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pom.xml
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pom.xml
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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>
<parent>
<groupId>com.github.celldynamics</groupId>
<artifactId>pom-quimp-root</artifactId>
<version>25.0.0</version>
<relativePath />
</parent>
<!-- Project's coordinates -->
<groupId>com.github.celldynamics.quimp</groupId>
<artifactId>QuimP_</artifactId>
<packaging>jar</packaging>
<version>19.08.02-SNAPSHOT</version>
<!-- Name and licencing and other project informations -->
<name>QuimP</name>
<url>www.warwick.ac.uk/quimp</url>
<description>QuimP software, a set of plugins for ImageJ to quantify spatio-temporal patterns of fluorescently labeled proteins in the cortex of moving cells.</description>
<inceptionYear>2002</inceptionYear>
<!-- Root of URL for documentation. MUST have / at end -->
<properties>
<manual.rootlocation>https://pilip.lnx.warwick.ac.uk/docs/</manual.rootlocation>
<site.rootlocation>https://pilip.lnx.warwick.ac.uk/site/</site.rootlocation>
<site.historylocation>${site.rootlocation}changes-report.html</site.historylocation>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<!--package-name>com.mycompany.imagej</package-name-->
<!--main-class>com.mycompany.imagej.Process_Pixels</main-class-->
<license.licenseName>QuimP License</license.licenseName>
<license.copyrightOwners>University of Warwick</license.copyrightOwners>
</properties>
<scm>
<connection>scm:git:https://github.com/CellDynamics/QuimP.git</connection>
<developerConnection>scm:git:https://github.com/CellDynamics/QuimP.git</developerConnection>
<url>https://github.com/CellDynamics/QuimP/</url>
<tag>HEAD</tag>
</scm>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/CellDynamics/QuimP/issues/</url>
</issueManagement>
<licenses>
<license>
<name>QuimP License</name>
<url>https://pilip.lnx.warwick.ac.uk/LICENSE.txt</url>
<distribution>repo</distribution>
<comments>University of Warwick licence</comments>
</license>
</licenses>
<organization>
<name>Department of Computer Science, Warwick University</name>
<url>http://www2.warwick.ac.uk/fac/sci/dcs/</url>
</organization>
<developers>
<developer>
<id>pbaniukiewicz</id>
<name>Piotr Baniukiewicz</name>
<email>[email protected]</email>
<organization>University of Warwick</organization>
<roles>
<role>lead</role>
<role>developer</role>
<role>support</role>
<role>reviewer</role>
<role>maintainer</role>
</roles>
<timezone>London</timezone>
</developer>
<developer>
<id>smsgai</id>
<name>Till Bretschneider</name>
<email>[email protected]</email>
<organization>University of Warwick</organization>
<roles>
<role>lead</role>
<role>reviewer</role>
<role>maintainer</role>
<role>founder</role>
<role>support</role>
</roles>
<timezone>London</timezone>
</developer>
</developers>
<contributors>
<contributor>
<name>Richard Tyson</name>
<organization>University of Warwick</organization>
<roles>
<role>developer</role>
</roles>
<timezone>London</timezone>
</contributor>
</contributors>
<mailingLists>
<mailingList>
<name>ImageJ Forum</name>
<archive>http://forum.imagej.net/</archive>
</mailingList>
</mailingLists>
<ciManagement>
<system>None</system>
</ciManagement>
<dependencies>
<!-- https://mvnrepository.com/artifact/io.github.benas/random-beans -->
<dependency>
<groupId>io.github.benas</groupId>
<artifactId>random-beans</artifactId>
<version>3.7.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.github.baniuk</groupId>
<artifactId>ImageJTestSuite</artifactId>
<version>1.0.2</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>pl.pragmatists</groupId>
<artifactId>JUnitParams</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
<!-- https://github.com/CellDynamics/QuimP/issues/309 -->
<version>1.52n</version>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>scijava-config</artifactId>
</dependency>
<dependency>
<groupId>org.scijava</groupId>
<artifactId>vecmath</artifactId>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-omero</artifactId>
</dependency>
<dependency>
<groupId>omero</groupId>
<artifactId>blitz</artifactId>
<exclusions>
<exclusion>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<!-- http://www.javacodegeeks.com/2012/10/maven-build-number-plugin-sample-usage.html -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
</plugin>
<plugin>
<!-- https://books.sonatype.com/mvnex-book/reference/customizing-sect-creating-simple-weather.html -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<reuseForks>false</reuseForks>
<forkCount>1</forkCount>
</configuration>
</plugin>
<plugin>
<!-- Default PluginFactory - not mocked -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/maven</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<inherited>false</inherited>
