<commit_before><?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/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <groupId>com.github.jmchilton.blend4j</groupId>
  <artifactId>blend4j</artifactId>
  <packaging>jar</packaging>
  <version>0.1-alpha-9-SNAPSHOT</version>
  <name>blend4j</name>
  <description>blend4j is a JVM partial reimplemenation of the Python library bioblend (http://bioblend.readthedocs.org/en/latest/) for interacting with Galaxy, CloudMan, and BioCloudCentral.</description>
  <parent>
    <groupId>org.sonatype.oss</groupId>
    <artifactId>oss-parent</artifactId>
    <version>7</version>
  </parent>
  <scm>
    <connection>scm:git:git@github.com:jmchilton/blend4j.git</connection>
    <developerConnection>scm:git:git<EMAIL>:jmchilton/blend4j.git</developerConnection>
    <url><EMAIL>:jmchilton/blend4j.git</url>
  </scm>
  <dependencies>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-client</artifactId>
      <version>1.17.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-json</artifactId>
      <version>1.17.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-core</artifactId>
      <version>1.17.1</version>
    </dependency>
    <dependency>
        <groupId>com.sun.jersey.contribs</groupId>
        <artifactId>jersey-multipart</artifactId>
        <version>1.17.1</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-core-asl</artifactId>
      <version>1.9.12</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-mapper-asl</artifactId>
      <version>1.9.12</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-jaxrs</artifactId>
      <version>1.9.12</version>
    </dependency>
    <!-- Test Dependencies -->
    <dependency>
      <groupId>org.testng</groupId>
      <artifactId>testng</artifactId>
      <version>6.6</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>com.github.jmchilton.galaxybootstrap</groupId>
      <artifactId>galaxybootstrap</artifactId>
      <version>0.3.0-rc3</version>
      <scope>test</scope>
    </dependency>
  </dependencies>
  <profiles>
    <profile>
      <id>release-sign-artifacts</id>
      <activation>
        <property>
          <name>performRelease</name>
          <value>true</value>
        </property>
      </activation>
      <build>
        <plugins>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-gpg-plugin</artifactId>
            <version>1.4</version>
            <executions>
              <execution>
                <id>sign-artifacts</id>
                <phase>verify</phase>
                <goals>
                  <goal>sign</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>  
  <build>
    <pluginManagement>
      <plugins>
        <plugin>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>2.3.2</version>
          <configuration>
            <source>1.6</source>
            <target>1.6</target>
            <compilerArgument />
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <configuration>
            <preparationGoals>clean install verify</preparationGoals>
            <goals>clean install javadoc:jar source:jar gpg:sign verify deploy</goals>
            <arguments>-Dmaven.test.skip=true</arguments>
          </configuration>
        </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-javadoc-plugin</artifactId>
          <executions>
            <execution>
              <id>attach-javadocs</id>
              <goals>
                <goal>jar</goal>
              </goals>
            </execution>
          </executions>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

</project><commit_msg>Update maven to build and deploy site (with JavaDocs) to github.<commit_after><?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/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>
  <groupId>com.github.jmchilton.blend4j</groupId>
  <artifactId>blend4j</artifactId>
  <packaging>jar</packaging>
  <version>0.1-alpha-9-SNAPSHOT</version>
  <name>blend4j</name>
  <description>blend4j is a JVM partial reimplemenation of the Python library bioblend (http://bioblend.readthedocs.org/en/latest/) for interacting with Galaxy, CloudMan, and BioCloudCentral.</description>
  <parent>
    <groupId>org.sonatype.oss</groupId>
    <artifactId>oss-parent</artifactId>
    <version>7</version>
  </parent>
  <scm>
    <connection>scm:git:git<EMAIL>:jmchilton/blend4j.git</connection>
    <developerConnection>scm:git:<EMAIL>:jmchilton/blend4j.git</developerConnection>
    <url><EMAIL>:jmchilton/blend4j.git</url>
  </scm>
  <issueManagement>
    <system>Github</system>
    <url>http://github.com/jmchilton/blend4j/issues</url>
  </issueManagement>
  <licenses>
    <license>
      <name>Apache License, Version 2.0</name>
      <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
      <distribution>repo</distribution>
      <comments>A business-friendly OSS license</comments>
