<commit_before><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">


	<!-- for releasing to Maven Central / OSS Sonatype -->
	<parent>
		<groupId>org.sonatype.oss</groupId>
		<artifactId>oss-parent</artifactId>
		<version>9</version>
	</parent>


	<modelVersion>4.0.0</modelVersion>
	<groupId>org.rcsb</groupId>
	<artifactId>mmtf</artifactId>
	<packaging>pom</packaging>
	<version>0.0.1-alpha4-SNAPSHOT</version>
	<name>mmtf</name>
	<description>MMTF is a compressed, fast and useful format for serving macromolecular data.
    </description>
	<url>https://github.com/rcsb</url>
	<organization>
		<name>RCSB PDB</name>
		<url>http://www.rcsb.org/</url>
	</organization>
	<licenses>
		<license>
			<name>Apache 2.0</name>
			<url>https://www.apache.org/licenses/LICENSE-2.0</url>
			<distribution>repo</distribution>
		</license>
	</licenses>
	<properties>
		<jdk.version>1.8</jdk.version>
		<maven.enforcer.jdk-version>1.8</maven.enforcer.jdk-version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
		<maxmem>512M</maxmem>
		<slf4j.version>1.7.14</slf4j.version>
		<log4j.version>2.5</log4j.version>
	</properties>
	<scm>
		<connection>scm:git:git://github.com:rcsb/mmtf-java.git</connection>
		<developerConnection>scm:git:<EMAIL>:rcsb/mmtf-java.git</developerConnection>
		<url>https://github.com/rcsb/mmtf-java</url>

		<tag>HEAD</tag>
	</scm>
	<build>
		<pluginManagement>
			<plugins>
				<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-enforcer-plugin</artifactId>
										<versionRange>[1.0.0,)</versionRange>
										<goals>
											<goal>enforce</goal>
										</goals>
									</pluginExecutionFilter>
									<action>
										<ignore />
									</action>
								</pluginExecution>
							</pluginExecutions>
						</lifecycleMappingMetadata>
					</configuration>
				</plugin>
				<plugin>
					<artifactId>maven-clean-plugin</artifactId>
					<version>3.0.0</version>
				</plugin>
				<plugin>
					<artifactId>maven-compiler-plugin</artifactId>
					<version>3.3</version>
					<configuration>
						<source>${jdk.version}</source>
						<target>${jdk.version}</target>
					</configuration>
				</plugin>
				<plugin>
					<artifactId>maven-dependency-plugin</artifactId>
					<version>2.10</version>
				</plugin>
				<plugin>
					<artifactId>maven-jar-plugin</artifactId>
					<version>2.6</version>
				</plugin>
				<plugin>
					<artifactId>maven-scm-plugin</artifactId>
					<version>1.9.4</version>
				</plugin>
				<plugin>
					<artifactId>maven-source-plugin</artifactId>
					<version>2.4</version>
				</plugin>
				<plugin>
					<artifactId>maven-failsafe-plugin</artifactId>
					<version>2.19.1</version>
				</plugin>
				<plugin>
					<groupId>net.sf</groupId>
					<artifactId>stat-scm</artifactId>
					<version>1.2.0</version>
				</plugin>
				<plugin>
					<groupId>org.jvnet.jaxb2.maven2</groupId>
					<artifactId>maven-jaxb2-plugin</artifactId>
					<version>0.13.1</version>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-release-plugin</artifactId>
					<version>2.5.3</version>
					<configuration>
						<remoteTagging>true</remoteTagging>
						<preparationGoals>clean install</preparationGoals>
						<autoVersionSubmodules>true</autoVersionSubmodules>
						<!-- work around for GPG hanging issue http://jira.codehaus.org/browse/MGPG-9 -->
						<mavenExecutorId>forked-path</mavenExecutorId>
					</configuration>

				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-javadoc-plugin</artifactId>
					<version>2.10.3</version>
					<configuration>
						<additionalparam>-Xdoclint:none</additionalparam>

						<maxmemory>256m</maxmemory>
						<footer>&lt;script src="http://www.google-analytics.com/urchin.js"
							type="text/javascript"&gt;&lt;/script&gt;&lt;script
							type="text/javascript"&gt;_uacct =
							"UA-1326640-1";urchinTracker();&lt;/script&gt;</footer>
					</configuration>

				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-shade-plugin</artifactId>
					<version>2.4.2</version>
				</plugin>
				<plugin>
					<artifactId>maven-assembly-plugin</artifactId>
					<version>2.6</version>
					<configuration>
						<descriptors>
							<descriptor>src/main/assembly/assembly.xml</descriptor>
						</descriptors>
					</configuration>

