Description

<dependency>
    <groupId>io.github.compevol</groupId>
    <artifactId>beast3</artifactId>
    <version>2.8.0-beta6</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>beast3</artifactId>
    <version>2.8.0-beta6</version>
    <packaging>pom</packaging>

    <name>BEAST 3</name>
    <description>Bayesian Evolutionary Analysis Sampling Trees</description>
    <url>https://github.com/CompEvol/beast3</url>

    <licenses>
        <license>
            <name>GNU Lesser General Public License v2.1</name>
            <url>https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html</url>
            <distribution>repo</distribution>
        </license>
    </licenses>

    <developers>
        <developer>
            <id>alexeid</id>
            <name>Alexei Drummond</name>
            <url>https://github.com/alexeid</url>
        </developer>
    </developers>

    <scm>
        <connection>scm:git:https://github.com/CompEvol/beast3.git</connection>
        <developerConnection>scm:git:ssh://git@github.com/CompEvol/beast3.git</developerConnection>
        <url>https://github.com/CompEvol/beast3</url>
    </scm>

    <distributionManagement>
        <repository>
            <id>github</id>
            <url>https://maven.pkg.github.com/CompEvol/beast3</url>
        </repository>
    </distributionManagement>

    <modules>
        <module>beast-pkgmgmt</module>
        <module>beast-base</module>
        <module>beast-fx</module>
    </modules>

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

        <javafx.version>25.0.2</javafx.version>
        <commons-math4-legacy.version>4.0-beta1</commons-math4-legacy.version>
        <antlr4.version>4.13.2</antlr4.version>
        <commons-numbers.version>1.2</commons-numbers.version>
        <commons-rng.version>1.6</commons-rng.version>
        <commons-statistics.version>1.2</commons-statistics.version>
        <junit.version>5.8.2</junit.version>
        <junit4.version>4.13.2</junit4.version>
        <testfx.version>4.0.18</testfx.version>
        <assertj.version>3.20.2</assertj.version>
        <maven-resolver.version>2.0.16</maven-resolver.version>
        <slf4j.version>2.0.16</slf4j.version>
        <beagle.version>1.0.0</beagle.version>
        <surefire.excludedGroups>slow</surefire.excludedGroups>
    </properties>

    <dependencyManagement>
        <dependencies>
            <!-- Internal modules -->
            <dependency>
                <groupId>io.github.compevol</groupId>
                <artifactId>beast-pkgmgmt</artifactId>
                <version>${project.version}</version>
            </dependency>
            <dependency>
                <groupId>io.github.compevol</groupId>
                <artifactId>beast-base</artifactId>
                <version>${project.version}</version>
            </dependency>

            <!-- BEAGLE -->
            <dependency>
                <groupId>io.github.beagle-dev</groupId>
                <artifactId>beagle</artifactId>
                <version>${beagle.version}</version>
            </dependency>

            <!-- Commons Math 4 -->
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-math4-legacy</artifactId>
                <version>${commons-math4-legacy.version}</version>
            </dependency>

            <!-- ANTLR Runtime -->
            <dependency>
                <groupId>org.antlr</groupId>
                <artifactId>antlr4-runtime</artifactId>
                <version>${antlr4.version}</version>
            </dependency>

            <!-- Commons Numbers -->
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-numbers-gamma</artifactId>
                <version>${commons-numbers.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-numbers-core</artifactId>
                <version>${commons-numbers.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-numbers-combinatorics</artifactId>
                <version>${commons-numbers.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-numbers-rootfinder</artifactId>
                <version>${commons-numbers.version}</version>
            </dependency>

            <!-- Commons RNG -->
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-rng-simple</artifactId>
                <version>${commons-rng.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-rng-sampling</artifactId>
                <version>${commons-rng.version}</version>
            </dependency>

            <!-- Commons Statistics -->
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-statistics-distribution</artifactId>
                <version>${commons-statistics.version}</version>
            </dependency>

            <!-- Maven Resolver -->
            <dependency>
                <groupId>org.apache.maven.resolver</groupId>
                <artifactId>maven-resolver-supplier-mvn4</artifactId>
                <version>${maven-resolver.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-nop</artifactId>
                <version>${slf4j.version}</version>
            </dependency>

            <!-- JavaFX -->
            <dependency>
                <groupId>org.openjfx</groupId>
                <artifactId>javafx-controls</artifactId>
                <version>${javafx.version}</version>
            </dependency>
            <dependency>
                <groupId>org.openjfx</groupId>
                <artifactId>javafx-fxml</artifactId>
                <version>${javafx.version}</version>
            </dependency>
            <dependency>
                <groupId>org.openjfx</groupId>
                <artifactId>javafx-swing</artifactId>
                <version>${javafx.version}</version>
            </dependency>
            <dependency>
                <groupId>org.openjfx</groupId>
                <artifactId>javafx-web</artifactId>
                <version>${javafx.version}</version>
            </dependency>

            <!-- Testing -->
            <dependency>
                <groupId>org.junit.jupiter</groupId>
                <artifactId>junit-jupiter</artifactId>
                <version>${junit.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>junit</groupId>
                <artifactId>junit</artifactId>
                <version>${junit4.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.testfx</groupId>
                <artifactId>testfx-core</artifactId>
                <version>${testfx.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.testfx</groupId>
                <artifactId>testfx-junit5</artifactId>
                <version>${testfx.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.assertj</groupId>
                <artifactId>assertj-core</artifactId>
                <version>${assertj.version}</version>
                <scope>test</scope>
            </dependency>
            <dependency>
                <groupId>org.testfx</groupId>
                <artifactId>openjfx-monocle</artifactId>
                <version>21.0.2</version>
                <scope>test</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>

    <build>
        <pluginManagement>
            <plugins>
                <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>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-surefire-plugin</artifactId>
                    <version>3.5.2</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-dependency-plugin</artifactId>
                    <version>3.6.1</version>
                </plugin>
                <!--
                    Tell Eclipse m2e to ignore copy-dependencies during
                    incremental builds. The goal is bound to the package
                    phase and requires packaged artifacts, which don't
                    exist during Eclipse's compile-time builds (MDEP-187).
                -->
                <plugin>
                    <groupId>org.eclipse.m2e</groupId>
                    <artifactId>lifecycle-mapping</artifactId>
                    <version>1.0.0</version>
                    <configuration>
                        <lifecycleMappingMetadata>
                            <pluginExecutions>
                                <pluginExecution>
                                    <pluginExecutionFilter>
                                        <groupId>org.apache.maven.plugins</groupId>
                                        <artifactId>maven-dependency-plugin</artifactId>
                                        <versionRange>[3.0,)</versionRange>
                                        <goals>
                                            <goal>copy-dependencies</goal>
                                        </goals>
                                    </pluginExecutionFilter>
                                    <action><ignore/></action>
                                </pluginExecution>
                            </pluginExecutions>
                        </lifecycleMappingMetadata>
                    </configuration>
                </plugin>
            </plugins>
        </pluginManagement>
        <plugins>
            <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>
            <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>
        </plugins>
    </build>

    <profiles>
        <profile>
            <id>slow-tests</id>
            <properties>
                <surefire.excludedGroups/>
            </properties>
        </profile>
        <profile>
            <id>release</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <version>3.2.7</version>
                        <configuration>
                            <gpgArguments>
                                <arg>--pinentry-mode</arg>
                                <arg>loopback</arg>
                            </gpgArguments>
                        </configuration>
                        <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>