PAMGuard/pom.xml

<project xmlns="http://maven.apache.org/POM/4.0.0" 
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.pamguard</groupId>
  <artifactId>Pamguard</artifactId>
  <version>2.02.14b</version>
  <name>Pamguard</name>
  <description>Pamguard using Maven to control dependencies</description>
	<url>www.pamguard.org</url>
	<organization>
		<name>Sea Mammal Research Unit, University of St. Andrews</name>
		<url>http://www.smru.st-andrews.ac.uk</url>
	</organization>


	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<javafx.version>21</javafx.version>
		<maven.compiler.source>11</maven.compiler.source>
		<maven.compiler.target>11</maven.compiler.target>
		<!-- Tethys version control -->
		<jaxb.runtime.version>2.4.0-b180830.0438</jaxb.runtime.version>
		<jaxb.api.version>2.4.0-b180830.0359</jaxb.api.version>
		<jaxb.xjc.version>2.4.0-b180830.0438</jaxb.xjc.version>
		<mockito.version>1.10.19</mockito.version>
		<powermock.version>1.6.6</powermock.version>
	</properties>

	<build>
		<!-- Define where the source and test directories are -->
		<sourceDirectory>${basedir}/src</sourceDirectory>
		<testSourceDirectory>${basedir}/src/test</testSourceDirectory> <!-- where the Unit tets are located -->
		<resources>
			<resource>
				<directory>src</directory>
				<excludes>
					<exclude>META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA</exclude>
					<exclude>**/*.java</exclude> <!--  don't include any source files -->
					<exclude>jars/*.*</exclude> <!--  don't include files in the jars folder -->
				</excludes>
			</resource>
		</resources>


		<plugins>
			<!-- original maven compiler definition - uses the JRE's javac compiler, not the one Eclipse uses 
	        <artifactId>maven-compiler-plugin</artifactId>
	        <version>3.8.0</version>
	        <configuration>
	          <release>13</release>
	        </configuration>
	      -->

			<!--  attempt to use the Eclipse JDT compiler, so that the errors match when building
			https://stackoverflow.com/questions/38070326/java-generics-compiler-error-not-shown-in-eclipse
			https://wiki.eclipse.org/JDT/FAQ#Can_I_use_JDT_outside_Eclipse_to_compile_Java_code.3F
			https://wiki.eclipse.org/Tycho/FAQ#Can_I_use_the_Tycho_compiler_support_in_non-OSGi_projects.2C_too.3F
			-->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.12.1</version>
				<configuration>
					<!--  set compiler to use Java version 11 API https://docs.oracle.com/javase/9/tools/javac.htm#JSWOR627 -->
					<release>21</release>
					<compilerId>jdt</compilerId>
				</configuration>
				<dependencies>
					<!-- https://mvnrepository.com/artifact/org.eclipse.tycho/tycho-compiler-jdt -->
					<dependency>
						<groupId>org.eclipse.tycho</groupId>
						<artifactId>tycho-compiler-jdt</artifactId>
						<version>1.5.1</version>
					</dependency>
				</dependencies>
			</plugin>

			<!-- Set up javafx properly.  -->
			<plugin>
				<groupId>org.openjfx</groupId>
				<artifactId>javafx-maven-plugin</artifactId>
				<version>0.0.8</version>
			</plugin>

			<!--  Maven Shade plugin - for creating the uberjar / fatjar -->
			<!--  see http://maven.apache.org/plugins/maven-shade-plugin/index.html for details -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-shade-plugin</artifactId>
				<version>3.2.1</version>
				<configuration>
					<transformers>
						<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
					</transformers>
					<filters>
						<!-- Moved these filters up to here from where they were int <executions><execution><configurtion> 
						based on advice at https://stackoverflow.com/questions/34738653/maven-shade-plugin-does-not-exclude-the-manifest-signature-files
						and the are now working -->
						<filter>
							<artifact>*:*</artifact>
							<excludes>
								<exclude>META-INF/*.SF</exclude> <!--  get rid of manifests from library jars - also done in orig ant build file -->
								<exclude>META-INF/*.DSA</exclude>
								<exclude>META-INF/*.RSA</exclude>
								<exclude>test/resources/**</exclude> <!--  get rid of deep learning moduels and wav files used for unit tests -->
							</excludes>
						</filter>
					</filters>
				</configuration>

