Merge pull request #1766 from cmu-phil/development

Update code to 7.6.4

INSTALL_APPLICATION.md

@@ -1,17 +1,22 @@
 # Tetrad Application
 
-This is a user interface tool that divides the analysis of causal problems into modular pieces which can be connected together to reflect how causal problems should ideally be analyzed. This can helpful as an educational tool or for data analysis for those who prefer a point and click interface. 
+This is a user interface tool that divides the analysis of causal problems into modular pieces which can be connected
+together to reflect how causal problems should ideally be analyzed. This can helpful as an educational tool or for data
+analysis for those who prefer a point and click interface.
 
-Please use a recent Java JDK. See [Setting up Java for Tetrad](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Java-for-Tetrad). 
+Please use a recent Java JDK.
+See [Setting up Java for Tetrad](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Java-for-Tetrad).
 
 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/7.6.2/tetrad-gui-7.6.2-launch.jar
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.6.3/tetrad-gui-7.6.3-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 will allow it to use) using this command: 
+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
+will allow it to use) using this command:
 
 java -Xmx[g]G -jar *-launch.jar
 
-Here, [g] is the maximum number of Gigabytes you wish to allocate to the process. 
+Here, [g] is the maximum number of Gigabytes you wish to allocate to the process.
 
 See our Documentation for more details about the Tetrad application.

README.md

@@ -1,24 +1,31 @@
 # Tetrad
 
-Please visit our [[Tetrad web page](https://www.cmu.edu/dietrich/philosophy/tetrad/)) for current links, a list of contributors, some history, documentation, descriptions, links for our various projects, Javadocs, and more.
+Please visit our [[Tetrad web page](https://www.cmu.edu/dietrich/philosophy/tetrad/)) for current links, a list of
+contributors, some history, documentation, descriptions, links for our various projects, Javadocs, and more.
 
 ## Tetrad Application
 
-See out insructions for [Installing the Tetrad Application](https://github.com/cmu-phil/tetrad/blob/development/INSTALL_APPLICATION.md).
+See our instructions
+for [Installing the Tetrad Application](https://github.com/cmu-phil/tetrad/blob/development/INSTALL_APPLICATION.md).
 
 ## Tetrad in Python
 
-We have a project, [py-tetrad](https://github.com/cmu-phil/py-tetrad), that allows you to incorporate arbitrary Tetrad code into a Python workflow. It's new, and the installation is still nonstandard, but it had a good response. This requires Python 3.5+. and Java JDK 9+.
+We have a project, [py-tetrad](https://github.com/cmu-phil/py-tetrad), that allows you to incorporate arbitrary Tetrad
+code into a Python workflow. It's new, and the installation is still nonstandard, but it had a good response. This
+requires Python 3.5+. and Java JDK 17+.
 
 ## Tetrad in R
 
-We also have a project, [rpy-tetrad](https://github.com/cmu-phil/py-tetrad/tree/main/pytetrad/R), that allows you to incorporate _some_ Tetrad functionality in R. It's also new, and the installation for it is also still nonstandard, but has gotten good feedback. This requires Python 3.5+ and Java JDK 9+.
+We also have a project, [rpy-tetrad](https://github.com/cmu-phil/py-tetrad/tree/main/pytetrad/R), that allows you to
+incorporate _some_ Tetrad functionality in R. It's also new, and the installation for it is also still nonstandard, but
+has gotten good feedback. This requires Python 3.5+ and Java JDK 17+.
 
 Please see our [description](https://sites.google.com/view/tetradcausal/tetrad-in-r?authuser=0).
 
 ## Tetrad at the Command Line
 
-In addition, we have a fully-developed tool, [Causal Command](https://github.com/bd2kccd/causal-cmd), that lets you run arbitrary Tetrad searches at the command likne.
+In addition, we have a fully developed tool, [Causal Command](https://github.com/bd2kccd/causal-cmd), that lets you run
+arbitrary Tetrad searches at the command line.
 
