Merge branch 'hotfix-1.1.3'

PavlidisLab · Jul 6, 2022 · 40b9ae7 · 40b9ae7
2 parents 49bca56 + 9d2073b
commit 40b9ae7
Show file tree

Hide file tree

Showing 14 changed files with 791 additions and 269 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.2</version>
+	<version>1.1.3</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -49,7 +49,7 @@
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi</artifactId>
-			<version>5.1.0</version>
+			<version>5.2.2</version>
 		</dependency>
 		<dependency>
 			<groupId>colt</groupId>
@@ -71,7 +71,7 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-configuration2</artifactId>
-			<version>2.7</version>
+			<version>2.8.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -93,7 +93,7 @@
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpcore</artifactId>
-			<version>4.4.14</version>
+			<version>4.4.15</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
@@ -142,7 +142,7 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
-			<version>1.7.32</version>
+			<version>1.7.36</version>
 		</dependency>
 
 		<!-- Jena -->
@@ -218,12 +218,13 @@
 		<dependency>
 			<groupId>xml-apis</groupId>
 			<artifactId>xml-apis</artifactId>
+			<!--suppress MavenPackageUpdate -->
 			<version>1.4.01</version>
 		</dependency>
 		<dependency>
 			<groupId>com.opencsv</groupId>
 			<artifactId>opencsv</artifactId>
-			<version>5.5.2</version>
+			<version>5.6</version>
 		</dependency>
 
 		<!-- Testing utilities -->
@@ -233,6 +234,24 @@
 			<version>4.13.2</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.mockito</groupId>
+			<artifactId>mockito-core</artifactId>
+			<version>4.6.1</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-core</artifactId>
+			<version>2.17.2</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-slf4j-impl</artifactId>
+			<version>2.17.2</version>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 	<build>
 		<directory>target</directory>
@@ -267,10 +286,30 @@
 			</testResource>
 		</testResources>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-enforcer-plugin</artifactId>
+				<version>1.4.1</version>
+				<executions>
+					<execution>
+						<id>enforce-maven</id>
+						<goals>
+							<goal>enforce</goal>
+						</goals>
+						<configuration>
+							<rules>
+								<requireMavenVersion>
+									<version>[3.0.5,)</version>
+								</requireMavenVersion>
+							</rules>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>com.amashchenko.maven.plugin</groupId>
 				<artifactId>gitflow-maven-plugin</artifactId>
-				<version>1.6.0</version>
+				<version>1.16.0</version>
 				<configuration>
 					<!-- Do not push to remote -->
 					<pushRemote>false</pushRemote>
@@ -280,7 +319,7 @@
 						<productionBranch>master</productionBranch>
 						<developmentBranch>development</developmentBranch>
 						<releaseBranchPrefix>release-</releaseBranchPrefix>
-						<versionTagPrefix></versionTagPrefix>
+						<versionTagPrefix/>
 						<origin>origin</origin>
 						<!-- Unused for releasing -->
 						<featureBranchPrefix>feature-</featureBranchPrefix>
@@ -363,7 +402,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>3.3.0</version>
+				<version>3.3.1</version>
 				<configuration>
 					<quiet>true</quiet>
 					<source>8</source>

diff --git a/src/ubic/basecode/math/linearmodels/LeastSquaresFit.java b/src/ubic/basecode/math/linearmodels/LeastSquaresFit.java
@@ -234,7 +234,7 @@ public LeastSquaresFit( DesignMatrix designMatrix, DoubleMatrix<String, String>
      * Preferred interface for weighted least squares fit between two matrices
      *
      * @param designMatrix
-     * @param data
+     * @param b the data
      * @param weights      to be used in modifying the influence of the observations in vectorB.
      */
     public LeastSquaresFit( DesignMatrix designMatrix, DoubleMatrix2D b, final DoubleMatrix2D weights ) {
@@ -338,7 +338,7 @@ public LeastSquaresFit( DoubleMatrix2D A, DoubleMatrix2D b, final DoubleMatrix2D
     }
 
     /**
-     * @param sample information that will be converted to a design matrix; intercept term is added.
+     * @param sampleInfo information that will be converted to a design matrix; intercept term is added.
      * @param data   Data matrix
      */
     public LeastSquaresFit( ObjectMatrix<String, String, Object> sampleInfo, DenseDoubleMatrix2D data ) {
@@ -378,7 +378,7 @@ public LeastSquaresFit( ObjectMatrix<String, String, Object> sampleInfo, DenseDo
     /**
      * NamedMatrix allows easier handling of the results.
      *
-     * @param sample information that will be converted to a design matrix; intercept term is added.
+     * @param design information that will be converted to a design matrix; intercept term is added.
      * @param b      Data matrix
      */
     public LeastSquaresFit( ObjectMatrix<String, String, Object> design, DoubleMatrix<String, String> b ) {
@@ -396,7 +396,7 @@ public LeastSquaresFit( ObjectMatrix<String, String, Object> design, DoubleMatri
     /**
      * NamedMatrix allows easier handling of the results.
      *
-     * @param sample information that will be converted to a design matrix; intercept term is added.
+     * @param design information that will be converted to a design matrix; intercept term is added.
      * @param data   Data matrix
      */
     public LeastSquaresFit( ObjectMatrix<String, String, Object> design, DoubleMatrix<String, String> data,
@@ -756,9 +756,9 @@ protected List<GenericAnovaResult> anova() {
     /**
      * Provide results of limma eBayes algorithm. These will be used next time summarize is called on this.
      * 
-     * @param dfPrior
-     * @param varPrior
-     * @param varPost
+     * @param d dfPrior
+     * @param v varPrior
+     * @param vp varPost
      */
     protected void ebayesUpdate( double d, double v, DoubleMatrix1D vp ) {
         this.dfPrior = d;