pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<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/maven-v4_0_0.xsd">

	<modelVersion>4.0.0</modelVersion>
	<packaging>pom</packaging>
	
	<groupId>org.biopax.paxtools</groupId>
	<artifactId>paxtools</artifactId>
	<version>5.0.2-SNAPSHOT</version>

	<name>Paxtools</name>
	
	<description>Paxtools is a Java library that allows software to read, write, analyze and manipulate BioPAX models.
		Paxtools provide a consistent, fully implemented, validating BioPAX API that significantly reduces development
		time of oftware that require programmatic access to BioPAX. Paxtools is modular, lightweight and platform
		independent to be easily embedded into applications.
	</description>
	
	<url>https://biopax.github.io/Paxtools</url>
	
	<organization>
		<name>BioPAX</name>
		<url>http://www.biopax.org</url>
	</organization>

	<modules>
		<module>paxtools-core</module>
		<module>gsea-converter</module>
		<module>psimi-converter</module>
		<module>sbgn-converter</module>
		<module>paxtools-console</module>
		<module>paxtools-query</module>
		<module>paxtools-trove</module>
		<module>paxtools-archetype</module>
		<module>json-converter</module>
 		<module>paxtools-search</module>
		<module>pattern</module>
		<module>normalizer</module>
	</modules>

	<properties>
		<java.version>1.6</java.version>
		<github.global.server>github</github.global.server>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
		<junit.version>4.10</junit.version>
		<slf4j.version>1.7.25</slf4j.version>
		<logback.version>1.1.2</logback.version>
		<commons-lang.version>3.4</commons-lang.version>
		<collections-generic.version>4.01</collections-generic.version>
		<maven.version.range>[3.0,4)</maven.version.range>
		<maven-compiler-plugin.version>3.3</maven-compiler-plugin.version>
		<maven-war-plugin.version>2.6</maven-war-plugin.version>
		<maven-resources-plugin>2.7</maven-resources-plugin>
		<maven-release-plugin.version>2.5.1</maven-release-plugin.version>
		<wagon-ssh.version>2.8</wagon-ssh.version>
		<wagon-scm.version>2.8</wagon-scm.version>
		<maven-surefire-plugin.version>2.18.1</maven-surefire-plugin.version>
		<maven-jar-plugin.version>2.6</maven-jar-plugin.version>
		<maven-source-plugin.version>2.4</maven-source-plugin.version>
		<maven-site-plugin.version>3.4</maven-site-plugin.version>
		<maven-javadoc-plugin.version>2.10.2</maven-javadoc-plugin.version>
		<maven-jxr-plugin.version>2.5</maven-jxr-plugin.version>
		<maven-project-info-reports-plugin.version>2.8</maven-project-info-reports-plugin.version>
		<maven-deploy-plugin.version>2.8.2</maven-deploy-plugin.version>
		<maven-gpg-plugin.version>1.6</maven-gpg-plugin.version>
		<nexus-staging-maven-plugin.version>1.6.5</nexus-staging-maven-plugin.version>
		<doxia-integration-tools.version>1.6</doxia-integration-tools.version>
		<maven-enforcer-plugin>1.4</maven-enforcer-plugin>
	</properties>

	<developers>
		<developer>
			<id>emekdemir</id>
			<name>Emek Demir</name>
			<organization>CBIO MSKCC</organization>
			<roles>
				<role>architect</role>
				<role>developer</role>
			</roles>
		</developer>
		<developer>
			<id>rodche</id>
			<name>Igor Rodchenkov</name>
			<organization>University of Toronto</organization>
			<roles>
				<role>developer</role>
			</roles>
		</developer>
		<developer>
			<id>ozgunbabur</id>
			<name>Ozgun Babur</name>
			<organization>CBIO MSKCC</organization>
			<roles>
				<role>developer</role>
			</roles>
		</developer>
		<developer>
			<id>kenichirofukuda</id>
			<name>Ken-Ichiro Fukuda</name>
			<organization />
			<roles>
				<role>developer</role>
			</roles>
		</developer>
		<developer>
			<id>armanaksoy</id>
			<name>B. Arman Aksoy</name>
			<organization>CBIO MSKCC</organization>
			<roles>
				<role>developer</role>
			</roles>
		</developer>
		<developer>
			<id>benjamingross</id>
			<name>Benjamin Gross</name>
			<organization>CBIO MSKCC</organization>
			<roles>
				<role>developer</role>
			</roles>
		</developer>		
	</developers>

