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pom.xml
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pom.xml
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<?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>uk.ac.ebi.rdt</groupId>
<artifactId>rdt</artifactId>
<description>Reaction Decoder Tool</description>
<version>2.5.0-SNAPSHOT</version>
<packaging>jar</packaging>
<properties>
<jdk.version>11</jdk.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
</properties>
<scm>
<connection>scm:git:git://github.com/asad/ReactionDecoder.git</connection>
<developerConnection>scm:git:git@github.com:asad/ReactionDecoder.git
</developerConnection>
<url>https://github.com/asad/ReactionDecoder.git</url>
<tag>HEAD</tag>
</scm>
<issueManagement>
<url>https://github.com/asad/ReactionDecoder/issues</url>
<system>GitHub Issues</system>
</issueManagement>
<!-- <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> -->
<distributionManagement>
<repository>
<id>github</id>
<name>GitHub Packages</name>
<url>https://maven.pkg.github.com/asad/ReactionDecoder</url>
</repository>
</distributionManagement>
<licenses>
<license>
<name>GNU General Lesser Public License (LGPL) version 3.0</name>
<url>https://www.gnu.org/licenses/lgpl-3.0.en.html</url>
</license>
</licenses>
<prerequisites>
<maven>3.0</maven>
</prerequisites>
<developers>
<developer>
<name>Syed Asad Rahman</name>
<email>s9asad@gmail.com</email>
<url>https://github.com/asad</url>
</developer>
<developer>
<name>Gilliean Torrance</name>
</developer>
<developer>
<name>Lorenzo Baldacci</name>
</developer>
<developer>
<name>Franz Fenninger</name>
</developer>
<developer>
<name>Nimish Gopal</name>
</developer>
<developer>
<name>John May</name>
</developer>
</developers>
<contributors>
<contributor>
<name>Sergio Martínez Cuesta</name>
</contributor>
<contributor>
<name>Gemma L. Holliday</name>
</contributor>
<contributor>
<name>Saket Choudhary</name>
</contributor>
<contributor>
<name>Christoph Steinbeck</name>
</contributor>
<contributor>
<name>Janet M. Thornton</name>
</contributor>
</contributors>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.13.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
<version>1.4.0</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-bundle</artifactId>
<version>2.4-SNAPSHOT</version>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>org.apache.directory.studio</groupId>
<artifactId>org.apache.commons.io</artifactId>
<version>2.4</version>
</dependency>
</dependencies>
<profiles>
<profile>
<id>local</id>
<build>
<plugins>
<!-- download source code in Eclipse, best practice -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.10</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>false</downloadJavadocs>
</configuration>
</plugin>
<!-- Set a compiler level -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<!-- Maven Assembly Plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.3.0</version>
<configuration>
<!-- get all project dependencies -->
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<!-- MainClass in mainfest make a executable jar -->
<archive>
<manifest>
<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<!-- bind to the packaging phase -->
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>ossrh</id>
<build>
<plugins>
<!-- download source code in Eclipse, best practice -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.10</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>false</downloadJavadocs>
</configuration>
</plugin>
<!-- Set a compiler level -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
<!-- Maven Assembly Plugin -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.3.0</version>
<configuration>
<!-- get all project dependencies -->
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<!-- MainClass in mainfest make a executable jar -->
<archive>
<manifest>
<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<!-- bind to the packaging phase -->
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>uk.ac.ebi.aamtool.ReactionDecoder</mainClass>
</manifest>
</archive>
</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>
<!--phase>deploy</phase-->
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<!-- explicitly define maven-deploy-plugin after other to force exec order -->
<artifactId>maven-deploy-plugin</artifactId>
<executions>
<execution>
<id>deploy</id>
<phase>deploy</phase>
<goals>
<goal>deploy</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-javadoc-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<id>attach-javadocs</id>
<!--phase>deploy</phase-->
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</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>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.2</version>
<configuration>
<excludes>
<!-- skip test class -->
<exclude>**/MCSTest.java</exclude>
<exclude>**/ComplexCases.java</exclude>
<exclude>**/RXNMappingTest.java</exclude>
</excludes>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>disable-java8-doclint</id>
<activation>
<jdk>[1.8,)</jdk>
</activation>
<properties>
<!--<additionalparam>-Xdoclint:none</additionalparam>-->
<doclint>none</doclint>
</properties>
</profile>
</profiles>
<name>ReactionDecoderTool</name>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<showDeprecation>true</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>