pom.xml

<?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/maven-v4_0_0.xsd">
	<modelVersion>4.0.0</modelVersion>
	<groupId>org.biojava</groupId>
	<artifactId>symmetry</artifactId>
	<version>2.3.1-SNAPSHOT</version>
	<packaging>pom</packaging>

	<name>RCSB Symmetry</name>
	<url>https://github.com/rcsb/symmetry</url>
	<description>Tools to detect, analyze, and visualize protein symmetry.

- Detect symmetry in biological assemblies
- Detect internal pseudo-symmetry in protein chains
- Visualize results in Jmol

This project contains developmental features for CE-Symm, as well as accessory
functions such as benchmarking. The core algorithms are gradually incorporated
into BioJava as they mature.</description>
	<organization>
		<name>RCSB</name>
		<url>http://www.rcsb.org</url>
	</organization>

	<properties>
		<jdk.version>11</jdk.version>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
		<maven.build.timestamp.format>yyyyMMdd-HHmm</maven.build.timestamp.format>
		<timestamp>${maven.build.timestamp}</timestamp>
		<slf4j.version>2.0.12</slf4j.version>
		<log4j.version>2.23.1</log4j.version>
		<biojava.version>7.1.3</biojava.version>
	</properties>

	<scm>
		<connection>scm:git:git@github.com:rcsb/symmetry.git</connection>
		<developerConnection>scm:git:git@github.com:rcsb/symmetry.git</developerConnection>
		<url>https://github.com/rcsb/symmetry</url>
		<tag>HEAD</tag>
	</scm>
	<issueManagement>
		<url>https://github.com/rcsb/symmetry/issues</url>
		<system>Github</system>
	</issueManagement>

	<!-- where Maven deploy will deploy project jars/wars -->
	<distributionManagement>
		<snapshotRepository>
			<id>ossrh</id>
			<url>https://oss.sonatype.org/content/repositories/snapshots</url>
		</snapshotRepository>
		<repository>
			<id>ossrh</id>
			<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
		</repository>
	</distributionManagement>

	<dependencyManagement>
		<dependencies>
			<dependency>
				<groupId>javax.vecmath</groupId>
				<artifactId>vecmath</artifactId>
				<version>1.5.2</version>
			</dependency>

			<dependency>
				<groupId>org.biojava</groupId>
				<artifactId>biojava-structure</artifactId>
				<version>${biojava.version}</version>
			</dependency>
			<dependency>
				<groupId>org.biojava</groupId>
				<artifactId>biojava-structure-gui</artifactId>
				<version>${biojava.version}</version>
			</dependency>
			<dependency>
				<groupId>org.biojava</groupId>
				<artifactId>biojava-ws</artifactId>
				<version>${biojava.version}</version>
			</dependency>

			<dependency>
				<groupId>org.jfree</groupId>
				<artifactId>jfreechart</artifactId>
				<version>1.5.5</version>
			</dependency>
			<dependency>
				<groupId>junit</groupId>
				<artifactId>junit</artifactId>
				<version>4.13.2</version>
				<scope>test</scope>
			</dependency>

			<dependency>
				<groupId>org.mockito</groupId>
				<artifactId>mockito-all</artifactId>
				<version>1.10.19</version>
			</dependency>

			<dependency>
				<groupId>commons-cli</groupId>
				<artifactId>commons-cli</artifactId>
				<version>1.8.0</version>
			</dependency>

			<dependency>
				<groupId>org.apache.commons</groupId>
				<artifactId>commons-math3</artifactId>
				<version>3.6.1</version>
			</dependency>

			<!-- SLF4J API, for compiling -->
			<dependency>
				<groupId>org.slf4j</groupId>
				<artifactId>slf4j-api</artifactId>
				<version>${slf4j.version}</version>
			</dependency>
			<!-- binding for log4j 2 at runtime-->
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-slf4j-impl</artifactId>
				<version>${log4j.version}</version>
				<!-- runtime scope includes the test scope as well -->
				<scope>runtime</scope>
			</dependency>
			<!-- Log4j API and Core implementation required for binding -->
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-api</artifactId>
				<version>${log4j.version}</version>
				<!-- runtime scope includes the test scope as well -->
				<scope>runtime</scope>
			</dependency>
			<dependency>
				<groupId>org.apache.logging.log4j</groupId>
				<artifactId>log4j-core</artifactId>
				<version>${log4j.version}</version>
				<!-- runtime scope includes the test scope as well -->
				<scope>runtime</scope>
			</dependency>

			<dependency>
				<groupId>xmlunit</groupId>
				<artifactId>xmlunit</artifactId>
				<version>1.6</version>
			</dependency>

		</dependencies>
	</dependencyManagement>

	<build>
		<pluginManagement>
			<plugins>
				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-compiler-plugin</artifactId>
					<version>3.13.0</version>
					<configuration>
						<source>${jdk.version}</source>
						<target>${jdk.version}</target>
					</configuration>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-jar-plugin</artifactId>
					<version>3.4.2</version>
					<configuration>
						<archive>
							<manifestEntries>
								<Multi-Release>true</Multi-Release>
							</manifestEntries>
						</archive>
					</configuration>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-resources-plugin</artifactId>
					<version>3.3.1</version>
				</plugin>

				<plugin>
					<artifactId>maven-surefire-plugin</artifactId>
					<version>3.3.1</version>
					<configuration>
						<argLine>-Xms256m -Xmx2000M</argLine>
					</configuration>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-release-plugin</artifactId>
					<version>3.1.1</version>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-shade-plugin</artifactId>
					<version>3.6.0</version>
				</plugin>

				<plugin>
					<groupId>org.apache.maven.plugins</groupId>
					<artifactId>maven-assembly-plugin</artifactId>
					<version>2.6</version>
				</plugin>
			</plugins>
		</pluginManagement>


		<extensions>
			<extension>
				<groupId>org.apache.maven.wagon</groupId>
				<artifactId>wagon-ssh</artifactId>
				<version>3.5.3</version>
			</extension>
		</extensions>

	</build>

	<profiles>

		<!-- Note: before you can use this build profile you need to set up an
			environment that contains correctly signed keys. Configure the keystore properties
			and the profile in ~/.m2/settings.xml -->
		<profile>
			<id>codesigning</id>
			<activation>
				<activeByDefault>false</activeByDefault>
			</activation>
			<build>
				<plugins>
					<plugin>

						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-jarsigner-plugin</artifactId>
						<version>1.4</version>
						<executions>
							<execution>
								<id>sign</id>
								<goals>
									<goal>sign</goal>
								</goals>
							</execution>
						</executions>

						<configuration>

							<verbose>true</verbose>
							<certs>true</certs>
							<storetype>${keystore.type}</storetype>
							<keystore>${keystore.path}</keystore>
							<alias>${keystore.alias}</alias>
							<storepass>${keystore.store.password}</storepass>
							<keypass>${keystore.key.password}</keypass>
							<signedjar>${project.build.directory}/${project.build.finalName}.jar</signedjar>
							<verify>true</verify>
							<verbose>true</verbose>
							<goal>sign</goal>
							<arguments>
								<argument>-tsa</argument>
								<argument>https://timestamp.geotrust.com/tsa</argument>
							</arguments>
						</configuration>
					</plugin>
				</plugins>
			</build>
		</profile>
	</profiles>

	<modules>
		<module>symmetry-core</module>
		<module>symmetry-tools</module>
	</modules>

</project>