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add release for lphy, studio, lphybeast part #56
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@walterxie
walterxie committed Aug 5, 2024
1 parent 4015472 commit 86a9573
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Showing 8 changed files with 197 additions and 45 deletions.
1 change: 1 addition & 0 deletions phylonco-beast/pom.xml
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</parent>

<artifactId>phylonco-beast</artifactId>
<!-- must be consisting with version.xml -->
<version>1.2.0-SNAPSHOT</version>

<properties>
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30 changes: 28 additions & 2 deletions phylonco-lphy-studio/pom.xml
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Expand Up @@ -7,6 +7,7 @@
</parent>

<artifactId>phylonco-lphy-studio</artifactId>
<version>1.2.0-SNAPSHOT</version>

<dependencies>
<dependency>
Expand All @@ -18,9 +19,34 @@
<dependency>
<groupId>io.github.linguaphylo</groupId>
<artifactId>lphy-studio</artifactId>
<version>1.6.0-SNAPSHOT</version>
<version>${lphy.vision}</version>
</dependency>
</dependencies>


<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.7.1</version>
<configuration>
<descriptors>
<descriptor>src/assembly/phylonco-lphy-studio-assembly.xml</descriptor>
</descriptors>
<outputDirectory>${project.build.directory}</outputDirectory>
<appendAssemblyId>false</appendAssemblyId>
<finalName>${project.artifactId}-${project.version}</finalName>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>
76 changes: 76 additions & 0 deletions phylonco-lphy-studio/src/assembly/phylonco-lphy-studio-assembly.xml
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<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.2.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.2.0 http://maven.apache.org/xsd/assembly-2.2.0.xsd">
<id>phylonco-lphy-studio-assembly</id>
<formats>
<format>dir</format>
<!-- <format>zip</format>-->
</formats>
<includeBaseDirectory>false</includeBaseDirectory>

<moduleSets>
<moduleSet>
<useAllReactorProjects>true</useAllReactorProjects>
<includes>
<include>io.github.linguaphylo:phylonco-lphy</include>
<include>io.github.linguaphylo:phylonco-lphy-studio</include>
</includes>

<sources>
<includeModuleDirectory>false</includeModuleDirectory>
<fileSets>
<fileSet>
<outputDirectory>src/${module.artifactId}</outputDirectory>
<excludes>
<exclude>${project.build.directory}/**</exclude>
<exclude>**/target/**</exclude>
<exclude>**/lib/**</exclude>
<exclude>**/examples/**</exclude>
</excludes>
</fileSet>
</fileSets>
</sources>
</moduleSet>
</moduleSets>
<fileSets>
<fileSet>
<directory>${project.basedir}/src/main/resources</directory>
<outputDirectory>src</outputDirectory>
<includes>
<include>lphy*.*</include>
</includes>
</fileSet>
<fileSet>
<directory>../examples</directory>
<outputDirectory>examples</outputDirectory>
<includes>
<include>**/*.lphy</include>
<include>**/data/**</include>
</includes>
<excludes>
<exclude>**/todo/**</exclude>
<exclude>**/*.log</exclude>
<exclude>**/*.trees</exclude>
<exclude>**/*.txt</exclude>
</excludes>
</fileSet>
</fileSets>
<!-- <files>-->
<!-- <file>-->
<!-- <source>../README.md</source>-->
<!-- </file>-->
<!-- <file>-->
<!-- <source>../LICENSE</source>-->
<!-- </file>-->
<!-- </files>-->
<dependencySets>
<dependencySet>
<outputDirectory>/lib</outputDirectory>
<includes>
<!-- only phylonco jars -->
<include>io.github.linguaphylo:phylonco-lphy</include>
<include>io.github.linguaphylo:phylonco-lphy-studio</include>
</includes>
</dependencySet>
</dependencySets>
</assembly>
6 changes: 3 additions & 3 deletions phylonco-lphy/pom.xml
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@@ -1,21 +1,21 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>io.github.linguaphylo</groupId>
<artifactId>beast-phylonco</artifactId>
<version>${revision}</version>
</parent>

<artifactId>phylonco-lphy</artifactId>
<version>1.2.0-SNAPSHOT</version>

<dependencies>
<dependency>
<groupId>io.github.linguaphylo</groupId>
<artifactId>lphy-base</artifactId>
<version>1.6.0-SNAPSHOT</version>
<version>${lphy.vision}</version>
</dependency>
</dependencies>


</project>
32 changes: 29 additions & 3 deletions phylonco-lphybeast/pom.xml
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</parent>

<artifactId>phylonco-lphybeast</artifactId>
<!-- must be consisting with version.xml -->
<version>1.2.0-SNAPSHOT</version>

<dependencies>
<dependency>
<groupId>io.github.linguaphylo</groupId>
<artifactId>lphybeast</artifactId>
<version>1.2.0-SNAPSHOT</version>
<version>${lphybeast.vision}</version>
</dependency>

<dependency>
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<artifactId>phylonco-lphy</artifactId>
<version>${project.version}</version>
</dependency>


</dependencies>

<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.7.1</version>
<configuration>
<descriptors>
<descriptor>src/assembly/phylonco-lphybeast-assembly.xml</descriptor>
</descriptors>
<outputDirectory>${project.build.directory}</outputDirectory>
<appendAssemblyId>false</appendAssemblyId>
<finalName>${project.artifactId}-${project.version}</finalName>
</configuration>
<executions>
<execution>
<id>make-assembly</id> <!-- this is used for inheritance merges -->
<phase>package</phase> <!-- bind to the packaging phase -->
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>