	<mailingLists>
		<mailingList>
			<name>BioPAX Discussion Group</name>
			<post>biopax-discuss@googlegroups.com</post>
		</mailingList>
	</mailingLists>

	<licenses>
		<license>
			<name>LGPL 2.0 license</name>
			<url>http://www.gnu.org/licenses/lgpl-2.0.html</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

	<issueManagement>
		<system>GitHub Issues</system>
		<url>https://github.com/BioPAX/Paxtools/issues</url>
	</issueManagement>	

	<ciManagement>
		<system>Travis CI</system>
        <url>https://travis-ci.org/BioPAX/Paxtools</url>
	</ciManagement>
	
	<profiles>
        <profile>
	<!-- It's auto-enabled during mvn release:perform; 
	for manual releasing (not snapshots): mvn clean deploy -P sonatype-release 
	-->
            <id>sonatype-release</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.sonatype.plugins</groupId>
                        <artifactId>nexus-staging-maven-plugin</artifactId>
                        <extensions>true</extensions>
                        <configuration>
                            <serverId>ossrh</serverId>
                            <nexusUrl>https://oss.sonatype.org/</nexusUrl>
<!--                             <autoReleaseAfterClose>true</autoReleaseAfterClose> -->
                        </configuration>
                    </plugin>
                    <plugin>
                        <artifactId>maven-source-plugin</artifactId>
                        <executions>
                            <execution>
                                <id>attach-sources</id>
                                <goals>
                                    <goal>jar-no-fork</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <artifactId>maven-javadoc-plugin</artifactId>
                        <executions>
                            <execution>
                                <id>attach-javadocs</id>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <groupId>org.apache.maven.plugins</groupId>
                        <executions>
                            <execution>
                                <id>sign-artifacts</id>
                                <phase>verify</phase>
                                <goals>
                                    <goal>sign</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
	</profiles>

	<scm>
		<connection>scm:git:git://github.com/BioPAX/Paxtools.git</connection>
		<developerConnection>scm:git:git@github.com:BioPAX/Paxtools.git</developerConnection>
		<url>https://github.com/BioPAX/Paxtools</url>
		<tag>HEAD</tag>
	</scm>
	
	<distributionManagement>
		<site>
			<id>github</id>
			<name>BioPAX/Paxtools Maven site</name>
			<url>https://biopax.github.io/Paxtools/${project.version}</url>
		</site>
		<repository>
			<id>ossrh</id>
			<name>Nexus Release Repository</name>
			<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
		</repository>
		<snapshotRepository>
			<id>ossrh</id>
			<name>Sonatype Nexus Snapshots</name>
			<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
		</snapshotRepository>
		<downloadUrl>http://www.biopax.org/downloads/paxtools/</downloadUrl>
	</distributionManagement>	

