manual merge in repeated_meaures -> integrated_OU

beast-dev · Nov 16, 2023 · 89b2fd4 · 89b2fd4
1 parent d5baf08
commit 89b2fd4
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Showing 496 changed files with 55,620 additions and 3,021 deletions.
diff --git a/.gitignore b/.gitignore
@@ -16,3 +16,6 @@ out/
 !ci/**/*.xml
 
 zig_zag
+
+*.dmg
+release/Mac
diff --git a/build.xml b/build.xml
@@ -203,13 +203,14 @@
                 <include name="dr/evomodel/branchratemodel/**/*.class"/>
                 <include name="dr/evomodel/clock/**/*.class"/>
                 <include name="dr/evomodel/coalescent/**/*.class"/>
+                <include name="dr/evomodel/continuous/**/*.class"/>
                 <include name="dr/evomodel/operators/**/*.class"/>
                 <include name="dr/evomodel/sitemodel/**/*.class"/>
                 <include name="dr/evomodel/speciation/**/*.class"/>
                 <include name="dr/evomodel/substmodel/**/*.class"/>
                 <include name="dr/evomodel/tree/**/*.class"/>
                 <include name="dr/evomodel/treelikelihood/**/*.class"/>
-                <exclude name="dr/evomodel/treedatalikelihood/MultiPartitionDataLikelihoodDelegate*"/>
+                <include name="dr/evomodel/treedatalikelihood/**/*.class"/>
                 <include name="dr/evomodelxml/**/*.class"/>
                 <exclude name="dr/evomodelxml/treedatalikelihood/MultiPartitionDataLikelihoodDelegate*"/>
                 <include name="dr/evoxml/**/*.class"/>

diff --git a/ci/TestXML/ToyLogisticHMCPrec.xml b/ci/TestXML/ToyLogisticHMCPrec.xml
@@ -202,6 +202,11 @@
 		<populationTree>
 			<treeModel idref="treeModel"/>
 		</populationTree>
+		<intervals>
+			<bigFastTreeIntervals id="bigFastTreeIntervals">
+				<treeModel idref="treeModel"/>
+			</bigFastTreeIntervals>
+		</intervals>
 	</coalescentLikelihood>
 
 	<coalescentGradient id="coalescentGradient">
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,3 +16,6 @@ out/ @@
     !ci/**/*.xml
     zig_zag
+    *.dmg
+    release/Mac