Merge pull request #12 from BEAST2-Dev/main

correct release and CI

Author: walterxie

.github/workflows/ci-publish.yml

@@ -2,30 +2,30 @@ name: CI & Publish
 
 on:
   push:
-    branches: [ master ]
+    branches: [ main ]
     tags: [ 'v*' ]
   pull_request:
-    branches: [ master ]
+    branches: [ main ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up JDK 25 (Azul Zulu)
         if: "!startsWith(github.ref, 'refs/tags/v')"
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           distribution: zulu
           java-version: '25'
           cache: maven
 
       - name: Set up JDK 25 (Azul Zulu) for Maven Central
         if: startsWith(github.ref, 'refs/tags/v')
-        uses: actions/setup-java@v4
+        uses: actions/setup-java@v5
         with:
           distribution: zulu
           java-version: '25'
@@ -44,11 +44,12 @@ jobs:
           mvn versions:set -DnewVersion=$VERSION -DgenerateBackupPoms=false
 
       - name: Build and test
+        if: "!startsWith(github.ref, 'refs/tags/v')"
         run: mvn verify
 
       - name: Publish to Maven Central
         if: startsWith(github.ref, 'refs/tags/v')
-        run: mvn deploy -Prelease -DskipTests
+        run: mvn -Prelease clean deploy
         env:
           CENTRAL_USERNAME: ${{ secrets.CENTRAL_USERNAME }}
           CENTRAL_TOKEN: ${{ secrets.CENTRAL_TOKEN }}

pom.xml

@@ -4,14 +4,14 @@
          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.compevol</groupId>
+    <groupId>io.github.beast2-dev</groupId>
     <artifactId>mutable-alignment</artifactId>
     <version>0.1.0-SNAPSHOT</version>
 
     <name>Mutable Alignment</name>
     <description>Mutable alignment support for BEAST</description>
 
-    <url>https://github.com/rbouckaert/MutableAlignment</url>
+    <url>https://github.com/BEAST2-Dev/MutableAlignment</url>
 
     <licenses>
         <license>
@@ -28,21 +28,20 @@
     </developers>
 
     <scm>
-        <connection>scm:git:git://github.com/rbouckaert/MutableAlignment.git</connection>
-        <developerConnection>scm:git:ssh://github.com:rbouckaert/MutableAlignment.git</developerConnection>
-        <url>https://github.com/rbouckaert/MutableAlignment</url>
+        <connection>scm:git:git://github.com/BEAST2-Dev/MutableAlignment.git</connection>
+        <developerConnection>scm:git:ssh://github.com:BEAST2-Dev/MutableAlignment.git</developerConnection>
+        <url>https://github.com/BEAST2-Dev/MutableAlignment</url>
     </scm>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <maven.compiler.release>25</maven.compiler.release>
-        <beast.version>2.8.0-beta2</beast.version>
+        <beast.version>2.8.0-beta7</beast.version>
         <beast.module>beast.base</beast.module>
         <beast.main>beast.base.minimal.BeastMain</beast.main>
         <beast.args/>
         <beast.pkg.name>MutableAlignment</beast.pkg.name>
-        <beast.pkg.version>0.1.0</beast.pkg.version>
     </properties>
 
     <dependencies>
@@ -75,6 +74,28 @@
 
     <build>
         <plugins>
+            <!-- Derive beast.pkg.version from project.version (strip -SNAPSHOT) so the
+                 version is declared once, in <version> above -->
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>3.6.0</version>
+                <executions>
+                    <execution>
+                        <id>set-beast-pkg-version</id>
+                        <phase>validate</phase>
+                        <goals><goal>regex-property</goal></goals>
+                        <configuration>
+                            <name>beast.pkg.version</name>
+                            <value>${project.version}</value>
+                            <regex>-SNAPSHOT$</regex>
+                            <replacement></replacement>
+                            <failIfNoMatch>false</failIfNoMatch>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <!-- Compiler -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -228,7 +249,7 @@
                     <plugin>
                         <groupId>org.sonatype.central</groupId>
                         <artifactId>central-publishing-maven-plugin</artifactId>
-                        <version>0.6.0</version>
+                        <version>0.11.0</version>
                         <extensions>true</extensions>
                         <configuration>
                             <publishingServerId>central</publishingServerId>

src/assembly/beast-package.xml

@@ -28,7 +28,7 @@
             <useProjectArtifact>true</useProjectArtifact>
             <scope>runtime</scope>
             <includes>
-                <include>io.github.compevol:mutable-alignment</include>
+                <include>io.github.beast2-dev:mutable-alignment</include>
             </includes>
         </dependencySet>
     </dependencySets>