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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>org.openscience.cdk</groupId>
<artifactId>cdk</artifactId>
<name>cdk</name>
<description>Modular library for Cheminformatics</description>
<version>2.2-SNAPSHOT</version>
<packaging>pom</packaging>
<url>http://sourceforge.net/projects/cdk/</url>
<modules>
<module>bundle</module>
<module>base</module>
<module>descriptor</module>
<module>display</module>
<module>misc</module>
<module>storage</module>
<module>tool</module>
<module>legacy</module>
<module>app</module>
</modules>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
</properties>
<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>
<url>https://github.com/cdk/cdk</url>
<connection>scm:git:git://github.com/cdk/cdk.git</connection>
<developerConnection>scm:git:git@github.com:cdk/cdk.git
</developerConnection>
</scm>
<issueManagement>
<url>http://sourceforge.net/p/cdk/bugs/</url>
<system>SourceForge Tracker</system>
</issueManagement>
<!-- define the cdk.repo.url and cdk.repo.snapshots.url properties in
~/.m2/settings.xml -->
<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>
<!-- site is staged and then copied to a sub-folder of gh-pages, no
url is provided but the field is needed to stage the site. -->
<site>
<id>cdk.github.com</id>
<url>http://cdk.github.io/cdk/</url>
</site>
</distributionManagement>
<repositories>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</repository>
</repositories>
<prerequisites>
<maven>3.0</maven>
</prerequisites>
<!-- developer = commit access -->
<developers>
<developer>
<name>Christoph Steinbeck</name>
</developer>
<developer>
<name>Egon Willighagen</name>
<email>egonw@users.sf.net</email>
<url>http://chem-bla-ics.blogspot.com</url>
</developer>
<developer>
<name>Rajarshi Guha</name>
</developer>
<developer>
<name>Miguel Rojas Cherto</name>
</developer>
<developer>
<name>John Mayfield</name>
<email>john@nextmovesoftware.com</email>
<url>http://www.github.com/johnmay/</url>
<timezone>GMT</timezone>
</developer>
</developers>
<contributors>
<contributor>
<name>Sam Adams</name>
</contributor>
<contributor>
<name>Jonathan Alvarsson</name>
</contributor>
<contributor>
<name>Rich Apodaca</name>
</contributor>
<contributor>
<name>Saravanaraj N Ayyampalayam</name>
</contributor>
<contributor>
<name>Ulrich Bauer</name>
</contributor>
<contributor>
<name>Stephan Beisken</name>
</contributor>
<contributor>
<name>Arvid Berg</name>
</contributor>
<contributor>
<name>Lyle D. Burgoon</name>
</contributor>
<contributor>
<name>Ed Cannon</name>
</contributor>
<contributor>
<name>Alex Clark</name>
</contributor>
<contributor>
<name>Fabian Dortu</name>
</contributor>
<contributor>
<name>Krishna Dole</name>
</contributor>
<contributor>
<name>Kai Dührkop</name>
</contributor>
<contributor>
<name>Martin Eklund</name>
</contributor>
<contributor>
<name>Luis de Figueiredo</name>
</contributor>
<contributor>
<name>Matteo Floris</name>
</contributor>
<contributor>
<name>Sambit Gaan</name>
</contributor>
<contributor>
<name>Jakub Galgonek</name>
</contributor>
<contributor>
<name>Dan Gezelter</name>
</contributor>
<contributor>
<name>Uli Fechner</name>
</contributor>
<contributor>
<name>Thorsten Flügel</name>
</contributor>
<contributor>
<name>Nimish Gopal</name>
</contributor>
<contributor>
<name>Saulius Gražulis</name>
</contributor>
<contributor>
<name>Yonquan Han</name>
</contributor>
<contributor>
<name>Thierry Hanser</name>
</contributor>
<contributor>
<name>Kai Hartmann</name>
</contributor>
<contributor>
<name>Cyrus Harmon</name>
</contributor>
<contributor>
<name>Tobias Helmus</name>
</contributor>
<contributor>
<name>Christian Hoppe</name>
</contributor>
<contributor>
<name>Oliver Horlacher</name>
</contributor>
<contributor>
<name>Miguel Howard</name>
</contributor>
<contributor>
<name>Andy Howlett</name>
</contributor>
<contributor>
<name>Nina Jeliazkova</name>
</contributor>
<contributor>
<name>Geert Josten</name>
</contributor>
<contributor>
<name>Klas Jönsson</name>
</contributor>
<contributor>
<name>Dmitry Katsubo</name>
</contributor>
<contributor>
<name>Jules Kerssemakers</name>
</contributor>
<contributor>
<name>Joos Kiener</name>
</contributor>
<contributor>
<name>Anatoli Krassavine</name>
</contributor>
<contributor>
<name>Stefan Kuhn</name>
</contributor>
<contributor>
<name>Uli Köhler</name>
</contributor>
<contributor>
<name>Violeta Labarta</name>
</contributor>
<contributor>
<name>Jonty Lawson</name>
</contributor>
<contributor>
