Merge pull request #1802 from cmu-phil/joe-work-2024-8-14

joe-work-2024-8-14
cmu-phil · Aug 15, 2024 · 2558025 · 2558025
2 parents 37ebfeb + d2abdef
commit 2558025
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Showing 36 changed files with 263 additions and 164 deletions.
diff --git a/data-reader/pom.xml b/data-reader/pom.xml
@@ -5,16 +5,16 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.5-SNAPSHOT</version>
+        <version>7.6.5</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>
     <packaging>jar</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven.compiler.source>17</maven.compiler.source>
-        <maven.compiler.target>17</maven.compiler.target>
+        <maven.compiler.source>21</maven.compiler.source>
+        <maven.compiler.target>21</maven.compiler.target>
     </properties>
 
     <build>
@@ -24,8 +24,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.11.0</version>
                 <configuration>
-                    <source>17</source>
-                    <target>17</target>
+                    <source>21</source>
+                    <target>21</target>
                 </configuration>
             </plugin>
         </plugins>

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.github.cmu-phil</groupId>
     <artifactId>tetrad</artifactId>
-    <version>7.6.5-SNAPSHOT</version>
+    <version>7.6.5</version>
     <packaging>pom</packaging>
 
     <name>Tetrad Project</name>
@@ -64,8 +64,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.13.0</version>
                 <configuration>
-                    <source>17</source>
-                    <target>17</target>
+                    <source>21</source>
+                    <target>21</target>
                 </configuration>
             </plugin>
             <plugin>
@@ -193,8 +193,8 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <additionalparam>-Xdoclint:none</additionalparam>
-        <maven.compiler.source>17</maven.compiler.source>
-        <maven.compiler.target>17</maven.compiler.target>
+        <maven.compiler.source>21</maven.compiler.source>
+        <maven.compiler.target>21</maven.compiler.target>
     </properties>
 
     <dependencies>

diff --git a/tetrad-gui/dependency-reduced-pom.xml b/tetrad-gui/dependency-reduced-pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>tetrad</artifactId>
     <groupId>io.github.cmu-phil</groupId>
-    <version>7.6.5-SNAPSHOT</version>
+    <version>7.6.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>tetrad-gui</artifactId>
@@ -35,8 +35,8 @@
         <artifactId>maven-compiler-plugin</artifactId>
         <version>3.13.0</version>
         <configuration>
-          <source>17</source>
-          <target>17</target>
+          <source>21</source>
+          <target>21</target>
         </configuration>
       </plugin>
       <plugin>
@@ -68,7 +68,7 @@
     </plugins>
   </build>
   <properties>
-    <java.version>17</java.version>
+    <java.version>21</java.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
   </properties>
 </project>
diff --git a/tetrad-gui/pom.xml b/tetrad-gui/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.5-SNAPSHOT</version>
+        <version>7.6.5</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>
@@ -33,8 +33,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.13.0</version>
                 <configuration>
-                    <source>17</source>
-                    <target>17</target>
+                    <source>21</source>
+                    <target>21</target>
                 </configuration>
             </plugin>
             <plugin>
@@ -186,7 +186,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <java.version>17</java.version>
+        <java.version>21</java.version>
     </properties>
 
     <!--<scm>-->

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AbstractSearchEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AbstractSearchEditor.java
@@ -483,34 +483,32 @@ GraphHistory getGraphHistory() {
     }
 
     /**
-     * <p>getTestType.</p>
-     *
-     * @return a {@link edu.cmu.tetradapp.util.IndTestType} object
-     */
     public IndTestType getTestType() {
         return (IndTestType) getAlgorithmRunner().getParams().get("indTestType", IndTestType.FISHER_Z);
     }
 
     /**
-     * {@inheritDoc}
+     * Sets the test type for the search algorithm.
+     *
+     * @param testType The test type to be set.
      */
     public void setTestType(IndTestType testType) {
         getAlgorithmRunner().getParams().set("indTestType", testType);
     }
 
     /**
-     * <p>getDataModel.</p>
+     * Retrieves the data model used to execute the algorithm.
      *
-     * @return a {@link edu.cmu.tetrad.data.DataModel} object
+     * @return the data model used to execute the algorithm, which might possibly be a graph.
      */
     public DataModel getDataModel() {
         return getAlgorithmRunner().getDataModel();
     }
 
     /**
-     * <p>getSourceGraph.</p>
+     * Retrieves the source graph used for the search algorithm.
      *
-     * @return a {@link java.lang.Object} object
+     * @return the source graph used for the search algorithm, or null if not set.
      */
     public Object getSourceGraph() {
         return getAlgorithmRunner().getParams().get("sourceGraph", null);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/FactorAnalysisEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/FactorAnalysisEditor.java
@@ -24,6 +24,7 @@
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.graph.LayoutUtil;
 import edu.cmu.tetradapp.model.FactorAnalysisRunner;
+import edu.cmu.tetradapp.util.IndTestType;
 import edu.cmu.tetradapp.workbench.GraphWorkbench;
 
 import javax.swing.*;
@@ -132,6 +133,16 @@ protected void addSpecialMenus(JMenuBar menuBar) {
 
