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Improvements made in response to JOSS reviewer suggestions #84

Merged
merged 8 commits into from
Jul 7, 2021
Merged

Improvements made in response to JOSS reviewer suggestions #84

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b34c9dc
Clarify README: the webserver does not serve content at `/`.
gaurav Apr 19, 2021
683e3f2
Added a separate note on running just the test suite.
gaurav Apr 19, 2021
783dbc2
Added some Java installation instructions.
gaurav Jun 17, 2021
f93568e
Merge branch 'master' into improvements-from-joss-review
gaurav Jun 17, 2021
1525a2e
Removed unused JSONLD package.
gaurav Jun 17, 2021
47c6df8
Replaced owlapi-distribution with owlapi-apibinding.
gaurav Jun 17, 2021
bbf672c
Recreate JAR file on each run.
gaurav Jun 17, 2021
e59ebda
Merge branch 'master' into improvements-from-joss-review
gaurav Jul 7, 2021
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9 changes: 9 additions & 0 deletions README.md
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Expand Up @@ -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,
Expand Down Expand Up @@ -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
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21 changes: 12 additions & 9 deletions pom.xml
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Expand Up @@ -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 -->
Expand All @@ -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>

Expand Down Expand Up @@ -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>
Expand Down