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<?xml version="1.0" encoding="UTF-8"?>
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<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>
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    <name>MosacSuite ImageJ/Fiji plugin</name>
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    <groupId>mosaic</groupId>
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    <artifactId>MosaicSuite</artifactId>
    <packaging>jar</packaging>
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    <version>1.0.19</version>
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    <description>Package contains image processing algorithms developed in MOSAIC Group</description>
    <url>http://mosaic.mpi-cbg.de/?q=downloads/imageJ</url>
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    <inceptionYear>2010</inceptionYear>
        <organization>
        <name>MOSAIC group</name>
        <url>http://mosaic.mpi-cbg.de</url>
    </organization>
    <licenses>
        <license>
            <name>GNU General Public License v3+</name>
            <url>https://www.gnu.org/licenses/gpl.html</url>
            <distribution>repo</distribution>
        </license>
    </licenses>

    <mailingLists>
        <mailingList>
            <name>ImageJ Forum</name>
            <archive>http://forum.imagej.net/</archive>
        </mailingList>
    </mailingLists>

    <scm>
        <connection>scm:git:git://git.mpi-cbg.de/mosaic/MosaicSuite</connection>
        <developerConnection>scm:git:git@git.mpi-cbg.de:mosaic/MosaicSuite</developerConnection>
        <tag>HEAD</tag>
        <url>https://git.mpi-cbg.de/mosaic/MosaicSuite</url>
    </scm>
    <issueManagement>
        <system>Mosaic Issues</system>
        <url>https://git.mpi-cbg.de/mosaic/MosaicSuite/issues</url>
    </issueManagement>
    <ciManagement>
        <system>None</system>
    </ciManagement>

    <properties>
        <package-name>mosaic</package-name>
        <license.licenseName>gpl_v3</license.licenseName>
        <license.copyrightOwners>MOSAIC group</license.copyrightOwners>
    </properties>
    
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    <developers>
        <developer>
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            <id>Krzysztof.Gonciarz</id>
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            <name>Krzysztof Gonciarz</name>
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            <url>http://imagej.net/User:Krzysztof.Gonciarz</url>
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            <email>gonciarz@mpi-cbg.de</email>
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            <roles>
                <role>developer</role>
                <role>support</role>
                <role>maintainer</role>
            </roles>            
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        </developer>
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    </developers>
    <contributors>
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        <contributor>
            <properties><id>Krzysztof.Gonciarz</id></properties>
            <name>Krzysztof Gonciarz</name>
            <email>gonciarz@mpi-cbg.de</email>
        </contributor>    
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        <contributor>
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            <name>Pietro Incardona</name>
            <email>incardon@mpi-cbg.de</email>
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        </contributor>
        <contributor>
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            <name>Aurélien Rizk</name>
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        </contributor>
        <contributor>
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            <name>Arun Shivanandan</name>
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        </contributor>
        <contributor>
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            <name>Janick Cardinale</name>
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        </contributor>
    </contributors>
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    <parent>
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        <groupId>org.scijava</groupId>
        <artifactId>pom-scijava</artifactId>
        <version> 16.1.0</version>
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        <relativePath />
    </parent>
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    <repositories>
        <repository>
            <id>imagej.public</id>
            <url>http://maven.imagej.net/content/groups/public</url>
        </repository>
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        <!--  temporary (but remotely accessible repository for not available otherwise jars -->
<!--         <repository>
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            <id>mosaic.public</id>
            <url>http://mosaic.mpi-cbg.de/maven/</url>
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         </repository> -->
         <!-- use instead above mosaic repository local one embedded in source tree -->
        <repository>
            <id>local-repo</id>
            <name>repo</name>
            <url>file://${project.basedir}/repo</url>
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        </repository>
    </repositories>

