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pom.xml
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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>19.2.0</version>
<relativePath />
</parent>
<groupId>ch.epfl.leb</groupId>
<artifactId>SASS_</artifactId>
<version>0.9.0-SNAPSHOT</version>
<packaging>jar</packaging>
<name>SASS</name>
<description>SMLM Acquisition Simulation Software</description>
<url>https://github.com/LEB-EPFL/SASS</url>
<inceptionYear>2017</inceptionYear>
<organization>
<name>The Laboratory of Experimental Biophysics</name>
<url>https://leb.epfl.ch</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>
<developers>
<developer>
<id>kmdouglass</id>
<name>Kyle M. Douglass</name>
<url>https://kmdouglass.github.io</url>
<roles>
<role>lead</role>
<role>developer</role>
<role>debugger</role>
<role>reviewer</role>
<role>support</role>
<role>maintainer</role>
</roles>
</developer>
</developers>
<contributors>
<contributor>
<name>Marcel Stefko</name>
<url>https://github.com/mstefko</url>
<roles>
<role>founder</role>
<role>developer</role>
</roles>
</contributor>
<contributor>
<name>Baptiste Ottino</name>
<url>https://github.com/bottino</url>
<roles>
<role>developer</role>
</roles>
</contributor>
</contributors>
<mailingLists>
<mailingList>
<name>Gitter</name>
<archive>https://gitter.im/leb_epfl/SASS</archive>
</mailingList>
</mailingLists>
<scm>
<connection>scm:git:git://github.com/LEB-EPFL/SASS</connection>
<developerConnection>scm:git:[email protected]:LEB-EPFL/SASS</developerConnection>
<tag>HEAD</tag>
<url>https://github.com/LEB-EPFL/SASS</url>
</scm>
<issueManagement>
<system>GitHub Issues</system>
<url>https://github.com/LEB-EPFL/SASS/issues</url>
</issueManagement>
<ciManagement>
<system>https://travis-ci.org/LEB-EPFL/SASS</system>
</ciManagement>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>1.8</maven.compiler.source>
<maven.compiler.target>1.8</maven.compiler.target>
<mainClass>ch.epfl.leb.sass.commandline.CommandLineInterface</mainClass>
<license.licenseName>gpl_v3</license.licenseName>
<license.copyrightOwners>The Laboratory of Experimental Biophysics, EPFL</license.copyrightOwners>
<!-- Used by Surefire incase JaCoCo gets skipped. -->
<argLine/>
<!-- Dependency versions not already in pom-scijava. -->
<bsh.version>2.0b4</bsh.version>
<commons-cli.version>1.4</commons-cli.version>
<colt.version>1.2.0</colt.version>
<commons-math2.version>2.2</commons-math2.version>
<thrift.version>0.11.0</thrift.version>
<json.version>20160810</json.version>
<alica_interfaces.version>0.0.1</alica_interfaces.version>
<alica_acpack.version>0.0.0</alica_acpack.version>
<slf4j-api.version>1.7.25</slf4j-api.version>
<!-- Plugins -->
<jacoco.version>0.8.1</jacoco.version>
<maven-dependency-plugin.version>3.1.0</maven-dependency-plugin.version>
<maven-shade-plugin.version>3.1.0</maven-shade-plugin.version>
<maven-failsafe-plugin.version>2.21.0</maven-failsafe-plugin.version>
<maven-surefire-plugin.version>2.21.0</maven-surefire-plugin.version>
</properties>
<repositories>
<repository>
<id>jitpack.io</id>
<url>https://jitpack.io</url>
</repository>
</repositories>
<dependencies>
<!-- ALICA Suite dependency -->
<dependency>
<groupId>com.github.LEB-EPFL</groupId>
<artifactId>ALICA_interfaces</artifactId>
<version>${alica_interfaces.version}</version>
</dependency>
<!-- ALICA Suite dependency -->
<dependency>
<groupId>com.github.LEB-EPFL</groupId>
<artifactId>ALICA_ACPack</artifactId>
<version>${alica_acpack.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/bsh/bsh -->
<dependency>
<groupId>org.beanshell</groupId>
<artifactId>bsh</artifactId>
<version>${bsh.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>${commons-cli.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.jfree/jfreechart -->
<dependency>
<groupId>org.jfree</groupId>
<artifactId>jfreechart</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/colt/colt -->
<dependency>
<groupId>colt</groupId>
<artifactId>colt</artifactId>
<version>${colt.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math</artifactId>
<version>${commons-math2.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.thrift/libthrift -->
<dependency>
<groupId>org.apache.thrift</groupId>
<artifactId>libthrift</artifactId>
<version>${thrift.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j-api.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/com.google.code.gson/gson -->
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.json/json -->
<dependency>
<groupId>org.json</groupId>
<artifactId>json</artifactId>
<version>${json.version}</version>
</dependency>
<!-- https://mvnrepository.com/artifact/junit/junit -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<!-- https://mvnrepository.com/artifact/org.mockito/mockito-core -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-java</artifactId>
<scope>test</scope>
<version>2.44.0</version>
</dependency>
<dependency>
<groupId>com.opera</groupId>
<artifactId>operadriver</artifactId>
<scope>test</scope>
<version>1.5</version>
<exclusions>
<exclusion>
<groupId>org.seleniumhq.selenium</groupId>
<artifactId>selenium-remote-driver</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
<profiles>
<!-- Builds an Uber jar that contains run-time dependencies.