	<build>
		<pluginManagement>
			<plugins>
				<plugin>
					<artifactId>maven-compiler-plugin</artifactId>
					<version>${maven-compiler-plugin.version}</version>
					<configuration>
						<source>${java.version}</source>
						<target>${java.version}</target>
					</configuration>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-jar-plugin</artifactId>
					<version>${maven-jar-plugin.version}</version>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-source-plugin</artifactId>
					<version>${maven-source-plugin.version}</version>
					<executions>
						<execution>
							<id>attach-sources</id>
							<goals>
								<goal>jar-no-fork</goal>
							</goals>
						</execution>
					</executions>					
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-release-plugin</artifactId>
					<version>${maven-release-plugin.version}</version>
						<configuration>
							<goals>deploy site-deploy</goals>
							<autoVersionSubmodules>true</autoVersionSubmodules>
							<useReleaseProfile>false</useReleaseProfile>
							<releaseProfiles>sonatype-release</releaseProfiles>
						</configuration>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-surefire-plugin</artifactId>
					<version>${maven-surefire-plugin.version}</version>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-javadoc-plugin</artifactId>
					<version>${maven-javadoc-plugin.version}</version>
					<configuration>
						<excludePackageNames>org.biopax.validator.*:net.biomodels.*</excludePackageNames>
						<failOnError>false</failOnError>
					</configuration>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-jxr-plugin</artifactId>
					<version>${maven-jxr-plugin.version}</version>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-project-info-reports-plugin</artifactId>
					<version>${maven-project-info-reports-plugin.version}</version>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-site-plugin</artifactId>
					<version>${maven-site-plugin.version}</version>
					<!--<configuration>-->
						<!--<skipDeploy>true</skipDeploy>-->
					<!--</configuration>-->
				</plugin>
				<plugin>
					<groupId>org.sonatype.plugins</groupId>
					<artifactId>nexus-staging-maven-plugin</artifactId>
					<version>${nexus-staging-maven-plugin.version}</version>
				</plugin>
				<plugin>
					<artifactId>maven-gpg-plugin</artifactId>
					<groupId>org.apache.maven.plugins</groupId>
					<version>${maven-gpg-plugin.version}</version>
				</plugin>
			</plugins>
		</pluginManagement>
		<extensions>
			<extension>
				<groupId>org.apache.maven.wagon</groupId>
				<artifactId>wagon-ssh</artifactId>
				<version>${wagon-ssh.version}</version>
			</extension>
			<extension>
				<groupId>org.apache.maven.wagon</groupId>
				<artifactId>wagon-scm</artifactId>
				<version>${wagon-scm.version}</version>
			</extension>
        		<extension>
					<groupId>org.apache.maven.doxia</groupId>
					<artifactId>doxia-integration-tools</artifactId>
           			<version>${doxia-integration-tools.version}</version>
        		</extension>
			</extensions>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-enforcer-plugin</artifactId>
				<version>${maven-enforcer-plugin}</version>
				<executions>
					<execution>
						<id>enforce-banned-dependencies</id>
						<goals>
							<goal>enforce</goal>
						</goals>
						<configuration>
							<rules>
								<bannedDependencies>
									<searchTransitive>true</searchTransitive>
									<excludes>
										<exclude>javassist:javassist</exclude><!-- org.javassist is the new one -->
										<exclude>commons-logging</exclude>
										<exclude>aspectj:aspectj*</exclude> <!-- org.aspectj is the new one -->
										<exclude>hsqldb:hsqldb</exclude> <!-- org.hsqldb is the new one -->
										<exclude>org.springframework</exclude>
										<exclude>com.sun.xml.bind</exclude>
										<exclude>javax.xml.bind</exclude>
										<exclude>net.sf.saxon</exclude>
										<exclude>c3p0:c3p0</exclude> <!-- com.mchange:c3p0 is the new one -->
										<exclude>org.apache.commons:com.springsource.org.apache.commons.logging</exclude>
										<exclude>log4j:log4j</exclude>
									</excludes>
								</bannedDependencies>
								<requireMavenVersion>
									<version>${maven.version.range}</version>
								</requireMavenVersion>
								<requireJavaVersion>
									<version>${java.version}</version>
								</requireJavaVersion>
							</rules>
							<fail>true</fail>
						</configuration>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-source-plugin</artifactId>
				<executions>
					<execution>
						<id>attach-sources</id>
						<goals>
							<goal>jar</goal>
						</goals>
					</execution>
				</executions>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-surefire-plugin</artifactId>
				<configuration>
					<testFailureIgnore>false</testFailureIgnore>
					<!-- enable assertions during the tests -->
					<argLine>-ea</argLine>
				</configuration>
			</plugin>
     	 	<plugin>
        		<groupId>org.apache.maven.plugins</groupId>
        		<artifactId>maven-release-plugin</artifactId>
      		</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-site-plugin</artifactId>
				<executions>
					<execution>
						<id>attach-descriptor</id>
						<goals>
							<goal>attach-descriptor</goal>
						</goals>
					</execution>
				</executions>
				<configuration>
					<skipDeploy>true</skipDeploy>
				</configuration>
			</plugin>
			
			<plugin>
				<artifactId>maven-assembly-plugin</artifactId>
				<version>2.2.1</version>
				<configuration>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
				</configuration>
			</plugin>

