Merge pull request #1803 from cmu-phil/development

Version 7.6.5 code
cmu-phil · Aug 15, 2024 · 69fdb1c · 69fdb1c
2 parents 1611de7 + db3fc5b
commit 69fdb1c
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diff --git a/INSTALL_APPLICATION.md b/INSTALL_APPLICATION.md
@@ -9,7 +9,7 @@ See [Setting up Java for Tetrad](https://github.com/cmu-phil/tetrad/wiki/Setting
 
 To download the Tetrad jar, please click the following link (which will always be updated to the latest version):
 
-https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.6.3/tetrad-gui-7.6.3-launch.jar
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.6.4/tetrad-gui-7.6.4-launch.jar
 
 You may be able to launch this jar by double-clicking the jar file name. However, on a Mac, this presents some security
 challenges. On all platforms, the jar may be launched at the command line (with a specification of the amount of RAM you

diff --git a/data-reader/pom.xml b/data-reader/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.5</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>
@@ -22,7 +22,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.11.0</version>
+                <version>3.13.0</version>
                 <configuration>
                     <source>17</source>
                     <target>17</target>

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>7.6.4</version>
+    <version>7.6.5</version>
     <packaging>pom</packaging>
 
     <name>Tetrad Project</name>
@@ -62,7 +62,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.11.0</version>
+                <version>3.13.0</version>
                 <configuration>
                     <source>17</source>
                     <target>17</target>
@@ -163,7 +163,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-gpg-plugin</artifactId>
-                <version>1.5</version>
+                <version>3.2.4</version>
                 <executions>
                     <execution>
                         <id>sign-artifacts</id>
@@ -198,11 +198,6 @@
     </properties>
 
     <dependencies>
-        <!--        <dependency>-->
-        <!--            <groupId>org.slf4j</groupId>-->
-        <!--            <artifactId>slf4j-log4j12</artifactId>-->
-        <!--            <version>1.7.36</version>-->
-        <!--        </dependency>-->
         <dependency> <!--For java annotations used by annotated algorithms-->
             <groupId>org.reflections</groupId>
             <artifactId>reflections</artifactId>

diff --git a/testTrueGraphForCheckNodewiseMarkov.txt b/testTrueGraphForCheckNodewiseMarkov.txt
@@ -0,0 +1,49 @@
+Graph Nodes:
+X1;X2;X3;X4;X5;X6;X7;X8;X9;X10
+
+Graph Edges:
+1. X1 --> X2
+2. X1 --> X3
+3. X1 --> X5
+4. X1 --> X6
+5. X1 --> X7
+6. X1 --> X8
+7. X1 --> X9
+8. X1 --> X10
+9. X2 --> X3
+10. X2 --> X4
+11. X2 --> X5
+12. X2 --> X8
+13. X2 --> X9
+14. X2 --> X10
+15. X3 --> X4
+16. X3 --> X5
+17. X3 --> X6
+18. X3 --> X7
+19. X3 --> X8
+20. X3 --> X9
+21. X3 --> X10
+22. X4 --> X5
+23. X4 --> X6
+24. X4 --> X9
+25. X4 --> X10
+26. X5 --> X6
+27. X5 --> X7
+28. X5 --> X8
+29. X5 --> X9
+30. X5 --> X10
+31. X6 --> X7
+32. X6 --> X8
+33. X6 --> X9
+34. X6 --> X10
+35. X7 --> X8
+36. X7 --> X9
+37. X7 --> X10
+38. X8 --> X9
+39. X8 --> X10
+40. X9 --> X10
+
+
+Test True Graph size: 10
+Test Estimated CPDAG Graph: Graph Nodes:
+X1;X2;X3;X4;X5;X6;X7;X8;X9;X10
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>7.6.4</version>
+    <version>7.6.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>tetrad-gui</artifactId>
@@ -33,15 +33,15 @@
     <plugins>
       <plugin>
         <artifactId>maven-compiler-plugin</artifactId>
-        <version>3.11.0</version>
+        <version>3.13.0</version>
         <configuration>
           <source>17</source>
           <target>17</target>
         </configuration>
       </plugin>
       <plugin>
         <artifactId>maven-shade-plugin</artifactId>
-        <version>3.5.1</version>
+        <version>3.6.0</version>
         <executions>
           <execution>
             <phase>package</phase>
@@ -68,7 +68,7 @@
     </plugins>
   </build>
   <properties>
-    <java.version>1.8</java.version>
+    <java.version>17</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>7.6.4</version>
+        <version>7.6.5</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>
@@ -31,7 +31,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.11.0</version>
+                <version>3.13.0</version>
                 <configuration>
                     <source>17</source>
                     <target>17</target>
@@ -40,7 +40,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>
-                <version>3.5.1</version>
+                <version>3.6.0</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -186,7 +186,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <java.version>1.8</java.version>
+        <java.version>17</java.version>
     </properties>
 
     <!--<scm>-->

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java
@@ -20,7 +20,6 @@
 ///////////////////////////////////////////////////////////////////////////////
 package edu.cmu.tetradapp;
 
-import edu.cmu.tetrad.search.work_in_progress.DMSearch;
 import edu.cmu.tetrad.util.JOptionUtils;
 import edu.cmu.tetrad.util.TetradLogger;
 import edu.cmu.tetrad.util.Version;
@@ -52,7 +51,7 @@ public final class Tetrad implements PropertyChangeListener {
      */
     private static final String EXP_OPT = "--experimental";
     /**
-     * Whether to enable experimental features
+     * Whether to enable experimental featuresj
      */
     public static boolean enableExperimental;
     /**
@@ -122,7 +121,7 @@ private static void setLookAndFeel() {
                         UIManager.getSystemLookAndFeelClassName());
             }
         } catch (Exception e) {
-            TetradLogger.getInstance().forceLogMessage("Couldn't set look and feel.");
+            TetradLogger.getInstance().log("Couldn't set look and feel.");
         }
     }
 