					<!-- Attach the creation of the assembly to the package phase. -->
					<executions>
						<execution>
							<id>assemble</id>
							<phase>package</phase>
							<goals>
								<goal>single</goal>
							</goals>
						</execution>
					</executions>

				</plugin>
				<plugin>
					<groupId>org.codehaus.mojo</groupId>
					<artifactId>findbugs-maven-plugin</artifactId>
					<version>3.0.3</version>
				</plugin>

				<plugin>
					<groupId>org.codehaus.mojo</groupId>
					<artifactId>buildnumber-maven-plugin</artifactId>
					<version>1.4</version>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-checkstyle-plugin</artifactId>
					<version>2.17</version>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-resources-plugin</artifactId>
					<version>2.7</version>
				</plugin>

				<plugin>
					<artifactId>maven-enforcer-plugin</artifactId>
					<version>1.4.1</version>
					<executions>
						<execution>
							<id>enforce-java</id>
							<goals>
								<goal>enforce</goal>
							</goals>
							<configuration>
								<rules>
									<requireJavaVersion>
										<version>${maven.enforcer.jdk-version}</version>
									</requireJavaVersion>
								</rules>
							</configuration>
						</execution>
					</executions>
				</plugin>

			</plugins>
		</pluginManagement>


		<plugins>

			<!-- for deployment on OSS Sonatype -->
			<plugin>
				<groupId>org.sonatype.plugins</groupId>
				<artifactId>nexus-staging-maven-plugin</artifactId>
				<version>1.6.6</version>
				<extensions>true</extensions>
				<configuration>
					<serverId>ossrh</serverId>
					<nexusUrl>https://oss.sonatype.org/</nexusUrl>
					<autoReleaseAfterClose>true</autoReleaseAfterClose>
				</configuration>
			</plugin>

			<!-- for digital signing of code -->
			<!--<plugin> -->
			<!--<groupId>org.apache.maven.plugins</groupId> -->
			<!--<artifactId>maven-gpg-plugin</artifactId> -->
			<!--<version>1.5</version> -->
			<!--<executions> -->
			<!--<execution> -->
			<!--<id>sign-artifacts</id> -->
			<!--<phase>verify</phase> -->
			<!--<goals> -->
			<!--<goal>sign</goal> -->
			<!--</goals> -->
			<!--</execution> -->
			<!--</executions> -->
			<!--</plugin> -->

			<!-- give more memory for junit tests -->
			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.19.1</version>
				<configuration>
					<argLine>-Xmx1500M</argLine>
					<reuseForks>false</reuseForks>
					<forkCount>1</forkCount>
				</configuration>
			</plugin>


			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jar-plugin</artifactId>

				<configuration>
					<archive>
						<addMavenDescriptor>false</addMavenDescriptor>
						<manifest>
							<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
							<addDefaultImplementationEntries>true</addDefaultImplementationEntries>

						</manifest>
						<manifestEntries>
							<Trusted-Library>true</Trusted-Library>
							<Permissions>all-permissions</Permissions>
							<Codebase>*</Codebase>
							<Application-Name>MMTF</Application-Name>
						</manifestEntries>
					</archive>
				</configuration>

			</plugin>


			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>findbugs-maven-plugin</artifactId>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-checkstyle-plugin</artifactId>
				<configuration>
					<!-- <enableFilesSummary>true</enableFilesSummary> <enableSeveritySummary>true</enableSeveritySummary> -->
					<enableRulesSummary>false</enableRulesSummary>
					<!-- <consoleOutput>true</consoleOutput> -->
				</configuration>
			</plugin>

			<plugin>
				<groupId>com.versioneye</groupId>
				<artifactId>versioneye-maven-plugin</artifactId>
				<version>3.5.1</version>
			</plugin>

		</plugins>

		<extensions>
			<extension>
				<groupId>org.apache.maven.wagon</groupId>
				<artifactId>wagon-ssh</artifactId>
				<version>2.6</version>
			</extension>
		</extensions>

	</build>


	<reporting>
		<plugins>
			<plugin>
				<artifactId>maven-javadoc-plugin</artifactId>
				<version>2.10.1</version>
				<configuration>
					<additionalparam>-Xdoclint:none</additionalparam>
					<aggregate>true</aggregate>
					<breakiterator>true</breakiterator>
					<quiet>true</quiet>
					<source>1.8</source>
					<verbose>false</verbose>
					<linksource>true</linksource>
				</configuration>
			</plugin>
			<plugin><commit_msg>Update to latest verions of maven and nexus plugins<commit_after><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">


	<!-- for releasing to Maven Central / OSS Sonatype -->
	<parent>
		<groupId>org.sonatype.oss</groupId>
		<artifactId>oss-parent</artifactId>
		<version>9</version>
	</parent>


