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>

  <properties>
    <project.build.sourceEncoding>utf-8</project.build.sourceEncoding>
  </properties>

  <groupId>org.fairsim</groupId>
  <artifactId>fairSIM</artifactId>
  <version>1.4.1</version>
  <packaging>jar</packaging>

  <name>fairSIM</name>
  <description>Free Analysis and Interactive Reconstruction for Structured Illumination Microscopy</description>
  <url>http://www.fairsim.org</url>
  <inceptionYear>2013</inceptionYear>

  <licenses>
    <license>
      <name>GNU General Public License</name>
      <url>https://gnu.org/licenses/gpl.html</url>
      <distribution>repo</distribution>
      <comments>Version 2 of the License or (at your option) any later version.</comments>
    </license>
  </licenses>

  <developers>
    <developer>
      <name>Marcel Müller</name>
      <email>muellerphysics@gmail.com</email>
      <roles>
        <role>developer</role>
      </roles>
    </developer>
  </developers>

  <scm>
    <connection>scm:git:git://github.com/fairSIM/fairSIM</connection>
    <developerConnection>scm:git:git@github.com:fairSIM/fairSIM</developerConnection>
    <tag>HEAD</tag>
    <url>http://github.com/fairSIM/fairSIM</url>
  </scm>
  <issueManagement>
    <system>GitHub Issues</system>
    <url>http://github.com/fairSIM/fairSIM/issues</url>
  </issueManagement>

  <dependencies>
    <dependency>
      <groupId>net.imagej</groupId>
      <artifactId>ij</artifactId>
      <version>1.48v</version>
    </dependency>

    <dependency>
	<groupId>com.github.wendykierp</groupId>
	<artifactId>JTransforms</artifactId>
	<version>3.1</version>
    </dependency>

    <!-- Test dependencies -->
<!-- not yet 
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>RELEASE</version>
      <scope>test</scope>
    </dependency>
-->

  </dependencies>

  <repositories>
    <repository>
      <id>imagej.public</id>
      <url>http://maven.imagej.net/content/groups/public</url>
    </repository>
  </repositories>


  <build>

    <!-- ImageJ plugins need an underscore on the filename of the jar. -->
    <finalName>${project.artifactId}_plugin_mvn-${buildNumber}</finalName>

    <sourceDirectory>./</sourceDirectory>

    <resources>
	<resource>
	    <directory>./</directory>
	    <filtering>true</filtering>
	    <includes>
		<include>org/fairsim/git-version-maven.txt</include>
	    </includes>
	</resource>
	<resource>
	    <directory>./</directory>
	    <filtering>false</filtering>
	    <includes>
		<include>org/fairsim/resources/*</include>
		<include>plugins.config</include>
	    </includes>
	</resource>
    </resources>

    <plugins>
      <plugin>
         <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <!--
          Since Maven 3, we really need to specify a version number for
          plugins, but RELEASE and LATEST are only valid for dependencies.
        -->
        <version>2.3.2</version>
        <configuration>
          <source>1.6</source>
          <target>1.6</target>
	  <!-- this keeps the forked/internal version of JTransform from being build
	       with maven dependencies, we can just rely on the original being there instead -->
	  <excludes>
	    <exclude>org/fairsim/linalg/JTransformsForkConnector.java</exclude>
	  </excludes>
	</configuration>
      </plugin>


      <plugin>
        <groupId>org.codehaus.mojo</groupId>
        <artifactId>buildnumber-maven-plugin</artifactId>
        <version>1.4</version>
        <executions>
          <execution>
            <phase>validate</phase>
            <goals>
              <goal>create</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
        	<doCheck>false</doCheck>
		<doUpdate>false</doUpdate>
		<shortRevisionLength>10</shortRevisionLength>
	</configuration>
      </plugin>

     <!-- Javadoc and Sources attachments are OSSRH requirements -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-source-plugin</artifactId>
        <version>2.2.1</version>
	<configuration>
	    <excludeResources>true</excludeResources>
	    <includes>
		<include>org/fairsim/**/*.java</include>
		<include>org/fairsim/resources/*</include>
	    </includes>
	    <excludes>
		<exclude>target</exclude>
		<exclude>org/fairsim/linalg/JTransformsForkConnector.java</exclude>
	    </excludes>
	</configuration>
        <executions>
          <execution>
            <id>attach-sources</id>
            <goals>
              <goal>jar-no-fork</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <version>2.9.1</version>
        <executions>
          <execution>
            <id>attach-javadocs</id>
            <goals>
              <goal>jar</goal>
            </goals>
            <configuration>
		<quiet>true</quiet>
		<excludes>
		    <exclude>org/fairsim/linalg/JTransformsForkConnector.java</exclude>
		</excludes>
	    
            </configuration>
          </execution>
        </executions>
      </plugin>

     </plugins>
  </build>
</project>