Merge pull request #1528 from cmu-phil/development

7.2.1 code
cmu-phil · Feb 19, 2023 · b4b6502 · b4b6502
2 parents 3caee6e + 265e0be
commit b4b6502
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diff --git a/README b/README
@@ -8,11 +8,11 @@ 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/7.1.3-1/tetrad-gui-7.1.3-1-launch.jar
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.2.0/tetrad-gui-7.2.0-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--
 
-https://github.com/cmu-phil/tetrad/wiki/Dealing-with-Tetrad-on-a-Mac--security-issues
+https://github.com/cmu-phil/tetrad/wiki/Dealing-with-Tetrad-on-a-Mac:--Security-Issues
 
 On all platforms, the jar may be launched at the command line (with a specification of the amount of RAM you will allow it to use) using this command:
 

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>7.2.0</version>
+        <version>7.2.1</version>
     </parent>
 <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>

diff --git a/docs/manual/index.html b/docs/manual/index.html
@@ -2889,7 +2889,7 @@ <h3>The IMaGES Algorithm</h3>
 
     <h4>Description</h4>
 
-    <div id="imgs_cont">
+    <div id="images">
 
         <p>Adjusts the selected score for FGES so
             allow for multiple datasets as input. The linear, Gaussian BIC scores
@@ -3118,7 +3118,7 @@ <h3>The GRaSP-FCI Algorithm</h3>
 
     <h4>Description</h4>
 
-    <div id="graspfci">
+    <div id="grasp-fci">
 
         <p>GRaSP-FCI is wrapper around the GRaSP algorithm that replaces
             the FGES step in GFCI with the more accurate GRaSP algrorithm, which
@@ -3829,7 +3829,7 @@ <h4>Description</h4>
 
     <h4>Input Assumptions</h4>
 
-    <p>Continuous, linear data in which all of the variables are
+    <p>Continuous, linear data in which all the variables are
         skewed.</p>
 
     <h4>Output Format</h4>
@@ -3946,6 +3946,40 @@ <h4>Parameters</h4>
 
     <p><a href="#maxit">alpha</a>, <a href="#depth">depth</a></p>
 
+    <h3>The CStaR Algorithm</h3>
+
+    <h4>Description</h4>
+
+    <div id="cstar">
+
+        <p>The CStaR algorithm (Causal Stability Ranking, Stekhoven,
+            D. J., Moraes, I., Sveinbjörnsson, G., Hennig, L.,
+            Maathuis, M. H., & Bühlmann, P. 2012. Causal stability
+            ranking. Bioinformatics, 28(21), 2819-2823) calculates
+            lower bounds on estimated parameters for the causally
+            sufficient case. It first runs a CPDAG algorithm and then
+            for X->Y locally about Y finds all possible orientation of
+            the edges in the CPDAG and does an estimation for each of
+            these and finds their lower bound. In the interface,
+            all nodes that are found to have significant impace on
+            a given target nodes are marked as into that target node.
+            However, the more useful thing is to look at the CStaR
+            table produced by the procedure. To see this table, either
+            run CStaR on a dataset, specifying a target node, and the
+            table will be printed out, or run Tetrad using java -jar
+            and look at the console output, or if these methods are
+            not available, turn on logging in the interface before
+            running the methods, and the table will be printed out.
+            The table is to interpreted as in the Steckhoven et al.
+            paper cited above (see), and is in the same format.
+        </p>
+
+    </div>
+
+    <h4>Input Assumptions</h4>
+
+    <p>Same as for PC.</p>
+
 
     <h2>Statistical Tests</h2>
 
@@ -8483,9 +8517,10 @@ <h3 class="parameter_description" id="checkType">checkType</h3>
             <li>Short Description: <span
                     id="checkType_short_desc">
                     Model significance check type: 1 = Significance, 2 = Clique, 3 = None
+            </span></li>
             <li>Long Description: <span id="checkType_long_desc">
         		Model significance check type: 1 = Significance, 2 = Clique, 3 = None
-         </span></li>
+                </span></li>
             <li>Default Value: <span
                     id="checkType_default_value">1</span></li>
             <li>Lower Bound: <span

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>7.2.0</version>
+    <version>7.2.1</version>
     <packaging>pom</packaging>
 
     <name>Tetrad Project</name>
@@ -80,27 +80,39 @@
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-site-plugin</artifactId>
-                <version>3.4</version>
-                <configuration>
-                    <port>9000</port>
-                    <tempWebappDirectory>${basedir}/target/site/tempdir</tempWebappDirectory>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-source-plugin</artifactId>
-                <version>2.2.1</version>
+                <artifactId>maven-resources-plugin</artifactId>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
-                        <id>attach-sources</id>
+                        <id>copy-dist-resources</id>
+                        <phase>validate</phase>
                         <goals>
-                            <goal>jar-no-fork</goal>
+                            <goal>copy-resources</goal>
                         </goals>
+                        <configuration>
+                            <outputDirectory>${project.build.directory}/dist</outputDirectory>
+                            <resources>
+                                <resource>
+                                    <directory>${project.basedir}/dist</directory>
+                                    <filtering>true</filtering>
+                                </resource>
+                            </resources>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.3.0</version>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
@@ -117,17 +129,48 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-site-plugin</artifactId>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.apache.velocity</groupId>
+                        <artifactId>velocity</artifactId>
+                        <version>1.5</version>
+                    </dependency>
+                </dependencies>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-source-plugin</artifactId>
+                <version>3.2.1</version>
+                <executions>
+                    <execution>
+                        <id>attach-sources</id>
+                        <goals>
+                            <goal>jar-no-fork</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-gpg-plugin</artifactId>
-                <version>3.0.1</version>
+                <version>1.5</version>
                 <executions>
                     <execution>
                         <id>sign-artifacts</id>
                         <phase>verify</phase>
                         <goals>
                             <goal>sign</goal>
                         </goals>
+                        <configuration>
+                            <gpgArguments>
+                                <arg>--pinentry-mode</arg>
+                                <arg>loopback</arg>
+                            </gpgArguments>
+                        </configuration>
                     </execution>
                 </executions>
             </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>7.2.0</version>
+        <version>7.2.1</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/RandomMimParamsEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/RandomMimParamsEditor.java
@@ -227,7 +227,7 @@ public RandomMimParamsEditor(Parameters parameters) {
         b1.add(b18);
 