				<executions>
					<execution>
						<phase>package</phase>
						<goals>
							<goal>shade</goal>
						</goals>
						<configuration>
							<transformers>
								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
									<manifestEntries>
										<Main-Class>pamguard.Pamguard</Main-Class>
										<Class-Path>.</Class-Path> <!--  this is from the orig ant build file -->
										<SplashScreen-Image>Resources/pgBlankSplash.png</SplashScreen-Image> <!--  this is from the orig ant build file -->
									</manifestEntries>
								</transformer>
								<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
							</transformers>
						</configuration>
					</execution>
				</executions>
			</plugin>


			<!--  The Maven-JDEPS plugin, to analyze necessary JDK dependencies.  See
		  this site for details: https://maven.apache.org/plugins/maven-jdeps-plugin/index.html -->
			<plugin>
				<groupId>com.github.marschall</groupId>
				<artifactId>jdeps-maven-plugin</artifactId>
				<version>0.5.1</version>
			</plugin>

			<!-- The Maven dependency plugin, which can copy all dependencies into a temp folder for jdeps analysis -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-dependency-plugin</artifactId>
				<version>3.1.1</version>
				<executions>
					<execution>
						<id>copy-dependencies</id>
						<phase>package</phase>
						<goals>
							<goal>copy-dependencies</goal>
						</goals>
						<configuration>
							<outputDirectory>${project.build.directory}/tempDependencies</outputDirectory>
							<overWriteReleases>false</overWriteReleases>
							<overWriteSnapshots>false</overWriteSnapshots>
							<overWriteIfNewer>true</overWriteIfNewer>
						</configuration>
					</execution>
					<!--  this deletes all the dependencies in the local repository and downloads them again.  
	          Run a Maven > Update after doing this in order to properly reset the dependencies.  Also, you
	          will need to add the 3 jar files (x3, JasioHost and jave) back into the local repository after
	          running this command -->

					<!-- I'm not sure why, but every time I try to run the shade:shade build to create a
			fatjar it first runs this, which deletes all of the dependencies and completely fails.
			I think it has something to do with the lifecycle mapping, but that's beyond my Maven
			abilities right now.
			I can't even remember why I added this in the first place, so I'm going to comment
			it out 
	          <execution>
	            <id>purge-local-dependencies</id>
	            <phase>process-sources</phase>
	            <goals>
	              <goal>purge-local-repository</goal>
	            </goals>
	            <configuration>
	            </configuration>
	          </execution>
	          -->
				</executions>
			</plugin>
			
			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>3.5.1</version>
				<configuration>
					<reuseForks>false</reuseForks>
				</configuration>
			</plugin>
		

<!--			 Plugin which creates a .dmg file for MacOS. 
		    <plugin>
		        <groupId>de.perdian.maven.plugins</groupId>
		        <artifactId>macosappbundler-maven-plugin</artifactId>
		        <version>1.21.1</version>
		        <configuration>
		            <plist>
		                <JVMMainClassName>pamguard.Pamguard</JVMMainClassName>
		               <CFBundleIconFile>src/Resources/PamguardIcon2.icns</CFBundleIconFile>
		                <CFBundleDisplayName>PAMGuard</CFBundleDisplayName>
		                <CFBundleDevelopmentRegion>English</CFBundleDevelopmentRegion>
		                <CFBundleURLTypes>
		                    <string>msa</string>
		                </CFBundleURLTypes>
		                <JVMVersion>21+</JVMVersion>
		                <JVMArguments>
		                    <string>-v</string>
		                </JVMArguments>
		            </plist>
		              <dmg>
		                <generate>true</generate>
		                <additionalResources>
		                    <additionalResource>
		                        <directory>src/target/macos/</directory>
		                    </additionalResource>
		                </additionalResources>
		            </dmg>
		             <jdk>
			            <include>false</include>
			            <location>/Library/Java/JavaVirtualMachines/amazon-corretto-21.jdk</location>
			        </jdk>
		             <codesign>
		                <identity>3rd Party Mac Developer Application: PAMGuard</identity>
		            </codesign> 
		        </configuration>
		        <executions>
		            <execution>
		                <phase>package</phase>
		                <goals>
		                    <goal>bundle</goal>
		                </goals>
		            </execution>
		        </executions>
		    </plugin> -->
		</plugins>


