cleaner jar generation, updated readme

README.md

@@ -37,10 +37,11 @@ Please see below for the experiment replication instructions.
 `upDoc` is written in Java 11 and developed with `java-11-openjdk-amd64`.
 
 
-### Compiling the sources
+### Compiling and building the sources
 
-Execute: `$ mvn clean compile`
+To compile the sources execute: `$ mvn clean compile`
 
+To build a jar execute: `$ mvn package`
 
 ## Test and Run
 
@@ -65,11 +66,18 @@ Use maven to run the unit tests: `$ mvn test`
 
 ### Code-comment mapping demo
 
-To see how `upDoc` maps code to comments, you can run this command:
+To see how `upDoc` maps code to comments, you can run these commands:
+
+1) execution from the sources
 
 `mvn exec:java -Dexec.mainClass="upDoc" -Dexec.args="analysis:mapping src/test/resources/paper-example/ FromAdaptiveIsomorphismInspectorFactory.java 0.2"`
 
-It will run `upDoc` on a single method and report the similarities of the sentences of the javadoc comment to the method signature.
+2) executing the jar
+
+`java -jar upDoc-1.0.jar analysis:mapping ../src/test/resources/paper-example/ FromAdaptiveIsomorphismInspectorFactory.java 0.2
+`
+
+The demo will run `upDoc` on a single method and report the similarities of the sentences of the javadoc comment to the method signature.
 
 ### Replicate the experimental results from the publication
 
@@ -82,5 +90,3 @@ Execute `$ mvn -Dtest=PaperExampleStatTest test`
 Execute `$ mvn -Dtest=ICPC19StatsTest test -DuseWMD="true"`
 
 Please note that while in the paper we talk about 67 changes, in the outputs you will read a total of 40. It is because some changes were essentially equivalent, and it was not worth it to write a test for each duplicate (check the [google doc](https://docs.google.com/spreadsheets/d/1maRH6YY0OVuKSB2ACDhrz1-CQCS7sRHHoaZJDvLWi2Y/edit?usp=sharing) for the manual ICPC19 dataset analysis, where we list al lthe 67 changes in question)
-
-

pom.xml

@@ -9,7 +9,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>doc-code-analysis</groupId>
     <artifactId>upDoc</artifactId>
-    <version>1.0-SNAPSHOT</version>
+    <version>1.0</version>
     <!-- Output to jar format -->
     <packaging>jar</packaging>
 
@@ -41,7 +41,7 @@
             <version>3.9.2</version>
             <classifier>models</classifier>
         </dependency>
-        <!-- added because of the models dependency above. TODO: remove output -->
+        <!-- added because of the models dependency above. -->
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
@@ -132,28 +132,31 @@
             <!-- For downloading and unzipping WMD models -->
             <!-- NOTE: if for any reason these tasks fail, just follow the URL and
             download + unzip the models manually. The unzipped .txt model (it is a single file)
-            must be under src/main/resources-->
+            must be under src/main/resources -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-antrun-plugin</artifactId>
                 <executions>
                     <execution>
                         <id>download-files</id>
                         <phase>prepare-package</phase>
+<!--                        <phase>compile</phase>-->
                         <goals>
                             <goal>run</goal>
                         </goals>
                         <configuration>
+                            <!-- see https://ant.apache.org/manual/Tasks/ for reference -->
                             <tasks>
                                 <!-- download file -->
-                                <get src="http://star-rep.inf.usi.ch/alberto/glove/raw/master/glove-models.zip"
-                                     dest="${project.build.directory}/downloads/"
-                                     verbose="false"
-                                     usetimestamp="true"/>
+                                <get src="https://star-rep.inf.usi.ch/alberto/glove/raw/master/glove-models.zip"
+                                     dest="${project.build.directory}/glove-models.zip"
+                                     verbose="off"
+                                     usetimestamp="false"
+                                />
                                 <!-- unzip file -->
-                                <unzip src="${project.build.directory}/downloads/"
+                                <unzip src="${project.build.directory}/glove-models.zip"
                                        dest="${project.basedir}/src/main/resources"/>
-
+                                <delete file="${project.build.directory}/glove-models.zip"/>
                             </tasks>
                         </configuration>
                     </execution>
@@ -163,6 +166,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.12.4</version>
                 <configuration>
                     <systemProperties>
                         <property>