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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!--
* This file is part of Simulation Core Library, a Java-based library
* for efficient numerical simulation of biological models.
*
* Copyright (C) 2007-2022 jointly by the following organizations:
* 1. University of Tuebingen, Germany
* 2. Keio University, Japan
* 3. Harvard University, USA
* 4. The University of Edinburgh, UK
* 5. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 6. The University of California, San Diego, La Jolla, CA, USA
* 7. The Babraham Institute, Cambridge, UK
* 8. Duke University, Durham, NC, US
*
* This library is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation. A copy of the license
* agreement is provided in the file named "LICENSE.txt" included with
* this software distribution and also available online as
* <http://www.gnu.org/licenses/lgpl-3.0-standalone.html>.
-->
<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.draegerlab</groupId>
<artifactId>sbscl</artifactId>
<!-- Output to jar format -->
<packaging>jar</packaging>
<!--
Hints for deployment:
mvn clean verify source:jar source:jar-no-fork javadoc:jar install:install gpg:sign deploy:deploy release:clean release:prepare release:perform deploy
Optionally also add: -Dmaven.test.skip=true
Minimal execution with: mvn deploy
mvn clean verify source:jar source:jar-no-fork javadoc:jar gpg:sign deploy -Dgpg.passphrase=<pw>
-->
<!-- =================================================================== -->
<!-- General project information -->
<!-- =================================================================== -->
<name>Systems Biology Simulation Core Library (SBSCL)</name>
<version>2.1.1</version>
<url>https://github.com/draeger-lab/SBSCL/</url>
<inceptionYear>2007</inceptionYear>
<description>
The Systems Biology Simulation Core Library provides an efficient and
exhaustive Java™ implementation of methods to interpret the content of
models encoded in the Systems Biology Markup Language (SBML) and its
numerical solution. This library is based on the JSBML project. It can be
used on every operating system for which a Java Virtual Machine is available.
Version 2.0 and beyond support simulation in three frameworks:
constraint-based analysis, stochastic simulation, and ordinary differential
equation systems. SBSCL supports SED-ML and COMBINE archives in OMEX format.
</description>
<properties>
<jdk.version>1.8</jdk.version>
<maven.build.timestamp.format>yyyy</maven.build.timestamp.format>
<year>${maven.build.timestamp}</year>
<!-- This property is used for filtering the variable ${year} in some resource
files -->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.license.url>https://www.gnu.org/licenses/lgpl-3.0-standalone.html</project.license.url>
<junit.version>4.13.1</junit.version>
<javadoc.version>3.2.0</javadoc.version>
<site.path>https://draeger-lab.github.io/SBSCL/docs/</site.path>
</properties>
<issueManagement>
<system>GitHub Issues</system>
<url>${project.url}/issues</url>
</issueManagement>
<distributionManagement>
<site>
<id>SBSCL</id>
<url>https://draeger-lab.github.io/SBSCL</url>
</site>
<downloadUrl>${project.url}</downloadUrl>
<repository>
<uniqueVersion>false</uniqueVersion>
<id>ossrh</id>
<name>Releases</name>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
<layout>default</layout>
</repository>
<snapshotRepository>
<uniqueVersion>true</uniqueVersion>
<id>ossrh</id>
<name>Snapshots</name>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
<layout>default</layout>
</snapshotRepository>
</distributionManagement>
<ciManagement>
<system>Travis CI</system>
<url>https://travis-ci.com/github/draeger-lab/SBSCL</url>
</ciManagement>
<licenses>
<license>
<name>GNU Lesser General Public License</name>
<url>${project.license.url}</url>
<distribution>repo</distribution>
</license>
</licenses>
<!-- =================================================================== -->
<!-- Source Control Management -->
<!-- =================================================================== -->
<scm>
<connection>scm:git:git://github.com/draeger-lab/SBSCL.git</connection>
<developerConnection>scm:git:ssh://github.com/draeger-lab/SBSCL.git</developerConnection>
<url>https://github.com/draeger-lab/SBSCL/tree/master/</url> <!-- Expanding ${project.url} does not work in Maven Central -->
</scm>
<!-- =================================================================== -->
<!-- The team of developers and contributors -->
<!-- =================================================================== -->
<developers>
<developer>
<name>Richard Adams</name>
<id>otter606</id>
<email>[email protected]</email>
<url>https://github.com/otter606</url>
<roles>
<role>developer</role>
</roles>
</developer>
<developer>
<name>Alexander Dörr</name>
<email>[email protected]</email>