		<pluginManagement>
			<plugins>
				<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
				<plugin>
					<groupId>org.eclipse.m2e</groupId>
					<artifactId>lifecycle-mapping</artifactId>
					<version>1.0.0</version>
					<configuration>
						<lifecycleMappingMetadata>
							<pluginExecutions>
								<pluginExecution>
									<pluginExecutionFilter>
										<groupId>
	    									org.apache.maven.plugins
	    								</groupId>
										<artifactId>
	    									maven-dependency-plugin
	    								</artifactId>
										<versionRange>
	    									[3.1.1,)
	    								</versionRange>
										<goals>
											<goal>
	    										purge-local-repository
	    									</goal>
										</goals>
									</pluginExecutionFilter>
									<action>
										<ignore></ignore>
									</action>
								</pluginExecution>
							</pluginExecutions>
						</lifecycleMappingMetadata>
					</configuration>
				</plugin>
			</plugins>
		</pluginManagement>
	</build>

	<reporting>
		<plugins>
			<plugin>
				<groupId>com.github.marschall</groupId>
				<artifactId>jdeps-maven-plugin</artifactId>
				<version>0.5.1</version>
			</plugin>
		</plugins>
	</reporting>


	<!--  ************************* Extra Repositories ************************************* -->
	<repositories>
		<!--  Project repo to hold the custom jar files that are not available in Maven.  Do
		this so that we don't have to do the extra step of manually installing jar files in the local repo -->
		<repository>
			<id>repo</id>
			<releases>
				<enabled>true</enabled>
				<checksumPolicy>ignore</checksumPolicy>
			</releases>
			<snapshots>
				<enabled>false</enabled>
			</snapshots>
			<url>file://${project.basedir}/repo</url>
		</repository>

		<!-- Repo for netCDF -->
		<repository>
			<snapshots>
				<enabled>false</enabled>
			</snapshots>
			<id>unidata-all</id>
			<name>Unidata netCDF</name>
			<url>https://artifacts.unidata.ucar.edu/repository/unidata-all/</url>
		</repository>

		<!--  
	    <repository>
	        <snapshots>
	            <enabled>false</enabled>
	        </snapshots>
	        <id>geomajas</id>
	        <name>geomajas</name>
	        <url>http://maven.geomajas.org/</url>
	    </repository>-->

		<!-- Repo for Renjin Script Engine -->
		<repository>
			<id>bedatadriven</id>
			<name>bedatadriven public repo</name>
			<url>https://nexus.bedatadriven.com/content/groups/public/</url>
		</repository>

		<repository>
			<id>central</id>
			<url>https://repo1.maven.org/maven2</url>
		</repository>

	</repositories>


	<!--  ************************* Dependencies ************************************* -->
	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>org.junit</groupId>
				<artifactId>junit-bom</artifactId>
				<version>5.11.3</version>
				<type>pom</type>
				<scope>import</scope>
			</dependency>
		</dependencies>
	</dependencyManagement>
	<dependencies>