<name>Kevin Lawson</name>
</contributor>
<contributor>
<name>Daniel Leidert</name>
</contributor>
<contributor>
<name>Katrin Leinweber</name>
</contributor>
<contributor>
<name>Edgar Luttmann</name>
</contributor>
<contributor>
<name>Todd Martin</name>
</contributor>
<contributor>
<name>Nathanaël Mazuir</name>
</contributor>
<contributor>
<name>Stephan Michels</name>
</contributor>
<contributor>
<name>Hirotomo Moriwaki</name>
</contributor>
<contributor>
<name>Scooter Morris</name>
</contributor>
<contributor>
<name>Peter Murray-Rust</name>
</contributor>
<contributor>
<name>Carl Mäsak</name>
</contributor>
<contributor>
<name>Irilenia Nobeli</name>
</contributor>
<contributor>
<name>Noel O'Boyle</name>
</contributor>
<contributor>
<name>Peter Odéus</name>
</contributor>
<contributor>
<name>Niels Out</name>
</contributor>
<contributor>
<name>Jerome Pansanel</name>
</contributor>
<contributor>
<name>Julio Peironcely</name>
</contributor>
<contributor>
<name>Diego Pedrosa</name>
</contributor>
<contributor>
<name>Tomáš Pluskal</name>
</contributor>
<contributor>
<name>Chris Pudney</name>
</contributor>
<contributor>
<name>Syed Asad Rahman</name>
</contributor>
<contributor>
<name>Jonathan Rienstra-Kiracofe</name>
</contributor>
<contributor>
<name>Mark Rijnbeek</name>
</contributor>
<contributor>
<name>David Robinson</name>
</contributor>
<contributor>
<name>Bhupinder Sandhu</name>
</contributor>
<contributor>
<name>Jean-Sebastien Senecal</name>
</contributor>
<contributor>
<name>Onkar Shinde</name>
</contributor>
<contributor>
<name>Sulev Sild</name>
</contributor>
<contributor>
<name>Bradley Smith</name>
</contributor>
<contributor>
<name>Ola Spjuth</name>
</contributor>
<contributor>
<name>Christoph Steinbeck</name>
</contributor>
<contributor>
<name>Ralf Stephan</name>
</contributor>
<contributor>
<name>Daniel Szisz</name>
</contributor>
<contributor>
<name>Aleksey Tarkhov</name>
</contributor>
<contributor>
<name>Stephan Tomkinson</name>
</contributor>
<contributor>
<name>Gilleain Torrance</name>
</contributor>
<contributor>
<name>Andreas Truszkowski</name>
</contributor>
<contributor>
<name>Paul Turner</name>
</contributor>
<contributor>
<name>Kazuya Ujihara</name>
</contributor>
<contributor>
<name>Mark B Vine</name>
</contributor>
<contributor>
<name>Joerg Wegner</name>
</contributor>
<contributor>
<name>Yap Chun Wei</name>
</contributor>
<contributor>
<name>Stephane Werner</name>
</contributor>
<contributor>
<name>Mark Williamson</name>
</contributor>
<contributor>
<name>Lars Willighagen</name>
</contributor>
<contributor>
<name>Yong Zhang</name>
</contributor>
<contributor>
<name>Daniel Zaharevitz</name>
</contributor>
</contributors>
<!-- Plugin repository (EBI) is required for cdk-build-utils and
ojdcheck to build the javadoc. -->
<pluginRepositories>
<pluginRepository>
<id>ebi-repo</id>
<name>EBI Maven Repository</name>
<url>
http://www.ebi.ac.uk/~maven/m2repo
</url>
<releases>
<enabled>true</enabled>
<updatePolicy>never</updatePolicy>
</releases>
<snapshots>
<enabled>false</enabled>
</snapshots>
</pluginRepository>
</pluginRepositories>
<!-- centralised versions for common dependencies -->
<dependencyManagement>
<dependencies>
<dependency>
<groupId>uk.ac.ebi.beam</groupId>
<artifactId>beam-core</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>uk.ac.ebi.beam</groupId>
<artifactId>beam-func</artifactId>
<version>1.1</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>17.0</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
</dependency>
<dependency>
<groupId>javax.vecmath</groupId>
<artifactId>vecmath</artifactId>
<version>1.5.2</version>
</dependency>
<dependency>
<groupId>gov.nist.math</groupId>
<artifactId>jama</artifactId>
<version>1.0.3</version>
</dependency>
<dependency>
<groupId>net.sf.jni-inchi</groupId>
<artifactId>jni-inchi</artifactId>
<version>0.8</version>
</dependency>
</dependencies>
</dependencyManagement>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<configuration>
<source>1.7</source>
<target>1.7</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.20</version>
<configuration>
<!-- prevent the annoying ForkedBooter process from stealing
window focus on Mac OS -->
<argLine>-Djava.awt.headless=true</argLine>
<excludes>
<!-- not a test class -->
<exclude>**/TestMoleculeFactory.java</exclude>
<!-- missing functionality -->
<exclude>**/cdk/limitations/**</exclude>
<!-- coverage tests need updating -->
<exclude>**/*CoverageTest.java</exclude>
<!-- module suites not needed -->
<exclude>**/modulesuites/M*Tests.java</exclude>