<!-- only execute these in the parent -->
<executions>
<execution>
<id>git submodule update</id>
<phase>initialize</phase>
<configuration>
<executable>git</executable>
<arguments>
<argument>submodule</argument>
<argument>update</argument>
<argument>--init</argument>
<argument>--recursive</argument>
</arguments>
</configuration>
<goals>
<goal>exec</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<configuration>
<tagNameFormat>v@{project.version}</tagNameFormat>
<pushChanges>false</pushChanges>
<localCheckout>true</localCheckout>
<releaseProfiles>installation</releaseProfiles>
<goals>install</goals>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
</plugin>
<plugin>
<groupId>com.github.jeluard</groupId>
<artifactId>plantuml-maven-plugin</artifactId>
<version>1.2</version>
<configuration>
<sourceFiles>
<directory>${basedir}/src/main/java</directory>
<includes>
<include>**/*.java</include>
</includes>
</sourceFiles>
<outputDirectory>${basedir}/target/apidocs</outputDirectory>
</configuration>
<dependencies>
<dependency>
<groupId>net.sourceforge.plantuml</groupId>
<artifactId>plantuml</artifactId>
<version>1.2019.3</version>
</dependency>
</dependencies>
<executions>
<execution>
<id>plantuml-javadoc-site</id>
<goals>
<goal>generate</goal>
</goals>
<phase>pre-site</phase>
<configuration>
<outputDirectory>${basedir}/target/site/apidocs</outputDirectory>
</configuration>
</execution>
<execution>
<id>plantuml-javadoc</id>
<goals>
<goal>generate</goal>
</goals>
<phase>generate-sources</phase>
<configuration>
<outputDirectory>${basedir}/target/apidocs</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<profiles>
<profile>
<!-- Set PluginFactory to mocked version and add sources of plugins -->
<!-- Most of this settings is dependend from folder structure -->
<!-- Use of this profile will cause that current state of Working Directory will be utilized -->
<id>development</id>
<properties>
<manual.location>${manual.rootlocation}develop/QuimP_Guide.html</manual.location>
<test.mode>true</test.mode>
</properties>
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<dependencies>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>2.7.22</version>
<scope>compile</scope>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>1.10</version>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>${basedir}/src/eclipse</source>
<source>${basedir}/../HatSnakeFilter_quimp/src/main/java</source>
<source>${basedir}/../HedgehogSnakeFilter_quimp/src/main/java</source>
<source>${basedir}/../MeanSnakeFilter_quimp/src/main/java</source>
<source>${basedir}/../SetHeadSnakeFilter_quimp/src/main/java</source>
<source>${basedir}/../RandomWalkSnakeFilter_quimp/src/main/java</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>testing</id>
<!-- Default profile for testing and building pure jar-->
<!-- Disables Reg Window -->
<activation>
<activeByDefault>false</activeByDefault>
</activation>
<properties>
<manual.location>${manual.rootlocation}develop/QuimP_Guide.html</manual.location>
<test.mode>true</test.mode>
</properties>
</profile>
<profile>
<id>installation</id>
<!--Default profile for building pure jar-->
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<manual.location>${manual.rootlocation}master/QuimP_Guide.html</manual.location>
<test.mode>false</test.mode>
</properties>
</profile>
</profiles>
<repositories>
<repository>
<id>ome.maven</id>
<url>http://artifacts.openmicroscopy.org/artifactory/maven/</url>
</repository>
<repository>
<id>net.imagej</id>
<url>http://maven.imagej.net/content/repositories/releases/</url>
</repository>
</repositories>
<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jxr-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<aggregate>true</aggregate>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
<version>2.17</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>findbugs-maven-plugin</artifactId>
<version>3.0.3</version>
<configuration>
<findbugsXmlOutput>true</findbugsXmlOutput>
<findbugsXmlWithMessages>true</findbugsXmlWithMessages>
<xmlOutput>true</xmlOutput>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-pmd-plugin</artifactId>
<version>3.11.0</version>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.3</version>
<configuration>
<!-- Sets the path to the file which contains the execution data. -->
<dataFile>${project.build.directory}/coverage-reports/jacoco-ut.exec</dataFile>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-changes-plugin</artifactId>
<version>2.12.1</version>
<reportSets>
<reportSet>
<reports>
<report>changes-report</report>
</reports>
</reportSet>
</reportSets>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.1.0</version>
<configuration>
<show>protected</show>
<quiet>false</quiet>
<doclint>none</doclint>
</configuration>
</plugin>
</plugins>
</reporting>
</project>