build_release.xml

<!--
  build_release.xml

  ANT build file used by GitHub Actions to package BEAST X releases for
  Mac, Windows and Linux. It is intentionally separate from build.xml so
  that CI packaging concerns (pre-built JARs, hardened-runtime signing,
  GNU-tar archives) do not pollute the local development build.

  Usage (all three targets run on a macOS runner):

    ant -f build_release.xml package-mac \
        -Dversion=10.5.1 \
        -Dapple.signer.app="Developer ID Application: ..."

    ant -f build_release.xml package-windows \
        -Dversion=10.5.1

    ant -f build_release.xml package-linux \
        -Dversion=10.5.1

  Required property (must be supplied via -D):
    version              e.g. 10.5.1

  Optional properties (all have sensible defaults):
    extra_release_tag    e.g. -beta4   (default: empty)
    dist.dir             directory containing pre-built beast.jar / beauti.jar
                         (default: build/dist)

  package-mac-bundled-jvm (optional, depends on package-mac):
    Embeds a JDK inside each .app bundle so the app is self-contained and
    runs without requiring a system-installed Java.

    Required extra property:
      jdk.bundle.dir     Absolute path to the JDK .jdk directory to embed.
                         On macOS this is typically a directory such as:
                           /Library/Java/JavaVirtualMachines/zulu-21.jdk
                         (install with Homebrew: brew install -cask zulu@21)
                         The Azul Zulu cask installs a universal binary
                         (aarch64 + x86_64) so one DMG runs natively on
                         both Apple Silicon and Intel Macs.

    The last path component (e.g. zulu-21.jdk) becomes the PlugIns sub-
    directory name and is written into each Info.plist as JVMRuntime so that
    universalJavaApplicationStub can locate the bundled JVM.

    Example:
      ant -f build_release.xml package-mac-bundled-jvm \\
          -Dversion=10.5.1 \\
          -Djdk.bundle.dir=/Library/Java/JavaVirtualMachines/zulu-21.jdk
-->
<project basedir="." default="package-all" name="BEAST-Release">

    <!-- ============================================================
         Version / release properties  (override with -D on CLI)
         ============================================================ -->
    <property name="version"           value="10.5.0"/>
    <property name="version_number"    value="${version}"/>
    <property name="extra_release_tag" value=""/>
    <property name="jvm_version"       value="1.8+"/>
    <property name="copyright"         value="Copyright 2002-2025"/>

    <!-- Pre-built JARs location -->
    <property name="dist.dir"          value="build/dist"/>

    <!-- ============================================================
         Directory layout  (mirrors build.xml conventions)
         ============================================================ -->
    <property name="release_dir"   value="release"/>
    <property name="common_dir"    value="${release_dir}/common"/>
    <property name="Mac_dir"       value="${release_dir}/Mac"/>
    <property name="Linux_dir"     value="${release_dir}/Linux"/>
    <property name="Windows_dir"   value="${release_dir}/Windows"/>
    <property name="packaging_tools" value="packaging_tools"/>
    <property name="Packaging_dir" value="${packaging_tools}/windows"/>

    <!-- Package / app names -->
    <property name="BEAST_name"              value="BEAST"/>
    <property name="BEAST_package_name"      value="BEAST X"/>
    <property name="BEAST_package_name_linux" value="BEAST_X"/>
    <property name="BEAUti_name"             value="BEAUti"/>
    <property name="TreeAnnotator_name"      value="TreeAnnotator"/>
    <property name="LogCombiner_name"        value="LogCombiner"/>

    <!-- Platform package staging directories -->
    <property name="Mac_package_dir"
              value="${Mac_dir}/${BEAST_package_name} v${version}"/>
    <property name="Linux_package_dir"
              value="${Linux_dir}/${BEAST_package_name_linux}_v${version}"/>
    <property name="Windows_package_dir"
              value="${Windows_dir}/${BEAST_package_name} v${version}"/>


    <!-- ==============================================================
         package-linux
         Produces:  release/BEAST_X_v<version><tag>.tgz
         Runs on:   macOS or Linux runner
         Uses GNU tar format (via ANT tar task) for Linux compatibility.
         ============================================================== -->
    <target name="package-linux" description="Package Linux/Unix release">
        <delete dir="${Linux_package_dir}"/>
        <mkdir  dir="${Linux_package_dir}"/>

        <copy todir="${Linux_package_dir}/bin">
            <fileset dir="${Linux_dir}/scripts"/>
        </copy>
        <!-- Preserve executable bits on the shell scripts -->
        <chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>

        <copy todir="${Linux_package_dir}/examples">
            <fileset dir="examples"/>
        </copy>

