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Upgrade to Maven by egonw · Pull Request #2 · cdk/chemojava · GitHub

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Upgrade to Maven #2

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7e9c434
Removed development jars
egonw Jun 6, 2021
37deae6
Replaced Ant by Maven
egonw Jun 6, 2021
6ceed13
Maven dir structure
egonw Jun 6, 2021
297b536
Is a separate package nowadays
egonw Jun 6, 2021
86da514
First dependencies defined
egonw Jun 6, 2021
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bin/
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186 changes: 186 additions & 0 deletions 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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-chemojava</artifactId>
<version>1.5.0</version>
<packaging>jar</packaging>
<name>ChemoJava</name>
<description>CDK extensions with GPL-licensed code</description>

<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
</properties>

<dependencies>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-qsar</artifactId>
<version>2.5</version>
</dependency>
<dependency>
<groupId>nz.ac.waikato.cms.weka</groupId>
<artifactId>weka-stable</artifactId>
<version>3.6.6</version>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.2</version>
<configuration>
<!-- prevent the annoying ForkedBooter process from stealing
window focus on Mac OS -->
<argLine>@{argLine} -Djava.awt.headless=true -Dcdk.logging.level=ERROR</argLine>
<excludes>
<!-- not a test class -->
<exclude>**/TestMoleculeFactory.java</exclude>
<!-- missing functionality -->
<exclude>**/cdk/limitations/**</exclude>
<!-- coverage tests need updating -->
<exclude>**/*CoverageTest.java</exclude>
<!-- module suites not needed -->
<exclude>**/modulesuites/M*Tests.java</exclude>
<!-- format tests do not work (cyclic dependency) -->
<exclude>**/io/formats/*FormatTest.java</exclude>
</excludes>
<excludedGroups>org.openscience.cdk.SlowTest</excludedGroups>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
<inherited>true</inherited>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<tags>
<!--cdk.depends and cdk.builddepends no longer used-->
<tag>
<name>cdk.set</name>
<placement>a</placement>

<head>Belongs to the set:</head>
</tag>
<tag>
<name>cdk.keyword</name>
<placement>a</placement>

<head>Keywords:</head>
</tag>
<tag>
<name>cdk.created</name>
<placement>a</placement>

<head>Created on:</head>
</tag>
<tag>
<name>cdk.require</name>
<placement>a</placement>

<head>Requires:</head>
</tag>
<tag>
<name>cdk.todo</name>
<placement>a</placement>

<head>To do:</head>
</tag>
<tag>
<name>cdk.license</name>
<placement>a</placement>

<head>License:</head>
</tag>
</tags>
<taglets>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKCiteTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKBugTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKDictRefTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKGitTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKInChITaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKIOOptionsTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKModuleTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKThreadSafeTaglet</tagletClass>
</taglet>
<taglet>
<tagletClass>net.sf.cdk.tools.doclets.CDKThreadNonSafeTaglet
</tagletClass>
</taglet>
</taglets>
<tagletArtifact>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-build-utils</artifactId>
<version>1.0.2.8</version>
</tagletArtifact>
<failOnError>false</failOnError>
<doctitle>ChemoJava ${project.version} API</doctitle>
<stylesheetfile>${basedir}/doc/javadoc/stylesheet.css</stylesheetfile>
</configuration>
<executions>
<execution>
<id>aggregate</id>
<goals>
<goal>aggregate</goal>
</goals>
<phase>site</phase>
<configuration>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>

</project>
0 ...rg/openscience/cdk/qsar/model/IModel.java → ...rg/openscience/cdk/qsar/model/IModel.java
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0 ...ce/cdk/qsar/model/QSARModelException.java → ...ce/cdk/qsar/model/QSARModelException.java
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0 .../cdk/qsar/model/R/CNNRegressionModel.java → .../cdk/qsar/model/R/CNNRegressionModel.java
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0 .../cdk/qsar/model/R/PLSRegressionModel.java → .../cdk/qsar/model/R/PLSRegressionModel.java
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0 .../openscience/cdk/qsar/model/R/RModel.java → .../openscience/cdk/qsar/model/R/RModel.java
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0 ...rg/openscience/cdk/qsar/model/data/lm_2.R → ...rg/openscience/cdk/qsar/model/data/lm_2.R
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