<url>http://www.cogsys.cs.uni-tuebingen.de/mitarb/doerr/</url>
<timezone>Europe/Berlin</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
http://www.cogsys.cs.uni-tuebingen.de/mitarb/doerr/portrait.jpg
</picUrl>
</properties>
</developer>
<developer>
<name>Andreas Dräger</name>
<id>draeger</id>
<email>[email protected]</email>
<url>https://github.com/draeger</url>
<organization>University of Tübingen</organization>
<organizationUrl>https://uni-tuebingen.de/en/127116</organizationUrl>
<roles>
<role>architect</role>
<role>developer</role>
</roles>
<timezone>Europe/Berlin</timezone>
<properties>
<picUrl>
https://publons.com/media/thumbs/academic/photos/dd5f988fb8ee4bc8a8cbecbb7b71c58e.jpg.200x200_q95_crop_detail_upscale.jpg
</picUrl>
</properties>
</developer>
<developer>
<name>Akira Funahashi</name>
<id>funasoul</id>
<email>[email protected]</email>
<url>http://fun.bio.keio.ac.jp/people/</url>
<organization>Keio University</organization>
<timezone>Japan/Tokyo</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
https://groups.oist.jp/sites/default/files/styles/group_image/public/eventimg/1611/funahashi-sensei_0.jpeg
</picUrl>
</properties>
</developer>
<developer>
<name>Roland Keller</name>
<id>RolandKeller5</id>
<email>http://www.cogsys.cs.uni-tuebingen.de/mitarb/keller/</email>
<url>[email protected]</url>
<timezone>Europe/Berlin</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
http://www.cogsys.cs.uni-tuebingen.de/mitarb/keller/portrait.jpg
</picUrl>
</properties>
</developer>
<developer>
<name>Matthias König</name>
<id>matthiaskoenig</id>
<email>[email protected]</email>
<url>https://github.com/matthiaskoenig</url>
<organization>Humboldt University</organization>
<timezone>Europe/Berlin</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
https://seek.lisym.org/assets/avatar-images/134-120x120.png
</picUrl>
</properties>
</developer>
<developer>
<name>Hannes Planatscher</name>
<id>planatscher</id>
<email>[email protected]</email>
<url>https://github.com/planatscher</url>
<timezone>Europe/Berlin</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
http://www.ra.cs.uni-tuebingen.de/mitarb/planatsc/img/PlanatscherHannes_small.png
</picUrl>
</properties>
</developer>
<developer>
<name>Nicolas Rodriguez</name>
<id>niko-rodrigue</id>
<email>[email protected]</email>
<url>https://github.com/niko-rodrigue</url>
<organization>The Babraham Institute</organization>
<timezone>UK/London</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
https://www.lenoverelab.org/sites/default/files/pictures/Nicolas_Rodriguez-170x150.jpg
</picUrl>
</properties>
</developer>
<developer>
<name>Shalin Shah</name>
<id>shalinshah1993</id>
<email>[email protected]</email>
<url>https://github.com/shalinshah1993</url>
<organization>Duke University</organization>
<timezone>US/EST</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>
https://uni-tuebingen.de/fileadmin/_processed_/3/d/csm_Shalin_Shah_85b583dd09.png
</picUrl>
</properties>
</developer>
<developer>
<name>Hemil Panchiwala</name>
<id>hemilpanchiwala</id>
<email>[email protected]</email>
<url>https://github.com/hemilpanchiwala</url>
<organization>Indian Institute of Technology, Roorkee</organization>
<timezone>India/IST</timezone>
<roles>
<role>developer</role>
</roles>
<properties>
<picUrl>https://avatars1.githubusercontent.com/u/42446679?s=60&u=b37bc60ef87d9b485be04913305c1903f9e77f92&v=4</picUrl>
</properties>
</developer>
<developer>
<name>Akito Tabira</name>
<id>mythosil</id>
<email>[email protected]</email>
<url>https://github.com/mythosil</url>
<organization>Keio University</organization>
<timezone>Japan/Tokyo</timezone>
<roles>
<role>developer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>Leonhard Markert</name>
<url>https://github.com/curiousleo</url>
</contributor>
<contributor>
<name>Max Zwießele</name>
<url>https://github.com/mzwiessele</url>
</contributor>
<contributor>
<name>Nicolas Le Novère</name>
<email>[email protected]</email>
<url>http://lenoverelab.org/perso/lenov/</url>
<organization>The Babraham Institute</organization>
<timezone>UK/London</timezone>
</contributor>
<contributor>
<name>Michael T. Cooling</name>
<url>https://www.linkedin.com/in/mikecooling/</url>
<organization>University of Auckland</organization>
</contributor>
<contributor>
<name>Noriko Hiroi</name>
<email>[email protected]</email>
<url>http://fun.bio.keio.ac.jp/~hiroi/</url>
<organization>Keio University</organization>
</contributor>
<contributor>
<name>Marcel Kronfeld</name>
<url>http://www.cogsys.cs.uni-tuebingen.de/mitarb/kronfeld</url>
<organization>University of Tübingen</organization>
</contributor>
<contributor>
<name>Adrian Schröder</name>
<url>http://www.cogsys.cs.uni-tuebingen.de/mitarb/schroeder/</url>
<organization>University of Tübingen</organization>
</contributor>
<contributor>
<name>Dieudonné M. Wouamba</name>