 ## Installallation for Programmers
 
@@ -48,9 +55,12 @@ To generate an executable jar:
 mvn clean package
 ```
 
-The (launch) jar for the Tetrad Application will appear in the tetrad-gui/target directory. For links to our Python and R projects or our command line tool, please see our [Tetrad web page](https://sites.google.com/view/tetradcausal).
+The (launch) jar for the Tetrad Application will appear in the tetrad-gui/target directory. For links to our Python and
+R projects or our command line tool, please see our [Tetrad web page](https://sites.google.com/view/tetradcausal).
 
-Here are some [instructions on how to set this project up in IntelliJ IDEA](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Tetrad-in-IntelliJ-IDEA). You can run the Tetrad lifecycle package target and launch the "-launch" jar built in the target directory.
+Here are
+some [instructions on how to set this project up in IntelliJ IDEA](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Tetrad-in-IntelliJ-IDEA).
+You can run the Tetrad lifecycle package target and launch the "-launch" jar built in the target directory.
 
 The project contains well-developed code in these packages:
 

data-reader/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.3</version>
+        <version>7.6.4</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>

data-reader/src/main/java/edu/pitt/dbmi/data/reader/ContinuousData.java

@@ -22,6 +22,7 @@
  * Dec 10, 2018 3:14:46 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface ContinuousData extends Data {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/Data.java

@@ -22,6 +22,7 @@
  * Nov 20, 2018 4:28:27 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface Data {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataColumn.java

@@ -22,6 +22,7 @@
  * Dec 8, 2018 4:14:30 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface DataColumn {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataColumns.java

@@ -32,6 +32,7 @@
  * Jan 2, 2019 10:46:41 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public final class DataColumns {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataFileReader.java

@@ -28,6 +28,7 @@
  * Dec 12, 2018 11:16:14 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public abstract class DataFileReader implements DataReader {
 
@@ -88,7 +89,7 @@ public DataFileReader(Path dataFile, Delimiter delimiter) {
      * Counts number of column from the first non-blank line.
      *
      * @return the number of column from the first non-blank line
-     * @throws IOException if an I/O error occurs
+     * @throws java.io.IOException if an I/O error occurs
      */
     protected int countNumberOfColumns() throws IOException {
         int count = 0;
@@ -184,7 +185,7 @@ protected int countNumberOfColumns() throws IOException {
      * Counts number of non-blank lines.
      *
      * @return the number of non-blank and non-commented lines
-     * @throws IOException if an I/O error occurs
+     * @throws java.io.IOException if an I/O error occurs
      */
     protected int countNumberOfLines() throws IOException {
         int count = 0;
@@ -253,7 +254,7 @@ protected int countNumberOfLines() throws IOException {
     /**
      * Sets the quote character.
      *
-     * @param quoteCharacter the quote character
+     * @param quoteCharacter the quote character to be set
      */
     @Override
     public void setQuoteCharacter(char quoteCharacter) {
@@ -265,7 +266,7 @@ public void setQuoteCharacter(char quoteCharacter) {
     /**
      * Sets the comment marker.
      *
-     * @param commentMarker the comment marker
+     * @param commentMarker the comment marker to be set
      */
     @Override
     public void setCommentMarker(String commentMarker) {

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataReader.java

@@ -22,6 +22,7 @@
  * Dec 12, 2018 11:16:53 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface DataReader {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataReaderException.java

@@ -24,6 +24,7 @@
  * Nov 6, 2018 2:26:59 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public class DataReaderException extends RuntimeException {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DatasetFileReader.java

@@ -24,6 +24,7 @@
  * Dec 7, 2018 3:43:12 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public abstract class DatasetFileReader extends DataFileReader implements DatasetReader {
 
@@ -45,9 +46,9 @@ public DatasetFileReader(Path dataFile, Delimiter delimiter) {
     }
 
     /**
-     * Get the missing data marker.
+     * Sets the missing data marker.
      *
-     * @param missingDataMarker the missing data marker
+     * @param missingDataMarker the missing data marker to be set
      */
     @Override
     public void setMissingDataMarker(String missingDataMarker) {

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DatasetReader.java