		<!--jpam project - utilities -->
		<dependency>
			<groupId>io.github.macster110</groupId>
			<artifactId>jpamutils</artifactId>
			<version>0.0.59d</version>
			<exclusions>
				<exclusion>
					<!-- com.github.psambit9791:wavfile:jar:0.1 pulls in various junit dependencies which breaks our own testing -->
					<groupId>org.junit.platform</groupId>
					<artifactId>junit-platform-surefire-provider</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<!--jpam project - Deep learning java library -->
		<dependency>
			<groupId>io.github.macster110</groupId>
			<artifactId>jdl4pam</artifactId>
			<version>0.0.99d</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/gov.nist.math/jama -->
		<dependency>
			<groupId>gov.nist.math</groupId>
			<artifactId>jama</artifactId>
			<version>1.0.3</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-controls -->
		<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
		but it does.  To fix, comment out the repository (in
		the <repositories> section above, let Maven download the JavaFX
		files, and then uncomment the repository again.    -->
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-controls</artifactId>
			<version>${javafx.version}</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-swing -->
		<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
		but it does.  To fix, comment out the repository (in
		the <repositories> section above, let Maven download the JavaFX
		files, and then uncomment the repository again.    -->
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-swing</artifactId>
			<version>${javafx.version}</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-media -->
		<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
		but it does.  To fix, comment out the repository (in
		the <repositories> section above, let Maven download the JavaFX
		files, and then uncomment the repository again.    -->
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-media</artifactId>
			<version>${javafx.version}</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.openjfx/javafx-web -->
		<!--  IMPORTANT - IF MAVEN IS NOT DOWNLOADING THE JAVAFX FILES AND
		INSTEAD THROWING AN ERROR, IT MIGHT BE BECAUSE THERE IS AN
		INTERFERENCE WITH JAMIE'S REPOSITORY.  I'm not sure why this happens,
		but it does.  To fix, comment out the repository (in
		the <repositories> section above, let Maven download the JavaFX
		files, and then uncomment the repository again.    -->
		<dependency>
			<groupId>org.openjfx</groupId>
			<artifactId>javafx-web</artifactId>
			<version>${javafx.version}</version>
		</dependency>
		
		<!-- Swing theme for MacOS -->
		<dependency>
		  <groupId>com.formdev</groupId>
		  <artifactId>flatlaf</artifactId>
		  <version>3.5.1</version>
		</dependency>

		<!-- Decorates JavaFX components with error icons if inputs are incorrect-->
		<dependency>
			<groupId>net.synedra</groupId>
			<artifactId>validatorfx</artifactId>
			<version>0.4.2</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-compress -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-compress</artifactId>
			<version>1.19</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-csv</artifactId>
			<version>1.7</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/commons-io/commons-io -->
		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.6</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-lang3 -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-lang3</artifactId>
			<version>3.9</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>3.6.1</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math -->
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math</artifactId>
			<version>2.2</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/commons-net/commons-net -->
		<dependency>
			<groupId>commons-net</groupId>
			<artifactId>commons-net</artifactId>
			<version>3.6</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.controlsfx/controlsfx -->
		<dependency>
			<groupId>org.controlsfx</groupId>
			<artifactId>controlsfx</artifactId>
			<version>11.2.0</version>
			<exclusions>
				<exclusion>
					<groupId>org.openjfx</groupId>
					<artifactId>javafx-base</artifactId>
				</exclusion>
				<exclusion>
					<groupId>org.openjfx</groupId>
					<artifactId>javafx-controls</artifactId>
				</exclusion>
				<exclusion>
					<groupId>org.openjfx</groupId>
					<artifactId>javafx-graphics</artifactId>
				</exclusion>
				<exclusion>
					<groupId>org.openjfx</groupId>
					<artifactId>javafx-media</artifactId>
				</exclusion>
				<exclusion>
					<groupId>org.openjfx</groupId>
					<artifactId>javafx-web</artifactId>
				</exclusion>
			</exclusions>
		</dependency>

		<!-- https://search.maven.org/artifact/org.kordamp.ikonli/ikonli-javafx/12.2.0/jar -->
		<!-- Icon symbol pack to replace FontAwesome.  This is the core library, and the
	     actual symbol packs need to be added separately (see below) -->
		<dependency>
			<groupId>org.kordamp.ikonli</groupId>
			<artifactId>ikonli-javafx</artifactId>
			<version>12.3.1</version>
		</dependency>

		<!-- Icon symbol pack for swing icons . -->
		<dependency>
			<groupId>org.kordamp.ikonli</groupId>
			<artifactId>ikonli-swing</artifactId>
			<version>12.3.1</version>
		</dependency>

		<!-- Ikonli MaterialDesign2 (Latest) font pack https://kordamp.org/ikonli/cheat-sheet-materialdesign2.html -->
		<dependency>
			<groupId>org.kordamp.ikonli</groupId>
			<artifactId>ikonli-materialdesign2-pack</artifactId>
			<version>12.3.1</version>
		</dependency>

