Migrate morph-models to BEAST 3

.github/workflows/main.yml

@@ -0,0 +1,18 @@
+name: Unit/integration tests
+on: [ push, pull_request, workflow_dispatch ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: 25
+          server-id: github
+          server-username: GITHUB_ACTOR
+          server-password: GITHUB_TOKEN
+      - run: mvn test
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -2,3 +2,9 @@
 /.idea
 /morph-models.iml
 /out
+
+# Maven build output
+target/
+
+# Package ZIPs
+*.v*.zip

README.md

@@ -1,8 +1,102 @@
 morph-models
 ============
 
-Models for dealing with standard discrete morphological data.
+Models for discrete morphological character data in [BEAST 3](https://github.com/CompEvol/beast3).
 
-Aiming at MK and MKv models from Lewis, 2001 (http://sysbio.oxfordjournals.org/content/50/6/913.short)
+Implements the Lewis MK and MKv substitution models (Lewis, 2001), along with ordinal and nested ordinal variants for ordered character data.
 
-A tutorial is available [here](http://www.beast2.org/morphological-models/)
+## Modules
+
+- **beast-morph-models** — core substitution models and alignment classes (depends on `beast-base`)
+- **beast-morph-models-fx** — BEAUti integration (depends on `beast-fx`)
+
+## Substitution models
+
+| Class | Description |
+|-------|-------------|
+| `LewisMK` | Equal or user-specified frequency Mk model |
+| `Ordinal` | Tridiagonal rate matrix for ordered characters |
+| `NestedOrdinal` | Nested ordinal rate matrix (state 0 transitions to all others) |
+
+## Building
+
+BEAST 3 dependencies are resolved from [GitHub Packages](https://github.com/CompEvol/beast3/packages) (or Maven Central, if published there). For GitHub Packages, add a [personal access token](https://github.com/settings/tokens) (classic) with `read:packages` scope to `~/.m2/settings.xml`:
+
+```xml
+<settings>
+  <servers>
+    <server>
+      <id>github</id>
+      <username>YOUR_GITHUB_USERNAME</username>
+      <password>YOUR_GITHUB_PAT</password>
+    </server>
+  </servers>
+</settings>
+```
+
+Then build morph-models:
+
+```bash
+cd ~/Git/morph-models
+mvn compile
+mvn test -pl beast-morph-models
+```
+
+Alternatively, you can install BEAST 3 from source (no GitHub auth needed):
+
+```bash
+cd ~/Git/beast3
+mvn install -DskipTests
+```
+
+## Running
+
+```bash
+# Validate an XML
+mvn -pl beast-morph-models exec:exec -Dbeast.args="-validate examples/M3982.xml"
+
+# Run an analysis
+mvn -pl beast-morph-models exec:exec -Dbeast.args="-overwrite examples/M3982.xml"
+```
+
+## Examples
+
+- `examples/M3982.xml` — Anolis lizard morphological analysis using BEAST 3 spec classes
+- `examples/legacy-2.7/` — original BEAST 2.7 XML files (some require external packages)
+
+## Releasing
+
+### ZIP / CBAN
+
+The existing `release.sh` script builds a BEAST package ZIP and optionally
+creates a GitHub release for submission to [CBAN](https://github.com/CompEvol/CBAN):
+
+```bash
+./release.sh            # build ZIP only
+./release.sh --release  # build ZIP + create GitHub release
+```
+
+### Maven Central
+
+```bash
+mvn clean deploy -Prelease
+```
+
+This builds the JARs (with `version.xml` embedded for service discovery), generates
+sources and javadoc JARs, signs everything with GPG, and uploads to Maven Central.
+
+BEAST 3 users can then install with:
+
+```
+Package Manager > Install from Maven > io.github.compevol:beast-morph-models:1.3.0
+```
+
+Or from the command line:
+
+```bash
+packagemanager -maven io.github.compevol:beast-morph-models:1.3.0
+```
+
+## References
+
+Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. *Systematic Biology*, 50(6), 913–925.