@@ -22,6 +22,7 @@
  * Dec 3, 2018 2:24:32 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface DatasetReader extends DataReader {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/Delimiter.java

@@ -22,6 +22,7 @@
  * Nov 5, 2018 2:27:47 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public enum Delimiter {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DiscreteData.java

@@ -22,6 +22,7 @@
  * Dec 10, 2018 3:50:45 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface DiscreteData extends Data {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DiscreteDataColumn.java

@@ -24,6 +24,7 @@
  * Dec 10, 2018 3:24:22 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface DiscreteDataColumn {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/MixedData.java

@@ -22,6 +22,7 @@
  * Dec 10, 2018 3:57:59 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface MixedData extends Data {
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/covariance/CovarianceData.java

@@ -26,20 +26,27 @@
  * Nov 19, 2018 2:20:52 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface CovarianceData extends Data {
 
     /**
+     * <p>getNumberOfCases.</p>
+     *
      * @return the number of cases in the data.
      */
     int getNumberOfCases();
 
     /**
+     * <p>getVariables.</p>
+     *
      * @return the number of variables in the data.
      */
     List<String> getVariables();
 
     /**
+     * <p>getData.</p>
+     *
      * @return the data in a 2D array.
      */
     double[][] getData();

data-reader/src/main/java/edu/pitt/dbmi/data/reader/covariance/CovarianceDataReader.java

@@ -26,14 +26,15 @@
  * Feb 22, 2017 2:31:13 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public interface CovarianceDataReader extends DataReader {
 
     /**
      * Reads in the covariance data.
      *
      * @return the covariance data.
-     * @throws IOException if an I/O error occurs.
+     * @throws java.io.IOException if an I/O error occurs.
      */
     CovarianceData readInData() throws IOException;
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/covariance/LowerCovarianceDataFileReader.java

@@ -34,6 +34,7 @@
  * Nov 19, 2018 11:04:51 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public class LowerCovarianceDataFileReader extends DataFileReader implements CovarianceDataReader {
 
@@ -48,10 +49,9 @@ public LowerCovarianceDataFileReader(Path dataFile, Delimiter delimiter) {
     }
 
     /**
+     * {@inheritDoc}
+     * <p>
      * Reads in the covariance data.
-     *
-     * @return the covariance data.
-     * @throws IOException if an I/O error occurs.
      */
     @Override
     public CovarianceData readInData() throws IOException {

data-reader/src/main/java/edu/pitt/dbmi/data/reader/metadata/ColumnMetadata.java

@@ -24,6 +24,7 @@
  * Dec 18, 2018 11:21:23 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public class ColumnMetadata {
 
@@ -75,9 +76,9 @@ public ColumnMetadata(String name, int columnNumber, boolean discrete) {
     }
 
     /**
+     * {@inheritDoc}
+     * <p>
      * Return a string representation of the column metadata.
-     *
-     * @return a string representation of the column metadata.
      */
     @Override
     public String toString() {

data-reader/src/main/java/edu/pitt/dbmi/data/reader/metadata/InterventionalColumn.java

@@ -24,6 +24,7 @@
  * Dec 20, 2018 11:42:01 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public class InterventionalColumn {
 
@@ -51,9 +52,9 @@ public InterventionalColumn(ColumnMetadata valueColumn, ColumnMetadata statusCol
     }
 
     /**
+     * {@inheritDoc}
+     * <p>
      * Returns a string representation of this object.
-     *
-     * @return a string representation of this object.
      */
     @Override
     public String toString() {

data-reader/src/main/java/edu/pitt/dbmi/data/reader/metadata/Metadata.java

@@ -27,6 +27,7 @@
  * Dec 18, 2018 11:21:23 AM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public class Metadata {
 
@@ -58,9 +59,9 @@ public Metadata(List<ColumnMetadata> domainColumnns, List<InterventionalColumn>
     }
 
     /**
+     * {@inheritDoc}
+     * <p>
      * Returns a string representation of this object.
-     *
-     * @return a string representation of this object.
      */
     @Override
     public String toString() {

data-reader/src/main/java/edu/pitt/dbmi/data/reader/metadata/MetadataFileReader.java

@@ -29,6 +29,7 @@
  * Dec 18, 2018 2:05:46 PM
  *
  * @author Kevin V. Bui (kvb2@pitt.edu)
+ * @version $Id: $Id
  */
 public class MetadataFileReader implements MetadataReader {
 
@@ -47,10 +48,9 @@ public MetadataFileReader(Path metadataFile) {
     }
 
     /**
+     * {@inheritDoc}
+     * <p>
      * Reads in the metadata.
-     *
-     * @return the metadata.
-     * @throws IOException if an I/O error occurs.
      */
     @Override
     public Metadata read() throws IOException {