sru

Description

<dependency>
    <groupId>io.github.jonasschaub</groupId>
    <artifactId>sru</artifactId>
    <version>1.5.0.0</version>
</dependency>

<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ MIT License
  ~
  ~ Copyright (c) 2025 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>1.5.0.0</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>2.10</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>
        <repository>
            <id>oss-sonatype</id>
            <name>oss-sonatype</name>
            <url>https://central.sonatype.org/content/repositories/</url>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
        </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>${cdk.version}</version>
        </dependency>
        <dependency>
            <groupId>org.openscience.cdk</groupId>
            <artifactId>cdk-extra</artifactId>
            <version>${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>11</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>1.7.0</version>
                <extensions>true</extensions>
                <configuration>
                    <serverId>ossrh</serverId>
                    <nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
                    <autoReleaseAfterClose>false</autoReleaseAfterClose>
                    <keepStagingRepositoryOnCloseRuleFailure>true</keepStagingRepositoryOnCloseRuleFailure>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-release-plugin</artifactId>
                <version>3.1.1</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>3.2.7</version>
                <executions>
                    <execution>
                        <id>sign-artifacts</id>
                        <phase>verify</phase>
                        <goals>
                            <goal>sign</goal>
                        </goals>
                        <configuration>
                            <executable>gpg</executable>
                            <gpgArguments>
                                <arg>--pinentry-mode</arg>
                                <arg>loopback</arg>
                            </gpgArguments>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>
<profiles>
    <profile>
        <id>coverage</id>
        <build>
            <plugins>
                <plugin>
                    <groupId>org.jacoco</groupId>
                    <artifactId>jacoco-maven-plugin</artifactId>
                    <version>0.8.12</version>
                    <executions>
                        <execution>
                            <id>prepare-agent</id>
                            <goals>
                                <goal>prepare-agent</goal>
                            </goals>
                        </execution>
                        <execution>
                            <id>report</id>
                            <goals>
                                <goal>report</goal>
                            </goals>
                            <configuration>
                                <formats>
                                    <format>XML</format>
                                </formats>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>
            </plugins>
        </build>
    </profile>
</profiles>
</project>