Merge pull request #1837 from cmu-phil/development

7.6.6 final commits.
cmu-phil · Dec 11, 2024 · 72ba5aa · 72ba5aa
2 parents 69fdb1c + 520dc64
commit 72ba5aa
Show file tree

Hide file tree

Showing 486 changed files with 17,572 additions and 7,855 deletions.
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/7.6.4/tetrad-gui-7.6.4-launch.jar
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.6.5/tetrad-gui-7.6.5-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>7.6.5</version>
+        <version>7.6.6</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>
@@ -24,8 +24,8 @@
                 <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>
         </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</version>
+    <version>7.6.6</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>

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</version>
+    <version>7.6.6-SNAPSHOT</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>

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</version>
+        <version>7.6.6</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>

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AlgorithmParameterPanel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/AlgorithmParameterPanel.java
@@ -96,7 +96,7 @@ public void addToPanel(GeneralAlgorithmRunner algorithmRunner) {
             Set<String> params = new LinkedHashSet<>();
             // RFCI
             params.add(Params.DEPTH);
-            params.add(Params.MAX_PATH_LENGTH);
+            params.add(Params.MAX_DISCRIMINATING_PATH_LENGTH);
             params.add(Params.COMPLETE_RULE_SET_USED);
             params.add(Params.VERBOSE);
             this.mainPanel.add(createSubPanel(title, params, parameters));

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/ApplyMeekRules.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/ApplyMeekRules.java
@@ -89,6 +89,7 @@ public void actionPerformed(ActionEvent e) {
         MeekRules meekRules = new MeekRules();
         meekRules.setMeekPreventCycles(true);
         meekRules.setRevertToUnshieldedColliders(false);
+        meekRules.setVerbose(false);
         meekRules.orientImplied(graph);
         workbench.setGraph(graph);
     }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/CheckGraphForMagAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/CheckGraphForMagAction.java
@@ -30,6 +30,7 @@
 
 import javax.swing.*;
 import java.awt.event.ActionEvent;
+import java.util.HashSet;
 
 /**
  * CheckGraphForMpdagAction is an action class that checks if a given graph is a legal MPDAG (Mixed Ancestral Graph) and
@@ -80,7 +81,7 @@ class MyWatchedProcess extends WatchedProcess {
             @Override
             public void watch() {
                 Graph _graph = new EdgeListGraph(workbench.getGraph());
-                legalMag = GraphSearchUtils.isLegalMag(_graph);
+                legalMag = GraphSearchUtils.isLegalMag(_graph, new HashSet<>());
             }
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/CheckGraphForPagAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/CheckGraphForPagAction.java
@@ -30,6 +30,7 @@
 
 import javax.swing.*;
 import java.awt.event.ActionEvent;
+import java.util.HashSet;
 
 /**
  * CheckGraphForMpdagAction is an action class that checks if a given graph is a legal PAG (Mixed Ancesgral Graph) and
@@ -80,7 +81,7 @@ class MyWatchedProcess extends WatchedProcess {
             @Override
             public void watch() {
                 Graph _graph = new EdgeListGraph(workbench.getGraph());
-                legalPag = GraphSearchUtils.isLegalPag(_graph);
+                legalPag = GraphSearchUtils.isLegalPag(_graph, new HashSet<>());
             }
         }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStats.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStats.java
@@ -146,8 +146,8 @@ public static String generateDescriptiveStats(DataSet dataSet, Node variable,
     /**
      * <p>median.</p>
      *
-     * @param data an array of {@link double} objects
-     * @return an array of {@link double} objects
+     * @param data an array of  objects
+     * @return an array of  objects
      */
     public static double[] median(double[] data) {
         Arrays.sort(data);
@@ -183,7 +183,7 @@ public static double standardErrorMean(double stdDev, double sampleSize) {
     /**
      * Given some variable, returns the mean, standard deviation, and variance.
      *
-     * @param data an array of {@link double} objects
+     * @param data an array of  objects
      * @return [0] -&gt; mean, [1] -&gt; standard deviation, [2] -&gt; variance
      */
     public static double[] normalParams(double[] data) {

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DirichletEstimatorParamsEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DirichletEstimatorParamsEditor.java
@@ -94,8 +94,8 @@ public void setup() {
                           "<br>provide below as pseudocount for every cell. This Dirichlet" +
                           "<br>Bayes IM will be used as the prior for the estimation. If" +
                           "<br>you would like to have more control over how this prior is" +
-                          "<br>created, please remove the PM-->Estimator edge, add a new" +
-                          "<br>IM box, connect it as PM-->IM-->Estimator, and create the" +
+                          "<br>created, please remove the PM--&gt;Estimator edge, add a new" +
+                          "<br>IM box, connect it as PM--&gt;IM--&gt;Estimator, and create the" +
                           "<br>prior you want as a Dirichlet Bayes IM in the IM box." +
                           "</html>"));
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/EdgeTypeTable.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/EdgeTypeTable.java
@@ -46,21 +46,29 @@ public class EdgeTypeTable extends JPanel {
             "Node 2"
     };
 
