Merge pull request #1531 from cmu-phil/development

Pushing version 7.2.2 to master

README

@@ -8,7 +8,7 @@ https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/
 
 The jar to launch the Tetrad GUI is here (please download this one and delete any old ones):
 
-https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.2.0/tetrad-gui-7.2.0-launch.jar
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.2.1/tetrad-gui-7.2.1-launch.jar
 
 The application will work on all major platforms once a recent version of the Java JRE is installed. (Corretto 18 is fine, for instance.) You may be able to launch it by double clicking the jar file name, though on a Mac, this presents some security challenges--
 

data-reader/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.2.1</version>
+        <version>7.2.2</version>
     </parent>
 <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>

pom.xml

@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.github.cmu-phil</groupId>
     <artifactId>tetrad</artifactId>
-    <version>7.2.1</version>
+    <version>7.2.2</version>
     <packaging>pom</packaging>
 
     <name>Tetrad Project</name>
@@ -132,6 +132,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-site-plugin</artifactId>
+                <version>3.12.0</version>
                 <dependencies>
                     <dependency>
                         <groupId>org.apache.velocity</groupId>

tetrad-gui/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.2.1</version>
+        <version>7.2.2</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>

tetrad-lib/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.2.1</version>
+        <version>7.2.2</version>
     </parent>
 
     <artifactId>tetrad-lib</artifactId>

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/mixed/Mgm.java

@@ -33,6 +33,10 @@ public Mgm() {
 
     @Override
     public Graph search(DataModel ds, Parameters parameters) {
+        if (!(ds instanceof DataSet)) {
+            throw new IllegalArgumentException("Expecting tabular data for MGM.");
+        }
+
         DataSet _data = (DataSet) ds;
 
         for (int j = 0; j < _data.getNumColumns(); j++) {

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/CCD.java

@@ -5,6 +5,7 @@
 import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
 import edu.cmu.tetrad.annotation.AlgType;
 import edu.cmu.tetrad.annotation.Bootstrapping;
+import edu.cmu.tetrad.annotation.Experimental;
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataSet;
 import edu.cmu.tetrad.data.DataType;
@@ -27,6 +28,7 @@
         algoType = AlgType.forbid_latent_common_causes
 )
 @Bootstrapping
+@Experimental
 public class CCD implements Algorithm, TakesIndependenceWrapper {
     static final long serialVersionUID = 23L;
     private IndependenceWrapper test;

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/PagSamplingRfci.java

@@ -29,7 +29,7 @@
         command = "pag-sampling-rfci",
         algoType = AlgType.allow_latent_common_causes
 )
-@Experimental
+//@Experimental
 public class PagSamplingRfci implements Algorithm, HasKnowledge {
 
     public static final List<String> PAG_SAMPLING_RFCI_PARAMETERS = new LinkedList<>();

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pattern/CStaR.java

@@ -53,25 +53,30 @@ public Graph search(DataModel dataSet, Parameters parameters) {
 
         List<Node> possibleEffects = new ArrayList<>();
 
-        String targetName = parameters.getString(Params.TARGETS);
+        String targetNames = parameters.getString(Params.TARGETS);
 
-        if (targetName.trim().equalsIgnoreCase("")) {
+        if (targetNames.trim().equalsIgnoreCase("")) {
             throw new IllegalStateException("Please specify target name(s).");
         }
 
-        if (targetName.trim().equalsIgnoreCase("all")) {
+        if (targetNames.trim().equalsIgnoreCase("all")) {
             for (String name : dataSet.getVariableNames()) {
                 possibleEffects.add(dataSet.getVariable(name));
             }
         } else {
-            String[] names = targetName.split(",");
+            String[] names = targetNames.split(",");
 
             for (String name : names) {
                 possibleEffects.add(dataSet.getVariable(name.trim()));
             }
         }
 
         List<Node> possibleCauses = new ArrayList<>(dataSet.getVariables());
+//        possibleCauses.removeAll(possibleEffects);
+
+        if (!(dataSet instanceof DataSet)) {
+            throw new IllegalArgumentException("Expecting tabular data for CStaR.");
+        }
 
         LinkedList<LinkedList<Cstar.Record>> allRecords
                 = cStaR.getRecords((DataSet) dataSet, possibleCauses, possibleEffects, test.getTest(dataSet, parameters));

tetrad-lib/src/main/java/edu/cmu/tetrad/search/BuildPureClusters.java

@@ -857,7 +857,7 @@ private List<List<int[]>> filterAndOrderClusterings(List<List<int[]>> baseListOf
                 ClusterSignificance clusterSignificance = new ClusterSignificance(variables, covarianceMatrix);
                 clusterSignificance.setCheckType(checkType);
                 List<Integer> cluster = ClusterSignificance.getInts(currentCluster);
-                if (clusterSignificance.significant(cluster, alpha)) {
+                if (!clusterSignificance.significant(cluster, alpha)) {
                     continue;
                 }
 

tetrad-lib/src/main/java/edu/cmu/tetrad/search/Cstar.java

@@ -178,10 +178,8 @@ public LinkedList<LinkedList<Record>> getRecords(DataSet dataSet, List<Node> pos
             this.test = test;
         } else if (test instanceof ChiSquare) {
             this.test = test;
-        } else if (test instanceof IndTestScore && ((IndTestScore) test).getWrappedScore() instanceof ConditionalGaussianScore) {
-            this.test = test;
         } else {
-            throw new IllegalArgumentException("Expecting Fisher Z, Chi Square, Sem BIC, or Conditional Gaussian Score.");
+            throw new IllegalArgumentException("Expecting Fisher Z, Chi Square, or Sem BIC.");
         }
 
         List<Map<Integer, Map<Node, Double>>> minimalEffects = new ArrayList<>();
@@ -244,6 +242,8 @@ public double[][] call() {
                             pattern = getPatternFges(sample);
                         } else if (Cstar.this.patternAlgorithm == PatternAlgorithm.PC_STABLE) {
                             pattern = getPatternPcStable(sample);
+                        } else if (Cstar.this.patternAlgorithm == PatternAlgorithm.GRaSP) {
+                            pattern = getPatternPcStable(sample);
                         } else {
                             throw new IllegalArgumentException("That type of of pattern algorithm is not configured: " + Cstar.this.patternAlgorithm);
                         }
@@ -600,6 +600,14 @@ private Graph getPatternPcStable(DataSet sample) {
         return pc.search();
     }
 
+    private Graph getPatternGRaSP(DataSet sample) {
+        test.setVerbose(false);
+        Grasp alg = new Grasp(new SemBicScore(sample));
+        alg.setVerbose(false);
+        alg.bestOrder(sample.getVariables());
+        return alg.getGraph(true);
+    }
+
     //=============================PRIVATE==============================//
 
     private Graph getPatternFges(DataSet sample) {
@@ -687,7 +695,7 @@ private List<double[][]> runCallablesDoubleArray(List<Callable<double[][]>> task
         return results;
     }
 
-    public enum PatternAlgorithm {FGES, PC_STABLE}
+    public enum PatternAlgorithm {FGES, PC_STABLE, GRaSP}
 
     public enum SampleStyle {BOOTSTRAP, SPLIT}
 

tetrad-lib/src/main/java/edu/cmu/tetrad/util/ConcurrencyUtils.java

@@ -8,7 +8,7 @@ public class ConcurrencyUtils {
     public static void runCallables(List<Callable<Boolean>> tasks, boolean parallelized) {
         if (tasks.isEmpty()) return;
 
-        if (parallelized) {
+        if (!parallelized) {
             for (Callable<Boolean> task : tasks) {
                 try {
                     task.call();