        <copy file="${common_dir}/icons/beast.png"   todir="${Linux_package_dir}/images"/>
        <copy file="${common_dir}/icons/beauti.png"  todir="${Linux_package_dir}/images"/>
        <copy file="${common_dir}/icons/utility.png" todir="${Linux_package_dir}/images"/>

        <copy file="${dist.dir}/beast.jar"  todir="${Linux_package_dir}/lib"/>
        <copy file="${dist.dir}/beauti.jar" todir="${Linux_package_dir}/lib"/>



        <!--
            ANT's built-in tar task is Java-based and writes a POSIX-compatible
            archive that GNU tar (Linux) reads correctly.  The filemode attribute
            on the bin tarfileset preserves executable permissions for scripts.
        -->
        <tar destfile="${release_dir}/${BEAST_package_name_linux}_v${version}${extra_release_tag}.tgz"
             compression="gzip"
             longfile="gnu">
            <tarfileset dir="${Linux_package_dir}"
                        prefix="${BEAST_name}v${version}"
                        filemode="755">
                <include name="bin/**"/>
            </tarfileset>
            <tarfileset dir="${Linux_package_dir}"
                        prefix="${BEAST_name}v${version}">
                <exclude name="bin/**"/>
                <include name="**/**"/>
            </tarfileset>
        </tar>

        <echo message="Linux/Unix package: ${release_dir}/${BEAST_package_name_linux}_v${version}${extra_release_tag}.tgz"/>
    </target>


    <!-- ==============================================================
         package-windows
         Produces:  release/BEAST X v<version><tag>.zip
         Runs on:   macOS runner (the repo ships the macOS launch4j binaries,
                    which cross-compile Windows PE executables on macOS).
         ============================================================== -->
    <target name="package-windows" description="Package Windows release (cross-compiled on macOS)">
        <delete dir="${Windows_package_dir}"/>
        <mkdir  dir="${Windows_package_dir}"/>

        <!-- launch4j is bundled with macOS binaries in packaging_tools/windows/launch4j -->
        <property name="launch4j.dir" location="${Packaging_dir}/launch4j"/>
        <taskdef name="launch4j"
                 classname="net.sf.launch4j.ant.Launch4jTask"
                 classpath="${launch4j.dir}/launch4j.jar${path.separator}${launch4j.dir}/lib/xstream.jar"/>

        <copy todir="${Windows_package_dir}/examples">
            <fileset dir="examples"/>
        </copy>
        <copy todir="${Windows_package_dir}/bin">
            <fileset dir="${Windows_dir}/scripts"/>
        </copy>
        <copy file="${dist.dir}/beast.jar"  todir="${Windows_package_dir}/lib"/>
        <copy file="${dist.dir}/beauti.jar" todir="${Windows_package_dir}/lib"/>


        <!-- BEAUti -->
        <launch4j configFile="${Windows_dir}/BEAUti_launch4j.xml"
                  jar="${dist.dir}/beauti.jar"
                  outfile="${Windows_package_dir}/${BEAUti_name} v${version}.exe"
                  fileVersion="${version_number}.0"
                  txtFileVersion="${version}"
                  productVersion="${version_number}.0"
                  txtProductVersion="${version}"/>

        <!-- BEAST -->
        <launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"
                  jar="${dist.dir}/beast.jar"
                  outfile="${Windows_package_dir}/${BEAST_name} v${version}.exe"
                  fileVersion="${version_number}.0"
                  txtFileVersion="${version}"
                  productVersion="${version_number}.0"
                  txtProductVersion="${version}"/>

        <!-- TreeAnnotator -->
        <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"
                  jar="${dist.dir}/beast.jar"
                  outfile="${Windows_package_dir}/${TreeAnnotator_name} v${version}.exe"
                  fileVersion="${version_number}.0"
                  txtFileVersion="${version}"
                  productVersion="${version_number}.0"
                  txtProductVersion="${version}"/>

        <!-- LogCombiner -->
        <launch4j configFile="${Windows_dir}/LogCombiner_launch4j.xml"
                  jar="${dist.dir}/beast.jar"
                  outfile="${Windows_package_dir}/${LogCombiner_name} v${version}.exe"
                  fileVersion="${version_number}.0"
                  txtFileVersion="${version}"
                  productVersion="${version_number}.0"
                  txtProductVersion="${version}"/>

        <zip destfile="${release_dir}/${BEAST_package_name} v${version}${extra_release_tag}.zip">
            <zipfileset dir="${Windows_package_dir}"
                        prefix="${BEAST_package_name} v${version}"/>
        </zip>

        <echo message="Windows package: ${release_dir}/${BEAST_package_name} v${version}${extra_release_tag}.zip"/>
    </target>


    <!-- ==============================================================
         package-mac
         Produces:  release/Mac/BEAST X v<version>/  — staging directory
                    containing the four unsigned .app bundles.

