diff --git a/build.xml b/build.xml index 85ee2c0..12a3c99 100644 --- a/build.xml +++ b/build.xml @@ -117,7 +117,7 @@ Downloading dependencies... BDSKY: - @@ -191,7 +191,7 @@ - + @@ -217,7 +217,7 @@ - + diff --git a/examples/smoothingpriors/comparison/hcv_bdsky.xml b/examples/smoothingpriors/comparison/hcv_bdsky.xml index 3586c09..cb78bdf 100644 --- a/examples/smoothingpriors/comparison/hcv_bdsky.xml +++ b/examples/smoothingpriors/comparison/hcv_bdsky.xml @@ -1,5 +1,5 @@ -beast.math.distributions.Uniform -beast.math.distributions.Exponential -beast.math.distributions.LogNormalDistributionModel -beast.math.distributions.Normal -beast.math.distributions.Beta -beast.math.distributions.Gamma -beast.math.distributions.LaplaceDistribution -beast.math.distributions.Prior -beast.math.distributions.InverseGamma -beast.math.distributions.OneOnX +beast.base.inference.distribution.Uniform +beast.base.inference.distribution.Exponential +beast.base.inference.distribution.LogNormalDistributionModel +beast.base.inference.distribution.Normal +beast.base.inference.distribution.Beta +beast.base.inference.distribution.Gamma +beast.base.inference.distribution.LaplaceDistribution +beast.base.inference.distribution.Prior +beast.base.inference.distribution.InverseGamma +beast.base.inference.distribution.OneOnX @@ -119,21 +119,21 @@ - + 1.0 - + - + - + @@ -202,7 +202,7 @@ - + 7.9E-4 @@ -267,21 +267,21 @@ - + - + - + - + @@ -295,7 +295,7 @@ diff --git a/examples/smoothingpriors/ouprior_test1.xml b/examples/smoothingpriors/ouprior_test1.xml index 7bc36a6..f45283a 100644 --- a/examples/smoothingpriors/ouprior_test1.xml +++ b/examples/smoothingpriors/ouprior_test1.xml @@ -1,5 +1,5 @@ + namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'> diff --git a/examples/smoothingpriors/ouprior_test2.xml b/examples/smoothingpriors/ouprior_test2.xml index 1b11c9a..21ca903 100644 --- a/examples/smoothingpriors/ouprior_test2.xml +++ b/examples/smoothingpriors/ouprior_test2.xml @@ -1,5 +1,5 @@ + namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'> diff --git a/examples/smoothingpriors/ouprior_test3.xml b/examples/smoothingpriors/ouprior_test3.xml index acfae63..b06e991 100644 --- a/examples/smoothingpriors/ouprior_test3.xml +++ b/examples/smoothingpriors/ouprior_test3.xml @@ -1,18 +1,18 @@ + namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions'> - beast.math.distributions.Uniform - beast.math.distributions.Exponential - beast.math.distributions.LogNormalDistributionModel - beast.math.distributions.Normal - beast.math.distributions.Beta - beast.math.distributions.Gamma - beast.math.distributions.LaplaceDistribution - beast.math.distributions.Prior - beast.math.distributions.InverseGamma - beast.math.distributions.OneOnX + beast.base.inference.distribution.Uniform + beast.base.inference.distribution.Exponential + beast.base.inference.distribution.LogNormalDistributionModel + beast.base.inference.distribution.Normal + beast.base.inference.distribution.Beta + beast.base.inference.distribution.Gamma + beast.base.inference.distribution.LaplaceDistribution + beast.base.inference.distribution.Prior + beast.base.inference.distribution.InverseGamma + beast.base.inference.distribution.OneOnX @@ -29,7 +29,7 @@ - + diff --git a/examples/smoothingpriors/ouprior_test4.xml b/examples/smoothingpriors/ouprior_test4.xml index 88e8421..b7423be 100644 --- a/examples/smoothingpriors/ouprior_test4.xml +++ b/examples/smoothingpriors/ouprior_test4.xml @@ -1,18 +1,18 @@ + namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions:skylinetools.parameter'> - beast.math.distributions.Uniform - beast.math.distributions.Exponential - beast.math.distributions.LogNormalDistributionModel - beast.math.distributions.Normal - beast.math.distributions.Beta - beast.math.distributions.Gamma - beast.math.distributions.LaplaceDistribution - beast.math.distributions.Prior - beast.math.distributions.InverseGamma - beast.math.distributions.OneOnX + beast.base.inference.distribution.Uniform + beast.base.inference.distribution.Exponential + beast.base.inference.distribution.LogNormalDistributionModel + beast.base.inference.distribution.Normal + beast.base.inference.distribution.Beta + beast.base.inference.distribution.Gamma + beast.base.inference.distribution.LaplaceDistribution + beast.base.inference.distribution.Prior + beast.base.inference.distribution.InverseGamma + beast.base.inference.distribution.OneOnX diff --git a/examples/smoothingpriors/ouprior_test5.xml b/examples/smoothingpriors/ouprior_test5.xml index f1fde50..94eb793 100644 --- a/examples/smoothingpriors/ouprior_test5.xml +++ b/examples/smoothingpriors/ouprior_test5.xml @@ -1,5 +1,5 @@ + namespace='beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.speciation:beast.base.util:beast.base.math:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.math.distributions:beast.base.evolution.branchratemodel:beast.base.evolution.likelihood:beast.base.inference.parameter:skylinetools.distributions:skylinetools.parameter'> diff --git a/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java b/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java index 470e567..38dfe57 100755 --- a/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java +++ b/src/beast/evolution/speciation/BirthDeathSkylineModelTestHelper.java @@ -1,5 +1,6 @@ package beast.evolution.speciation; +import bdsky.evolution.speciation.BirthDeathSkylineModel; import java.util.List; /** @@ -17,4 +18,4 @@ public class BirthDeathSkylineModelTestHelper extends BirthDeathSkylineModel { public List rChangeTimes() { return rChangeTimes; } -} \ No newline at end of file +} diff --git a/src/skylinetools/distributions/BMPrior.java b/src/skylinetools/distributions/BMPrior.java index 64d45f0..30e60ef 100644 --- a/src/skylinetools/distributions/BMPrior.java +++ b/src/skylinetools/distributions/BMPrior.java @@ -1,11 +1,11 @@ package skylinetools.distributions; -import beast.core.Distribution; -import beast.core.Function; -import beast.core.Input; -import beast.core.State; -import beast.core.parameter.RealParameter; -import beast.math.distributions.ParametricDistribution; +import beast.base.inference.Distribution; +import beast.base.core.Function; +import beast.base.core.Input; +import beast.base.inference.State; +import beast.base.inference.parameter.RealParameter; +import beast.base.inference.distribution.ParametricDistribution; import java.util.List; import java.util.Random; diff --git a/src/skylinetools/distributions/OUPrior.java b/src/skylinetools/distributions/OUPrior.java index 4a452c0..e2e85e0 100644 --- a/src/skylinetools/distributions/OUPrior.java +++ b/src/skylinetools/distributions/OUPrior.java @@ -1,11 +1,11 @@ package skylinetools.distributions; -import beast.core.Distribution; -import beast.core.Function; -import beast.core.Input; -import beast.core.State; -import beast.core.parameter.RealParameter; -import beast.math.distributions.ParametricDistribution; +import beast.base.inference.Distribution; +import beast.base.core.Function; +import beast.base.core.Input; +import beast.base.inference.State; +import beast.base.inference.parameter.RealParameter; +import