evomodel.trace.DnDsPerSiteAnalysis
+dr.evomodel.trace.CnCsPerSiteAnalysis
+dr.evomodel.trace.CnCsToDnDsPerSiteAnalysis
 
 # MARGINAL LIKELIHOOD ESTIMATION
 dr.inference.mcmc.MarginalLikelihoodEstimator