<url>https://www.linkedin.com/in/dieudonné-motsou-wouamba-2952a018/</url>
<organization>University of Tübingen</organization>
</contributor>
<contributor>
<name>Andreas Zell</name>
<email>[email protected]</email>
<url>http://www.cogsys.cs.uni-tuebingen.de/mitarb/zell/</url>
<organization>University of Tübingen</organization>
</contributor>
<contributor>
<name>Michael J. Ziller</name>
<email>[email protected]</email>
<url>https://www.psych.mpg.de/person/47510/2176252</url>
<organization>Max Planck Institute of Psychatry</organization>
</contributor>
</contributors>
<!-- =================================================================== -->
<!-- Repositories -->
<!-- =================================================================== -->
<repositories>
<repository>
<id>in-project</id>
<name>In project repository</name>
<url>file:${project.basedir}/src/lib/maven</url>
</repository>
<repository>
<id>libs</id>
<url>file://${project.basedir}/lib</url>
</repository>
<!-- Adding repository to download latest jlibSBML -->
<repository>
<id>JSBML-SNAPSHOT</id>
<name>The JSBML Snapshot repository</name>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
<!-- Adding repository to download CombineArchive -->
<repository>
<id>sems-maven-repository-releases</id>
<name>SEMS Maven Repo</name>
<url>https://mvn.bio.informatik.uni-rostock.de/releases/</url>
<layout>default</layout>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<!-- =================================================================== -->
<!-- Dependencies -->
<!-- =================================================================== -->
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>org.sbml.jsbml</groupId>
<artifactId>jsbml</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.jdom</groupId>
<artifactId>jdom2</artifactId>
<version>2.0.5</version>
</dependency>
<dependency>
<groupId>org.jmathml</groupId>
<artifactId>jmathml</artifactId>
<version>2.1.0</version>
</dependency>
<dependency>
<groupId>org.jlibsedml</groupId>
<artifactId>jlibsedml</artifactId>
<version>2.2.3</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
<version>2.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.7</version>
</dependency>
<dependency>
<groupId>org.jfree</groupId>
<artifactId>jfreechart</artifactId>
<version>1.0.19</version>
</dependency>
<dependency>
<groupId>com.blazegraph</groupId>
<artifactId>colt</artifactId>
<version>2.1.4</version>
</dependency>
<!-- LP solvers -->
<dependency>
<groupId>scpsolver</groupId>
<artifactId>SCPSolver</artifactId>
<version>1.0v2</version>
</dependency>
<dependency>
<groupId>scpsolver</groupId>
<artifactId>GLPKSolverPack</artifactId>
<version>4.35v2</version>
</dependency>
<dependency>
<groupId>scpsolver</groupId>
<artifactId>LPSOLVESolverPack</artifactId>
<version>5.5.2.5</version>
</dependency>
<dependency>
<groupId>kisao</groupId>
<artifactId>libkisao</artifactId>
<version>1.0.3.1-rc</version>
</dependency>
<!-- OMEX archive -->
<dependency>
<groupId>de.uni-rostock.sbi</groupId>
<artifactId>CombineArchive</artifactId>
<version>1.3.6</version>
<exclusions>
<exclusion>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<!-- =================================================================== -->
<!-- Building -->
<!-- =================================================================== -->
<!-- To build the project run: -->
<!-- mvn clean compile package assembly:single -->
<build>
<!--<finalName>${project.artifactId}-${project.version}</finalName>-->
<pluginManagement>
<plugins>
<!-- Run mvn license:third-party-report to build report of licenses -->
<!-- Download license files for 3rd party libraries and put them in website code -->
<!-- at src/target/generated-sources/THIRD-PARTY.txt and src/target/site/third-party-report.html -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>license-maven-plugin</artifactId>
<version>1.16</version>
<executions>
<execution>
<id>download-licenses</id>
<goals>
<goal>download-licenses</goal>
</goals>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.apache.maven.doxia</groupId>
<artifactId>doxia-core</artifactId>
<version>1.9.1</version>
</dependency>
<dependency>
<groupId>org.apache.maven.doxia</groupId>
<artifactId>doxia-site-renderer</artifactId>
<version>1.9.2</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.9.1</version>
<configuration>
<locales>en</locales>
<pomPackagingOnly>false</pomPackagingOnly>
</configuration>
<executions>
<execution>
<id>attach-descriptor</id>
<goals>
<goal>attach-descriptor</goal>
<goal>site</goal>
</goals>
<!-- select the Maven phase in which the plugin will be executed -->
<phase>site-deploy</phase>
<configuration>
<!-- Plugin configuration ges here -->
<server>github</server>
<!-- The commit message -->
<message>Building site for my project</message>
<!-- The location where the site is uploaded -->
<path>${site.path}</path>
