Merge pull request #2 from cicirello/development

Various updated in preparation for publishing to GitHub package registry

Author: cicirello

README.md

@@ -37,67 +37,46 @@ Javadoc documentation is in the /docs folder as well as at https://jpt.cicirello
 Source code is found in the /src folder.  JUnit test classes are found in the /tests folder, which
 mirrors the package structure of /src.
 
-Compiled jar files of the library are in the /lib folder.
+Compiled jar files of the library are in the /dist folder.
 
 The /examples folder includes source code to illustrate how to use the library.  The /replication
 folder includes source code that recreates results found in publications associated with the library.
 
 ## Building the Library (with ant)
 
-The /build directory contains an ant build file.  The build file also executes the JUnit tests, and the build directory contains
-the relevant jar files for the JUnit libraries.  If you prefer, you can replace these with the latest versions available
-from https://junit.org/junit4/ (just be sure to edit the property fields in the build.xml to point to the locations of the JUnit jar files).
-
-To execute the build process do one of the following.  If your working directory is the build directory, then simply execute
-`ant` from the command line.  If your working directory is the parent of build, then execute: `ant -f build/build.xml`
-
-The default of the provided ant build file, compiles all source files and all JUnit tests, executes all test cases,
-and generates the jar file of the library. The build process will terminate on any test case failures.  The default 
-does not compile the example programs or the experiment replication programs.  To include those in the build as well
-then execute `ant all` (if your working directory is the build directory) or `ant -f build/build.xml all` (if your 
-working directory is the parent of build).
-
-If you use the ant build file, the build will generate the following directories: bin (for the compiled Java classes),
-testbin (for the compiled JUnit tests), lib (for the jar file of the library), and exbin (for the compiled example
+The /build directory contains an ant build file.  The build file 
+also executes the JUnit tests, and the build directory contains
+the relevant jar files for the JUnit libraries.  If you prefer, 
+you can replace these with the latest versions available
+from https://junit.org/junit4/ (just be sure to edit the property 
+fields in the build.xml to point to the locations of the JUnit jar files).
+
+To execute the build process do one of the following.  If your working 
+directory is the build directory, then simply execute
+`ant` from the command line.  If your working directory is the 
+parent of build, then execute: `ant -f build/build.xml`
+
+The default of the provided ant build file, compiles all source 
+files and all JUnit tests, executes all test cases,
+generates the jar file of the library, and compiles the example 
+programs and the experiment replication programs. The 
+build process will terminate on any test case failures.  
+
+If you use the ant build file, the build will generate the 
+following directories: bin (for the compiled Java classes),
+testbin (for the compiled JUnit tests), dist (for the jar file of the library), 
+and exbin (for the compiled example
 programs and experiment replication programs).
 
 ## Running the Example Programs
 
 The examples directory contains example usage of several of the classes of the API.
 The replication directory additionally contains more complex examples that replicate the
 experiments from published papers that have used the library.  Those directories contain
-readmes that provide more detail on the examples.
-
-Assuming the build was successful, the compiled examples and replication programs will be
-in the exbin directory.  If your working directory is the root
-of the repository, then you can run these programs from the command line with the following:
-
-```
-java -cp "lib/jpt2.jar;exbin" org.cicirello.examples.jpt.AverageDistance
-java -cp "lib/jpt2.jar;exbin" org.cicirello.examples.jpt.TableOfDistances
-java -cp "lib/jpt2.jar;exbin" org.cicirello.examples.jpt.PermutationExamples
-java -cp "lib/jpt2.jar;exbin" org.cicirello.examples.jpt.SimpleDistanceExamples
-java -cp "lib/jpt2.jar;exbin" org.cicirello.examples.jpt.SequenceDistanceExamples
-java -cp "lib/jpt2.jar;exbin" org.cicirello.examples.jpt.PermutationHashCodes
-java -cp "lib/jpt2.jar;exbin" org.cicirello.replication.flairs2013.Flairs2013
-java -cp "lib/jpt2.jar;exbin" org.cicirello.replication.ieeetevc2016.FDC
-java -cp "lib/jpt2.jar;exbin" org.cicirello.replication.bict2019.BICT2019
-```
-
-In each of the above cases, the source code includes comments explaining the example
-usage of the library.
-
-**Memory Intensive Example**: Note that depending on your processor speed, 
-the experiment replication programs may be slow (certainly slower than
-the examples from the examples folder).  Additionally, the `org.cicirello.replication.ieeetevc2016.FDC` is memory intensive, 
-and depending upon your system may require increasing the heap allocation to the Java virtual machine.
-If it throws an `OutOfMemoryError`, then execute as follows (note the additional command line argument):
-
-```
-java -Xms1g -cp "lib/jpt2.jar;exbin" org.cicirello.replication.ieeetevc2016.FDC
-```
-
+READMEs that provide more detail on the examples, including on running the examples.
 