		</plugins>
	</build>

	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>junit</groupId>
				<artifactId>junit</artifactId>
				<version>${junit.version}</version>
				<scope>test</scope>
			</dependency>
			<dependency>
				<groupId>net.sourceforge.collections</groupId>
				<artifactId>collections-generic</artifactId>
				<version>${collections-generic.version}</version>
			</dependency>
			<dependency>
				<groupId>org.apache.commons</groupId>
				<artifactId>commons-lang3</artifactId>
				<version>${commons-lang.version}</version>
			</dependency>
			<dependency>
				<groupId>org.codehaus.jackson</groupId>
				<artifactId>jackson-mapper-asl</artifactId>
				<version>1.9.12</version>
			</dependency>
			<dependency>
				<groupId>com.hp.hpl.jena</groupId>
				<artifactId>jena</artifactId>
				<version>2.6.4</version>
			</dependency>
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>slf4j-api</artifactId>
				<version>${slf4j.version}</version>
			</dependency>
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>jcl-over-slf4j</artifactId>
				<version>${slf4j.version}</version>
				<scope>runtime</scope>
			</dependency>
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>jul-to-slf4j</artifactId>
				<version>${slf4j.version}</version>
				<scope>runtime</scope>
			</dependency>
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>log4j-over-slf4j</artifactId>
				<version>${slf4j.version}</version>
			</dependency>
			<dependency>
				<groupId>ch.qos.logback</groupId>
				<artifactId>logback-classic</artifactId>
				<version>${logback.version}</version>
				<optional>true</optional>
			</dependency>
		</dependencies>
	</dependencyManagement>

	<dependencies>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
		</dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>jcl-over-slf4j</artifactId>
			<scope>runtime</scope>
		</dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>jul-to-slf4j</artifactId>
			<scope>runtime</scope>
		</dependency>
		<dependency>
			<groupId>ch.qos.logback</groupId>
			<artifactId>logback-classic</artifactId>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<scope>test</scope>
		</dependency>
	</dependencies>

	<repositories>
		<!-- we'd remove repos below if everything were on OSSRH and Maven Central... -->
        <repository>
            <id>ossrh</id>
            <name>OSSRH Repository</name>
            <url>https://oss.sonatype.org/content/groups/public/</url>
        </repository>
		<repository><!-- currently, it's only to get org.sbgn:libsbgn:0.2 -->
        	<id>biopax.releases</id>
        	<name>BioPAX.org Repository</name>
        	<url>http://www.biopax.org/m2repo/releases/</url>
        	<snapshots>
        		<enabled>false</enabled>
			</snapshots>
        </repository>
		<repository>
			<id>ebi-repo</id>
			<name>The EBI internal repository</name>
			<url>http://www.ebi.ac.uk/~maven/m2repo</url>
			<snapshots>
				<enabled>false</enabled>
			</snapshots>
		</repository>
	</repositories>

	<!-- the following is used both by Maven 3.x and 2.x -->
	<reporting>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-javadoc-plugin</artifactId>
				<configuration>
              		<linksource>true</linksource>
              		<notimestamp>true</notimestamp>
              		<links combine.children="append">
              			<link>http://download.oracle.com/javase/7/docs/api/</link>
              		</links>
              		<level>public</level>
					<excludePackageNames>org.biopax.validator.*:net.biomodels.*</excludePackageNames>
					<failOnError>false</failOnError>
            	</configuration>
				<reportSets>
					<reportSet>
						<id>default</id>
						<reports>
							<!-- no test-javadoc -->
							<report>javadoc</report>
						</reports>
					</reportSet>				
					<reportSet>
						<id>aggregate</id>
						<inherited>false</inherited>
						<reports>
							<report>aggregate</report>
						</reports>
					</reportSet>
				</reportSets>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jxr-plugin</artifactId>
				<reportSets>
              		<reportSet>
                		<id>aggregate</id>
                		<inherited>false</inherited>
                		<reports>
                  			<report>aggregate</report>
                		</reports>
              		</reportSet>
            	</reportSets>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-project-info-reports-plugin</artifactId>
				<configuration>
					<dependencyDetailsEnabled>false</dependencyDetailsEnabled>
					<dependencyLocationsEnabled>false</dependencyLocationsEnabled>
				</configuration>				
				<reportSets>
                    <reportSet>
                        <reports>
                        	<report>index</report>
                        	<report>summary</report>
                            <report>modules</report>                       	
<!--                             <report>cim</report> -->
                            <report>dependencies</report>
<!--                             <report>dependency-convergence</report> -->
                            <report>dependency-info</report>
                            <report>dependency-management</report>
                            <report>distribution-management</report>
                            <report>issue-tracking</report>
                            <report>license</report>
<!--                             <report>plugin-management</report> -->
<!--                             <report>plugins</report> -->
                            <report>project-team</report>
                            <report>mailing-list</report>
                            <report>scm</report>
                        </reports>
                    </reportSet>
                </reportSets>				
			</plugin>
		</plugins>
	</reporting>
</project>