	<modelVersion>4.0.0</modelVersion>
	<groupId>org.rcsb</groupId>
	<artifactId>mmtf</artifactId>
	<packaging>pom</packaging>
	<version>0.0.1-alpha4-SNAPSHOT</version>
	<name>mmtf</name>
	<description>MMTF is a compressed, fast and useful format for serving macromolecular data.
    </description>
	<url>https://github.com/rcsb</url>
	<organization>
		<name>RCSB PDB</name>
		<url>http://www.rcsb.org/</url>
	</organization>
	<licenses>
		<license>
			<name>Apache 2.0</name>
			<url>https://www.apache.org/licenses/LICENSE-2.0</url>
			<distribution>repo</distribution>
		</license>
	</licenses>
	<properties>
		<jdk.version>1.8</jdk.version>
		<maven.enforcer.jdk-version>1.8</maven.enforcer.jdk-version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
		<maxmem>512M</maxmem>
		<slf4j.version>1.7.14</slf4j.version>
		<log4j.version>2.5</log4j.version>
	</properties>
	<scm>
		<connection>scm:git:git://github.com:rcsb/mmtf-java.git</connection>
		<developerConnection>scm:git:git@github.com:rcsb/mmtf-java.git</developerConnection>
		<url>https://github.com/rcsb/mmtf-java</url>

		<tag>HEAD</tag>
	</scm>
	<build>
		<pluginManagement>
			<plugins>
				<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-enforcer-plugin</artifactId>
										<versionRange>[1.0.0,)</versionRange>
										<goals>
											<goal>enforce</goal>
										</goals>
									</pluginExecutionFilter>
									<action>
										<ignore />
									</action>
								</pluginExecution>
							</pluginExecutions>
						</lifecycleMappingMetadata>
					</configuration>
				</plugin>
				<plugin>
					<artifactId>maven-clean-plugin</artifactId>
					<version>3.0.0</version>
				</plugin>
				<plugin>
					<artifactId>maven-compiler-plugin</artifactId>
					<version>3.5.1</version>
					<configuration>
						<source>${jdk.version}</source>
						<target>${jdk.version}</target>
					</configuration>
				</plugin>
				<plugin>
					<artifactId>maven-dependency-plugin</artifactId>
					<version>2.10</version>
				</plugin>
				<plugin>
					<artifactId>maven-jar-plugin</artifactId>
					<version>2.6</version>
				</plugin>
				<plugin>
					<artifactId>maven-scm-plugin</artifactId>
					<version>1.9.4</version>
				</plugin>
				<plugin>
					<artifactId>maven-source-plugin</artifactId>
					<version>3.0.0</version>
				</plugin>
				<plugin>
					<artifactId>maven-failsafe-plugin</artifactId>
					<version>2.19.1</version>
				</plugin>
				<plugin>
					<groupId>net.sf</groupId>
					<artifactId>stat-scm</artifactId>
					<version>1.2.0</version>
				</plugin>
				<plugin>
					<groupId>org.jvnet.jaxb2.maven2</groupId>
					<artifactId>maven-jaxb2-plugin</artifactId>
					<version>0.13.1</version>
				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-release-plugin</artifactId>
					<version>2.5.3</version>
					<configuration>
						<remoteTagging>true</remoteTagging>
						<preparationGoals>clean install</preparationGoals>
						<autoVersionSubmodules>true</autoVersionSubmodules>
						<!-- work around for GPG hanging issue http://jira.codehaus.org/browse/MGPG-9 -->
						<mavenExecutorId>forked-path</mavenExecutorId>
					</configuration>

				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-javadoc-plugin</artifactId>
					<version>2.10.3</version>
					<configuration>
						<additionalparam>-Xdoclint:none</additionalparam>

						<maxmemory>256m</maxmemory>
						<footer>&lt;script src="http://www.google-analytics.com/urchin.js"
							type="text/javascript"&gt;&lt;/script&gt;&lt;script
							type="text/javascript"&gt;_uacct =
							"UA-1326640-1";urchinTracker();&lt;/script&gt;</footer>
					</configuration>

				</plugin>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-shade-plugin</artifactId>
					<version>2.4.3</version>
				</plugin>
				<plugin>
					<artifactId>maven-assembly-plugin</artifactId>
					<version>2.6</version>
					<configuration>
						<descriptors>
							<descriptor>src/main/assembly/assembly.xml</descriptor>
						</descriptors>
					</configuration>

					<!-- Attach the creation of the assembly to the package phase. -->
					<executions>
						<execution>
							<id>assemble</id>
							<phase>package</phase>
							<goals>
								<goal>single</goal>
							</goals>
						</execution>
					</executions>