@@ -271,7 +270,7 @@ public void componentMoved(ComponentEvent e) {
                     }
                 });
             } catch (Exception e) {
-                TetradLogger.getInstance().forceLogMessage("Could not set quit handler on this platform..");
+                TetradLogger.getInstance().log("Could not set quit handler on this platform..");
             }
         }
     }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LoadSessionAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LoadSessionAction.java
@@ -122,7 +122,8 @@ public void watch() {
 
                             throw e1;
                         } catch (Exception e2) {
-                            TetradLogger.getInstance().forceLogMessage("Exception: " + e2.getMessage());
+                            e2.printStackTrace();
+                            TetradLogger.getInstance().log("Exception: " + e2.getMessage());
                         }
                     } else if (o instanceof SessionWrapper) {
                         sessionWrapper = (SessionWrapper) o;
@@ -158,8 +159,10 @@ public void watch() {
                     DesktopController.getInstance().closeEmptySessions();
                     DesktopController.getInstance().putMetadata(sessionWrapper, metadata);
                 } catch (FileNotFoundException ex) {
+                    ex.printStackTrace();
                     JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "That wasn't a TETRAD session file: " + file);
                 } catch (Exception ex) {
+                    ex.printStackTrace();
                     JOptionPane.showMessageDialog(JOptionUtils.centeringComp(), "An error occurred attempting to load the session.");
                 }
             }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SaveSessionAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SaveSessionAction.java
@@ -30,6 +30,7 @@
 import javax.swing.*;
 import java.awt.event.ActionEvent;
 import java.io.IOException;
+import java.io.NotSerializableException;
 import java.io.ObjectOutputStream;
 import java.io.Serial;
 import java.nio.file.Files;
@@ -106,6 +107,11 @@ public void watch() {
                     sessionWrapper.setNewSession(false);
                     objOut.writeObject(metadata);
                     objOut.writeObject(sessionWrapper);
+                } catch (NotSerializableException exception) {
+                    exception.printStackTrace(System.err);
+                    JOptionPane.showMessageDialog(
+                            JOptionUtils.centeringComp(),
+                            "An error occurred while attempting to save the session. The session could not be saved.");
                 } catch (IOException exception) {
                     exception.printStackTrace(System.err);
                     JOptionPane.showMessageDialog(

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorNode.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorNode.java
@@ -260,14 +260,19 @@ public void doDoubleClickAction() {
     public void doDoubleClickAction(Graph sessionWrapper) {
         this.sessionWrapper = (SessionWrapper) sessionWrapper;
 
-        class MyWatchedProcess extends WatchedProcess {
-            public void watch() {
-                TetradLogger.getInstance().setTetradLoggerConfig(getSessionNode().getLoggerConfig());
-                launchEditorVisit();
-            }
-        }
+        SwingUtilities.invokeLater(() -> {
+            TetradLogger.getInstance().setTetradLoggerConfig(getSessionNode().getLoggerConfig());
+            launchEditorVisit();
+        });
 
-        new MyWatchedProcess();
+//        class MyWatchedProcess extends WatchedProcess {
+//            public void watch() {
+//                TetradLogger.getInstance().setTetradLoggerConfig(getSessionNode().getLoggerConfig());
+//                launchEditorVisit();
+//            }
+//        }
+//
+//        new MyWatchedProcess();
     }
 
     private void launchEditorVisit() {
@@ -816,7 +821,7 @@ private void showLogConfig(TetradLoggerConfig config) {
     }
 
     private void executeSessionNode(SessionNode sessionNode) {
-        class MyWatchedProcess extends WatchedProcess {
+        new WatchedProcess() {
             @Override
             public void watch() {
                 final Class c = SessionEditorWorkbench.class;
@@ -829,13 +834,11 @@ public void watch() {
 
                 workbench.getSimulationStudy().execute(sessionNode, true);
             }
-        }
-
-        new MyWatchedProcess();
+        };
     }
 
     private void createDescendantModels() {
-        class MyWatchedProcess extends WatchedProcess {
+        new WatchedProcess() {
             @Override
             public void watch() {
                 final Class clazz = SessionEditorWorkbench.class;
@@ -849,9 +852,7 @@ public void watch() {
                             getSessionNode(), true);
                 }
             }
-        }
-
-        new MyWatchedProcess();
+        };
     }
 
     /**

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorToolbar.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorToolbar.java
@@ -99,6 +99,8 @@ public SessionEditorToolbar(SessionEditorWorkbench workbench) {
                 new ButtonInfo("Graph", "Graph", "graph", "<html>Add a graph node.</html>"),
                 new ButtonInfo("Compare", "Compare", "compare",
                         "<html>Add a node to compare graphs or SEM IM's.</html>"),
+                new ButtonInfo("GridSearch", "Grid Search", "search",
+                        "<html>Add a node to do a grid search.</html>"),
                 new ButtonInfo("PM", "Parametric Model", "pm",
                         "<html>Add a node for a parametric model.</html>"),
                 new ButtonInfo("IM", "Instantiated Model", "im",

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/TetradDesktop.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/app/TetradDesktop.java
@@ -532,7 +532,7 @@ public void setDisplayLogging(boolean displayLogging) {
             try {
                 TetradLogger.getInstance().setNextOutputStream();
             } catch (IllegalStateException e2) {
-                TetradLogger.getInstance().forceLogMessage(
+                TetradLogger.getInstance().log(
                         "Unable to setup logging, please restart Tetrad.");
                 return;
             }

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);