try to fix tests #8

BEAST2-Dev · Nov 16, 2022 · 52645e2 · 52645e2
1 parent f46ff65
commit 52645e2
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Showing 12 changed files with 47 additions and 19 deletions.
diff --git a/build.xml b/build.xml
@@ -217,9 +217,10 @@
 
         <mkdir dir="${pack}"/>
         <mkdir dir="${pack}/examples"/>
+        <mkdir dir="${pack}/examples/data"/>
         <mkdir dir="${pack}/fxtemplates"/>
         <!--mkdir dir="${pack}/lib"/-->
-        <mkdir dir="${pack}/doc"/>
+<!--        <mkdir dir="${pack}/doc"/>-->
 
         <jar jarfile="${pack}/${fullName}.src.jar" basedir="${src}" />
 
@@ -234,16 +235,19 @@
 
         <copy todir="${pack}/examples">
             <fileset dir="${examples}" includes="**/*.xml" />
-            <fileset dir="${examples}" includes="**/*.nex" />
+        </copy>
+        <copy todir="${pack}/examples/data">
+            <fileset dir="${examples}/data" includes="benchmarkData1024T1K.xml" />
+            <fileset dir="${examples}/data" includes="**/*.nex" />
         </copy>
 
         <copy todir="${pack}/fxtemplates">
             <fileset dir="${fxtemplates}" includes="*.xml" />
         </copy>
 
-        <copy todir="${pack}/doc">
-            <fileset dir="${doc}" includes="*.tex,*.doc,*.lyx,*.txt"/>
-        </copy>
+<!--        <copy todir="${pack}/doc">-->
+<!--            <fileset dir="${doc}" includes="*.tex,*.doc,*.lyx,*.txt"/>-->
+<!--        </copy>-->
 
         <copy file="version.xml" todir="${pack}" />
 

diff --git a/fxtemplates/CMSubstModels.xml b/fxtemplates/CMSubstModels.xml
@@ -1,8 +1,9 @@
 <beast version='2.7'
        namespace='beast.base.core:beast.base.inference:beast.base.inference.util:
        beast.evolution.nuc:beast.base.evolution.alignment:beast.base.evolution.datatype:
-       beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:
-       beast.base.evolution.operator:beast.base.inference.operator:beast.evolution:beast.base.math.distributions:
+       beast.base.evolution.branchratemodel:beast.base.evolution.speciation:
+       beast.base.evolution.tree.coalescent:beast.base.math.distributions:
+       beast.base.evolution.operator:beast.base.inference.operator:beast.evolution:
        beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:
        codonmodels:codonmodels.evolution:codonmodels.evolution.alignment:codonmodels.evolution.datatype:
        codonmodels.evolution.likelihood:codonmodels.evolution.operators:codonmodels.evolution.tree'

diff --git a/fxtemplates/CodonSubstModels.xml b/fxtemplates/CodonSubstModels.xml
@@ -1,8 +1,9 @@
 <beast version='2.7'
        namespace='beast.base.core:beast.base.inference:beast.base.inference.util:
        beast.evolution.nuc:beast.base.evolution.alignment:beast.base.evolution.datatype:
-       beast.base.evolution.branchratemodel:beast.base.evolution.speciation:beast.base.evolution.tree.coalescent:
-       beast.base.evolution.operator:beast.base.inference.operator:beast.evolution:beast.base.math.distributions:
+       beast.base.evolution.branchratemodel:beast.base.evolution.speciation:
+       beast.base.evolution.tree.coalescent:beast.base.math.distributions:
+       beast.base.evolution.operator:beast.base.inference.operator:beast.evolution:
        beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood:
        codonmodels:codonmodels.evolution:codonmodels.evolution.alignment:codonmodels.evolution.datatype:
        codonmodels.evolution.likelihood:codonmodels.evolution.operators:codonmodels.evolution.tree'

diff --git a/test/codonmodels/evolution/CodonData.java b/test/codonmodels/evolution/CodonData.java
@@ -7,17 +7,30 @@
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeParser;
 import beast.base.inference.parameter.RealParameter;
+import beast.pkgmgmt.BEASTClassLoader;
 import codonmodels.CodonFrequencies;
 import codonmodels.M0Model;
 import codonmodels.evolution.datatype.Codon;
 
+import java.io.File;
+
 /**
  * @author Walter Xie
  */
 public class CodonData {
 
     public static final Codon codonUNIVERSAL = new Codon();
 
+    public static void initDataTypes() {
+        String PROJECT_DIR = System.getProperty("user.dir");
+        System.out.println("user.dir = " + PROJECT_DIR);
+        File versionXML = new File(PROJECT_DIR + File.separator + "version.xml");
+        if (!versionXML.exists())
+            throw new IllegalArgumentException("Cannot locate codonsubstmodels/version.xml !");
+        BEASTClassLoader.initServices();
+        BEASTClassLoader.addServices(versionXML.getAbsolutePath());
+    }
+
 
     // create a Sequence obj using Codon.codeMap
     public static Sequence getSeqCodeMap() {

diff --git a/test/codonmodels/evolution/alignment/CodonAlignmentTest.java b/test/codonmodels/evolution/alignment/CodonAlignmentTest.java
@@ -4,12 +4,11 @@
 import beast.base.evolution.alignment.Sequence;
 import beast.base.evolution.datatype.DataType;
 import beast.pkgmgmt.BEASTClassLoader;
-import beast.pkgmgmt.PackageManager;
 import codonmodels.evolution.CodonData;
 import codonmodels.evolution.datatype.Codon;
+import org.junit.Before;
 import org.junit.Test;
 
