<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">
  <modelVersion>4.0.0</modelVersion>
  <groupId>io.github.egonw</groupId>
  <artifactId>nanojava</artifactId>
  <name>NanoJava</name>
  <version>2.0.0</version>

  <scm>
    <connection>scm:git:git://github.com/egonw/nanojava.git</connection>
    <developerConnection>scm:git:ssh://git@github.com/egonw/nanojava.git</developerConnection>
    <url>http://github.com/egonw/nanojava/tree/master</url>
    <tag>HEAD</tag>
  </scm>

  <distributionManagement>
    <snapshotRepository>
      <id>ossrh</id>
      <url>https://s01.oss.sonatype.org/content/repositories/snapshots</url>
    </snapshotRepository>
    <repository>
      <id>ossrh</id>
      <url>https://s01.oss.sonatype.org/service/local/staging/deploy/maven2</url>
    </repository>
  </distributionManagement>

  <dependencies>
    <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>${junit.version}</version>
        <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.blueobelisk</groupId>
      <artifactId>cmlxom</artifactId>
      <version>4.0</version>
    </dependency>
	<dependency>
	    <groupId>org.openscience.cdk</groupId>
	    <artifactId>cdk-bundle</artifactId>
	    <version>${cdk.version}</version>
	</dependency>
	<dependency>
		<groupId>info.picocli</groupId>
		<artifactId>picocli</artifactId>
		<version>3.1.0</version>
	</dependency>
	<dependency>
	    <groupId>com.github.egonw</groupId>
	    <artifactId>jqudt</artifactId>
	    <version>1.4.0</version>
	</dependency>
    <dependency>
        <groupId>com.github.stefanbirkner</groupId>
        <artifactId>system-rules</artifactId>
        <version>1.19.0</version>
        <scope>test</scope>
    </dependency>
  </dependencies>

  <properties>
    <cdk.version>2.7.1</cdk.version>
    <junit.version>4.13.1</junit.version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <maven.compiler.source>1.8</maven.compiler.source>
    <maven.compiler.target>1.8</maven.compiler.target>
  </properties>

  <!-- developer = commit access -->
  <developers>
    <developer>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://chem-bla-ics.blogspot.com</url>
    </developer>
  </developers>

  <contributors>
    <contributor>
      <name><NAME></name>
    </contributor>
    <contributor>
      <name><NAME></name>
    </contributor>
  </contributors>

  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>true</filtering>
      </resource>
    </resources>
    <plugins>
		<plugin>
			<artifactId>maven-assembly-plugin</artifactId>
			<configuration>
				<descriptorRefs>
					<descriptorRef>jar-with-dependencies</descriptorRef>
				</descriptorRefs>
				<archive>
					<manifest>
						<mainClass>io.github.egonw.nanojava.NanoJava</mainClass>
					</manifest>
				</archive>
			</configuration>
			<executions>
				<execution>
					<id>make-assembly</id>
					<phase>package</phase>
					<goals>
						<goal>single</goal>
					</goals>
				</execution>
			</executions>
		</plugin>
            <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>0.8.7</version>
                <executions>
                    <execution>
                        <id>start-agent</id>
                        <goals>
                            <goal>prepare-agent</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>generate-report</id>
                        <goals>
                            <goal>report</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.sonatype.plugins</groupId>
                <artifactId>nexus-staging-maven-plugin</artifactId>
                <version>1.6.8</version>
                <extensions>true</extensions>
                <configuration>
                    <serverId>ossrh</serverId>
                    <nexusUrl>https://oss.sonatype.org/</nexusUrl>
                    <autoReleaseAfterClose>true</autoReleaseAfterClose>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-gpg-plugin</artifactId>
                <version>1.6</version>
                <executions>
                    <execution>
                        <id>sign-artifacts</id>
                        <phase>verify</phase>
                        <goals>
                            <goal>sign</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.22.2</version>
                <configuration>
                    <groups>${junit5.groups}</groups>
                    <excludedGroups>${junit5.excludeGroups}</excludedGroups>
                </configuration>
            </plugin><commit_msg>Added missing pom.xml content: license, url, description, and plugins for JavaDoc and source jar<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">
  <modelVersion>4.0.0</modelVersion>
  <groupId>io.github.egonw</groupId>
  <artifactId>nanojava</artifactId>
  <description>Java library extending the Chemistry Development Kit with functionality for nanomaterials.</description>  
  <name>NanoJava</name>
  <version>2.0.0</version>
  <url>https://github.com/enanomapper/nanojava</url>