</project>
51 changes: 51 additions & 0 deletions phylonco-lphybeast/src/assembly/phylonco-lphybeast-assembly.xml
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<assembly xmlns="http://maven.apache.org/ASSEMBLY/2.2.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/ASSEMBLY/2.2.0 http://maven.apache.org/xsd/assembly-2.2.0.xsd">
<id>phylonco-lphybeast-assembly</id>
<formats>
<format>dir</format>
<format>zip</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<!-- <baseDirectory>${project.artifactId}-${project.version}</baseDirectory>-->

<moduleSets>
<moduleSet>
<useAllReactorProjects>true</useAllReactorProjects>
<includes>
<include>io.github.linguaphylo:phylonco-lphybeast</include>
</includes>

<sources>
<includeModuleDirectory>false</includeModuleDirectory>
<fileSets>
<fileSet>
<outputDirectory>src/${module.artifactId}</outputDirectory>
<excludes>
<exclude>${project.build.directory}/**</exclude>
<exclude>**/target/**</exclude>
<exclude>**/lib/**</exclude>
</excludes>
</fileSet>
</fileSets>
</sources>
</moduleSet>
</moduleSets>
<files>
<file>
<source>version.xml</source>
</file>
</files>
<dependencySets>
<!-- Dependency set for lphybeast with useTransitiveDependencies set to false -->
<dependencySet>
<outputDirectory>/lib</outputDirectory>
<includes>
<include>io.github.linguaphylo:phylonco-lphybeast</include>
</includes>
<useTransitiveDependencies>false</useTransitiveDependencies>
</dependencySet>

</dependencySets>

</assembly>
40 changes: 6 additions & 34 deletions phylonco-lphybeast/version.xml
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<package name='phylonco' version='1.1.0'>
<package name='phylonco.lphybeast' version='1.2.0'>
<!-- phylonco beast -->
<depends on='BEAST.base' atleast='2.7.6'/>
<depends on='BEAST.app' atleast='2.7.6'/>
<depends on='BEASTLabs' atleast='2.0.2'/>
<depends on='lphybeast' atleast='1.1.0'/>
<depends on='phylonco' atleast='1.2.0'/>
<depends on='lphybeast' atleast='1.2.0'/>

<!-- add BEAST2 service below -->
<service type="beast.base.evolution.datatype.DataType">
<provider classname="phylonco.beast.evolution.datatype.NucleotideDiploid10"/>
<provider classname="phylonco.beast.evolution.datatype.NucleotideDiploid16"/>
<provider classname="phylonco.beast.evolution.datatype.NucleotideMethylation"/>
<provider classname="phylonco.beast.evolution.datatype.Ternary"/>
<!-- any ? -->
<!-- <provider classname="phylonco.beast.evolution.datatype.NucleotideDiploid10"/>-->
</service>
<service type="beast.base.core.BEASTInterface">
<provider classname="phylonco.beast.evolution.datatype.NucleotideDiploid10"/>
<provider classname="phylonco.beast.evolution.datatype.NucleotideDiploid16"/>
<provider classname="phylonco.beast.evolution.datatype.NucleotideMethylation"/>
<provider classname="phylonco.beast.evolution.datatype.Ternary"/>
<provider classname="phylonco.beast.evolution.errormodel.BinaryErrorModel"/>
<provider classname="phylonco.beast.evolution.errormodel.ErrorModel"/>
<provider classname="phylonco.beast.evolution.errormodel.ErrorModelBase"/>
<provider classname="phylonco.beast.evolution.errormodel.GT16ErrorModel"/>
<provider classname="phylonco.beast.evolution.likelihood.BeagleTreeLikelihoodWithError"/>
<provider classname="phylonco.beast.evolution.likelihood.TreeLikelihoodWithError"/>
<provider classname="phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorFast"/>
<provider classname="phylonco.beast.evolution.likelihood.TreeLikelihoodWithErrorSlow"/>
<provider classname="phylonco.beast.evolution.substitutionmodel.BinarySubstitutionModel"/>
<provider classname="phylonco.beast.evolution.substitutionmodel.GT16"/>
<provider classname="phylonco.beast.evolution.substitutionmodel.MethylationHKY"/>
<provider classname="phylonco.beast.evolution.substitutionmodel.SiFit2"/>
<provider classname="phylonco.beast.evolution.substitutionmodel.SiFit3"/>
<provider classname="phylonco.beast.evolution.populationmodel.GompertzGrowth_f0"/>
<provider classname="phylonco.beast.evolution.populationmodel.ExponentialGrowth"/>
<provider classname="phylonco.beast.evolution.populationmodel.LogisticGrowth"/>
<provider classname="phylonco.beast.evolution.populationmodel.GompertzGrowth_t50"/>
<provider classname="phylonco.beast.evolution.populationmodel.ConstantGrowth"/>
<provider classname="phylonco.beast.evolution.populationmodel.StochasticVariableSelection"/>


<!-- any ? -->
</service>

<!-- add lphybeast ext below -->
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6 changes: 3 additions & 3 deletions pom.xml
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<name>beast-phylonco</name>

<properties>
<!-- https://maven.apache.org/maven-ci-friendly.html -->
<lphy.vision>1.6.0-SNAPSHOT</lphy.vision>
<lphybeast.vision>1.2.0-SNAPSHOT</lphybeast.vision>
<!-- project.version https://maven.apache.org/maven-ci-friendly.html -->
<revision>1.2.0-SNAPSHOT</revision>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

<!-- <lphyVersion>1.6.0-SNAPSHOT</lphyVersion>-->
</properties>

<modules>
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