<!-- format tests do not work (cyclic dependency) -->
<exclude>**/io/formats/*FormatTest.java</exclude>
</excludes>
<excludedGroups>org.openscience.cdk.SlowTest</excludedGroups>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.2</version>
<inherited>true</inherited>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9</version>
<configuration>
<tags>
<!--cdk.depends and cdk.builddepends no longer used-->
<tag>
<name>cdk.set</name>
<placement>a</placement>
<head>Belongs to the set:</head>
</tag>
<tag>
<name>cdk.keyword</name>
<placement>a</placement>
<head>Keywords:</head>
</tag>
<tag>
<name>cdk.created</name>
<placement>a</placement>
<head>Created on:</head>
</tag>
<tag>
<name>cdk.require</name>
<placement>a</placement>
<head>Requires:</head>
</tag>
<tag>
<name>cdk.todo</name>
<placement>a</placement>
<head>To do:</head>
</tag>
<tag>
<name>cdk.license</name>
<placement>a</placement>
<head>License:</head>
</tag>
</tags>
<taglets>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKCiteTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKBugTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKDictRefTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKGitTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKInChITaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKIOOptionsTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKModuleTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKThreadSafeTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKThreadNonSafeTaglet
</tagletClass>
</taglet>
</taglets>
<tagletArtifact>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-build-utils</artifactId>
<version>1.0.2.5</version>
</tagletArtifact>
<failOnError>false</failOnError>
</configuration>
<executions>
<execution>
<id>aggregate</id>
<goals>
<goal>aggregate</goal>
</goals>
<phase>site</phase>
<configuration>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>3.6</version>
<configuration>
<rulesets>
<ruleset>/pmd/custom.xml</ruleset>
</rulesets>
<excludes>
<exclude>.*/smsd/*.java</exclude>
</excludes>
<excludeRoots>
<excludeRoot>${basedir}/target/generated-sources/javacc</excludeRoot>
</excludeRoots>
</configuration>
<dependencies>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-build-utils</artifactId>
<version>1.0.2.4</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>com.googlecode.maven-java-formatter-plugin</groupId>
<artifactId>maven-java-formatter-plugin</artifactId>
<version>0.4</version>
<configuration>
<configFile>cdk-formatting-conventions.xml</configFile>
<lineEnding>LF</lineEnding>
</configuration>
<dependencies>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-build-utils</artifactId>
<version>1.0.2.3</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
<configuration>
<configLocation>checkstyle.xml</configLocation>
<linkXRef>false</linkXRef>
<logViolationsToConsole>true</logViolationsToConsole>
</configuration>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.7.1.201405082137</version>
</plugin>
</plugins>
</pluginManagement>
</build>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9</version>
<reportSets>
<reportSet>
<id>default</id>
<configuration>
<aggregate>false</aggregate>
</configuration>
<reports>
<report>javadoc</report>
</reports>
</reportSet>
</reportSets>
<configuration>
<failOnError>false</failOnError>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>3.1</version>
<configuration>
<rulesets>
<ruleset>/pmd/custom.xml</ruleset>
</rulesets>
<excludeRoots>
<excludeRoot>${basedir}/target/generated-sources/javacc</excludeRoot>
</excludeRoots>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>RELEASE</version>
</plugin>
</plugins>
</reporting>
<profiles>
<profile>
<id>slow-tests</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.16</version>
<configuration combine.self="override">
<!-- prevent the annoying ForkedBooter process from stealing
window focus on Mac OS -->
<argLine>-Djava.awt.headless=true</argLine>
<excludes>
<!-- not a test class -->
<exclude>**/TestMoleculeFactory.java</exclude>
</excludes>
<groups>org.openscience.cdk.SlowTest</groups>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>ossrh</id>
<build>
<plugins>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.3</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>1.5</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-source-plugin</artifactId>
<version>2.2.1</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>2.10.4</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
</project>