Merge pull request #84 from phyloref/improvements-from-joss-review

This PR collects improvements made in response to JOSS reviewer suggestions. This includes:
* A note about the `JAVA_HOME` environment variable. Closes #81.
* Cleaned up dependencies, removing overlapped JARs in the final output shaded JAR. Closes #82.

README.md

@@ -33,6 +33,11 @@ Development of JPhyloRef takes place in [our GitHub repository]. This includes [
 
 # Build and execution instructions
 
+You will need [Java] and [Apache Maven] to build the software from source. We recommend installing these
+tools using a package manager, such as [Homebrew] on macOS. You can use [jEnv] instead if you want to install
+multiple Java versions on the same computer. Installation should set up the `JAVA_HOME` environment
+variable; if not, you will need to set it to point at the directory containing your Java installation.
+
 Once you have downloaded the source code to your computer, you can compile and test the code by running `mvn test`.
 
 JPhyloRef can be built from source by running `mvn package` from the root directory of this repository. This will create a JAR file in the `target/` directory, which can be executed by running,
@@ -88,6 +93,10 @@ Once you're set up, you can run `mvn clean deploy` to publish the package
 to the OSSRH. If your version number ends in `-SNAPSHOT`, this will be
 published to the OSSRH Snapshots repository.
 
+  [Java]: https://www.java.com/en/
+  [Apache Maven]: https://maven.apache.org/
+  [Homebrew]: https://brew.sh/
+  [jEnv]: https://www.jenv.be/
   [Sonatype OSSRH]: https://central.sonatype.org/pages/ossrh-guide.html
   [the Sonatype website]: https://central.sonatype.org/pages/apache-maven.html
   [Maven settings.xml file]: https://central.sonatype.org/pages/apache-maven.html

pom.xml

@@ -97,13 +97,6 @@
             <version>2.3.2</version>
         </dependency>
 
-        <!-- https://mvnrepository.com/artifact/com.github.jsonld-java/jsonld-java -->
-        <dependency>
-            <groupId>com.github.jsonld-java</groupId>
-            <artifactId>jsonld-java</artifactId>
-            <version>0.12.0</version>
-        </dependency>
-
         <!-- REASONERS -->
 
         <!-- Elk is an OWL 2 EL reasoner -->
@@ -115,10 +108,10 @@
         </dependency>
 
         <!-- To access OWL-API -->
-        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-distribution -->
+        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-apibinding -->
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
-            <artifactId>owlapi-distribution</artifactId>
+            <artifactId>owlapi-apibinding</artifactId>
             <version>4.5.19</version>
         </dependency>
 
@@ -249,6 +242,16 @@
               </configuration>
             </plugin>
 
+            <!-- Recreate JAR file on every run -->
+            <plugin>
+              <groupId>org.apache.maven.plugins</groupId>
+	      <artifactId>maven-jar-plugin</artifactId>
+	      <version>3.2.0</version>
+	      <configuration>
+                <forceCreation>true</forceCreation>
+	      </configuration>
+	    </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>