<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>compmolbio</groupId>
	<artifactId>stallone</artifactId>
	<version>1.0.0.0-SNAPSHOT</version>
	<packaging>jar</packaging>

	<url>http://compmolbio.biocomputing-berlin.de/index.php</url>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<base.jar.name>${project.artifactId}-${project.version}</base.jar.name>
	</properties>

	<!-- TODO: describe build process -->
	<build>
		<sourceDirectory>src</sourceDirectory>
		<testSourceDirectory>test</testSourceDirectory>

		<plugins>
			<plugin>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.1</version>
				<configuration>
					<source>1.6</source>
					<target>1.6</target>
					<optimize>true</optimize>
					<useIncrementalCompilation>false</useIncrementalCompilation>
					<showWarnings>true</showWarnings>
					<showDeprecation>true</showDeprecation>
					<compilerArgs>
						<arg>-Xlint:unchecked</arg>
					</compilerArgs>
				</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-assembly-plugin</artifactId>
				<!-- Goal assembly:single is bound to maven execution phase "prepare-package" -->
				<executions>
					<execution>
						<id>distro-assembly</id>
						<phase>package</phase>
						<goals>
							<goal>single</goal>
						</goals>
						<!-- HERE, the configuration (which is loaded from file assemblyDescriptor.xml) 
							of the assembly is setup -->
						<configuration>
							<descriptorRefs>
								<descriptorRef>jar-with-dependencies</descriptorRef>
							</descriptorRefs>
							<archive>
								<index>true</index>
								<manifest>
									<addClasspath>true</addClasspath>
								</manifest>
								<manifestEntries>
									<version>${project.version}</version>
								</manifestEntries>
							</archive>
						</configuration>
					</execution>
				</executions>
			</plugin>
			<!-- build runtime jar, which includes all dependencies -->
			<plugin>
				<artifactId>proguard-maven-plugin</artifactId>
				<groupId>com.github.wvengen</groupId>
				<version>2.0.6</version>
				<executions>
					<execution>
						<phase>package</phase>
						<goals>
							<goal>proguard</goal>
						</goals>
					</execution>
				</executions>
				<dependencies>
					<dependency>
						<groupId>net.sf.proguard</groupId>
						<artifactId>proguard-base</artifactId>
						<version>4.10</version>
						<scope>runtime</scope>
					</dependency>
				</dependencies>
				<configuration>
					<injar>${project.build.finalName}-jar-with-dependencies.jar</injar>
					<outjar>${project.build.finalName}-jar-with-dependencies-proguard.jar</outjar>
					<outputDirectory>${project.build.directory}</outputDirectory>
					<libs>
						<lib>${java.home}/lib/rt.jar</lib>
						<lib>${java.home}/lib/jsse.jar</lib>
					</libs>
					<addMavenDescriptor>false</addMavenDescriptor>
					<!-- do not include any libraries. we depend on: we are already working 
						on a jar which contains all dependencies in one jar See: previous package 
						step -->
					<includeDependency>false</includeDependency>
					<obfuscate>false</obfuscate>
					<proguardInclude>${basedir}/proguard.conf</proguardInclude>
				</configuration>
			</plugin>
		</plugins>
	</build>

	<dependencies>
		<!-- jep library, for function string parsing/evaluation -->
		<dependency><commit_msg>[pom] use proguard only if profile buildDistribution is active<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>compmolbio</groupId>
	<artifactId>stallone</artifactId>
	<version>1.0.0.0-SNAPSHOT</version>
	<packaging>jar</packaging>

	<url>http://compmolbio.biocomputing-berlin.de/index.php</url>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<base.jar.name>${project.artifactId}-${project.version}</base.jar.name>
	</properties>

	<!-- TODO: describe build process -->
	<build>
		<sourceDirectory>src</sourceDirectory>
		<testSourceDirectory>test</testSourceDirectory>

		<plugins>
			<plugin>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.1</version>
				<configuration>
					<source>1.6</source>
					<target>1.6</target>
					<optimize>true</optimize>
					<useIncrementalCompilation>false</useIncrementalCompilation>
					<showWarnings>true</showWarnings>
					<showDeprecation>true</showDeprecation>
					<compilerArgs>
						<arg>-Xlint:unchecked</arg>
					</compilerArgs>
				</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-assembly-plugin</artifactId>
				<!-- Goal assembly:single is bound to maven execution phase "prepare-package" -->
				<executions>
					<execution>
						<id>distro-assembly</id>
						<phase>package</phase>
						<goals>
							<goal>single</goal>
						</goals>
						<!-- HERE, the configuration (which is loaded from file assemblyDescriptor.xml) 
							of the assembly is setup -->
						<configuration>
							<descriptorRefs>
								<descriptorRef>jar-with-dependencies</descriptorRef>
							</descriptorRefs>
							<archive>
								<index>true</index>
								<manifest>
									<addClasspath>true</addClasspath>
								</manifest>
								<manifestEntries>
									<version>${project.version}</version>
								</manifestEntries>
							</archive>
						</configuration>
					</execution>
				</executions>
			</plugin>
		</plugins>
	</build>
	<profiles>
		<profile>
			<id>buildDistribution</id>
			<build>
				<plugins>
					<!-- build runtime jar, which includes all dependencies -->
					<plugin>
						<artifactId>proguard-maven-plugin</artifactId>
						<groupId>com.github.wvengen</groupId>
						<version>2.0.6</version>
						<executions>
							<execution>
								<phase>package</phase>
								<goals>
									<goal>proguard</goal>
								</goals>
							</execution>
						</executions>
						<dependencies>
							<dependency>
								<groupId>net.sf.proguard</groupId>
								<artifactId>proguard-base</artifactId>
								<version>4.10</version>
								<scope>runtime</scope>
							</dependency>
						</dependencies>
						<configuration>
							<injar>${project.build.finalName}-jar-with-dependencies.jar</injar>
							<outjar>${project.build.finalName}-jar-with-dependencies-proguard.jar</outjar>
							<outputDirectory>${project.build.directory}</outputDirectory>
							<libs>
								<lib>${java.home}/lib/rt.jar</lib>
								<lib>${java.home}/lib/jsse.jar</lib>
							</libs>
							<addMavenDescriptor>false</addMavenDescriptor>
							<!-- do not include any libraries. we depend on: we are already working 
								on a jar which contains all dependencies in one jar See: previous package 
								step -->
							<includeDependency>false</includeDependency>
							<obfuscate>false</obfuscate>
							<proguardInclude>${basedir}/proguard.conf</proguardInclude>
						</configuration>
					</plugin>
				</plugins>
			</build>
		</profile>
	</profiles>

	<dependencies>
		<!-- jep library, for function string parsing/evaluation -->
		<dependency>
{'fraction_non_alphanumeric': 0.15379412958203706, 'fraction_numerical': 0.009197889895847423, 'mean_word_length': 3.049288061336254, 'pattern_counts': {'":': 0, '<': 303, '<?xml version=': 0, '>': 303, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 6}, 'pii_count': 2, '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': '1702704', 'n_tokens_mistral': 3273, 'n_tokens_neox': 2303, 'n_words': 344}