beast-morph-models-fx/pom.xml

@@ -0,0 +1,80 @@
+<?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>
+
+    <parent>
+        <groupId>io.github.compevol</groupId>
+        <artifactId>morph-models-parent</artifactId>
+        <version>1.3.0-SNAPSHOT</version>
+    </parent>
+
+    <artifactId>beast-morph-models-fx</artifactId>
+    <name>BEAST Morph Models FX</name>
+
+    <dependencies>
+        <!-- Internal -->
+        <dependency>
+            <groupId>io.github.compevol</groupId>
+            <artifactId>beast-morph-models</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.github.compevol</groupId>
+            <artifactId>beast-base</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.github.compevol</groupId>
+            <artifactId>beast-fx</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.github.compevol</groupId>
+            <artifactId>beast-pkgmgmt</artifactId>
+        </dependency>
+
+        <!-- JavaFX -->
+        <dependency>
+            <groupId>org.openjfx</groupId>
+            <artifactId>javafx-controls</artifactId>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <!-- Run BEAUti with morph-models on module path:
+                 mvn -pl beast-morph-models-fx exec:exec
+                 mvn -pl beast-morph-models-fx exec:exec -Dbeast.main=beast.base.minimal.BeastMain -Dbeast.args="examples/M3982.xml" -->
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>exec-maven-plugin</artifactId>
+                <version>3.5.0</version>
+                <configuration>
+                    <executable>java</executable>
+                    <workingDirectory>${maven.multiModuleProjectDirectory}</workingDirectory>
+                    <commandlineArgs>--module-path %classpath -m beast.fx/${beast.main} ${beast.args}</commandlineArgs>
+                </configuration>
+            </plugin>
+
+            <!-- Assemble BEAST package ZIP -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <version>3.7.1</version>
+                <configuration>
+                    <descriptors>
+                        <descriptor>src/assembly/beast-package.xml</descriptor>
+                    </descriptors>
+                    <finalName>${beast.pkg.name}.v${beast.pkg.version}</finalName>
+                    <appendAssemblyId>false</appendAssemblyId>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>beast-package</id>
+                        <phase>package</phase>
+                        <goals><goal>single</goal></goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>

beast-morph-models-fx/src/assembly/beast-package.xml

@@ -0,0 +1,46 @@
+<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>beast-package</id>
+    <formats>
+        <format>zip</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+
+    <!-- version.xml from project root -->
+    <files>
+        <file>
+            <source>${project.parent.basedir}/version.xml</source>
+            <outputDirectory>/</outputDirectory>
+        </file>
+    </files>
+
+    <!-- Module JARs only (BEAST core, JavaFX, and their transitive deps are provided by the runtime) -->
+    <dependencySets>
+        <dependencySet>
+            <outputDirectory>/lib</outputDirectory>
+            <useProjectArtifact>true</useProjectArtifact>
+            <scope>runtime</scope>
+            <includes>
+                <include>io.github.compevol:beast-morph-models</include>
+                <include>io.github.compevol:beast-morph-models-fx</include>
+            </includes>
+        </dependencySet>
+    </dependencySets>
+
+    <fileSets>
+        <!-- fxtemplates/ -->
+        <fileSet>
+            <directory>${project.basedir}/src/main/resources/beast.morph.models.fx/fxtemplates</directory>
+            <outputDirectory>/fxtemplates</outputDirectory>
+        </fileSet>
+        <!-- examples/ from project root (excluding legacy directories) -->
+        <fileSet>
+            <directory>${project.parent.basedir}/examples</directory>
+            <outputDirectory>/examples</outputDirectory>
+            <excludes>
+                <exclude>legacy*/**</exclude>
+            </excludes>
+        </fileSet>
+    </fileSets>
+</assembly>

beast-morph-models-fx/src/main/java/module-info.java

@@ -0,0 +1,12 @@
+open module beast.morph.models.fx {
+    requires beast.morph.models;
+    requires beast.base;
+    requires beast.pkgmgmt;
+    requires beast.fx;
+    requires javafx.controls;
+
+    exports morphmodels.app.beauti;
+
+    provides beast.base.core.BEASTInterface with
+        morphmodels.app.beauti.BeautiMorphModelAlignmentProvider;
+}

src/morphmodels/app/beauti/BeautiMorphModelAlignmentProvider.java → beast-morph-models-fx/src/main/java/morphmodels/app/beauti/BeautiMorphModelAlignmentProvider.java

@@ -11,7 +11,7 @@
 import beastfx.app.inputeditor.BeautiAlignmentProvider;
 import beastfx.app.inputeditor.BeautiDoc;
 import beastfx.app.util.Alert;
-import beastfx.app.util.ExtensionFileFilter;
+
 import beastfx.app.util.FXUtils;
 import javafx.scene.control.ButtonType;
 import beast.base.core.BEASTInterface;