         Box b19 = Box.createHorizontalBox();
-        b19.add(new JLabel("Measured &lt;-> Measured"));
+        b19.add(new JLabel("Measured <-> Measured"));
         b19.add(Box.createHorizontalGlue());
         b19.add(numMeasuredMeasuredImpureAssociations);
         b1.add(b19);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralAlgorithmRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralAlgorithmRunner.java
@@ -243,8 +243,12 @@ public void execute() {
 
         Algorithm algo = getAlgorithm();
 
-        if (algo instanceof HasKnowledge) {
-            ((HasKnowledge) algo).setKnowledge(this.knowledge.copy());
+        if (this.knowledge != null && !knowledge.isEmpty()) {
+            if (algo instanceof HasKnowledge) {
+                ((HasKnowledge) algo).setKnowledge(this.knowledge.copy());
+            } else {
+                throw new IllegalArgumentException("Knowledge has been supplied, but this algorithm does not use knowledge.");
+            }
         }
 
         if (getDataModelList().size() == 0 && getSourceGraph() != null) {
@@ -286,10 +290,8 @@ public void execute() {
             if (getAlgorithm() instanceof MultiDataSetAlgorithm) {
                 for (int k = 0; k < this.parameters.getInt("numRuns"); k++) {
                     Knowledge knowledge1 = getDataModelList().get(0).getKnowledge();
-                    List<DataSet> dataSets = getDataModelList().stream()
-                            .map(e -> (DataSet) e)
-                            .collect(Collectors.toCollection(ArrayList::new));
-                    for (DataSet dataSet : dataSets) dataSet.setKnowledge(knowledge1);
+                    List<DataModel> dataSets = new ArrayList<>(getDataModelList());
+                    for (DataModel dataSet : dataSets) dataSet.setKnowledge(knowledge1);
                     int randomSelectionSize = this.parameters.getInt("randomSelectionSize");
                     if (randomSelectionSize == 0) {
                         randomSelectionSize = dataSets.size();

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemEstimatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemEstimatorWrapper.java
@@ -79,7 +79,7 @@ public SemEstimatorWrapper(DataModel dataModel, SemPm semPm, Parameters params)
             ICovarianceMatrix covMatrix = new CovarianceMatrix((ICovarianceMatrix) dataModel);
             SemEstimator estimator = new SemEstimator(covMatrix, semPm, getOptimizer());
             estimator.setNumRestarts(getParams().getInt("numRestarts", 1));
-            estimator.setScoreType((ScoreType) getParams().get("scoreType", ScoreType.SemBic));
+            estimator.setScoreType((ScoreType) getParams().get("scoreType", ScoreType.Fml));
             estimator.estimate();
             if (!degreesOfFreedomCheck(semPm)) {
                 throw new IllegalArgumentException("Cannot proceed.");

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>7.2.0</version>
+        <version>7.2.1</version>
     </parent>
 
     <artifactId>tetrad-lib</artifactId>

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/AlgorithmFactory.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/AlgorithmFactory.java
@@ -18,13 +18,15 @@
  */
 package edu.cmu.tetrad.algcomparison.algorithm;
 
+import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg;
 import edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper;
 import edu.cmu.tetrad.algcomparison.score.ScoreWrapper;
 import edu.cmu.tetrad.algcomparison.utils.TakesExternalGraph;
 import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
 import edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper;
 import edu.cmu.tetrad.annotation.AlgorithmAnnotations;
 import edu.cmu.tetrad.graph.Graph;
+import org.apache.commons.math3.analysis.function.Sin;
 
 /**
  * Aug 30, 2017 3:14:40 PM
@@ -68,7 +70,7 @@ public static Algorithm create(Class<? extends Algorithm> algoClass, Independenc
             throws IllegalAccessException, InstantiationException {
         Algorithm algorithm = AlgorithmFactory.create(algoClass, test, score);
         if (externalGraph != null && algorithm instanceof TakesExternalGraph) {
-            ((TakesExternalGraph) algorithm).setExternalGraph(externalGraph);
+            ((TakesExternalGraph) algorithm).setExternalGraph(new SingleGraphAlg(externalGraph));
         }
 
         return algorithm;
@@ -90,7 +92,7 @@ public static Algorithm create(Class<? extends Algorithm> algoClass, Class<? ext
             throws IllegalAccessException, InstantiationException {
         Algorithm algorithm = AlgorithmFactory.create(algoClass, indTestClass, scoreClass);
         if (externalGraph != null && algorithm instanceof TakesExternalGraph) {
-            ((TakesExternalGraph) algorithm).setExternalGraph(externalGraph);
+            ((TakesExternalGraph) algorithm).setExternalGraph(new SingleGraphAlg(externalGraph));
         }
 
         return algorithm;