		<!-- Ikonli File Icons (Latest) font pack https://kordamp.org/ikonli/cheat-sheet-materialdesign2.html -->
		<dependency>
			<groupId>org.kordamp.ikonli</groupId>
			<artifactId>ikonli-fileicons-pack</artifactId>
			<version>12.3.1</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/net.sf.geographiclib/GeographicLib-Java 
	 Used in the video range module-->
		<dependency>
			<groupId>net.sf.geographiclib</groupId>
			<artifactId>GeographicLib-Java</artifactId>
			<version>1.50</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.jogamp.gluegen/gluegen
	<dependency>
		<groupId>org.jogamp.gluegen</groupId>
		<artifactId>gluegen-rt-main</artifactId>
		<version>2.3.2</version>
	</dependency>-->


		<!-- https://mvnrepository.com/artifact/com.healthmarketscience.jackcess/jackcess
	<dependency>
		<groupId>com.healthmarketscience.jackcess</groupId>
		<artifactId>jackcess</artifactId>
		<version>3.0.1</version>
	</dependency>-->

		<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-databind -->
		<dependency>
			<groupId>com.fasterxml.jackson.core</groupId>
			<artifactId>jackson-databind</artifactId>
			<version>2.10.1</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.jogamp.jogl/jogl-all-main 
	<dependency>
		<groupId>org.jogamp.jogl</groupId>
		<artifactId>jogl-all-main</artifactId>
		<version>2.3.2</version>
	</dependency>-->

		<!-- NOT SURE IF WE NEED THE JAXB LIBRARIES HERE - NO ERRORS WHEN REMOVED
	<dependency>
	    <groupId>javax.xml.bind</groupId>
	    <artifactId>jaxb-api</artifactId>
	    <version>2.3.1</version>
	</dependency>
    <dependency>
	    <groupId>org.glassfish.jaxb</groupId>
	    <artifactId>jaxb-core</artifactId>
	    <version>2.3.0.1</version>
	</dependency>
    <dependency>
	    <groupId>com.sun.xml.bind</groupId>
 	   <artifactId>jaxb-impl</artifactId>
    	<version>2.3.2</version>
	</dependency>
	 -->

		<!-- https://mvnrepository.com/artifact/org.jflac/jflac-codec -->
		<dependency>
			<groupId>org.jflac</groupId>
			<artifactId>jflac-codec</artifactId>
			<version>1.5.2</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/javax.help/javahelp -->
		<dependency>
			<groupId>javax.help</groupId>
			<artifactId>javahelp</artifactId>
			<version>2.0.05</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/net.java.dev.jna/jna -->
		<dependency>
			<groupId>net.java.dev.jna</groupId>
			<artifactId>jna</artifactId>
			<version>5.5.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/net.java.dev.jna/jna-platform -->
		<dependency>
			<groupId>net.java.dev.jna</groupId>
			<artifactId>jna-platform</artifactId>
			<version>5.5.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.jcraft/jsch -->
		<dependency>
			<groupId>com.jcraft</groupId>
			<artifactId>jsch</artifactId>
			<version>0.1.55</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.fazecast/jSerialComm -->
		<dependency>
			<groupId>com.fazecast</groupId>
			<artifactId>jSerialComm</artifactId>
			<version>2.11.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/edu.emory.mathcs/JTransforms -->
		<dependency>
			<groupId>edu.emory.mathcs</groupId>
			<artifactId>JTransforms</artifactId>
			<version>2.4</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.sun.mail/javax.mail -->
		<dependency>
			<groupId>com.sun.mail</groupId>
			<artifactId>javax.mail</artifactId>
			<version>1.6.2</version>
		</dependency>


