Merge pull request #170 from CEGRcode/dev

Merge dev to master and deprecate use of dedicated dev branch

Author: owlang

.classpath

@@ -1,10 +1,32 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path="src"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
-	<classpathentry kind="lib" path="lib/jcommon-1.0.21.jar"/>
-	<classpathentry kind="lib" path="lib/jfreechart-1.0.17.jar"/>
-	<classpathentry kind="lib" path="lib/jfreesvg-3.0.jar"/>
-	<classpathentry kind="lib" path="lib/picard.jar"/>
-	<classpathentry kind="output" path="bin"/>
-</classpath>
+	<classpathentry kind="src" output="bin/main" path="src/main/resources">
+		<attributes>
+			<attribute name="gradle_scope" value="main"/>
+			<attribute name="gradle_used_by_scope" value="main,test"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/test" path="src/test/java">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/test" path="src/test/resources">
+		<attributes>
+			<attribute name="gradle_scope" value="test"/>
+			<attribute name="gradle_used_by_scope" value="test"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="bin/main" path="src/main/java">
+		<attributes>
+			<attribute name="gradle_scope" value="main"/>
+			<attribute name="gradle_used_by_scope" value="main,test"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8/"/>
+	<classpathentry kind="con" path="org.eclipse.buildship.core.gradleclasspathcontainer"/>
+	<classpathentry kind="output" path="bin/default"/>
+</classpath>

.github/workflows/gradle.yml

@@ -0,0 +1,40 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will build a Java project with Gradle and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-gradle
+
+# Modified to matrix test across three OS and two Temurin distributions of Java - two LTS versions (11 and 17)
+
+name: Java CI with Gradle
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master", "dev" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build on node ${{ matrix.java_version }} and ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        java_version: ['11', '17']
+        os: [ ubuntu-latest, windows-latest, macOS-latest ]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up JDK ${{ matrix.java_version }} on ${{ matrix.os }}
+      uses: actions/setup-java@v3
+      with:
+        java-version: ${{ matrix.java_version }}
+        distribution: 'temurin'
+    - name: Build with Gradle
+      uses: gradle/gradle-build-action@67421db6bd0bf253fb4bd25b31ebb98943c375e1
+      with:
+        arguments: build

.gitignore

@@ -3,3 +3,4 @@
 /.gradle/
 /build/
 .metadata
+.idea

.project

@@ -6,12 +6,12 @@
 	</projects>
 	<buildSpec>
 		<buildCommand>
-			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
+			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
 		<buildCommand>
-			<name>org.eclipse.jdt.core.javabuilder</name>
+			<name>org.eclipse.buildship.core.gradleprojectbuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>

.settings/org.eclipse.buildship.core.prefs

@@ -1,2 +1,2 @@
 connection.project.dir=
-eclipse.preferences.version=1
+eclipse.preferences.version=1

build.gradle

@@ -1,68 +1,60 @@
-// gradle 4.3
+/*
+ * This file was generated by the Gradle 'init' task.
+ *
+ * This generated file contains a sample Java Library project to get you started.
+ * For more details take a look at the Java Libraries chapter in the Gradle
+ * User Manual available at https://docs.gradle.org/7.5/userguide/java_library_plugin.html
+ */
+
+// 
+plugins {
+    // Apply the java-library plugin to add support for Java Library
+    id 'java-library'
+    id 'java'
+    id 'eclipse'
+    id 'application'
+//    id 'pmd'
+//    id 'checkstyle'
+    id 'com.github.johnrengelman.shadow' version '7.1.2'
+}
 
-apply plugin: 'java'
-//apply plugin: 'checkstyle'
-//apply plugin: 'findbugs'
-//apply plugin: 'pmd'
-apply plugin: 'application'
-apply plugin: 'eclipse'
+mainClassName = "scriptmanager.main.ScriptManager"
+version = 'v0.14-dev'
 
-sourceSets.main.java.srcDirs = ['src']
-mainClassName = "main.ScriptManager"
-version = 'v0.14'
 sourceCompatibility = 1.8
 targetCompatibility = 1.8
 
