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Merge branch 'release-staging/2.0.0' into release
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# Conflicts:
#	pom.xml
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@benknoll-umn
benknoll-umn committed Jun 29, 2018
2 parents 7b40858 + 15c3523 commit 1f5bb30
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15 changes: 15 additions & 0 deletions .travis.yml
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language: java
jdk:
- oraclejdk8
branches:
only:
- master
- release
cache:
directories:
- "$HOME/.m2"
notifications:
slack:
secure: 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
on_success: change
on_failure: always
295 changes: 243 additions & 52 deletions pom.xml
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@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright (C) 2016 Regents of the University of Minnesota
~ Copyright (C) 2018 Regents of the University of Minnesota
~
~ This program is free software: you can redistribute it and/or modify
~ it under the terms of the GNU General Public License as published by
Expand All @@ -20,49 +20,35 @@
xmlns="http://maven.apache.org/POM/4.0.0"
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>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-gpl</artifactId>
<packaging>jar</packaging>
<version>1.8.4</version>
<version>2.0.0</version>

<name>biomedicus-gpl</name>
<name>BioMedICUS GPL</name>
<description>BioMedICUS Annotation System - GPL Extensions</description>
<url>https://github.com/nlpie/biomedicus-gpl</url>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<biomedicus.version>1.8.4</biomedicus.version>
<java.version>1.8</java.version>
<biomedicus.version>2.0.0</biomedicus.version>
<kotlin.version>1.2.50</kotlin.version>
<maven.compiler.source>${java.version}</maven.compiler.source>
<maven.compiler.target>${java.version}</maven.compiler.target>
</properties>

<dependencies>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-core</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-uima</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.stanford.nlp</groupId>
<artifactId>stanford-corenlp</artifactId>
<version>3.6.0</version>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-stable</artifactId>
<version>3.8.0</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.0</version>
<optional>true</optional>
</dependency>
</dependencies>

<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
</repository>
</distributionManagement>

<build>
<resources>
Expand All @@ -83,8 +69,108 @@
</resources>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<artifactId>kotlin-maven-plugin</artifactId>
<groupId>org.jetbrains.kotlin</groupId>
<version>${kotlin.version}</version>
<configuration>
<apiVersion>1.2</apiVersion>
<jvmTarget>${java.version}</jvmTarget>
</configuration>
<executions>
<execution>
<id>compile</id>
<goals>
<goal>compile</goal>
</goals>
<configuration>
<sourceDirs>
<sourceDir>${project.basedir}/src/main/kotlin</sourceDir>
<sourceDir>${project.basedir}/src/main/java</sourceDir>
</sourceDirs>
</configuration>
</execution>
<execution>
<id>test-compile</id>
<goals>
<goal>test-compile</goal>
</goals>
<configuration>
<sourceDirs>
<sourceDir>${project.basedir}/src/test/kotlin</sourceDir>
<sourceDir>${project.basedir}/src/test/java</sourceDir>
</sourceDirs>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<compilerArgs>
<compilerArg>-Xlint:unchecked</compilerArg>
</compilerArgs>
</configuration>
<executions>
<!-- Replacing default-compile as it is treated specially by maven -->
<execution>
<id>default-compile</id>
<phase>none</phase>
</execution>
<!-- Replacing default-testCompile as it is treated specially by maven -->
<execution>
<id>default-testCompile</id>
<phase>none</phase>
</execution>
<execution>
<id>java-compile</id>
<phase>compile</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>java-test-compile</id>
<phase>test-compile</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.0</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.0.2</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.2</version>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.7</version>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>make-bundles</id>
Expand All @@ -100,20 +186,125 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.7</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
</plugins>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>

<profiles>
<profile>
<id>release</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.0.1</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>

<dependencies>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-stdlib-jdk8</artifactId>
<version>${kotlin.version}</version>
</dependency>
<dependency>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-reflect</artifactId>
<version>${kotlin.version}</version>
</dependency>

<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>nlpengine</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-core</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.umn.biomedicus</groupId>
<artifactId>biomedicus-uima</artifactId>
<version>${biomedicus.version}</version>
</dependency>
<dependency>
<groupId>edu.stanford.nlp</groupId>
<artifactId>stanford-corenlp</artifactId>
<version>3.9.1</version>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-stable</artifactId>
<version>3.8.2</version>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
<version>3.0.2</version>
<optional>true</optional>
</dependency>
</dependencies>

<reporting>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.0</version>
</plugin>
</plugins>
</reporting>

<organization>
<name>University of Minnesota Institute for Health Informatics NLP/IE Program</name>
<url>http://www.bmhi.umn.edu/ihi/research/nlpie/index.htm</url>
Expand All @@ -122,7 +313,8 @@
<developer>
<name>Ben Knoll</name>
<email>[email protected]</email>
<organization>NLP/IE Group at the University of Minnesota Institute for Health Informatics
<organization>
University of Minnesota Institute for Health Informatics NLP/IE Program
</organization>
<organizationUrl>http://www.bmhi.umn.edu/ihi/research/nlpie/index.htm</organizationUrl>
</developer>
Expand All @@ -135,9 +327,8 @@
</license>
</licenses>
<scm>
<url>https://github.com/NLPIE/BioMedICUS</url>
<connection>scm:git:https://github.com/NLPIE/BioMedICUS.git</connection>
<developerConnection>scm:git:https://github.com/NLPIE/BioMedICUS.git</developerConnection>
<connection>scm:git:git://github.com:nlpie/biomedicus-gpl.git</connection>
<developerConnection>scm:git:ssh://github.com:nlpie/biomedicus-gpl.git</developerConnection>
<url>https://github.com/nlpie/biomedicus-gpl</url>
</scm>

</project>
</project>
9 changes: 5 additions & 4 deletions src/assembly/descriptor.xml
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@@ -1,5 +1,5 @@
<!--
~ Copyright (C) 2016 Regents of the University of Minnesota
~ Copyright (C) 2018 Regents of the University of Minnesota
~
~ This program is free software: you can redistribute it and/or modify
~ it under the terms of the GNU General Public License as published by
Expand All @@ -15,9 +15,9 @@
~ along with this program. If not, see <http://www.gnu.org/licenses/>.
-->

<assembly xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.0.0 http://maven.apache.org/xsd/assembly-2.0.0.xsd">
<id>release</id>
<formats>
<format>zip</format>
Expand Down Expand Up @@ -54,6 +54,7 @@
<includes>
<include>**/*</include>
</includes>
<filtered>true</filtered>
</fileSet>
<fileSet>
<directory>src/main/top</directory>
Expand Down
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