		<!-- https://mvnrepository.com/artifact/com.drewnoakes/metadata-extractor -->
		<dependency>
			<groupId>com.drewnoakes</groupId>
			<artifactId>metadata-extractor</artifactId>
			<version>2.12.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/mysql/mysql-connector-java -->
		<dependency>
			<groupId>mysql</groupId>
			<artifactId>mysql-connector-java</artifactId>
			<version>8.0.18</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.google.protobuf/protobuf-java -->
		<!-- this is needed so that tensorflow models run properly (used in Deep Learning plugin) -->
		<!-- NOTE it is important this is included before edu.ucar.netcdfAll so 
		that this version is used instead of the internal version - exclusions do 
		not seem to work otherwise -->
		<dependency>
			<groupId>com.google.protobuf</groupId>
			<artifactId>protobuf-java</artifactId>
			<version>3.17.0</version>
		</dependency>

		<!-- https://docs.unidata.ucar.edu/netcdf-java/5.2/userguide/using_netcdf_java_artifacts.html -->
		<!--  exclusions have been added here to fix problem with Deep Learning plugin - see above -->
		<dependency>
			<groupId>edu.ucar</groupId>
			<artifactId>netcdfAll</artifactId>
			<version>4.6.14</version>
			<exclusions>
				<exclusion>
					<groupId>com.google.protobuf</groupId>
					<artifactId>protobuf-java</artifactId>
				</exclusion>
				<exclusion>
					<groupId>com.google.protobuf</groupId>
					<artifactId>protobuf-java-util</artifactId>
				</exclusion>
			</exclusions>
			<scope>compile</scope>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.opencsv/opencsv -->
		<dependency>
			<groupId>com.opencsv</groupId>
			<artifactId>opencsv</artifactId>
			<version>5.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.springframework/org.springframework.core -->

		<!-- https://mvnrepository.com/artifact/org.postgresql/postgresql -->
		<dependency>
			<groupId>org.postgresql</groupId>
			<artifactId>postgresql</artifactId>
			<version>42.2.24</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.renjin/renjin-script-engine
	Used to export data to R structures-->
		<dependency>
			<groupId>org.renjin</groupId>
			<artifactId>renjin-script-engine</artifactId>
			<version>0.9.2725</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api
	this one is only needed to get rid of an annoying warning that shows up during startup -->
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
			<version>1.8.0-beta4</version>
		</dependency>


		<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-nop
	this one is only needed to get rid of an annoying warning that shows up during startup -->
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-nop</artifactId>
			<version>1.8.0-beta4</version>
		</dependency>


		<!-- https://mvnrepository.com/artifact/org.docx4j/docx4j-JAXB-ReferenceImpl -->
		<!--  note that we are excluding slf4j-api here, because if we don't then one of the
	transitive dependencies of docx4j (jcl-over-slf4j) will try to load an older
	version of slf4j-api, resulting in a weird warning/error that shows up every time that
	PAMGuard start up -->
		<!--  DONT BOTHER WITH EXCLUSION, DOESN'T MAKE THE ERROR GO AWAY.  Leaving code here
	just in case the older version does cause a conflict at some point -->
		<dependency>
			<groupId>org.docx4j</groupId>
			<artifactId>docx4j-JAXB-ReferenceImpl</artifactId>
			<version>11.1.3</version>
			<!-- 
	    <exclusions>
	    	<exclusion>
			    <groupId>org.slf4j</groupId>
			    <artifactId>slf4j-api</artifactId>
	    	</exclusion>
	    </exclusions>
	     -->
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.xerial/sqlite-jdbc -->
		<dependency>
			<groupId>org.xerial</groupId>
			<artifactId>sqlite-jdbc</artifactId>
			<version>3.45.3.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/net.sf.ucanaccess/ucanaccess -->
		<dependency>
			<groupId>net.sf.ucanaccess</groupId>
			<artifactId>ucanaccess</artifactId>
			<version>4.0.4</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/nz.ac.waikato.cms.weka/weka-dev -->
		<dependency>
			<groupId>nz.ac.waikato.cms.weka</groupId>
			<artifactId>weka-dev</artifactId>
			<version>3.7.7</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/javax.vecmath/vecmath -->
		<dependency>
			<groupId>javax.vecmath</groupId>
			<artifactId>vecmath</artifactId>
			<version>1.5.2</version>
		</dependency>