				</plugin>
				<plugin>
					<groupId>org.codehaus.mojo</groupId>
					<artifactId>findbugs-maven-plugin</artifactId>
					<version>3.0.3</version>
				</plugin>

				<plugin>
					<groupId>org.codehaus.mojo</groupId>
					<artifactId>buildnumber-maven-plugin</artifactId>
					<version>1.4</version>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-checkstyle-plugin</artifactId>
					<version>2.17</version>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-resources-plugin</artifactId>
					<version>2.7</version>
				</plugin>

				<plugin>
					<artifactId>maven-enforcer-plugin</artifactId>
					<version>1.4.1</version>
					<executions>
						<execution>
							<id>enforce-java</id>
							<goals>
								<goal>enforce</goal>
							</goals>
							<configuration>
								<rules>
									<requireJavaVersion>
										<version>${maven.enforcer.jdk-version}</version>
									</requireJavaVersion>
								</rules>
							</configuration>
						</execution>
					</executions>
				</plugin>

			</plugins>
		</pluginManagement>


		<plugins>

			<!-- for deployment on OSS Sonatype -->
			<plugin>
				<groupId>org.sonatype.plugins</groupId>
				<artifactId>nexus-staging-maven-plugin</artifactId>
				<version>1.6.7</version>
				<extensions>true</extensions>
				<configuration>
					<serverId>ossrh</serverId>
					<nexusUrl>https://oss.sonatype.org/</nexusUrl>
					<autoReleaseAfterClose>true</autoReleaseAfterClose>
				</configuration>
			</plugin>

			<!-- for digital signing of code -->
			<!--<plugin> -->
			<!--<groupId>org.apache.maven.plugins</groupId> -->
			<!--<artifactId>maven-gpg-plugin</artifactId> -->
			<!--<version>1.5</version> -->
			<!--<executions> -->
			<!--<execution> -->
			<!--<id>sign-artifacts</id> -->
			<!--<phase>verify</phase> -->
			<!--<goals> -->
			<!--<goal>sign</goal> -->
			<!--</goals> -->
			<!--</execution> -->
			<!--</executions> -->
			<!--</plugin> -->

			<!-- give more memory for junit tests -->
			<plugin>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.19.1</version>
				<configuration>
					<argLine>-Xmx1500M</argLine>
					<reuseForks>false</reuseForks>
					<forkCount>1</forkCount>
				</configuration>
			</plugin>


			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jar-plugin</artifactId>

				<configuration>
					<archive>
						<addMavenDescriptor>false</addMavenDescriptor>
						<manifest>
							<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
							<addDefaultImplementationEntries>true</addDefaultImplementationEntries>

						</manifest>
						<manifestEntries>
							<Trusted-Library>true</Trusted-Library>
							<Permissions>all-permissions</Permissions>
							<Codebase>*</Codebase>
							<Application-Name>MMTF</Application-Name>
						</manifestEntries>
					</archive>
				</configuration>

			</plugin>


			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>findbugs-maven-plugin</artifactId>
			</plugin>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-checkstyle-plugin</artifactId>
				<configuration>
					<!-- <enableFilesSummary>true</enableFilesSummary> <enableSeveritySummary>true</enableSeveritySummary> -->
					<enableRulesSummary>false</enableRulesSummary>
					<!-- <consoleOutput>true</consoleOutput> -->
				</configuration>
			</plugin>

			<plugin>
				<groupId>com.versioneye</groupId>
				<artifactId>versioneye-maven-plugin</artifactId>
				<version>3.9.1</version>
			</plugin>

		</plugins>

		<extensions>
			<extension>
				<groupId>org.apache.maven.wagon</groupId>
				<artifactId>wagon-ssh</artifactId>
				<version>2.6</version>
			</extension>
		</extensions>

	</build>


	<reporting>
		<plugins>
			<plugin>
				<artifactId>maven-javadoc-plugin</artifactId>
				<version>2.10.3</version>
				<configuration>
					<additionalparam>-Xdoclint:none</additionalparam>
					<aggregate>true</aggregate>
					<breakiterator>true</breakiterator>
					<quiet>true</quiet>
					<source>1.8</source>
					<verbose>false</verbose>
					<linksource>true</linksource>
				</configuration>
			</plugin>
			<plugin>
{'fraction_non_alphanumeric': 0.17124769190187286, 'fraction_numerical': 0.015193880242680032, 'mean_word_length': 3.009306260575296, 'pattern_counts': {'":': 0, '<': 922, '<?xml version=': 0, '>': 922, 'https://': 8, 'lorem ipsum': 0, 'www.': 8, 'xml': 6}, 'pii_count': 1, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7596951', 'n_tokens_mistral': 8918, 'n_tokens_neox': 6206, 'n_words': 717}