Description

<dependency>
    <groupId>com.arosbio</groupId>
    <artifactId>parent</artifactId>
    <version>2.0.0</version>
</dependency>

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!--

    Copyright (C) Aros Bio AB.

    CPSign is an Open Source Software that is dual licensed to allow you to choose a license that best suits your requirements:

    1) GPLv3 (GNU General Public License Version 3) with Additional Terms, including an attribution clause as well as a limitation to use the software for commercial purposes.

    2) CPSign Proprietary License that allows you to use CPSign for commercial activities, such as in a revenue-generating operation or environment, or integrate CPSign in your proprietary software without worrying about disclosing the source code of your proprietary software, which is required if you choose to use the software under GPLv3 license. See arosbio.com/cpsign/commercial-license for details.

-->
<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>com.arosbio</groupId>
  <artifactId>parent</artifactId>
  <version>2.0.0</version>
  <packaging>pom</packaging>
  <name>${project.groupId}:${project.artifactId}</name>
  <description>The aggregation project for all cpsign child modules</description> 
  <url>http://arosbio.com</url>

  <organization>
    <name>Aros Bio</name>
    <url>http://arosbio.com</url>
  </organization>

  <modules>
    <module>fast-ivap</module>
    <module>depict</module>
    <module>test-utils</module>
    <module>confai</module>
    <module>cpsign-api</module>
    <module>cpsign</module>
  </modules>

  <licenses>

    <license>
      <name>GPLv3 (GNU General Public License Version 3) with Additional Terms</name>
      <comments>Non-commerical license</comments>
      <url>http://www.gnu.org/licenses/gpl-3.0.html</url>
      <distribution>repo</distribution>
    </license>

    <license>
      <name>Commercial license</name>
      <url>https://arosbio.com/cpsign/commercial-license</url>
      <distribution>repo</distribution>
    </license>

  </licenses>

  <scm>
    <connection>scm:git:git://github.com/arosbio/cpsign.git</connection>
    <developerConnection>scm:git:ssh://github.com:arosbio/cpsign.git</developerConnection>
    <url>http://github.com/arosbio/cpsign/tree/master</url>
  </scm>

  <distributionManagement>
    <repository>
      <id>ossrh</id>
      <url>https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/</url>
    </repository>
  </distributionManagement>

  <developers>
    <developer>
      <name>Staffan Arvidsson McShane</name>
      <email>staffan.arvidsson@gmail.com</email>
      <organization>Pharmb.io</organization>
      <organizationUrl>https://pharmb.io/</organizationUrl>
    </developer>
  </developers>


  <!-- Common properties -->
  <properties>

    <!-- This property should point to the base of the root-directory of the cpsign repo - need to be overwritten in all child-modules -->
    <parent.basedir>${project.basedir}</parent.basedir>

    <!-- general settings -->
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <maven.compiler.source>11</maven.compiler.source>
    <maven.compiler.target>11</maven.compiler.target>
    <maven.compiler.release>11</maven.compiler.release>
    <application.vendor>Aros Bio AB</application.vendor>
    <timestamp>${maven.build.timestamp}</timestamp>
    <mf.impl.vendor>Aros Bio AB</mf.impl.vendor>
    <test.pkg>com.arosbio.tests.suites</test.pkg>

    <!-- plugin versions -->
    <shade.plugin.version>3.2.4</shade.plugin.version>
    <javadoc.plugin.version>3.4.0</javadoc.plugin.version>
    <compiler.plugin.version>3.11.0</compiler.plugin.version>
    <dependency.plugin.version>3.6.0</dependency.plugin.version>
    <resources.plugin.version>3.3.1</resources.plugin.version>
    <jar.plugin.version>3.3.0</jar.plugin.version>
    <surefire.plugin.version>3.0.0-M7</surefire.plugin.version>
    <exec-maven-plugin.version>3.0.0</exec-maven-plugin.version>
    <source.plugin.version>3.2.1</source.plugin.version>
    <gpg.plugin.version>3.0.1</gpg.plugin.version>
    <nexus.staging.plugin.version>1.6.7</nexus.staging.plugin.version>

