pom.xml

<?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.pathvisio</groupId>
    <artifactId>githubplugin</artifactId>
    <version>1.0.2-SNAPSHOT</version>
    <packaging>jar</packaging>

    <name>PathVisio GitHub Integration Plugin</name>
    <description>
        Direct GitHub integration plugin for PathVisio that enables
        biologists to submit and update biological pathways to the
        WikiPathways GitHub repository directly from PathVisio.
    </description>

    <properties>
        <maven.compiler.source>11</maven.compiler.source>
        <maven.compiler.target>11</maven.compiler.target>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

        <junit.version>5.10.0</junit.version>
        <mockito.version>5.3.1</mockito.version>
        <maven.surefire.version>3.1.2</maven.surefire.version>
        <maven.compiler.version>3.11.0</maven.compiler.version>
        <maven.jar.version>3.3.0</maven.jar.version>
    </properties> 

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

    <dependency>
        <groupId>org.pathvisio</groupId>
        <artifactId>org.pathvisio.desktop</artifactId>
        <version>4.0.0-local</version>
    </dependency>

    <dependency>
        <groupId>org.pathvisio</groupId>
        <artifactId>org.pathvisio.core</artifactId>
        <version>4.0.0-local</version>
     </dependency>
        <dependency>
            <groupId>org.pathvisio</groupId>
            <artifactId>org.pathvisio.libgpml</artifactId>
            <version>4.0.4</version>
        </dependency>

        <dependency>
        <groupId>org.pathvisio</groupId>
        <artifactId>org.pathvisio.gui</artifactId>
        <version>4.0.0-local</version>
    </dependency>

        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-core</artifactId>
            <version>${mockito.version}</version>
            <scope>test</scope>
        </dependency>


        <!-- mockito-junit-jupiter: integrates Mockito with JUnit 5 via @ExtendWith(MockitoExtension.class).
             mockConstruction() (used to mock new URL(...)) is built into mockito-core in Mockito 5.x —
             no separate mockito-inline artifact needed. -->
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-junit-jupiter</artifactId>
            <version>${mockito.version}</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.osgi</groupId>
            <artifactId>org.osgi.framework</artifactId>
            <version>1.8.0</version>
            <scope>provided</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>${maven.compiler.version}</version>
                <configuration>
                    <source>11</source>
                    <target>11</target>
                    <encoding>UTF-8</encoding>
                    <showWarnings>true</showWarnings>
                </configuration>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>${maven.surefire.version}</version>
                <configuration>
                    <argLine>
                        -Djdk.attach.allowAttachSelf=true
                        --add-opens java.base/java.lang=ALL-UNNAMED
                    </argLine>
                    <useModulePath>false</useModulePath>
                    <useManifestOnlyJar>false</useManifestOnlyJar>
                </configuration>
            </plugin>

            <plugin>
    <groupId>org.apache.felix</groupId>
    <artifactId>maven-bundle-plugin</artifactId>
    <version>5.1.9</version>
    <executions>
        <execution>
            <id>generate-osgi-manifest</id>
            <goals>
                <goal>manifest</goal>
            </goals>
            <configuration>
                <instructions>
                    <Bundle-SymbolicName>org.pathvisio.githubplugin</Bundle-SymbolicName>
                    <Bundle-Name>PathVisio GitHub Integration Plugin</Bundle-Name>
                    <Bundle-Version>${project.version}</Bundle-Version>
                    <Bundle-Vendor>Snehashree Prusty</Bundle-Vendor>
                    <Bundle-Description>Direct GitHub integration for WikiPathways pathway submission</Bundle-Description>
                    <Require-Bundle>org.pathvisio.desktop;bundle-version="4.0.0"</Require-Bundle>
                    <Bundle-Activator>org.pathvisio.githubplugin.GUI.Activator</Bundle-Activator>
                </instructions>
            </configuration>
        </execution>
    </executions>
</plugin>

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-jar-plugin</artifactId>
    <version>${maven.jar.version}</version>
    <configuration>
        <archive>
            <manifestFile>${project.build.outputDirectory}/META-INF/MANIFEST.MF</manifestFile>
        </archive>
        <finalName>githubplugin</finalName>
    </configuration>
</plugin>
        </plugins>
    </build>
    <profiles>
    <profile>
        <id>cli</id>
        <build>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-shade-plugin</artifactId>
                    <version>3.5.1</version>
                    <executions>
                        <execution>
                            <phase>package</phase>
                            <goals><goal>shade</goal></goals>
                            <configuration>
                                <finalName>pathvisio-github-cli</finalName>
                                <transformers>
                                    <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                        <mainClass>org.pathvisio.githubplugin.PathVisioGitHubCli</mainClass>
                                    </transformer>
                                </transformers>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>
            </plugins>
        </build>
    </profile>
    <profile>
    <id>cli2</id>
    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>3.5.1</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals><goal>shade</goal></goals>
                        <configuration>
                            <finalName>pathvisio-github-cli2</finalName>
                            <transformers>
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                    <mainClass>org.pathvisio.githubplugin.PathVisioGitHubCli2</mainClass>
                                </transformer>
                            </transformers>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
</profile>
</profiles>
</project>