 ## Contribute
 
-Report bugs, suggestions, feature requests, etc via the [issues tracker](https://github.com/cicirello/JavaPermutationTools/issues).  If you would like to directly contribute new code, you may also fork the repository, and create pull requests.
+Report bugs, suggestions, feature requests, etc via the [issues tracker](https://github.com/cicirello/JavaPermutationTools/issues).  If you would 
+like to directly contribute new code, you may also fork the repository, 
+and create pull requests.

build/build.xml

@@ -3,14 +3,14 @@
   Build file for the Java Permutation Tools (JPT) API.
   </description>
   <!-- global properties for this build -->
-  <property name="VERSION" value="2"/>
+  <property name="VERSION" value="2.0.1"/>
   <property name="junit" location="build/junit-4.12.jar"/>
   <property name="hamcrest" location="build/hamcrest-core-1.3.jar"/>
   <property name="src" location="src"/>
   <property name="bin" location="bin"/>
   <property name="testsrc" location="tests"/>
   <property name="testbin" location="testbin"/>
-  <property name="dist" location="lib"/>
+  <property name="dist" location="dist"/>
   <property name="examples" location="examples"/>
   <property name="replication" location="replication"/>
   <property name="examplebin" location="exbin"/>
@@ -63,17 +63,17 @@
 	<!-- Create the distribution directory -->
     <mkdir dir="${dist}"/>
     <!-- Put everything in ${bin} into the jpt${VERSION}.jar file -->
-    <jar jarfile="${dist}/jpt${VERSION}.jar" basedir="${bin}"/>
+    <jar jarfile="${dist}/jpt-${VERSION}.jar" basedir="${bin}"/>
   </target>
 
   <target name="examples" depends="dist"
 		description="compiles example programs and experiment replication programs">
 	<!-- Create directory for bin of examples and replication programs -->
     <mkdir dir="${examplebin}"/>
 	<!-- Compile basic examples -->
-	<javac srcdir="${examples}" destdir="${examplebin}" classpath="${dist}/jpt${VERSION}.jar;${examples}" includeantruntime="false"/>
+	<javac srcdir="${examples}" destdir="${examplebin}" classpath="${dist}/jpt-${VERSION}.jar;${examples}" includeantruntime="false"/>
 	<!-- Compile experiment replication programs -->
-	<javac srcdir="${replication}" destdir="${examplebin}" classpath="${dist}/jpt${VERSION}.jar;${replication}" includeantruntime="false"/>
+	<javac srcdir="${replication}" destdir="${examplebin}" classpath="${dist}/jpt-${VERSION}.jar;${replication}" includeantruntime="false"/>
   </target>
 
   <target name="docs" depends="dist" 
@@ -84,7 +84,8 @@
 			doctitle="JavaPermutationTools - A Java API for computation on permutations"
 			overview="src/overview.html"
 			author="false"
-			version="false">
+			version="false"
+			additionalparam="-notimestamp">
 		<link href="https://docs.oracle.com/javase/8/docs/api/" packagelistLoc="build/java-package-list" offline="true" />
 		<bottom><![CDATA[Copyright &copy; 2005-2019 Vincent A. Cicirello. <a href=\"https://www.cicirello.org/\" target=_top>https://www.cicirello.org/</a>]]></bottom>
 	</javadoc>

dist/jpt-2.0.1.jar

@@ -2,9 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Wed Sep 25 12:39:57 EDT 2019 -->
+<!-- Generated by javadoc -->
 <title>All Classes (JavaPermutationTools - A Java API for computation on permutations)</title>
-<meta name="date" content="2019-09-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>

lib/jpt1.jar renamed to dist/jpt1.jar

@@ -2,9 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Wed Sep 25 12:39:57 EDT 2019 -->
+<!-- Generated by javadoc -->
 <title>All Classes (JavaPermutationTools - A Java API for computation on permutations)</title>
-<meta name="date" content="2019-09-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>

lib/jpt2.jar renamed to dist/jpt2.jar

@@ -2,9 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Wed Sep 25 12:39:57 EDT 2019 -->
+<!-- Generated by javadoc -->
 <title>Constant Field Values (JavaPermutationTools - A Java API for computation on permutations)</title>
-<meta name="date" content="2019-09-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>

docs/api/allclasses-frame.html

@@ -2,9 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Wed Sep 25 12:39:57 EDT 2019 -->
+<!-- Generated by javadoc -->
 <title>Deprecated List (JavaPermutationTools - A Java API for computation on permutations)</title>
-<meta name="date" content="2019-09-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>

docs/api/allclasses-noframe.html

@@ -2,9 +2,8 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_05) on Wed Sep 25 12:39:57 EDT 2019 -->
+<!-- Generated by javadoc -->
 <title>API Help (JavaPermutationTools - A Java API for computation on permutations)</title>
-<meta name="date" content="2019-09-25">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>