    <!-- Dependency versions -->
    <cdk.version>2.9</cdk.version>
    <slf4j.version>2.0.9</slf4j.version>
    <logback.version>1.4.14</logback.version>
    <json-simple.version>4.0.1</json-simple.version>
    <commons-csv.version>1.10.0</commons-csv.version>
    <commons-math3.version>3.6.1</commons-math3.version>
    <commons-io.version>2.11.0</commons-io.version>
    <commons-text.version>1.10.0</commons-text.version>
    <commons-lang.version>3.9</commons-lang.version>
    <guava.version>32.0.0-jre</guava.version>
    <filters.version>2.0.235-1</filters.version>
    <libsvm.version>3.24</libsvm.version>
    <liblinear.version>2.44</liblinear.version>
    <encrypt-api.version>2.0.2</encrypt-api.version>
  </properties>


  <!-- DEPENDENCY MANAGEMENT - SPECIFY SAME VERSIONS AND SIMPLIFY DEPS IN CHILDS -->
  <dependencyManagement>
    <dependencies>
      
      <!-- CDK DEP -->
      <dependency>
        <groupId>org.openscience.cdk</groupId>
        <artifactId>cdk-bundle</artifactId>
        <version>${cdk.version}</version>
        <!-- Trying to reduce the final JAR size and remove Log4j and unnecessary dependencies -->
        <exclusions>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-extra</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-iordf</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-jniinchi-support</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-legacy</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-qsarionpot</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-ionpot</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-qsarcml</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-libiomd</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-pdbcml</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-libiocml</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.freehep</groupId>
            <artifactId>freehep-graphicsio-svg</artifactId>
          </exclusion>
          <exclusion>
            <groupId>org.freehep</groupId>
            <artifactId>freehep-graphicsio-ps</artifactId>
          </exclusion>
        </exclusions>
      </dependency>

      <dependency>
        <groupId>com.github.cliftonlabs</groupId>
        <artifactId>json-simple</artifactId>
        <version>${json-simple.version}</version>
      </dependency>

      <dependency>
        <groupId>com.jhlabs</groupId>
        <artifactId>filters</artifactId>
        <version>${filters.version}</version>
      </dependency>

      <dependency>
        <groupId>com.google.guava</groupId>
        <artifactId>guava</artifactId>
        <version>${guava.version}</version>
      </dependency>

      <dependency>
        <groupId>commons-io</groupId>
        <artifactId>commons-io</artifactId>
        <version>${commons-io.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-lang3</artifactId>
        <version>${commons-lang.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-text</artifactId>
        <version>${commons-text.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-math3</artifactId>
        <version>${commons-math3.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-csv</artifactId>
        <version>${commons-csv.version}</version>
      </dependency>

      <dependency>
        <groupId>org.beryx</groupId>
        <artifactId>awt-color-factory</artifactId>
        <version>1.0.2</version>
      </dependency>

      <dependency>
        <groupId>tw.edu.ntu.csie</groupId>
        <artifactId>libsvm</artifactId>
        <version>${libsvm.version}</version>
      </dependency>

      <dependency>
        <groupId>de.bwaldvogel</groupId>
        <artifactId>liblinear</artifactId>
        <version>${liblinear.version}</version>
      </dependency>

      <!-- LOGGING -->
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-api</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>ch.qos.logback</groupId>
        <artifactId>logback-classic</artifactId>
        <version>${logback.version}</version>
      </dependency>
      <!-- 
      <dependency>
        <groupId>ch.qos.logback</groupId>
        <artifactId>logback-core</artifactId>
        <version>${logback.version}</version>
      </dependency>
    -->

      <!-- CLI DEPS -->
      <dependency>
        <groupId>me.tongfei</groupId>
        <artifactId>progressbar</artifactId>
        <version>0.9.4</version>
      </dependency>
      <dependency>
        <groupId>info.picocli</groupId>
        <artifactId>picocli</artifactId>
        <version>4.7.5</version>
      </dependency>
  
      <dependency>
        <groupId>org.fusesource.jansi</groupId>
        <artifactId>jansi</artifactId>
        <version>2.4.0</version>
      </dependency>

    </dependencies>

  </dependencyManagement>

  <dependencies>

    <!-- TEST DEPENDENCIES -->

    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>[4.13.1,)</version>
      <scope>test</scope>
    </dependency>
    <dependency>
        <groupId>org.hamcrest</groupId>
        <artifactId>hamcrest-library</artifactId>
        <version>2.2</version>
        <scope>test</scope>
    </dependency>
    <dependency>
      <groupId>org.hamcrest</groupId>
      <artifactId>hamcrest</artifactId>
      <version>2.2</version>
      <scope>test</scope>
    </dependency>