+    private static final String[] EDGES_WITH_PROPERTIES = {
+        "",
+        "Node 1",
+        "Interaction",
+        "Node 2",
+        "Property"
+    };
+
     private static final String[] EDGES_AND_EDGE_TYPES = {
             "",
             "Node 1",
             "Interaction",
             "Node 2",
             "Ensemble",
             "Edge",
-            "No edge",
-            "\u2192",
-            "\u2190",
-            "---",
-            "\u2192", // -G> pd nl
-            "\u2190", // <G- pd nl
-            "\u2192", // =G> dd nl
-            "\u2190", // <G= dd nl
+            "No edge",  // 6
+            "--> dd pl",   // 7
+            "<-- dd pl",   // 8
+            "---",         // 9
+            "--> pd nl", // -G> pd nl 10  nl pd
+            "<-- pd nl", // <G- pd nl 11
+            "--> dd nl", // =G> dd nl 12  nl dd
+            "<-- dd nl", // <G= dd nl 13
             "o->",
             "<-o",
             "o-o",
@@ -118,19 +126,19 @@ public void update(Graph graph) {
             tableModel.setColumnIdentifiers(EdgeTypeTable.EDGES_AND_EDGE_TYPES);
 
             JTableHeader header = this.table.getTableHeader();
-            Font boldFont = new Font(header.getFont().getFontName(), Font.BOLD, 18);
-            TableCellRenderer headerRenderer = header.getDefaultRenderer();
-            header.setDefaultRenderer((tbl, value, isSelected, hasFocus, row, column) -> {
-                Component comp = headerRenderer.getTableCellRendererComponent(tbl, value, isSelected, hasFocus, row, column);
-                if (column >= 10 && column <= 13) {
-                    comp.setForeground(Color.BLUE);
-                }
-                if (column >= 12 && column <= 13) {
-                    comp.setFont(boldFont);
-                }
-
-                return comp;
-            });
+//            Font boldFont = new Font(header.getFont().getFontName(), Font.BOLD, 18);
+//            TableCellRenderer headerRenderer = header.getDefaultRenderer();
+//            header.setDefaultRenderer((tbl, value, isSelected, hasFocus, row, column) -> {
+//                Component comp = headerRenderer.getTableCellRendererComponent(tbl, value, isSelected, hasFocus, row, column);
+//                if (column >= 10 && column <= 13) {
+//                    comp.setForeground(Color.BLUE);
+//                }
+//                if (column >= 12 && column <= 13) {
+//                    comp.setFont(boldFont);
+//                }
+//
+//                return comp;
+//            });
 
             edges.forEach(edge -> {
                 String[] rowData = new String[EdgeTypeTable.EDGES_AND_EDGE_TYPES.length];
@@ -140,17 +148,20 @@ public void update(Graph graph) {
                 tableModel.addRow(rowData);
             });
         } else {
+            boolean addProperty = hasEdgeProperties(graph);
+            String[] edgeHeaders = addProperty ? EDGES_WITH_PROPERTIES : EDGES;
+
             this.title.setText("Edges");
             this.table.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
-            tableModel.setColumnIdentifiers(EdgeTypeTable.EDGES);
+
+            tableModel.setColumnIdentifiers(edgeHeaders);
 
             edges.forEach(edge -> {
-                String[] rowData = new String[EdgeTypeTable.EDGES.length];
-                addEdgeData(edge, rowData);
+                String[] rowData = new String[edgeHeaders.length];
+                addEdgeData(edge, rowData, addProperty);
 
                 tableModel.addRow(rowData);
             });
-
         }
 
         tableModel.fireTableDataChanged();
@@ -241,6 +252,52 @@ private void addEdgeProbabilityData(Edge edge, String[] rowData) {
         rowData[5] = String.format("%.4f", edge.getProbability());
     }
 
