Upgrade to Maven

.gitignore

@@ -1,2 +1,3 @@
 bin/
 build/
+target/

pom.xml

@@ -0,0 +1,186 @@
+<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>org.openscience.cdk</groupId>
+  <artifactId>cdk-chemojava</artifactId>
+  <version>1.5.0</version>
+  <packaging>jar</packaging>
+  <name>ChemoJava</name>
+  <description>CDK extensions with GPL-licensed code</description>
+
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+    <maven.compiler.source>11</maven.compiler.source>
+    <maven.compiler.target>11</maven.compiler.target>		
+  </properties>
+
+  <dependencies>
+    <dependency>
+       <groupId>org.openscience.cdk</groupId>
+       <artifactId>cdk-qsar</artifactId>
+       <version>2.5</version>
+    </dependency>
+    <dependency>
+      <groupId>nz.ac.waikato.cms.weka</groupId>
+      <artifactId>weka-stable</artifactId>
+      <version>3.6.6</version>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
+                <configuration>
+                    <source>1.8</source>
+                    <target>1.8</target>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.22.2</version>
+                <configuration>
+                    <!-- prevent the annoying ForkedBooter process from stealing
+                         window focus on Mac OS -->
+                    <argLine>@{argLine} -Djava.awt.headless=true -Dcdk.logging.level=ERROR</argLine>
+                    <excludes>
+                        <!-- not a test class -->
+                        <exclude>**/TestMoleculeFactory.java</exclude>
+                        <!-- missing functionality -->
+                        <exclude>**/cdk/limitations/**</exclude>
+                        <!-- coverage tests need updating -->
+                        <exclude>**/*CoverageTest.java</exclude>
+                        <!-- module suites not needed -->
+                        <exclude>**/modulesuites/M*Tests.java</exclude>
+                        <!-- format tests do not work (cyclic dependency) -->
+                        <exclude>**/io/formats/*FormatTest.java</exclude>
+                    </excludes>
+                    <excludedGroups>org.openscience.cdk.SlowTest</excludedGroups>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <version>3.2.0</version>
+                <inherited>true</inherited>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
+                        </manifest>
+                    </archive>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>test-jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>3.2.0</version>
+                <configuration>
+                    <tags>
+                        <!--cdk.depends and cdk.builddepends no longer used-->
+                        <tag>
+                            <name>cdk.set</name>
+                            <placement>a</placement>
+
+                            <head>Belongs to the set:</head>
+                        </tag>
+                        <tag>
+                            <name>cdk.keyword</name>
+                            <placement>a</placement>
+
+                            <head>Keywords:</head>
+                        </tag>
+                        <tag>
+                            <name>cdk.created</name>
+                            <placement>a</placement>
+
+                            <head>Created on:</head>
+                        </tag>
+                        <tag>
+                            <name>cdk.require</name>
+                            <placement>a</placement>
+
+                            <head>Requires:</head>
+                        </tag>
+                        <tag>
+                            <name>cdk.todo</name>
+                            <placement>a</placement>
+
+                            <head>To do:</head>
+                        </tag>
+                        <tag>
+                            <name>cdk.license</name>
+                            <placement>a</placement>
+
+                            <head>License:</head>
+                        </tag>
+                    </tags>
+                    <taglets>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKCiteTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKBugTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKDictRefTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKGitTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKInChITaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKIOOptionsTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKModuleTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKThreadSafeTaglet</tagletClass>
+                        </taglet>
+                        <taglet>
+                            <tagletClass>net.sf.cdk.tools.doclets.CDKThreadNonSafeTaglet
+                            </tagletClass>
+                        </taglet>
+                    </taglets>
+                    <tagletArtifact>
+                        <groupId>org.openscience.cdk</groupId>
+                        <artifactId>cdk-build-utils</artifactId>
+                        <version>1.0.2.8</version>
+                    </tagletArtifact>
+                    <failOnError>false</failOnError>
+                    <doctitle>ChemoJava ${project.version} API</doctitle>
+                    <stylesheetfile>${basedir}/doc/javadoc/stylesheet.css</stylesheetfile>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>aggregate</id>
+                        <goals>
+                            <goal>aggregate</goal>
+                        </goals>
+                        <phase>site</phase>
+                        <configuration>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+    </plugins>   
+  </build>
+
+</project>