pom.xml

<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>
	
	<properties>
		<bundle.symbolicName>chemViz2</bundle.symbolicName>
		<bundle.namespace>edu.ucsf.rbvi.chemViz2.internal</bundle.namespace>
		<cytoscape.api.version>3.10.0</cytoscape.api.version>
    <maven-compiler-plugin.version>3.8.0</maven-compiler-plugin.version>
    <maven-surefire-plugin.version>3.0.0-M3</maven-surefire-plugin.version>
    <maven-bundle-plugin.version>5.1.9</maven-bundle-plugin.version>
    <osgi.api.version>6.0.0</osgi.api.version>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
	</properties>

	<groupId>edu.ucsf.rbvi</groupId>
	<artifactId>chemViz2</artifactId>
	<packaging>bundle</packaging>
	<name>${bundle.symbolicName}</name>

	<version>2.0.3</version>

	<build>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.2</version>
				<configuration>
					<source>1.8</source>
					<target>1.8</target>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.apache.felix</groupId>
				<artifactId>maven-bundle-plugin</artifactId>
				<version>${maven-bundle-plugin.version}</version>
				<extensions>true</extensions>
				<configuration>
					<instructions>
						<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
						<Bundle-Version>${project.version}</Bundle-Version>
						<Export-Package>!${bundle.namespace}.*</Export-Package>
						<Private-Package>${bundle.namespace}.*</Private-Package>
						<Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>
						<Embed-Dependency>*;scope=!provided</Embed-Dependency>
						<Embed-Transitive>true</Embed-Transitive>
						<Import-Package>*;resolution:=optional</Import-Package>
					</instructions>
				</configuration>
			</plugin>
		</plugins>
	</build>

	<!-- Links to the Cytoscape Maven repositories. -->
	<repositories>
		<repository>
			<id>cytoscape_releases</id>
			<snapshots>
				<enabled>false</enabled>
			</snapshots>
			<releases>
				<enabled>true</enabled>
			</releases>
			<name>Cytoscape Releases</name>
			<url>https://nrnb-nexus.ucsd.edu/nexus/content/repositories/releases/</url>
		</repository>
		<repository>
			<id>apache-repo-releases</id>
			<url>https://repository.apache.org/content/repositories/</url>
			<releases>
				<enabled>true</enabled>
			</releases>
		</repository>
	</repositories>

	<dependencies>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>model-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>group-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>application-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>swing-application-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>core-task-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>viewmodel-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>presentation-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>work-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>service-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>swing-util-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.cytoscape</groupId>
			<artifactId>command-executor-api</artifactId>
			<version>${cytoscape.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.ops4j.pax.logging</groupId>
			<artifactId>pax-logging-api</artifactId>
			<version>1.11.11</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.osgi</groupId>
			<artifactId>org.osgi.core</artifactId>
			<version>${osgi.api.version}</version>
			<scope>provided</scope>
		</dependency>
		<!-- Only loading in the CDK modules we want reduces the size of the app by about 20% -->
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-interfaces</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-core</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-smiles</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-smarts</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-inchi</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-qsar</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-qsarmolecular</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-render</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-renderbasic</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-renderextra</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-renderawt</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-builder3d</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-fingerprint</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-silent</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.openscience.cdk</groupId>
			<artifactId>cdk-legacy</artifactId>
			<version>2.9</version>
			<optional>true</optional>
		</dependency>

		<dependency>
			<groupId>xom</groupId>
			<artifactId>xom</artifactId>
			<version>1.2.5</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>xerces</groupId>
			<artifactId>xercesImpl</artifactId>
			<version>2.8.0</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>org.freehep</groupId>
			<artifactId>freehep-graphicsio-svg</artifactId>
			<version>2.4</version>
			<optional>true</optional>
		</dependency>
		<dependency>
			<groupId>org.freehep</groupId>
			<artifactId>freehep-graphicsio-pdf</artifactId>
			<version>2.4</version>
			<optional>true</optional>
		</dependency>
    <!-- https://mvnrepository.com/artifact/io.github.dan2097/jna-inchi -->
    <dependency>
      <groupId>io.github.dan2097</groupId>
      <artifactId>jna-inchi-api</artifactId>
      <version>1.2.1</version>
			<optional>true</optional>
    </dependency>
    <dependency>
      <groupId>io.github.dan2097</groupId>
      <artifactId>jna-inchi-smiles</artifactId>
      <version>1.2.1</version>
			<optional>true</optional>
    </dependency>
    <dependency>
      <groupId>io.github.dan2097</groupId>
      <artifactId>jna-inchi-linux-x86-64</artifactId>
      <version>1.2.1</version>
			<optional>true</optional>
    </dependency>
    <dependency>
      <groupId>io.github.dan2097</groupId>
      <artifactId>jna-inchi-darwin-aarch64</artifactId>
      <version>1.2.1</version>
			<optional>true</optional>
    </dependency>
    <dependency>
      <groupId>io.github.dan2097</groupId>
      <artifactId>jna-inchi-darwin-x86-64</artifactId>
      <version>1.2.1</version>
			<optional>true</optional>
    </dependency>
    <dependency>
      <groupId>io.github.dan2097</groupId>
      <artifactId>jna-inchi-win32-x86-64</artifactId>
      <version>1.2.1</version>
			<optional>true</optional>
    </dependency>

		<dependency>
			<groupId>xml-apis</groupId>
			<artifactId>xml-apis</artifactId>
			<version>1.3.03</version>
			<scope>provided</scope>
		</dependency>
		<dependency>
			<groupId>com.google.guava</groupId>
  		<artifactId>guava</artifactId>
  		<version>17.0</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>3.0</version>
			<optional>true</optional>
		</dependency>
	</dependencies>

</project>