<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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>

  <groupId>de.jstacs</groupId>
  <artifactId>jstacs-core</artifactId>
  <version>2.5.0</version>
  <packaging>jar</packaging>

  <name>Jstacs Core</name>
  <description>A library for statistical analysis of biological sequences.</description>
  <url>https://jstacs.de</url>

  <licenses>
    <license>
      <name>GNU General Public License, version 3 or later (GPL-3.0-or-later)</name>
      <url>https://www.gnu.org/licenses/gpl-3.0-standalone.html</url>
    </license>
  </licenses>

  <developers>
    <developer>
      <id>jgraux</id>
      <name>Jan Grau</name>
      <email>grau@informatik.uni-halle.de</email>
      <organization>Martin-Luther-Universität Halle-Wittenberg</organization>
      <organizationUrl>https://www.informatik.uni-halle.de</organizationUrl>
    </developer>
    <developer>
      <id>JensKeilwangen</id>
      <name>Jens Keilwangen</name>
      <organization>Julius Kühn-Institut</organization>
      <organizationUrl>https://www.julius-kuehn.de</organizationUrl>
    </developer>
    <developer>
      <id>aerkes</id>
      <name>Annett Erkes</name>
      <organization>Martin-Luther-Universität Halle-Wittenberg</organization>
      <organizationUrl>https://www.informatik.uni-halle.de</organizationUrl>
    </developer>
    <developer>
      <id>lemora</id>
      <name>Lea Morschel</name>
      <organization>Martin-Luther-Universität Halle-Wittenberg</organization>
      <organizationUrl>https://www.informatik.uni-halle.de</organizationUrl>
    </developer>
  </developers>

  <scm>
    <connection>scm:git:https://github.com/jstacs/jstacs-core.git</connection>
    <developerConnection>scm:git:ssh://git@github.com/jstacs/jstacs-core.git</developerConnection>
    <url>https://github.com/jstacs/jstacs-core</url>
    <tag>v2.5.0</tag>
  </scm>

  <properties>
    <maven.compiler.release>17</maven.compiler.release>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <maven.javadoc.skip>true</maven.javadoc.skip>
  </properties>

  <dependencies>
    <dependency>
      <groupId>gov.nist.math</groupId>
      <artifactId>jama</artifactId>
      <version>1.0.3</version>
    </dependency>
    <dependency>
      <groupId>org.rosuda.REngine</groupId>
      <artifactId>REngine</artifactId>
      <version>2.1.0</version>
    </dependency>
    <dependency>
      <groupId>org.rosuda.REngine</groupId>
      <artifactId>Rserve</artifactId>
      <version>1.8.1</version>
    </dependency>
    <dependency>
      <groupId>org.apache.commons</groupId>
      <artifactId>commons-math3</artifactId>
      <version>3.6.1</version>
    </dependency>
    <dependency>
      <groupId>org.apache.xmlgraphics</groupId>
      <artifactId>xmlgraphics-commons</artifactId>
      <version>2.9</version>
    </dependency>
    <dependency>
      <groupId>xml-apis</groupId>
      <artifactId>xml-apis</artifactId>
      <version>1.4.01</version>
    </dependency>
    <dependency>
      <groupId>org.apache.xmlgraphics</groupId>
      <artifactId>batik-all</artifactId>
      <version>1.17</version>
    </dependency>
    <dependency>
      <groupId>org.apache.xmlgraphics</groupId>
      <artifactId>fop-core</artifactId>
      <version>2.10</version>
    </dependency>
    <dependency>
      <groupId>ca.umontreal.iro.simul</groupId>
      <artifactId>ssj</artifactId>
      <version>3.3.2</version>
    </dependency>
    <dependency>
      <groupId>org.biojava</groupId>
      <artifactId>core</artifactId>
      <version>1.9.7</version>
    </dependency>
    <dependency>
      <groupId>org.junit.jupiter</groupId>
      <artifactId>junit-jupiter</artifactId>
      <version>5.10.2</version>
      <scope>test</scope>
    </dependency>
  </dependencies>

  <profiles>
    <profile>
      <id>release</id>
      <properties>
        <maven.javadoc.skip>false</maven.javadoc.skip>
      </properties>
      <build>
        <plugins>
          <plugin>
            <groupId>org.sonatype.central</groupId>
            <artifactId>central-publishing-maven-plugin</artifactId>
            <version>0.9.0</version>
            <extensions>true</extensions>
            <configuration>
              <publishingServerId>central</publishingServerId>
              <tokenAuth>true</tokenAuth>
              <autoPublish>true</autoPublish>
            </configuration>
          </plugin>
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
            <version>3.3.1</version>
            <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-gpg-plugin</artifactId>
            <version>3.2.8</version>
            <executions>
              <execution>
                <id>sign-artifacts</id>
                <phase>verify</phase>
                <goals>
                  <goal>sign</goal>
                </goals>
              </execution>
            </executions>
            <configuration>
              <gpgArguments>
                <arg>--pinentry-mode</arg>
                <arg>loopback</arg>
              </gpgArguments>
            </configuration>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>

  <build>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>3.11.0</version>
        <configuration>
          <encoding>${project.build.sourceEncoding}</encoding>
          <release>${maven.compiler.release}</release>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-jar-plugin</artifactId>
        <version>3.4.1</version>
        <configuration>
          <archive>
            <manifest>
              <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
              <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
            </manifest>
          </archive>
        </configuration>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>3.2.5</version>
      </plugin>
      <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>3.11.2</version>
          <configuration>
            <doclint>none</doclint>
            <additionalOptions>
              <additionalOption>--allow-script-in-comments</additionalOption>
              <additionalOption>-header</additionalOption>
              <additionalOption>'&lt;script type="text/javascript" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"&gt;&lt;/script&gt;'</additionalOption>
            </additionalOptions>
          </configuration>
          <executions>
            <execution>
              <id>attach-javadocs</id>
              <goals>
                <goal>jar</goal>
              </goals>
            </execution>
          </executions>
      </plugin>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-release-plugin</artifactId>
        <version>3.1.1</version>
        <configuration>
          <preparationProfiles>release</preparationProfiles>
          <releaseProfiles>release</releaseProfiles>
          <preparationGoals>clean verify</preparationGoals>
        </configuration>
      </plugin>
    </plugins>
  </build>
</project>