    <dependencies>
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        <dependency>
            <groupId>net.imagej</groupId>
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            <artifactId>ij</artifactId>
        </dependency>
        <dependency>
            <groupId>net.imglib2</groupId>
            <artifactId>imglib2</artifactId>
        </dependency>
        <dependency>
            <groupId>net.imglib2</groupId>
            <artifactId>imglib2-ij</artifactId>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
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            <!--<scope>compile</scope>-->
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        </dependency>
        <dependency>
            <groupId>io.scif</groupId>
            <artifactId>scifio</artifactId>
        </dependency>
        <dependency>
            <groupId>net.imglib2</groupId>
            <artifactId>imglib2-algorithm</artifactId>
        </dependency>
        <dependency>
            <groupId>net.imglib2</groupId>
            <artifactId>imglib2-algorithm-gpl</artifactId>
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        </dependency>
        <dependency>
            <groupId>edu.mines</groupId>
            <artifactId>mines-jtk</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math3</artifactId>
        </dependency>
        <dependency>
            <groupId>com.google.code.gson</groupId>
            <artifactId>gson</artifactId>
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        </dependency>
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        <dependency>
            <groupId>org.scijava</groupId>
            <artifactId>vecmath</artifactId>
        </dependency>
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        <dependency>
            <groupId>org.scijava</groupId>
            <artifactId>scijava-common</artifactId>
        </dependency>
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        <dependency>
            <groupId>sc.fiji</groupId>
            <artifactId>bij</artifactId>
        </dependency>
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        <dependency>
            <groupId>nz.ac.waikato.cms.weka</groupId>
            <artifactId>weka-dev</artifactId>
        </dependency>
        <dependency>
            <groupId>com.jcraft</groupId>
            <artifactId>jsch</artifactId>
        </dependency>
        <dependency>
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            <groupId>net.sf.jgrapht</groupId>
            <artifactId>jgrapht</artifactId>
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        </dependency>
        <dependency>
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            <groupId>sc.fiji</groupId>
            <artifactId>Skeletonize3D_</artifactId>
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        </dependency>
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        <!-- 3rd party stuff -->
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        <dependency>
            <groupId>com.googlecode.efficient-java-matrix-library</groupId>
            <artifactId>ejml</artifactId>
            <version>0.24</version>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
            <version>2.4</version>
        </dependency>
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        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-lang3</artifactId>
        </dependency>
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        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.17</version>
        </dependency>
        <dependency>
            <groupId>net.sf.supercsv</groupId>
            <artifactId>super-csv</artifactId>
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            <version>2.4.0</version>
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        </dependency>
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        <dependency>
            <groupId>net.sf.dozer</groupId>
            <artifactId>dozer</artifactId>
            <version>5.5.1</version>
        </dependency>
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        <dependency>
            <groupId>net.sf.supercsv</groupId>
            <artifactId>super-csv-dozer</artifactId>
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            <version>2.4.0</version>
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        </dependency>
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        <dependency>
            <groupId>com.github.rwl</groupId>
            <artifactId>jtransforms</artifactId>
            <version>2.4.0</version>
        </dependency>

        <!-- These dependencies are temporarily kept in mosaic maven -->
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        <dependency>
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            <groupId>net.jgeom.nurbs</groupId>
            <artifactId>net.jgeom.nurbs</artifactId>
            <version>1.0.0</version>
        </dependency>
        <dependency>
            <groupId>cmaes</groupId>
            <artifactId>cmaes</artifactId>
            <version>1.0.0</version>
        </dependency>
    </dependencies>
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    <build>
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        <plugins>
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            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.4.3</version>
                <executions>
                    <execution>
                        <id>generate-allIn1-jar</id>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <outputFile>target/${project.artifactId}-${project.version}_Full.jar</outputFile>
                            <!-- Intentionally not 'true' - removes too much 
                                from destination jar (like org.apache.commons.beanutils.ConvertUtils) -->
                            <minimizeJar>false</minimizeJar>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
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            <plugin>
                <artifactId>maven-resources-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-resources</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${env.FIJI_MOSAIC_PLUGIN_PATH}</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>target</directory>
                                    <includes>
                                        <include>${project.artifactId}-${project.version}_Full.jar</include>
                                    </includes>
                                    <filtering>false</filtering>
                                </resource>
                            </resources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
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            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <configuration>
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                    <!-- Disable assertions because of CMA-ES jar - seems 
                        some not finished implementation there throws assertion -->
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                    <argLine>-disableassertions</argLine>
                </configuration>
            </plugin>
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        </plugins>
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    </build>
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</project>