  <licenses>
    <license>
      <name>GNU LGPL 2.1 or later</name>
      <url>http://www.gnu.org/licenses/lgpl.html</url>
      <distribution>repo</distribution>
    </license>
  </licenses>

  <scm>
    <connection>scm:git:git://github.com/egonw/nanojava.git</connection>
    <developerConnection>scm:git:ssh://git@github.com/egonw/nanojava.git</developerConnection>
    <url>http://github.com/egonw/nanojava/tree/master</url>
    <tag>HEAD</tag>
  </scm>

  <distributionManagement>
    <snapshotRepository>
      <id>ossrh</id>
      <url>https://s01.oss.sonatype.org/content/repositories/snapshots</url>
    </snapshotRepository>
    <repository>
      <id>ossrh</id>
      <url>https://s01.oss.sonatype.org/service/local/staging/deploy/maven2</url>
    </repository>
  </distributionManagement>

  <dependencies>
    <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>${junit.version}</version>
        <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.blueobelisk</groupId>
      <artifactId>cmlxom</artifactId>
      <version>4.0</version>
    </dependency>
	<dependency>
	    <groupId>org.openscience.cdk</groupId>
	    <artifactId>cdk-bundle</artifactId>
	    <version>${cdk.version}</version>
	</dependency>
	<dependency>
		<groupId>info.picocli</groupId>
		<artifactId>picocli</artifactId>
		<version>3.1.0</version>
	</dependency>
	<dependency>
	    <groupId>com.github.egonw</groupId>
	    <artifactId>jqudt</artifactId>
	    <version>1.4.0</version>
	</dependency>
    <dependency>
        <groupId>com.github.stefanbirkner</groupId>
        <artifactId>system-rules</artifactId>
        <version>1.19.0</version>
        <scope>test</scope>
    </dependency>
  </dependencies>

  <properties>
    <cdk.version>2.7.1</cdk.version>
    <junit.version>4.13.1</junit.version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <maven.compiler.source>1.8</maven.compiler.source>
    <maven.compiler.target>1.8</maven.compiler.target>
  </properties>

  <!-- developer = commit access -->
  <developers>
    <developer>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://chem-bla-ics.blogspot.com</url>
    </developer>
  </developers>

  <contributors>
    <contributor>
      <name><NAME></name>
    </contributor>
    <contributor>
      <name><NAME></name>
    </contributor>
  </contributors>

  <build>
    <resources>
      <resource>
        <directory>src/main/resources</directory>
        <filtering>true</filtering>
      </resource>
    </resources>
    <plugins>
		<plugin>
			<artifactId>maven-assembly-plugin</artifactId>
			<configuration>
				<descriptorRefs>
					<descriptorRef>jar-with-dependencies</descriptorRef>
				</descriptorRefs>
				<archive>
					<manifest>
						<mainClass>io.github.egonw.nanojava.NanoJava</mainClass>
					</manifest>
				</archive>
			</configuration>
			<executions>
				<execution>
					<id>make-assembly</id>
					<phase>package</phase>
					<goals>
						<goal>single</goal>
					</goals>
				</execution>
			</executions>
		</plugin>
            <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>0.8.7</version>
                <executions>
                    <execution>
                        <id>start-agent</id>
                        <goals>
                            <goal>prepare-agent</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>generate-report</id>
                        <goals>
                            <goal>report</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.sonatype.plugins</groupId>
                <artifactId>nexus-staging-maven-plugin</artifactId>
                <version>1.6.8</version>
                <extensions>true</extensions>
                <configuration>
                    <serverId>ossrh</serverId>
                    <nexusUrl>https://oss.sonatype.org/</nexusUrl>
                    <autoReleaseAfterClose>true</autoReleaseAfterClose>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-gpg-plugin</artifactId>
                <version>1.6</version>
                <executions>
                    <execution>
                        <id>sign-artifacts</id>
                        <phase>verify</phase>
                        <goals>
                            <goal>sign</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.22.2</version>
                <configuration>
                    <groups>${junit5.groups}</groups>
                    <excludedGroups>${junit5.excludeGroups}</excludedGroups>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <version>3.2.1</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-javadoc-plugin</artifactId>
                <version>3.4.0</version>
                <executions>
                    <execution>
                        <id>attach-javadocs</id>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>aggregate</id>
                        <goals>
                            <goal>aggregate</goal>
                        </goals>
                        <phase>site</phase>
                        <configuration>
                        </configuration>
                    </execution>
                </executions>
                <configuration>
                    <source>8</source>
                </configuration>
            </plugin>
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{'dir': 'git-commits-cleaned', 'id': '542242', 'n_tokens_mistral': 4253, 'n_tokens_neox': 3637, 'n_words': 407}