     }
 
+    /**
+     * This method is called when the user selects "Save As..." from the File menu.
+     *
+     * @throws UnsupportedOperationException since this method is not supported by this class.
+     */
+    @Override
+    public IndTestType getTestType() {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
     /**
      * <p>getSourceGraph.</p>
      *

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MissingDataInjectorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MissingDataInjectorWrapper.java
@@ -42,6 +42,7 @@
  * @version $Id: $Id
  */
 public class MissingDataInjectorWrapper extends DataWrapper {
+    @Serial
     private static final long serialVersionUID = 23L;
 
     /**

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ReplaceMissingWithRandomWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ReplaceMissingWithRandomWrapper.java
@@ -43,11 +43,6 @@ public class ReplaceMissingWithRandomWrapper extends DataWrapper {
     @Serial
     private static final long serialVersionUID = 23L;
 
-    /**
-     * @serial Cannot be null.
-     */
-    private final DataSet outputDataSet;
-
     //============================CONSTRUCTORS=============================//
 
     /**
@@ -59,8 +54,8 @@ public ReplaceMissingWithRandomWrapper(DataWrapper wrapper) {
         DataSet dataSet =
                 (DataSet) wrapper.getSelectedDataModel();
 
-        this.outputDataSet = DataTransforms.replaceMissingWithRandom(dataSet);
-        setDataModel(this.outputDataSet);
+        DataSet outputDataSet = DataTransforms.replaceMissingWithRandom(dataSet);
+        setDataModel(outputDataSet);
         setSourceGraph(wrapper.getSourceGraph());
 
         LogDataUtils.logDataModelList("Parent data with missing values injected randomly.", getDataModelList());

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemImWrapper.java
@@ -55,7 +55,7 @@ public class SemImWrapper implements SessionModel {
     private List<SemIm> semIms;
 
     /**
-     * @serial Can be null.
+     * The name of the model.
      */
     private String name;
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemUpdaterWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemUpdaterWrapper.java
@@ -42,12 +42,12 @@ public class SemUpdaterWrapper implements SessionModel {
     private static final long serialVersionUID = 23L;
 
     /**
-     * @serial
+     * The wrapped Bayes Updater.
      */
     private final SemUpdater semUpdater;
 
     /**
-     * @serial Can be null.
+     * The name of the model.
      */
     private String name;
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StandardizedSemImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StandardizedSemImWrapper.java
@@ -44,11 +44,11 @@ public class StandardizedSemImWrapper implements KnowledgeBoxInput {
 
     private static final long serialVersionUID = 23L;
     /**
-     * @serial Cannot be null.
+     * The wrapped standardized SEM IM.
      */
     private final StandardizedSemIm standardizedSemIm;
     /**
-     * @serial Can be null.
+     * The name of the model.
      */
     private String name;
     /**

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StructEmBayesSearchRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StructEmBayesSearchRunner.java
@@ -52,17 +52,17 @@ public class StructEmBayesSearchRunner implements SessionModel, GraphSource {
     private String name;
 
     /**
-     * @serial Cannot be null.
+     * The Bayes PM.
      */
     private BayesPm bayesPm;
 
     /**
-     * @serial Cannot be null.
+     * The data set.
      */
     private DataSet dataSet;
 
     /**
-     * @serial Cannot be null.
+     * The estimated Bayes IM.
      */
     private BayesIm estimatedBayesIm;
 

diff --git a/tetrad-lib/dependency-reduced-pom.xml b/tetrad-lib/dependency-reduced-pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>tetrad</artifactId>
     <groupId>io.github.cmu-phil</groupId>
-    <version>7.6.5-SNAPSHOT</version>
+    <version>7.6.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>tetrad-lib</artifactId>
@@ -20,8 +20,8 @@
         <artifactId>maven-compiler-plugin</artifactId>
         <version>3.13.0</version>
         <configuration>
-          <source>17</source>
-          <target>17</target>
+          <source>21</source>
+          <target>21</target>
         </configuration>
       </plugin>
       <plugin>

diff --git a/tetrad-lib/pom.xml b/tetrad-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.5-SNAPSHOT</version>
+        <version>7.6.5</version>
     </parent>
 
     <artifactId>tetrad-lib</artifactId>
@@ -18,8 +18,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.13.0</version>
                 <configuration>
-                    <source>17</source>
-                    <target>17</target>
+                    <source>21</source>
+                    <target>21</target>
                 </configuration>
             </plugin>
             <plugin>

