Description

<dependency>
    <groupId>io.github.compevol</groupId>
    <artifactId>coupled-mcmc</artifactId>
    <version>1.3.0-beta1</version>
</dependency>

<?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>io.github.compevol</groupId>
    <artifactId>coupled-mcmc</artifactId>
    <version>1.3.0-beta1</version>

    <name>CoupledMCMC</name>
    <description>Coupled MCMC (MC3) for BEAST</description>

    <url>https://github.com/CompEvol/CoupledMCMC</url>

    <licenses>
        <license>
            <name>GNU General Public License v3.0</name>
            <url>https://www.gnu.org/licenses/gpl-3.0.html</url>
        </license>
    </licenses>

    <developers>
        <developer>
            <name>Nicola F. Müller</name>
            <url>https://github.com/nicfel</url>
        </developer>
        <developer>
            <name>Remco Bouckaert</name>
            <url>https://github.com/rbouckaert</url>
        </developer>
    </developers>

    <scm>
        <connection>scm:git:git://github.com/CompEvol/CoupledMCMC.git</connection>
        <developerConnection>scm:git:ssh://github.com:CompEvol/CoupledMCMC.git</developerConnection>
        <url>https://github.com/CompEvol/CoupledMCMC</url>
    </scm>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
        <maven.compiler.release>25</maven.compiler.release>

        <beast.version>2.8.0-beta5</beast.version>
        <javafx.version>25.0.2</javafx.version>
        <junit.version>5.8.2</junit.version>

        <beast.module>beast.base</beast.module>
        <beast.main>beast.base.minimal.BeastMain</beast.main>
        <beast.args/>
        <beast.pkg.name>CoupledMCMC</beast.pkg.name>
        <beast.pkg.version>1.3.0-SNAPSHOT</beast.pkg.version>
    </properties>

    <dependencies>
        <!-- BEAST 3 core -->
        <dependency>
            <groupId>io.github.compevol</groupId>
            <artifactId>beast-base</artifactId>
            <version>${beast.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>io.github.beagle-dev</groupId>
                    <artifactId>beagle</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>io.github.compevol</groupId>
            <artifactId>beast-pkgmgmt</artifactId>
            <version>${beast.version}</version>
        </dependency>

        <!-- GUI (optional at runtime) -->
        <dependency>
            <groupId>io.github.compevol</groupId>
            <artifactId>beast-fx</artifactId>
            <version>${beast.version}</version>
            <optional>true</optional>
            <exclusions>
                <exclusion>
                    <groupId>io.github.beagle-dev</groupId>
                    <artifactId>beagle</artifactId>
                </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.openjfx</groupId>
            <artifactId>javafx-controls</artifactId>
            <version>${javafx.version}</version>
            <optional>true</optional>
        </dependency>

        <!-- Testing -->
        <dependency>
            <groupId>org.junit.jupiter</groupId>
            <artifactId>junit-jupiter</artifactId>
            <version>${junit.version}</version>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <!-- Compiler -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.15.0</version>
                <configuration>
                    <release>25</release>
                    <encoding>UTF-8</encoding>
                </configuration>
            </plugin>

            <!-- Surefire (test runner) -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>3.5.2</version>
                <configuration>
                    <workingDirectory>${project.build.testOutputDirectory}</workingDirectory>
                    <argLine>
                        --add-reads coupled.mcmc=ALL-UNNAMED
                        --add-reads beast.base=ALL-UNNAMED
                        --add-reads beast.pkgmgmt=ALL-UNNAMED
                    </argLine>
                    <systemPropertyVariables>
                        <BEAST_PACKAGE_PATH>${project.build.outputDirectory}</BEAST_PACKAGE_PATH>
                    </systemPropertyVariables>
                </configuration>
            </plugin>

            <!-- Copy version.xml to target/ for BEASTClassLoader.initServices() -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <version>3.3.1</version>
                <executions>
                    <execution>
                        <id>copy-version-xml</id>
                        <phase>generate-resources</phase>
                        <goals><goal>copy-resources</goal></goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>${project.basedir}</directory>
                                    <includes>
                                        <include>version.xml</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                    <execution>
                        <id>embed-version-xml-in-jar</id>
                        <phase>generate-resources</phase>
                        <goals><goal>copy-resources</goal></goals>
                        <configuration>
                            <outputDirectory>${project.build.outputDirectory}</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>${project.basedir}</directory>
                                    <includes>
                                        <include>version.xml</include>
                                    </includes>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Run BEAST or BEAUti with coupled-mcmc on module path:
                 mvn exec:exec -Dbeast.args="examples/mcmc.xml"
                 mvn exec:exec -Dbeast.module=beast.fx -Dbeast.main=beastfx.app.beauti.Beauti -->
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <version>3.5.0</version>
                <configuration>
                    <executable>java</executable>
                    <workingDirectory>${project.basedir}</workingDirectory>
                    <commandlineArgs>--module-path %classpath -DBEAST_PACKAGE_PATH=${project.build.outputDirectory} -m ${beast.module}/${beast.main} ${beast.args}</commandlineArgs>
                </configuration>
            </plugin>

            <!-- Source JAR (included in BEAST package ZIP as CoupledMCMC.src.jar) -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <version>3.3.1</version>
                <executions>
                    <execution>
                        <id>attach-sources</id>
                        <goals><goal>jar-no-fork</goal></goals>
                    </execution>
                </executions>
            </plugin>

            <!-- Assemble BEAST package ZIP -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>3.7.1</version>
                <configuration>
                    <descriptors>
                        <descriptor>src/assembly/beast-package.xml</descriptor>
                    </descriptors>
                    <finalName>${beast.pkg.name}.v${beast.pkg.version}</finalName>
                    <appendAssemblyId>false</appendAssemblyId>
                </configuration>
                <executions>
                    <execution>
                        <id>beast-package</id>
                        <phase>package</phase>
                        <goals><goal>single</goal></goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <profiles>
        <profile>
            <id>release</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-javadoc-plugin</artifactId>
                        <version>3.11.2</version>
                        <configuration>
                            <doclint>none</doclint>
                        </configuration>
                        <executions>
                            <execution>
                                <id>attach-javadocs</id>
                                <goals><goal>jar</goal></goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <version>3.2.7</version>
                        <executions>
                            <execution>
                                <id>sign-artifacts</id>
                                <phase>verify</phase>
                                <goals><goal>sign</goal></goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.sonatype.central</groupId>
                        <artifactId>central-publishing-maven-plugin</artifactId>
                        <version>0.6.0</version>
                        <extensions>true</extensions>
                        <configuration>
                            <publishingServerId>central</publishingServerId>
                            <autoPublish>true</autoPublish>
                            <waitUntil>published</waitUntil>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>
</project>