Beast3

.github/workflows/ci-publish.yml

@@ -0,0 +1,55 @@
+name: CI & Publish
+
+on:
+  push:
+    branches: [ master ]
+    tags: [ 'v*' ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up JDK 25 (Azul Zulu)
+        if: "!startsWith(github.ref, 'refs/tags/v')"
+        uses: actions/setup-java@v4
+        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
+        with:
+          distribution: zulu
+          java-version: '25'
+          cache: maven
+          server-id: central
+          server-username: CENTRAL_USERNAME
+          server-password: CENTRAL_TOKEN
+          gpg-private-key: ${{ secrets.GPG_PRIVATE_KEY }}
+          gpg-passphrase: GPG_PASSPHRASE
+
+      - name: Set release version from tag
+        if: startsWith(github.ref, 'refs/tags/v')
+        run: |
+          VERSION=${GITHUB_REF_NAME#v}
+          echo "Publishing version: $VERSION"
+          mvn versions:set -DnewVersion=$VERSION -DgenerateBackupPoms=false
+
+      - name: Build and test
+        run: mvn verify
+
+      - name: Publish to Maven Central
+        if: startsWith(github.ref, 'refs/tags/v')
+        run: mvn deploy -Prelease -DskipTests
+        env:
+          CENTRAL_USERNAME: ${{ secrets.CENTRAL_USERNAME }}
+          CENTRAL_TOKEN: ${{ secrets.CENTRAL_TOKEN }}
+          GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}

README.md

@@ -7,3 +7,106 @@ Select models through path sampling/stepping stone analysis
 [Path sampling](http://www.beast2.org/path-sampling/)
 
 [Path sampling with a GUI](http://www.beast2.org/2014/07/14/path-sampling-with-a-gui.html)
+
+## For developer
+
+Build the package, skipping tests:
+
+```bash
+mvn clean package -DskipTests
+```
+
+Run an example XML through BEAST:
+
+```bash
+mvn exec:exec -Dbeast.args="src/test/resources/modelselection/examples/normalTest-1.xml"
+```
+### Project folder structure
+
+BEAUti templates and the example XMLs live under `src/`, not root directory:
+
+```
+src/
+├── main/resources/modelselection/
+│   ├── app/tools/ps.png
+│   └── fxtemplates/
+│       └── ModelSelection.xml
+└── test/resources/modelselection/examples/
+    ├── normalTest-1.xml, normalTest-2.xml, normalTestPS-1.xml, normalTestPS-2.xml,
+    │   testPairedPathSampler.xml, testPathSampler.xml, testPathSamplerForSimpleTree.xml
+    └── legacy/          (superseded example XMLs, excluded from the release ZIP)
+```
+
+`fxtemplates/` is a **main** resource, so it's bundled into the jar (see below).
+`examples/` is a **test** resource, so the assembly plugin copies it into the ZIP's
+top-level `/examples/` directly from `src/test/resources/`, excluding `legacy/**`
+(see `src/assembly/beast-package.xml`).
+
+
+## Releasing
+
+### Jar folder structure
+
+The release module jar, bundled into the BEAST package ZIP's `lib/`, contains:
+
+```
+META-INF/
+├── MANIFEST.MF
+└── maven/io.github.beast2-dev/model-selection/
+    ├── pom.xml
+    └── pom.properties
+modelselection/
+├── app/tools/          (PathSampler, PathSampleAnalyser, PairedPathSampler*, GeneralisedSteppingStone, ps.png)
+├── core/                (CPOLogger)
+├── cpo/                 (CPOAnalyser, BEASTRunAnalyser + inner classes)
+├── fxtemplates/
+│   └── ModelSelection.xml
+├── gss/                 (GeneralisedSteppingStone*, MCMC2GSS, MCMC2IS, GSSFromFile, TraceLog, ...)
+│   ├── coalescent/
+│   └── distribution/
+└── inference/           (PathSampler, PathSamplingStep, PairedPathSampler*, AICMAnalyser, DiffLogger, ...)
+version.xml
+module-info.class
+```
+
+`modelselection/fxtemplates/ModelSelection.xml` is loaded via module path resource
+lookup at runtime — `src/assembly/beast-package.xml` does not copy it anywhere else in
+the ZIP.
+
+### 1. Maven Central release (JARs)
+
+Push a `v*` tag to trigger `.github/workflows/ci-publish.yml`, which sets the Maven
+version from the tag, builds, tests, GPG-signs, and publishes to Maven Central:
+
+```bash
+git tag v1.7.0
+git push origin v1.7.0
+```
+
+Monitor the run at:
+https://github.com/BEAST2-Dev/model-selection/actions/workflows/ci-publish.yml
+
+### 2. GitHub release (BEAST package ZIP)
+
+First remove `-SNAPSHOT` from `<version>` in `pom.xml` so it matches the release
+(e.g. `1.7.0-SNAPSHOT` -> `1.7.0`), then build the installable BEAST package ZIP locally:
+
+```bash
+mvn clean package -DskipTests
+```
+
+**Note:** if you skip the manual edit above, the build still succeeds, but the module
+jar bundled inside the ZIP (`lib/model-selection-<version>.jar`) will carry the
+`-SNAPSHOT` suffix — that's meant for dev/testing builds, not an official release.
+Alternatively, instead of hand-editing `pom.xml`, run:
+
+```bash
+mvn versions:set -DnewVersion=<version> -DgenerateBackupPoms=false
+```
+
+The ZIP is written to `target/MODEL_SELECTION.v<version>.zip`. Then manually:
+
+1. Go to https://github.com/BEAST2-Dev/model-selection/releases/new
+2. Choose the matching tag (e.g. `v1.7.0`), fill in the release title/notes
+3. Upload `target/MODEL_SELECTION.v<version>.zip` as a release asset
+4. Publish