<?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>
    <artifactId>SilentGenes</artifactId>
    <packaging>pom</packaging>
    <modules>
        <module>silent-genes-model</module>
        <module>silent-genes-simple</module>
        <module>silent-genes-io</module>
        <module>silent-genes-gtf</module>
        <module>silent-genes-jannovar</module>
        <module>silent-genes-cli</module>
    </modules>

    <groupId>org.monarchinitiative.sgenes</groupId>
    <version>0.2.2</version>
    <name>SilentGenes</name>
    <inceptionYear>2021</inceptionYear>

    <parent>
        <groupId>org.springframework.boot</groupId>
        <artifactId>spring-boot-starter-parent</artifactId>
        <version>2.6.3</version>
    </parent>

    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
        <java.version>11</java.version>
        <maven.compiler.source>${java.version}</maven.compiler.source>
        <maven.compiler.target>${java.version}</maven.compiler.target>

        <spring-boot-starter.version>2.5.5</spring-boot-starter.version>
        <svart.version>2.0.0-RC1</svart.version>
        <jannovar.version>0.35</jannovar.version>
        <guava.version>31.0.1-jre</guava.version>
        <commons-compress.version>1.21</commons-compress.version>
        <commons-csv.version>1.9.0</commons-csv.version>
        <picocli.version>4.6.2</picocli.version>
        <slf4j.version>1.7.35</slf4j.version>
    </properties>

    <developers>
        <developer>
            <name>Daniel Danis</name>
            <email>daniel.danis@jax.org</email>
            <organization>The Jackson Laboratory for Genomic Medicine</organization>
            <organizationUrl>https://www.jax.org</organizationUrl>
        </developer>
        <developer>
            <name>Michael Gargano</name>
            <email>michael.gargano@jax.org</email>
            <organization>The Jackson Laboratory for Genomic Medicine</organization>
            <organizationUrl>https://www.jax.org</organizationUrl>
        </developer>
        <developer>
            <name>Peter N Robinson</name>
            <email>peter.robinson@jax.org</email>
            <organization>The Jackson Laboratory for Genomic Medicine</organization>
            <organizationUrl>https://www.jax.org</organizationUrl>
        </developer>
    </developers>

    <scm>
        <connection>scm:git:git@github.com:ielis/SilentGenes.git</connection>
        <developerConnection>scm:git:git@github.com:ielis/SilentGenes.git</developerConnection>
        <url>scm:git:git@github.com:ielis/SilentGenes.git</url>
        <tag>v0.2.2</tag>
    </scm>

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

    <licenses>
        <license>
            <name>BSD-3-Clause</name>
            <distribution>repo</distribution>
        </license>
    </licenses>

    <profiles>
        <profile>
            <!-- This profile should be activated only when a release is being built. -->
            <!-- Then, GPG plugin is used to sign the artifacts. Note that you need to set up your GPG key first. -->
            <!-- Activate the profile by running e.g. `mvn -DperformRelease=true clean deploy` -->
            <id>release-sign-artifacts</id>
            <activation>
                <property>
                    <name>performRelease</name>
                    <value>true</value>
                </property>
            </activation>
            <build>
                <plugins>

                    <plugin>
                        <!-- override version of GPG plugin to use new GPG signing features -->
                        <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>

    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>org.monarchinitiative.svart</groupId>
                <artifactId>svart</artifactId>
                <version>${svart.version}</version>
            </dependency>
            <dependency>
                <groupId>de.charite.compbio</groupId>
                <artifactId>jannovar-core</artifactId>
                <version>${jannovar.version}</version>
                <exclusions>
                    <exclusion>
                        <groupId>com.google.guava</groupId>
                        <artifactId>guava</artifactId>
                    </exclusion>
                </exclusions>
            </dependency>
            <dependency>
                <groupId>com.google.guava</groupId>
                <artifactId>guava</artifactId>
                <version>${guava.version}</version>
            </dependency>
            <dependency>
                <groupId>info.picocli</groupId>
                <artifactId>picocli</artifactId>
                <version>${picocli.version}</version>
            </dependency>
            <dependency>
                <groupId>org.apache.commons</groupId>
                <artifactId>commons-csv</artifactId>
                <version>${commons-csv.version}</version>
            </dependency>
            <dependency>
                <groupId>org.slf4j</groupId>
                <artifactId>slf4j-api</artifactId>
                <version>${slf4j.version}</version>
            </dependency>
        </dependencies>
    </dependencyManagement>

    <dependencies>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
        </dependency>
        <dependency>
            <groupId>org.junit.jupiter</groupId>
            <artifactId>junit-jupiter</artifactId>
            <version>5.8.2</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.hamcrest</groupId>
            <artifactId>hamcrest</artifactId>
            <version>2.2</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-simple</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-source-plugin</artifactId>
                    <version>2.2.1</version>
                    <executions>
                        <execution>
                            <id>attach-sources</id>
                            <goals>
                                <goal>jar-no-fork</goal>
                            </goals>
                        </execution>
                    </executions>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-javadoc-plugin</artifactId>
                    <version>3.1.0</version>
                    <configuration>
                        <javadocExecutable>${java.home}/bin/javadoc</javadocExecutable>
                        <doclint>none</doclint>
                        <quiet>true</quiet>
                    </configuration>
                    <executions>
                        <execution>
                            <id>attach-javadocs</id>
                            <goals>
                                <goal>jar</goal>
                            </goals>
                        </execution>
                    </executions>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-compiler-plugin</artifactId>
                    <version>3.8.0</version>
                    <configuration>
                        <compilerArgument>-Xlint:all</compilerArgument>
                        <showWarnings>true</showWarnings>
                        <showDeprecation>true</showDeprecation>
                        <source>${java.version}</source>
                        <target>${java.version}</target>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-surefire-plugin</artifactId>
                    <version>3.0.0-M5</version>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-jar-plugin</artifactId>
                    <version>3.2.0</version>
                </plugin>
            </plugins>
        </pluginManagement>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
            </plugin>
        </plugins>
    </build>
</project>