beast.base.inference.distribution.ParametricDistribution; import java.util.Arrays; import java.util.List; diff --git a/src/skylinetools/parameter/DateParser.java b/src/skylinetools/parameter/DateParser.java index 5ced97a..1fb2913 100644 --- a/src/skylinetools/parameter/DateParser.java +++ b/src/skylinetools/parameter/DateParser.java @@ -1,8 +1,8 @@ package skylinetools.parameter; -import beast.core.Input; -import beast.core.parameter.RealParameter; -import beast.core.util.Log; +import beast.base.core.Input; +import beast.base.inference.parameter.RealParameter; +import beast.base.core.Log; import java.time.LocalDate; import java.time.format.DateTimeFormatter; diff --git a/src/skylinetools/parameter/RealParameterSequence.java b/src/skylinetools/parameter/RealParameterSequence.java index c771e2b..9039520 100644 --- a/src/skylinetools/parameter/RealParameterSequence.java +++ b/src/skylinetools/parameter/RealParameterSequence.java @@ -1,8 +1,8 @@ package skylinetools.parameter; -import beast.core.Description; -import beast.core.Input; -import beast.core.parameter.RealParameter; +import beast.base.core.Description; +import beast.base.core.Input; +import beast.base.inference.parameter.RealParameter; import java.util.Arrays; diff --git a/src/skylinetools/util/TreeDateLogger.java b/src/skylinetools/util/TreeDateLogger.java index d52c2f6..b009947 100644 --- a/src/skylinetools/util/TreeDateLogger.java +++ b/src/skylinetools/util/TreeDateLogger.java @@ -1,12 +1,12 @@ package skylinetools.util; -import beast.core.CalculationNode; -import beast.core.Function; -import beast.core.Input; -import beast.core.Loggable; -import beast.core.parameter.RealParameter; -import beast.core.util.Log; -import beast.evolution.tree.Tree; +import beast.base.inference.CalculationNode; +import beast.base.core.Function; +import beast.base.core.Input; +import beast.base.core.Loggable; +import beast.base.inference.parameter.RealParameter; +import beast.base.core.Log; +import beast.base.evolution.tree.Tree; import java.io.PrintStream; diff --git a/src/skylinetools/util/TreeDateSlicer.java b/src/skylinetools/util/TreeDateSlicer.java index 2be3f76..e764171 100644 --- a/src/skylinetools/util/TreeDateSlicer.java +++ b/src/skylinetools/util/TreeDateSlicer.java @@ -1,9 +1,9 @@ package skylinetools.util; -import beast.core.Function; -import beast.core.Input; -import beast.evolution.tree.Tree; -import beast.util.HeapSort; +import beast.base.core.Function; +import beast.base.core.Input; +import beast.base.evolution.tree.Tree; +import beast.base.util.HeapSort; import java.util.Arrays; diff --git a/src/skylinetools/util/TreeSliceDateLogger.java b/src/skylinetools/util/TreeSliceDateLogger.java index ddb6942..6c49816 100644 --- a/src/skylinetools/util/TreeSliceDateLogger.java +++ b/src/skylinetools/util/TreeSliceDateLogger.java @@ -1,9 +1,9 @@ package skylinetools.util; -import beast.core.CalculationNode; -import beast.core.Function; -import beast.core.Input; -import beast.core.Loggable; +import beast.base.inference.CalculationNode; +import beast.base.core.Function; +import beast.base.core.Input; +import beast.base.core.Loggable; import java.io.PrintStream; diff --git a/src/skylinetools/util/TreeSlicer.java b/src/skylinetools/util/TreeSlicer.java index adb1b23..7923f92 100644 --- a/src/skylinetools/util/TreeSlicer.java +++ b/src/skylinetools/util/TreeSlicer.java @@ -1,11 +1,11 @@ package skylinetools.util; -import beast.core.*; -import beast.core.parameter.Parameter; -import beast.core.parameter.RealParameter; -import beast.evolution.tree.Node; -import beast.evolution.tree.Tree; -import beast.util.HeapSort; +import beast.base.core.