+    private void addEdgeData(Edge edge, String[] rowData, boolean addProperty) {
+        String node1Name = edge.getNode1().getName();
+        String node2Name = edge.getNode2().getName();
+
+        Endpoint endpoint1 = edge.getEndpoint1();
+        Endpoint endpoint2 = edge.getEndpoint2();
+
+        // These should not be flipped.
+        String endpoint1Str = switch (endpoint1) {
+            case TAIL ->
+                "-";
+            case ARROW ->
+                "<";
+            case CIRCLE ->
+                "o";
+            default ->
+                "";
+        };
+        String endpoint2Str = switch (endpoint2) {
+            case TAIL ->
+                "-";
+            case ARROW ->
+                ">";
+            case CIRCLE ->
+                "o";
+            default ->
+                "";
+        };
+        String edgeType = endpoint1Str + "-" + endpoint2Str;
+
+        rowData[1] = node1Name;
+        rowData[2] = edgeType;
+        rowData[3] = node2Name;
+
+        if (addProperty) {
+            List<Edge.Property> edgeProperties = edge.getProperties();
+            if (edgeProperties.isEmpty()) {
+                rowData[4] = "";
+            } else {
+                rowData[4] = edgeProperties.stream()
+                        .map(e -> e.toString())
+                        .collect(Collectors.joining(", "));
+            }
+        }
+    }
+
     private void addEdgeData(Edge edge, String[] rowData) {
         String node1Name = edge.getNode1().getName();
         String node2Name = edge.getNode2().getName();
@@ -282,6 +339,16 @@ private boolean hasEdgeProbabilities(Graph graph) {
         return false;
     }
 
+    private boolean hasEdgeProperties(Graph graph) {
+        for (Edge edge : graph.getEdges()) {
+            if (!edge.getProperties().isEmpty()) {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
     /**
      * <p>Getter for the field <code>graph</code>.</p>
      *

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphEditor.java
@@ -272,7 +272,7 @@ private void initUI(GraphWrapper graphWrapper) {
                     // Update the graphWrapper
                     graphWrapper.setGraph(targetGraph);
                     // Also need to update the UI
-                    updateBootstrapTable(targetGraph);
+//                    updateBootstrapTable(targetGraph);
                 }
             } else if ("modelChanged".equals(propertyName)) {
                 firePropertyChange("modelChanged", null, null);
@@ -350,6 +350,9 @@ private void initUI(GraphWrapper graphWrapper) {
 //        JSplitPane splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT, new PaddingPanel(topBox), new PaddingPanel(edgeTypeTable));
 //        splitPane.setDividerLocation((int) (splitPane.getPreferredSize().getHeight() - 150));
 
+        this.edgeTypeTable.update(graph);
+        updateBootstrapTable(graph);
+
         // Switching to tabbed pane because of resizing problems with the split pane... jdramsey 2021.08.25
         JTabbedPane tabbedPane = new JTabbedPane(SwingConstants.RIGHT);
         tabbedPane.addTab("Graph", new PaddingPanel(topBox));
@@ -359,8 +362,6 @@ private void initUI(GraphWrapper graphWrapper) {
         add(menuBar, BorderLayout.NORTH);
         add(tabbedPane, BorderLayout.CENTER);
 
-        this.edgeTypeTable.update(graph);
-
         // Performs relayout.
         // It means invalid content is asked for all the sizes and
         // all the subcomponents' sizes are set to proper values by LayoutManager.

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphFileMenu.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphFileMenu.java
@@ -59,15 +59,15 @@ public GraphFileMenu(GraphEditable editable, JComponent comp, boolean saveOnly)
         JMenu save = new JMenu("Save...");
         add(save);
 
-        save.add(new SaveGraph(editable, "Text...", SaveGraph.Type.text));
-        save.add(new SaveGraph(editable, "XML...", SaveGraph.Type.xml));
-        save.add(new SaveGraph(editable, "Json...", SaveGraph.Type.json));
-        save.add(new SaveGraph(editable, "R...", SaveGraph.Type.r));
-        save.add(new SaveGraph(editable, "Dot...", SaveGraph.Type.dot));
-        save.add(new SaveGraph(editable, "amat.cpdag...", SaveGraph.Type.amatCpdag));
-        save.add(new SaveGraph(editable, "amat.pag...", SaveGraph.Type.amatPag));
+        save.add(new SaveGraph(editable.getWorkbench(), "Text...", SaveGraph.Type.text));
+        save.add(new SaveGraph(editable.getWorkbench(), "XML...", SaveGraph.Type.xml));
+        save.add(new SaveGraph(editable.getWorkbench(), "Json...", SaveGraph.Type.json));
+        save.add(new SaveGraph(editable.getWorkbench(), "R...", SaveGraph.Type.r));
+        save.add(new SaveGraph(editable.getWorkbench(), "Dot...", SaveGraph.Type.dot));
+        save.add(new SaveGraph(editable.getWorkbench(), "amat.cpdag...", SaveGraph.Type.amatCpdag));
+        save.add(new SaveGraph(editable.getWorkbench(), "amat.pag...", SaveGraph.Type.amatPag));
 //        save.add(new SaveGraph(editable, "PCALG...", SaveGraph.Type.pcalg));
-        save.add(new SaveGraph(editable, "lavaan...", SaveGraph.Type.lavaan));
+        save.add(new SaveGraph(editable.getWorkbench(), "lavaan...", SaveGraph.Type.lavaan));
 
         addSeparator();
         add(new SaveComponentImage(comp, "Save Graph Image..."));