<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>
    <groupId>org.genemania</groupId>
    <artifactId>genemania-engine</artifactId>
    <packaging>jar</packaging>
    <version>3.1.1</version>
    <name>GeneManiaEngine</name>
    <url>http://localhost:8080/genemania</url>
    <repositories>
        <repository>
            <id>genemania_maven_repo</id>
            <name>GeneMANIA Maven Project Repository</name>
            <url>http://genemania.org/mvn</url>
        </repository>
        <repository>
            <id>maven2-repository.dev.java.net</id>
            <name>Java.net Repository for Maven</name>
            <url>http://download.java.net/maven/2/</url>
            <layout>default</layout>
        </repository>
    </repositories>
  <distributionManagement>
    <repository>
      <id>nexus.cs.toronto.edu</id>
      <name>Maven2 Remote Repository for Releases</name>
      <url>http://nexus.cs.toronto.edu/nexus/content/repositories/externals</url>
    </repository>
  </distributionManagement>
    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
    </properties>
    <dependencies>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math</artifactId>
            <version>2.1</version>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.7</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.genemania</groupId>
            <artifactId>genemania-common</artifactId>
            <version>3.1.1</version>
        </dependency>
        <!-- if we want to use the bundled apps against a derby db, need 
            these dependencies <dependency> <groupId>org.genemania</groupId> <artifactId>genemania-hibernate-support</artifactId> 
            <version>0.1</version> </dependency> <dependency> <groupId>org.apache.derby</groupId> 
            <artifactId>derby</artifactId> <version>10.4.2.0</version> </dependency> -->
        <!-- experimenting with avro for serialization <dependency> <groupId>org.apache.hadoop</groupId> 
            <artifactId>avro</artifactId> <version>1.3.2</version> </dependency> -->
        <dependency> 
            <groupId>com.googlecode.matrix-toolkits-java</groupId> 
            <artifactId>mtj</artifactId> 
            <version>0.9.14d</version> 
        </dependency>     
        
        <dependency>
            <artifactId>opencsv</artifactId>
            <groupId>net.sf.opencsv</groupId>
            <version>1.8</version>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.14</version>
        </dependency>
        <dependency>
            <groupId>args4j</groupId>
            <artifactId>args4j</artifactId>
            <version>2.0.9</version>
        </dependency>
        <dependency>
            <groupId>commons-configuration</groupId>
            <artifactId>commons-configuration</artifactId>
            <version>1.5</version>
        </dependency>
        <dependency>
            <groupId>commons-collections</groupId>
            <artifactId>commons-collections</artifactId>
            <version>3.2.1</version>
            <!-- <scope>test</scope> -->
        </dependency>
    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.3.2</version>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.4.3</version>
                <configuration>
                    <argLine>-Xmx512m</argLine>
                    <skip>false</skip>
                    <testFailureIgnore>true</testFailureIgnore>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <configuration>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                </configuration>
            </plugin>
            <plugin>
                <groupId>com.mycila.maven-license-plugin</groupId>
                <artifactId>maven-license-plugin</artifactId>
                <version>1.9.0</version>
                <configuration>
                    <header>src/etc/header.txt</header>
                    <strictCheck>true</strictCheck>
                    <includes>
                        <include>src/**/*.java</include>
                        <include>src/**/*.py</include>
                    </includes>
                </configuration>
            </plugin>
        </plugins>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
                <excludes>
                    <exclude>**/MATLAB/*</exclude>
                </excludes>
            </resource>
        </resources>
    </build>
    <reporting>
        <plugins>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>cobertura-maven-plugin</artifactId>
                <version>2.4</version>
                <configuration>
                    <formats>
                        <format>html</format>
                        <format>xml</format>
                    </formats>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-report-plugin</artifactId>
                <version>2.4.2</version>
            </plugin>
        </plugins>
    </reporting>
</project>