    <dependency>
      <groupId>com.github.stefanbirkner</groupId>
      <artifactId>system-rules</artifactId>
      <version>1.19.0</version>
      <scope>test</scope>
      <!-- junit:junit-dep is deprecated, and junit:junit replaces it. -->
      <exclusions>
        <exclusion>
          <groupId>junit</groupId>
          <artifactId>junit-dep</artifactId>
        </exclusion>
      </exclusions>
    </dependency>

    <dependency>
      <groupId>org.openjdk.jol</groupId>
      <artifactId>jol-core</artifactId>
      <version>0.10</version>
      <scope>test</scope>
    </dependency>

  </dependencies>


  <build>

    <plugins>

      <plugin>
        <artifactId>maven-dependency-plugin</artifactId>
        <version>${dependency.plugin.version}</version>
      </plugin>

      <plugin>
        <artifactId>maven-resources-plugin</artifactId>
        <version>${resources.plugin.version}</version>
        <configuration>
          <propertiesEncoding>UTF-8</propertiesEncoding>
        </configuration>
      </plugin>

      <plugin>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>${compiler.plugin.version}</version>
      </plugin>

      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-javadoc-plugin</artifactId>
        <version>${javadoc.plugin.version}</version>
        <configuration>
          <author>false</author>
          <bottom><![CDATA[<i>Copyright &#169; 2022, <a href="https://arosbio.com">Aros Bio AB</a>. All Rights Reserved.</i>]]></bottom>
        </configuration>
      </plugin>

      

      <!-- License management: updates the header of source files only 
      Run it using `mvn license:format` -->
      
      <plugin>
        <groupId>com.mycila</groupId>
        <artifactId>license-maven-plugin</artifactId>
        <version>4.1</version>
        <configuration>
          <licenseSets>
            <licenseSet>
              <inlineHeader>
Copyright (C) Aros Bio AB.

CPSign is an Open Source Software that is dual licensed to allow you to choose a license that best suits your requirements:

1) GPLv3 (GNU General Public License Version 3) with Additional Terms, including an attribution clause as well as a limitation to use the software for commercial purposes.

2) CPSign Proprietary License that allows you to use CPSign for commercial activities, such as in a revenue-generating operation or environment, or integrate CPSign in your proprietary software without worrying about disclosing the source code of your proprietary software, which is required if you choose to use the software under GPLv3 license. See arosbio.com/cpsign/commercial-license for details.
              </inlineHeader>

              <excludes>
                <exclude>**/README</exclude>
                <exclude>*.md</exclude>
                <exclude>src/test/resources/**</exclude>
                <exclude>src/main/resources/**</exclude>
                <exclude>**/*.txt</exclude>
              </excludes>
            </licenseSet>
          </licenseSets>
          
        </configuration>
      </plugin>
      
    

    </plugins>
  </build>

  <profiles>
    <!-- Profile for deploying to the maven central repo - builds and signs all required artifacts -->
    <profile>
      <id>deploy</id>
      <activation>
				<activeByDefault>false</activeByDefault>
			</activation>

      <build>
				<plugins>
          <!-- TODO - not sure if we need to specify this again -->
          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-javadoc-plugin</artifactId>
            <version>${javadoc.plugin.version}</version>
            <configuration>
              <author>false</author>
              <bottom><![CDATA[<i>Copyright &#169; 2022, <a href="https://arosbio.com">Aros Bio AB</a>. All Rights Reserved.</i>]]></bottom>
            </configuration>
            <executions>
              <execution>
                <id>attach-javadocs</id>
                <goals>
                  <goal>jar</goal>
                </goals>
              </execution>
            </executions>
          </plugin>

          <plugin>
            <groupId>org.apache.maven.plugins</groupId>
            <artifactId>maven-source-plugin</artifactId>
            <version>${source.plugin.version}</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-gpg-plugin</artifactId>
            <version>${gpg.plugin.version}</version>
            <executions>
              <execution>
                <id>sign-artifacts</id>
                <phase>verify</phase>
                <goals>
                  <goal>sign</goal>
                </goals>
              </execution>
            </executions>
          </plugin>
    
          <plugin>
            <groupId>org.sonatype.plugins</groupId>
            <artifactId>nexus-staging-maven-plugin</artifactId>
            <version>${nexus.staging.plugin.version}</version>
            <extensions>true</extensions>
            <configuration>
               <serverId>ossrh</serverId>
               <nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
               <autoReleaseAfterClose>true</autoReleaseAfterClose>
            </configuration>
          </plugin>

        </plugins>
      </build>

    </profile>
  </profiles>

</project>