(except for ALICA_ACPack*.jar). -->
<profile>
<id>build-uber-jar</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<directory>target-uber/</directory>
<plugins>
<!-- Runs the unit tests. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<configuration>
<argLine>@{argLine}</argLine>
</configuration>
</plugin>
<!-- Runs the integration tests. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${maven-failsafe-plugin.version}</version>
<executions>
<execution>
<id>integration-tests</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
<configuration>
<argLine>${itCoverageAgent}</argLine>
</configuration>
</execution>
</executions>
</plugin>
<!-- Runs the code coverage analysis. -->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<configuration>
<excludes>
<exclude>ch/epfl/leb/sass/server/RemoteSimulationService$*.class</exclude>
</excludes>
</configuration>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>default-prepare-agent-integration</id>
<goals>
<goal>prepare-agent-integration</goal>
</goals>
<configuration>
<propertyName>itCoverageAgent</propertyName>
</configuration>
</execution>
<execution>
<id>default-report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
<execution>
<id>default-report-integration</id>
<goals>
<goal>report-integration</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Pushes the coverage report to Coveralls. -->
<plugin>
<groupId>org.eluder.coveralls</groupId>
<artifactId>coveralls-maven-plugin</artifactId>
<version>4.3.0</version>
<configuration>
<timestampFormat>EpochMillis</timestampFormat>
</configuration>
</plugin>
<!-- Adds the ALICA_interfaces dependency to the final .jar. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${maven-shade-plugin.version}</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>ch.epfl.leb.sass.commandline.CommandLineInterface</mainClass>
</transformer>
</transformers>
<artifactSet>
<includes>
<include>com.github.LEB-EPFL:ALICA_interfaces</include>
<include>net.imagej:ij</include>
<include>org.beanshell:bsh</include>
<include>org.apache.commons:commons-math3</include>
<include>commons-cli:commons-cli</include>
<include>org.jfree:jfreechart</include>
<include>colt:colt</include>
<include>org.apache.commons:commons-math</include>
<include>org.apache.thrift:libthrift</include>
<include>org.slf4j:slf4j-api</include>
<include>com.google.code.gson:gson</include>
<include>org.json:json</include>
</includes>
</artifactSet>
</configuration>
</execution>
</executions>
</plugin>
<!-- Download ALICA_ACPack and put it in output directory. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>${maven-dependency-plugin.version}</version>
<executions>
<execution>
<id>copy</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
</execution>
</executions>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.github.LEB-EPFL</groupId>
<artifactId>ALICA_ACPack</artifactId>
<version>${alica_acpack.version}</version>
<type>jar</type>
<overWrite>false</overWrite>
<outputDirectory>${project.build.directory}</outputDirectory>
<destFileName>ALICA_ACPack-${alica_acpack.version}.jar</destFileName>
</artifactItem>
</artifactItems>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<!-- Builds the jar for Fiji plugins. -->
<profile>
<id>build-fiji</id>
<build>
<plugins>
<!-- Runs the unit tests. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>${maven-surefire-plugin.version}</version>
<configuration>
<argLine>@{argLine}</argLine>
</configuration>
</plugin>
<!-- Runs the integration tests. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
<version>${maven-failsafe-plugin.version}</version>
<executions>
<execution>
<id>integration-tests</id>
<goals>
<goal>integration-test</goal>
<goal>verify</goal>
</goals>
<configuration>
<argLine>${itCoverageAgent}</argLine>
</configuration>
</execution>
</executions>
</plugin>
<!-- Runs the code coverage analysis. -->
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>${jacoco.version}</version>
<executions>
<execution>
<id>default-prepare-agent</id>
<goals>
<goal>prepare-agent</goal>
</goals>
</execution>
<execution>
<id>default-prepare-agent-integration</id>
<goals>
<goal>prepare-agent-integration</goal>
</goals>
<configuration>
<propertyName>itCoverageAgent</propertyName>
</configuration>
</execution>
<execution>
<id>default-report</id>
<goals>
<goal>report</goal>
</goals>
</execution>
<execution>
<id>default-report-integration</id>
<goals>
<goal>report-integration</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Adds the ALICA_interfaces dependency to the final .jar. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>${maven-shade-plugin.version}</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>ch.epfl.leb.sass.commandline.CommandLineInterface</mainClass>
</transformer>
</transformers>
<artifactSet>
<includes>
<include>com.github.LEB-EPFL:ALICA_interfaces</include>
</includes>
</artifactSet>
</configuration>
</execution>
</executions>
</plugin>
<!-- Download ALICA_ACPack and put it in output directory. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>${maven-dependency-plugin.version}</version>
<executions>
<execution>
<id>copy</id>
<phase>package</phase>
<goals>
<goal>copy</goal>
</goals>
</execution>
</executions>
<configuration>
<artifactItems>
<artifactItem>
<groupId>com.github.LEB-EPFL</groupId>
<artifactId>ALICA_ACPack</artifactId>
<version>${alica_acpack.version}</version>
<type>jar</type>
<overWrite>false</overWrite>
<outputDirectory>${project.build.directory}</outputDirectory>
<destFileName>ALICA_ACPack-${alica_acpack.version}.jar</destFileName>
</artifactItem>
</artifactItems>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>