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Bfci.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Bfci.java
@@ -45,7 +45,7 @@
         algoType = AlgType.allow_latent_common_causes
 )
 @Bootstrapping
-@Experimental
+//@Experimental
 public class Bfci extends AbstractBootstrapAlgorithm implements Algorithm, UsesScoreWrapper,
         TakesIndependenceWrapper, HasKnowledge, ReturnsBootstrapGraphs,
         TakesCovarianceMatrix {
@@ -119,7 +119,7 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
         search.setDoDiscriminatingPathColliderRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
         search.setDepth(parameters.getInt(Params.DEPTH));
         search.setNumThreads(parameters.getInt(Params.NUM_THREADS));
-        search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
+        search.setGuaranteePag(parameters.getBoolean(Params.GUARANTEE_PAG));
         search.setVerbose(parameters.getBoolean(Params.VERBOSE));
 
         search.setKnowledge(knowledge);
@@ -182,7 +182,7 @@ public List<String> getParameters() {
         params.add(Params.TIME_LAG);
         params.add(Params.SEED);
         params.add(Params.NUM_THREADS);
-        params.add(Params.REPAIR_FAULTY_PAG);
+        params.add(Params.GUARANTEE_PAG);
         params.add(Params.VERBOSE);
 
         // Parameters

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Fci.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Fci.java
@@ -110,7 +110,7 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
         search.setVerbose(parameters.getBoolean(Params.VERBOSE));
         search.setPcHeuristicType(pcHeuristicType);
         search.setStable(parameters.getBoolean(Params.STABLE_FAS));
-        search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
+        search.setGuaranteePag(parameters.getBoolean(Params.GUARANTEE_PAG));
 
         return search.search();
     }
@@ -164,7 +164,7 @@ public List<String> getParameters() {
         parameters.add(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE);
         parameters.add(Params.COMPLETE_RULE_SET_USED);
         parameters.add(Params.TIME_LAG);
-        parameters.add(Params.REPAIR_FAULTY_PAG);
+        parameters.add(Params.GUARANTEE_PAG);
 
         parameters.add(Params.VERBOSE);
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/FciMax.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/FciMax.java
@@ -108,7 +108,7 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
         search.setDoDiscriminatingPathColliderRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
         search.setPossibleMsepSearchDone(parameters.getBoolean(Params.POSSIBLE_MSEP_DONE));
         search.setPcHeuristicType(pcHeuristicType);
-        search.setRepairFaultyPag(parameters.getBoolean(Params.REPAIR_FAULTY_PAG));
+        search.setGuaranteePag(parameters.getBoolean(Params.GUARANTEE_PAG));
         search.setVerbose(parameters.getBoolean(Params.VERBOSE));
 
         return search.search();
@@ -160,7 +160,7 @@ public List<String> getParameters() {
         parameters.add(Params.DO_DISCRIMINATING_PATH_TAIL_RULE);
         parameters.add(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE);
         parameters.add(Params.POSSIBLE_MSEP_DONE);
-        parameters.add(Params.REPAIR_FAULTY_PAG);
+        parameters.add(Params.GUARANTEE_PAG);
 //        parameters.add(Params.PC_HEURISTIC);
         parameters.add(Params.TIME_LAG);
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Gfci.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Gfci.java
@@ -105,7 +105,7 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
         search.setDoDiscriminatingPathTailRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_TAIL_RULE));
         search.setDoDiscriminatingPathColliderRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_COLLIDER_RULE));
         search.setNumThreads(parameters.getInt(Params.NUM_THREADS));
-        search.setRepairFaultyPag(parameters.getBoolean(Params.REMOVE_ALMOST_CYCLES));
+        search.setGuaranteePag(parameters.getBoolean(Params.REMOVE_ALMOST_CYCLES));
         search.setOut(System.out);
 
         return search.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/GraspFci.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/GraspFci.java
@@ -132,7 +132,7 @@ public Graph runSearch(DataModel dataModel, Parameters parameters) {
 
         // General
         search.setVerbose(parameters.getBoolean(Params.VERBOSE));
-        search.setRepairFaultyPag(parameters.getBoolean(Params.REMOVE_ALMOST_CYCLES));
+        search.setGuaranteePag(parameters.getBoolean(Params.REMOVE_ALMOST_CYCLES));
         search.setKnowledge(this.knowledge);
 
         return search.search();
-Original file line number
+Diff line change
@@ Expand Up / @@ -42,6 +42,7 @@ @@
      * @version $Id: $Id
      */
     public class MissingDataInjectorWrapper extends DataWrapper {
+        @Serial
         private static final long serialVersionUID = 23L;
         /**
@@ Expand Down @@