sru
Used in
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency>
<groupId>io.github.jonasschaub</groupId>
<artifactId>sru</artifactId>
<version>1.4.0.0</version>
</dependency><?xml version="1.0" encoding="UTF-8"?>
<!--
~ MIT License
~
~ Copyright (c) 2023 Jonas Schaub, Achim Zielesny, Christoph Steinbeck, Maria Sorokina
~
~ Permission is hereby granted, free of charge, to any person obtaining a copy
~ of this software and associated documentation files (the "Software"), to deal
~ in the Software without restriction, including without limitation the rights
~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the Software is
~ furnished to do so, subject to the following conditions:
~
~ The above copyright notice and this permission notice shall be included in all
~ copies or substantial portions of the Software.
~
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
~ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
~ SOFTWARE.
-->
<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>
<groupId>io.github.jonasschaub</groupId>
<artifactId>sru</artifactId>
<version>1.4.0.0</version>
<name>Sugar Removal Utility</name>
<packaging>jar</packaging>
<url>https://github.com/JonasSchaub/SugarRemoval</url>
<description>
The Sugar Removal Utility - An algorithmic approach for in silico removal of circular and linear sugars from molecular structures.
</description>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<sonar.organization>jonasschaub</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<project.build.source>17</project.build.source>
<project.build.target>17</project.build.target>
<java.version>17</java.version>
<cdk.version>2.9</cdk.version>
<junit.version>5.10.0</junit.version>
<hamcrest.version>2.2</hamcrest.version>
<spotless.version>2.40.0</spotless.version>
<sonar.organization>jonasschaub</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
</properties>
<licenses>
<license>
<name>MIT</name>
<url>https://opensource.org/license/mit/</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<url>https://github.com/JonasSchaub/SugarRemoval</url>
<connection>scm:git:git://github.com/JonasSchaub/SugarRemoval.git</connection>
<developerConnection>scm:git:git@github.com:JonasSchaub/SugarRemoval.git</developerConnection>
<tag>HEAD</tag>
</scm>
<issueManagement>
<url>https://github.com/JonasSchaub/SugarRemoval/issues</url>
</issueManagement>
<developers>
<developer>
<name>Jonas Schaub</name>
<email>jonas.schaub@uni-jena.de</email>
<organization>Friedrich Schiller University Jena</organization>
<organizationUrl>https://cheminf.uni-jena.de</organizationUrl>
</developer>
<developer>
<name>Achim Zielesny</name>
<email>achim.zielesny@w-hs.de</email>
<organization>Westphalian University of Applied Sciences</organization>
<organizationUrl>https://www.w-hs.de/service/informationen-zur-person/person/zielesny/</organizationUrl>
</developer>
<developer>
<name>Christoph Steinbeck</name>
<email>christoph.steinbeck@uni-jena.de</email>
<organization>Friedrich Schiller University Jena</organization>
<organizationUrl>https://cheminf.uni-jena.de</organizationUrl>
</developer>
<developer>
<name>Maria Sorokina</name>
<organization>Friedrich Schiller University Jena</organization>
<organizationUrl>https://cheminf.uni-jena.de</organizationUrl>
</developer>
</developers>
<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://s01.oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://s01.oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<repositories>
<repository>
<id>ossrh</id>
<url>https://s01.oss.sonatype.org/content/repositories/snapshots</url>
</repository>
</repositories>
<dependencies>
<!--
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-bundle</artifactId>
<version>${cdk.version}</version>
</dependency>
-->
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-core</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-smiles</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-model</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-depict</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-data</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-inchi</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-silent</artifactId>
<version>${cdk.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.4</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<scope>test</scope>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-params</artifactId>
<scope>test</scope>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<scope>test</scope>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-core</artifactId>
<scope>test</scope>
<version>${hamcrest.version}</version>
</dependency>
<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest</artifactId>
<scope>test</scope>
<version>${hamcrest.version}</version>
</dependency>
</dependencies>
<build>
<finalName>SugarRemovalUtility</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.10.1</version>
<configuration>
<release>17</release>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.2</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>de.unijena.cheminf.deglycosylation.Main</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.5.0</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.4.2</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>de.unijena.cheminf.deglycosylation.Main</mainClass>
</manifest>
</archive>
</configuration>
<executions>
<execution>
<id>assemble-all</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.2.1</version>
</plugin>
<plugin>
<groupId>com.diffplug.spotless</groupId>
<artifactId>spotless-maven-plugin</artifactId>
<version>${spotless.version}</version>
<configuration>
<!-- define a language-specific format -->
<java>
<includes>
<include>src/main/java/**/*.java</include>
<include>src/test/java/**/*.java</include>
</includes>
<excludes>
<exclude>src/main/java/org/openscience/cdk/cdkbook/SMILESFormatMatcher.java</exclude>
</excludes>
<encoding>UTF-8</encoding>
<!-- Cleanthat will refactor your code, but it may break your style: apply it before your formatter -->
<cleanthat />
<importOrder>
<order>de,org,com,java,javax</order>
</importOrder>
<removeUnusedImports>
<engine>cleanthat-javaparser-unnecessaryimport</engine>
</removeUnusedImports>
<trimTrailingWhitespace/>
<endWithNewline/>
<indent>
<tabs>false</tabs>
<spaces>true</spaces>
<spacesPerTab>4</spacesPerTab>
</indent>
<!-- make sure every file has the following copyright header.
optionally, Spotless can set copyright years by digging
through git history (see "license" section below) -->
<licenseHeader>
<file>${project.basedir}/License-header/License-header.txt</file>
</licenseHeader>
<replaceRegex>
<name>Remove wildcard imports</name>
<searchRegex>import\s+[^\*\s]+\*;(\r\n|\r|\n)</searchRegex>
<replacement>$1</replacement>
</replaceRegex>
</java>
</configuration>
<executions>
<execution>
<goals>
<goal>check</goal>
</goals>
<phase>compile</phase>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.13</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>false</autoReleaseAfterClose>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5.3</version>
<configuration>
<tagNameFormat>@{project.version}</tagNameFormat>
</configuration>
<executions>
<execution>
<id>default</id>
<goals>
<goal>perform</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>Open source consumption has exploded, with estimates placing this year’s downloads at over 6.6 trillion. This reliance on open source components, now making up to 90% of the modern software application, has ushered in both unprecedented innovation and complex challenges for software supply chains.
View the Report