		<!-- Jave2 (https://github.com/a-schild/jave2) - fork of original jave from sauronsoft.  A LOT bigger; the win64 files alone are > 60Mb compared
	to 14Mb originally.  Since the old one worked fine, let's stick with it for now and save the space
	<dependency>
    	<groupId>ws.schild</groupId>
	   	<artifactId>jave-core</artifactId>
   		<version>2.7.1</version>
	</dependency>
	<dependency>
		<groupId>ws.schild</groupId>
		<artifactId>jave-nativebin-win64</artifactId>
		<version>2.7.1</version>
	</dependency>
	-->

		<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave
	DOESN'T WORK - NOT IN THE ICM REPOSITORY ANYMORE.  STICK WITH ORIG JAR FILE
	<dependency>
	    <groupId>it.sauronsoftware</groupId>
	    <artifactId>jave</artifactId>
	    <version>1.0.2</version>
	</dependency>
	 -->


		<!-- From NilusXMLGenerator POM at https://bitbucket.org/tethysacousticmetadata/nilusxmlgenerator/src/master/-->
		<dependency>
			<groupId>org.eclipse.persistence</groupId>
			<artifactId>org.eclipse.persistence.moxy</artifactId>
			<version>2.5.0</version>
		</dependency>
		<dependency>
			<groupId>javax.xml.bind</groupId>
			<artifactId>jaxb-api</artifactId>
			<version>${jaxb.api.version}</version>
		</dependency>
		<dependency>
			<groupId>org.glassfish.jaxb</groupId>
			<artifactId>jaxb-runtime</artifactId>
			<version>${jaxb.runtime.version}</version>
		</dependency>
		<dependency>
			<groupId>org.glassfish.jaxb</groupId>
			<artifactId>jaxb-xjc</artifactId>
			<version>${jaxb.xjc.version}</version>
		</dependency>


		<!-- dependencies copied from TethysJavaClient -->
		<dependency>
			<groupId>com.sun.jersey.contribs</groupId>
			<artifactId>jersey-multipart</artifactId>
			<version>1.18.1</version>
		</dependency>


		<dependency>
			<groupId>commons-cli</groupId>
			<artifactId>commons-cli</artifactId>
			<version>1.2</version>
		</dependency>


		<dependency>
			<groupId>org.apache.poi</groupId>
			<artifactId>poi</artifactId>
			<version>3.10-beta1</version>
		</dependency>


		<dependency>
			<groupId>com.sun.jersey</groupId>
			<artifactId>jersey-client</artifactId>
			<version>1.18.1</version>
		</dependency>


		<dependency>
			<groupId>com.sun.jersey.contribs</groupId>
			<artifactId>jersey-apache-client</artifactId>
			<version>1.18.1</version>
		</dependency>


		<dependency>
			<groupId>com.miglayout</groupId>
			<artifactId>miglayout</artifactId>
			<version>3.7.4</version>
		</dependency>


		<dependency>
			<groupId>ca.juliusdavies</groupId>
			<artifactId>not-yet-commons-ssl</artifactId>
			<version>0.3.11</version>
		</dependency>


		<dependency>
			<groupId>javax.ws.rs</groupId>
			<artifactId>javax.ws.rs-api</artifactId>
			<version>2.1.1</version>
		</dependency>


		<dependency>
			<groupId>javax.xml.bind</groupId>
			<artifactId>jaxb-api</artifactId>
			<version>2.2.11</version>
		</dependency>


		<dependency>
			<groupId>com.sun.xml.bind</groupId>
			<artifactId>jaxb-impl</artifactId>
			<version>2.2.11</version>
		</dependency>


		<dependency>
			<groupId>javax.activation</groupId>
			<artifactId>activation</artifactId>
			<version>1.1</version>
		</dependency>


		<dependency>
			<groupId>org.glassfish.jaxb</groupId>
			<artifactId>jaxb-core</artifactId>
			<version>2.2.11</version>
		</dependency>


		<dependency>
			<groupId>org.glassfish.jersey.core</groupId>
			<artifactId>jersey-common</artifactId>
			<version>2.2</version>
		</dependency>


		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-text</artifactId>
			<version>1.9</version>
		</dependency>