    </license>
  </licenses>
  <properties>
    <!-- github server corresponds to entry in ~/.m2/settings.xml -->
    <github.global.server>github</github.global.server>
  </properties>
  <dependencies>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-client</artifactId>
      <version>1.17.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-json</artifactId>
      <version>1.17.1</version>
    </dependency>
    <dependency>
      <groupId>com.sun.jersey</groupId>
      <artifactId>jersey-core</artifactId>
      <version>1.17.1</version>
    </dependency>
    <dependency>
        <groupId>com.sun.jersey.contribs</groupId>
        <artifactId>jersey-multipart</artifactId>
        <version>1.17.1</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-core-asl</artifactId>
      <version>1.9.12</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-mapper-asl</artifactId>
      <version>1.9.12</version>
    </dependency>
    <dependency>
      <groupId>org.codehaus.jackson</groupId>
      <artifactId>jackson-jaxrs</artifactId>
      <version>1.9.12</version>
    </dependency>
    <!-- Test Dependencies -->
    <dependency>
      <groupId>org.testng</groupId>
      <artifactId>testng</artifactId>
      <version>6.6</version>
      <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>com.github.jmchilton.galaxybootstrap</groupId>
      <artifactId>galaxybootstrap</artifactId>
      <version>0.3.0-rc3</version>
      <scope>test</scope>
    </dependency>
  </dependencies>
  <reporting>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-project-info-reports-plugin</artifactId>
        <version>2.7</version>
        <reportSets>
          <reportSet>
            <reports>
              <report>index</report>
<!--              <report>dependencies</report> -->
              <report>issue-tracking</report>
              <report>license</report>
              <report>scm</report>
            </reports>
          </reportSet>
        </reportSets>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <version>2.9</version>
        <reportSets>
          <reportSet><!-- by default, id = "default" -->
            <reports><!-- select non-aggregate reports -->
              <report>javadoc</report>
            </reports>
          </reportSet>
          <reportSet><!-- aggregate reportSet, to define in poms having modules -->
            <id>aggregate</id>
            <inherited>false</inherited><!-- don't run aggregate in child modules -->
            <reports>
              <report>aggregate</report>
            </reports>
          </reportSet>
        </reportSets>
      </plugin>
    </plugins>
  </reporting>
  <profiles>
    <profile>
      <id>release-sign-artifacts</id>
      <activation>
        <property>
          <name>performRelease</name>
          <value>true</value>
        </property>
      </activation>
      <build>
        <plugins>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-gpg-plugin</artifactId>
            <version>1.4</version>
            <executions>
              <execution>
                <id>sign-artifacts</id>
                <phase>verify</phase>
                <goals>
                  <goal>sign</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>  
  <build>
    <plugins>
      <plugin>
        <groupId>com.github.github</groupId>
        <artifactId>site-maven-plugin</artifactId>
        <version>0.8</version>
        <configuration>
          <message>Creating site for ${project.version}</message>
        </configuration>
        <executions>
          <execution>
            <goals>
              <goal>site</goal>
            </goals>
            <phase>site</phase>
          </execution>
        </executions>
      </plugin>
    </plugins>
    <pluginManagement>
      <plugins>
        <plugin>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>2.3.2</version>
          <configuration>
            <source>1.6</source>
            <target>1.6</target>
            <compilerArgument />
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <configuration>
            <preparationGoals>clean install verify</preparationGoals>
            <goals>clean install javadoc:jar source:jar gpg:sign verify deploy</goals>
            <arguments>-Dmaven.test.skip=true</arguments>
          </configuration>
        </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-javadoc-plugin</artifactId>
          <executions>
            <execution>
              <id>attach-javadocs</id>
              <goals>
                <goal>jar</goal>
              </goals>
            </execution>
          </executions>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>
</project>
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{'dir': 'git-commits-cleaned', 'id': '2284668', 'n_tokens_mistral': 4079, 'n_tokens_neox': 3649, 'n_words': 478}