-import java.io.File;
 import java.util.List;
 import java.util.Set;
 
@@ -22,6 +21,11 @@
  */
 public class CodonAlignmentTest {
 
+    @Before
+    public void setUp() throws Exception {
+        CodonData.initDataTypes();
+    }
+
     @Test
     public void testGetSequence() {
         Sequence seq1 = CodonData.getSeqCodeMap();
@@ -39,13 +43,6 @@ public void testGetSequence() {
 
     @Test
     public void testGettingDataType() {
-        String PROJECT_DIR = System.getProperty("user.dir");
-        System.out.println("user.dir = " + PROJECT_DIR);
-        File versionXML = new File(PROJECT_DIR + File.separator + "version.xml");
-        if (!versionXML.exists())
-            throw new IllegalArgumentException("Cannot locate codonsubstmodels/version.xml !");
-        BEASTClassLoader.initServices();
-        BEASTClassLoader.addServices(versionXML.getAbsolutePath());
         Set<String> dataTypes = BEASTClassLoader.loadService(DataType.class);
         System.out.println(dataTypes);
         assertTrue("Cannot load Codon data type !", dataTypes.contains(Codon.class.getName()));

diff --git a/test/codonmodels/evolution/likelihood/DALikelihoodMultithreadingTest.java b/test/codonmodels/evolution/likelihood/DALikelihoodMultithreadingTest.java
@@ -29,6 +29,8 @@ public class DALikelihoodMultithreadingTest {
 
     @Before
     public void setUp() {
+        CodonData.initDataTypes();
+
         Alignment data = CodonData.getAlig6T333();
         // create Codon Alignment
         CodonAlignment codonAlignment = new CodonAlignment();

diff --git a/test/codonmodels/evolution/likelihood/DALikelihoodTest.java b/test/codonmodels/evolution/likelihood/DALikelihoodTest.java
@@ -31,6 +31,7 @@ public class DALikelihoodTest {
 
     @Before
     public void setUp() {
+        CodonData.initDataTypes();
 //        String newickTree = "(t1:0.5, t2:0.0):0.0;"; // TODO bug for 0 branch length ?
         String newickTree = "(t1:0.5, t2:0.1):0.0;";
 //        boolean adjustTipHeights = true;

diff --git a/test/codonmodels/evolution/likelihood/DAStatesLikelihoodCoreIndexTest.java b/test/codonmodels/evolution/likelihood/DAStatesLikelihoodCoreIndexTest.java
@@ -1,6 +1,7 @@
 package codonmodels.evolution.likelihood;
 
 
+import codonmodels.evolution.CodonData;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -27,6 +28,8 @@ public class DAStatesLikelihoodCoreIndexTest {
 
     @Before
     public void setUp() throws Exception {
+        CodonData.initDataTypes();
+
         final int nrOfState = 61;
 
         // ======= transition probability matrix =======

diff --git a/test/codonmodels/evolution/likelihood/M0TreeLikelihoodTest.java b/test/codonmodels/evolution/likelihood/M0TreeLikelihoodTest.java
@@ -18,6 +18,8 @@ public class M0TreeLikelihoodTest {
 
     @Before
     public void setUp() {
+        CodonData.initDataTypes();
+
         Alignment data = CodonData.getAlig6T333();
         // create Codon Alignment
         codonAlignment = new CodonAlignment();

diff --git a/test/codonmodels/evolution/substmodel/CodonFrequenciesTest.java b/test/codonmodels/evolution/substmodel/CodonFrequenciesTest.java
@@ -18,6 +18,8 @@ public class CodonFrequenciesTest {
 
     @Before
     public void setUp() {
+        CodonData.initDataTypes();
+
         Alignment data = CodonData.getAlig6T333();
         // create Codon Alignment
         codonAlignment = new CodonAlignment();

diff --git a/test/codonmodels/evolution/substmodel/M0ModelTest.java b/test/codonmodels/evolution/substmodel/M0ModelTest.java
@@ -28,6 +28,7 @@ public class M0ModelTest {
 
     @Before
     public void setUp() {
+        CodonData.initDataTypes();
 
         Alignment data = CodonData.getAlig6T333();
         // create Codon Alignment

diff --git a/version.xml b/version.xml
@@ -12,12 +12,13 @@
         <provider classname="codonmodels.CodonSubstitutionModel"/>
         <provider classname="codonmodels.evolution.alignment.CodonAlignment"/>
         <provider classname="codonmodels.evolution.datatype.Codon"/>
-<!--        <provider classname="codonmodels.evolution.datatype.GeneticCode"/>-->
+        <provider classname="codonmodels.evolution.datatype.GeneticCode"/>
         <provider classname="codonmodels.evolution.likelihood.DataAugTreeLikelihood"/>
         <provider classname="codonmodels.evolution.likelihood.GenericDATreeLikelihood"/>
         <provider classname="codonmodels.evolution.operators.GibbsSamplingOperator"/>
         <provider classname="codonmodels.evolution.operators.ScaleOperatorGibbs"/>
         <provider classname="codonmodels.evolution.operators.UniformGibbs"/>
+        <provider classname="codonmodels.evolution.tree.NodeStates"/>
         <provider classname="codonmodels.evolution.tree.NodeStatesArray"/>
         <provider classname="codonmodels.evolution.tree.NodeStatesLogger"/>
         <provider classname="codonmodels.util.Report"/>