		<!-- dependencies copied from TethysJavaClient END -->


		<!-- Thethy library not in Maven central, so you may need to copy the javaclient and nilus folders from 
	e.g. C:\Users\dg50\source\repos\**your projectfolder**\repo\tethys\org
	to C:\Users\dg50\.m2\repository\tethys\org -->
	<dependency>
		<groupId>tethys.org</groupId>
		<artifactId>nilus</artifactId>
		<version>3.1</version>
	</dependency>

		<dependency>
			<groupId>tethys.org</groupId>
			<artifactId>javaclient</artifactId>
			<version>3.0</version>
		</dependency>

		<!-- 
	X3 library for decompressing sud files. Not in Maven repository  
	you may need to copy files from your downloaded PAMGuard source code, 
	e.g. C:\Users\*yourreposfolder*\source\repos\PAMGuardPAMGuard\repo\pamguard\org\x3\2.2.2 to 
	C:\Users\*yourusername*\.m2\repository\pamguard\org\x3\2.2.2
	-->
		<dependency>
			<groupId>org.pamguard</groupId>
			<artifactId>x3</artifactId>
			<version>2.2.8</version>
		</dependency>


		<!-- https://mvnrepository.com/artifact/it.sauronsoftware/jave -->
		<dependency>
			<groupId>it.sauronsoftware</groupId>
			<artifactId>jave</artifactId>
			<version>1.0.2</version>
		</dependency>

		<!-- not in Maven repository -->
		<dependency>
			<groupId>com.synthbot</groupId>
			<artifactId>jasiohost</artifactId>
			<version>1.0.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.dataformat/jackson-dataformat-xml -->
		<!-- 
 	<dependency>
 		<groupId>com.fasterxml.jackson.dataformat</groupId>
 		<artifactId>jackson-dataformat-xml</artifactId>
 		<version>2.10.1</version>
 	</dependency>
 	 -->

		<!-- https://mvnrepository.com/artifact/org.springframework/spring-core -->
		<dependency>
			<groupId>org.springframework</groupId>
			<artifactId>spring-core</artifactId>
			<version>5.2.3.RELEASE</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/com.1stleg/jnativehook -->
		<!-- For global hotkeys, especially in Logger -->
		<dependency>
			<groupId>com.1stleg</groupId>
			<artifactId>jnativehook</artifactId>
			<version>2.1.0</version>
		</dependency>

		<!-- https://mvnrepository.com/artifact/org.swinglabs.swingx/swingx-all -->
		<!-- For new Network Receive Module -->
		<dependency>
			<groupId>org.swinglabs.swingx</groupId>
			<artifactId>swingx-all</artifactId>
			<version>1.6.5-1</version>
		</dependency>


		<!--  Extra 3D bits for JavaFX -->
		<dependency>
			<groupId>org.fxyz3d</groupId>
			<artifactId>fxyz3d</artifactId>
			<version>0.6.0</version>
		</dependency>

		<!--  Atlanta style for JavaFX -->
		<dependency>
			<groupId>io.github.mkpaz</groupId>
			<artifactId>atlantafx-base</artifactId>
			<version>2.0.1</version>
		</dependency>

		<!-- Four dependencies from xbee library that are needed for Genus module. -->
		<dependency>
			<groupId>javax.servlet</groupId>
			<artifactId>javax.servlet-api</artifactId>
			<version>4.0.1</version>
		</dependency>
		<dependency>
			<groupId>org.mockito</groupId>
			<artifactId>mockito-all</artifactId>
			<version>${mockito.version}</version>
		</dependency>
		<dependency>
			<groupId>org.powermock</groupId>
			<artifactId>powermock-module-junit4</artifactId>
			<version>${powermock.version}</version>
		</dependency>
		<dependency>
			<groupId>org.powermock</groupId>
			<artifactId>powermock-api-mockito</artifactId>
			<version>${powermock.version}</version>
		</dependency>



		<!-- Test dependencies -->
		<dependency>
			<groupId>org.junit.jupiter</groupId>
			<artifactId>junit-jupiter</artifactId>
			<scope>test</scope>
		</dependency>
	</dependencies>
</project>