<!-- Use merge or override the content -->
<merge>true</merge>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.apache.maven.doxia</groupId>
<artifactId>doxia-module-markdown</artifactId>
<version>1.7</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.0.0-M5</version>
<configuration>
<forkedProcessExitTimeoutInSeconds>60</forkedProcessExitTimeoutInSeconds>
</configuration>
</plugin>
<!-- Download source code in Eclipse, best practice [OPTIONAL!] -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<downloadSources>true</downloadSources>
<downloadJavadocs>false</downloadJavadocs>
</configuration>
</plugin>
<!-- Set a JDK compiler level -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
<!-- <excludes> <exclude>**/org/simulator/fba/COBRAsolver.java</exclude>
<exclude>**/org/simulator/fba/COBRAsolverExample.java</exclude> </excludes> -->
</configuration>
</plugin>
<!-- Assemble executable JAR -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.6</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<finalName>${project.artifactId}-${project.version}</finalName>
<appendAssemblyId>false</appendAssemblyId>
<descriptor>src/assembly/assembly.xml
</descriptor> <!-- Details of the assembly are described in this file -->
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<!-- This will create a JAR with all dependencies -->
<!-- mvn clean compile package assembly:single -->
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- This plug-in copies resources from target/site to docs/ so Github can render it -->
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.7</version>
<configuration>
</configuration>
</plugin>
<!-- Plugins for Maven Central -->
<!-- Needed for uploading the distriution to Maven Central -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.0</version>
<!--<configuration>
<attach>true</attach>
</configuration>-->
<executions>
<execution>
<id>attach-sources</id>
<phase>verify</phase>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>${javadoc.version}</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
<configuration>
<!-- add this to disable checking -->
<!-- <doclint>none</doclint> -->
<!-- <doclint>syntax</doclint> -->
<!-- <doclint>html</doclint> -->
<doclint>accessibility</doclint>
<doclint>reference</doclint>
<!--
This sets the command-line option -Xdoclint:none. In addition
to 'none' there are further options available, including 'all',
'html', 'syntax', 'accessibility', and more. For further information see
https://docs.oracle.com/javase/8/docs/technotes/tools/unix/javadoc.html
-->
</configuration>
</plugin>
<!-- Needed to upload the distribution to Maven Central to sign the JAR file -->
<!-- Execute with mvn clean deploy -Dgpg.passphrase=yourpassphrase -->
<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>
<configuration>
<keyname>${gpg.keyname}</keyname>
<passphraseServerId>${gpg.keyname}</passphraseServerId>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.7</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
<!-- Execute with "mvn release:clean release:prepare" followed by "mvn release:perform" -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</version>
<configuration>
<autoVersionSubmodules>true</autoVersionSubmodules>
<useReleaseProfile>false</useReleaseProfile>
<releaseProfiles>release</releaseProfiles>
<goals>deploy</goals>
</configuration>
</plugin>
</plugins>
</pluginManagement>
<!-- Resources copied by resources plug-in. Note that mvn site needs to run before mvn install to
make sure the website code exists inside target/site folder -->
<resources>
<resource>
<directory>${project.build.directory}/site/</directory>
<targetPath>${basedir}/docs/</targetPath>
</resource>
</resources>
</build>
<!-- =================================================================== -->
<!-- Profiles -->
<!-- =================================================================== -->
<!-- To stop maven errors from javadoc warnings -->
<profiles>
<profile>
<id>java8-doclint-disabled</id>
<activation>
<jdk>[1.8,)</jdk>
</activation>
<properties>
<javadoc.opts>-Xdoclint:none</javadoc.opts>
</properties>
</profile>
</profiles>
<!-- =================================================================== -->
<!-- Reporting -->
<!-- =================================================================== -->
<!-- Generate javadoc and integrate with generated website with 'mvn site' -->
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>${javadoc.version}</version>
<reportSets>
<reportSet>
<reports>
<report>javadoc</report>
</reports>
</reportSet>
</reportSets>
<configuration>
<overview>${project.basedir}/src/main/javadoc/overview.html</overview>
<additionalOptions>${javadoc.opts}</additionalOptions>
<failOnError>false</failOnError>
<show>public</show> <!-- Display only public methods and classes -->
</configuration>
</plugin>
</plugins>
</reporting>
</project>