*; +import beast.base.inference.parameter.Parameter; +import beast.base.inference.parameter.RealParameter; +import beast.base.evolution.tree.Node; +import beast.base.evolution.tree.Tree; +import beast.base.util.HeapSort; import java.util.ArrayList; import java.util.Arrays; diff --git a/test/beast/evolution/speciation/SkylineTimesTest.java b/test/beast/evolution/speciation/SkylineTimesTest.java index 42b881f..c47aa65 100755 --- a/test/beast/evolution/speciation/SkylineTimesTest.java +++ b/test/beast/evolution/speciation/SkylineTimesTest.java @@ -1,17 +1,17 @@ package beast.evolution.speciation; -import beast.core.parameter.BooleanParameter; -import beast.core.parameter.RealParameter; -import beast.evolution.speciation.BirthDeathSkylineModelTestHelper; -import beast.evolution.tree.Tree; -import beast.util.TreeParser; +import beast.base.inference.parameter.BooleanParameter; +import beast.base.inference.parameter.RealParameter; +import bdsky.evolution.speciation.BirthDeathSkylineModelTestHelper; +import beast.base.evolution.tree.Tree; +import beast.base.evolution.tree.TreeParser; import org.junit.Test; import junit.framework.TestCase; import java.util.List; /** - * This test is to check how bdsky (beast.evolution.speciation.BirthDeathSkylineModel) sets change-point times, depending + * This test is to check how bdsky (bdsky.evolution.speciation.BirthDeathSkylineModel) sets change-point times, depending * on the input. * * There are 5 different ways to set the change-point times: diff --git a/test/skylinetools/distributions/OUPriorLkTest.java b/test/skylinetools/distributions/OUPriorLkTest.java index 4fb983a..663027c 100644 --- a/test/skylinetools/distributions/OUPriorLkTest.java +++ b/test/skylinetools/distributions/OUPriorLkTest.java @@ -1,6 +1,6 @@ package skylinetools.distributions; -import beast.core.parameter.RealParameter; +import beast.base.inference.parameter.RealParameter; import junit.framework.TestCase; import org.junit.Test; import skylinetools.distributions.OUPrior; diff --git a/test/skylinetools/util/TreeDateSlicerTest.java b/test/skylinetools/util/TreeDateSlicerTest.java index 12be810..305b5be 100644 --- a/test/skylinetools/util/TreeDateSlicerTest.java +++ b/test/skylinetools/util/TreeDateSlicerTest.java @@ -1,10 +1,10 @@ package skylinetools.util; -import beast.evolution.alignment.Taxon; -import beast.evolution.alignment.TaxonSet; -import beast.evolution.tree.TraitSet; -import beast.evolution.tree.Tree; -import beast.util.TreeParser; +import beast.base.evolution.alignment.Taxon; +import beast.base.evolution.alignment.TaxonSet; +import beast.base.evolution.tree.TraitSet; +import beast.base.evolution.tree.Tree; +import beast.base.evolution.tree.TreeParser; import junit.framework.TestCase; import org.junit.Test; import skylinetools.parameter.DateParser; diff --git a/test/skylinetools/util/TreeSlicerTest.java b/test/skylinetools/util/TreeSlicerTest.java index 61c0e46..4613fff 100644 --- a/test/skylinetools/util/TreeSlicerTest.java +++ b/test/skylinetools/util/TreeSlicerTest.java @@ -1,7 +1,7 @@ package skylinetools.util; -import beast.evolution.tree.Tree; -import beast.util.TreeParser; +import beast.base.evolution.tree.Tree; +import beast.base.evolution.tree.TreeParser; import junit.framework.TestCase; import org.junit.Test; import test.beast.BEASTTestCase; diff --git a/version.xml b/version.xml index 7311e37..3b29826 100644 --- a/version.xml +++ b/version.xml @@ -1,7 +1,11 @@ - - - + + + + - - - + + + + + +