-// Gradle builds for dev
-jar {
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
-
-	baseName = "ScriptManager"
-
-	manifest {
-        attributes 'ScriptManager-Title': baseName,
-        	'ScriptManager-Version': version,
-        	'Main-Class': mainClassName
-    }
-}
-
-// Create a single JAR with all dependencies bundles - for production deployment
-task fatJar(type: Jar) {
-    exclude 'META-INF/*.RSA', 'META-INF/*.SF','META-INF/*.DSA'
-
-	manifest {
-        attributes 'ScriptManager-Title': 'Gradle jar of ScriptManager',
-        	'ScriptManager-Version': version,
-        	'Main-Class': mainClassName
-    }
-
-    baseName = 'ScriptManager' + version
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
-    with jar
-}
-
 // Get dependencies from Maven central repository
 repositories {
+    // Use jcenter for resolving dependencies.
+    //jcenter()
+    // You can declare any Maven/Ivy/file repository here.
     mavenCentral()
 }
 
 // Declare the dependencies for your production and test code
 dependencies {
-	compile group: 'org.slf4j', name: 'slf4j-api', version: '1.7.13'
-	// https://mvnrepository.com/artifact/javax.xml.bind/jaxb-api
-	compile group: 'javax.xml.bind', name: 'jaxb-api', version: '2.1'
-	// https://mvnrepository.com/artifact/info.picocli/picocli     #CommandLineInterface Parsing Args
-	compile group: 'info.picocli', name: 'picocli', version: '4.2.0'
-	compile group: 'org.jfree', name: 'jfreechart', version: '1.5.3'
-	compile group: 'org.jfree', name: 'jfreesvg', version: '3.4.2'
-	testCompile group: 'junit', name: 'junit', version: '4.12'
-	compile fileTree(dir: 'lib', include: ['*.jar'])
- }
+    implementation group: 'org.slf4j', name: 'slf4j-api', version: '1.7.13'
+    // https://mvnrepository.com/artifact/javax.xml.bind/jaxb-api
+    implementation group: 'javax.xml.bind', name: 'jaxb-api', version: '2.1'
+    // https://mvnrepository.com/artifact/info.picocli/picocli     #CommandLineInterface Parsing Args
+    implementation group: 'info.picocli', name: 'picocli', version: '4.2.0'
+    implementation group: 'org.jfree', name: 'jfreechart', version: '1.5.3'
+    implementation group: 'org.jfree', name: 'jfreesvg', version: '3.4.2'
+    implementation fileTree(dir: 'lib', include: ['*.jar'])
+}
+
+// Declare dependencies explicitly (for Gradle 7.X with Shadow)
+tasks.shadowJar.dependsOn ':distTar'
+tasks.shadowJar.dependsOn ':distZip'
+
+// Build fat jar executable with all dependencies bundled together
+shadowJar {
+    // Configure JAR file name
+    archiveBaseName.set('ScriptManager')
+    archiveClassifier.set('')
+    archiveVersion.set(version)
 
-uploadArchives {
-    repositories {
-       flatDir {
-           dirs 'repos'
-       }
-    }
+    // Reduce fat jar to only include dependencies used
+    minimize()
 }

docusaurus/docs/read-analysis/transpose-matrix.md

@@ -0,0 +1,41 @@
+---
+id: transpose-matrix
+title: Transpose Matrix
+sidebar_label: transpose-matrix
+---
+
+![transpose-matrix](/../static/icons/Read_Analysis/TransposeMatrix_square.svg)
+
+Interchange the rows and columns of a matrix, while optionally preserving labels.
+
+<img src={require('/../static/md-img/Read_Analysis/TransposeMatrixWindow.png').default} style={{width:70+'%'}}/> 
+
+## Command Line Interface
+
+Usage:
+```bash
+java -jar ScriptManager.jar read-analysis transpose-matrix [-hV] [-z] [-l=<startCOL>]
+[-o=<output>] [-r=<startROW>] <matrix>
+```
+
+## Positional Input
+
+This tool takes a single matrix file for input.
+
+
+### Output Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-o, --output=<output>` | specify output filename |
+| `-z, --compress` | output compressed .gz file |
+
+
+### Coord Start Options
+
+| Option | Description |
+| ------ | ----------- |
+| `-r, --start-row` | row to start transposing the matrix (zero indexed) |
+| `-l, --start-col` | column to start transposing the matrix (zero indexed) |
+
+[file-format]:file-formats.md

docusaurus/static/icons/Read_Analysis/TransposeMatrix_square.svg

@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.5-bin.zip
+networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.5.1-bin.zip