         Runs on:   macOS runner only (requires jarbundler).

         Signing, DMG creation, notarisation and stapling are all handled
         by the GitHub Actions workflow so that this target can be run
         locally without any Apple certificates.
         ============================================================== -->
    <target name="package-mac" description="Create Mac .app bundles (unsigned) in staging directory">
        <delete dir="${Mac_package_dir}"/>
        <mkdir  dir="${Mac_package_dir}"/>

        <copy todir="${Mac_package_dir}/bin">
            <fileset dir="${Mac_dir}/scripts"/>
        </copy>
        <chmod dir="${Mac_package_dir}/bin" perm="755" includes="**/**"/>

        <copy todir="${Mac_package_dir}/examples">
            <fileset dir="examples"/>
        </copy>

        <!-- beast.jar / beauti.jar from the pre-built dist directory -->
        <copy file="${dist.dir}/beast.jar"  todir="${Mac_package_dir}/lib"/>
        <copy file="${dist.dir}/beauti.jar" todir="${Mac_package_dir}/lib"/>
        <!-- Additional lib JARs (for BEAUti plugins etc.) -->
        <copy todir="${Mac_package_dir}/lib">
            <fileset dir="lib">
                <include name="*.jar"/>
            </fileset>
        </copy>



        <taskdef name="jarbundler"
                 classname="com.ultramixer.jarbundler.JarBundler"
                 classpath="${packaging_tools}/mac/jarbundler-core-3.3.0.jar"/>

        <!-- ── BEAST.app ────────────────────────────────────────── -->
        <jarbundler dir="${Mac_package_dir}"
                    name="${BEAST_name} v${version}"
                    mainclass="dr.app.beast.BeastMain"
                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
                    useJavaXKey="true"
                    icon="${common_dir}/icons/beast.icns"
                    jvmversion="${jvm_version}"
                    vmoptions="-Xmx2048M -Djava.library.path=/usr/local/lib"
                    arguments="-window -working -options"
                    highresolutioncapable="true"
                    version="${version}"
                    copyright="${BEAST_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                    bundleid="dr.app.beast">
            <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
            <jarfileset dir="${Mac_package_dir}/lib">
                <include name="**/beast.jar"/>
            </jarfileset>
        </jarbundler>

        <!-- ── BEAUti.app ───────────────────────────────────────── -->
        <jarbundler dir="${Mac_package_dir}"
                    name="${BEAUti_name} v${version}"
                    mainclass="dr.app.beauti.BeautiApp"
                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
                    useJavaXKey="true"
                    icon="${common_dir}/icons/beauti.icns"
                    jvmversion="${jvm_version}"
                    vmoptions="-Xmx2048M"
                    arguments=""
                    version="${version}"
                    highresolutioncapable="true"
                    copyright="${BEAUti_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                    bundleid="dr.app.beauti">
            <documenttype name="BEAUti document"
                          extensions="beauti bti"
                          iconFile="beautidoc.icns"
                          role="Editor"/>
            <jarfileset dir="${Mac_package_dir}/lib">
                <include name="**/beauti.jar"/>
            </jarfileset>
            <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
        </jarbundler>

        <!-- ── LogCombiner.app ──────────────────────────────────── -->
        <jarbundler dir="${Mac_package_dir}"
                    name="${LogCombiner_name} v${version}"
                    mainclass="dr.app.tools.logcombiner.LogCombiner"
                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
                    useJavaXKey="true"
                    icon="${common_dir}/icons/utility.icns"
                    jvmversion="${jvm_version}"
                    vmoptions="-Xmx2048M"
                    highresolutioncapable="true"
                    arguments=""
                    version="${version}"
                    copyright="${LogCombiner_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                    bundleid="dr.app.tools.logcombiner">
            <jarfileset dir="${Mac_package_dir}/lib">
                <include name="**/beast.jar"/>
            </jarfileset>
            <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
        </jarbundler>

        <!-- ── TreeAnnotator.app ────────────────────────────────── -->
        <jarbundler dir="${Mac_package_dir}"
                    name="${TreeAnnotator_name} v${version}"
                    mainclass="dr.app.tools.treeannotator.TreeAnnotator"
                    stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
                    useJavaXKey="true"
                    icon="${common_dir}/icons/utility.icns"
                    jvmversion="${jvm_version}"
                    vmoptions="-Xmx4096M"
                    highresolutioncapable="true"
                    arguments=""
                    version="${version}"
                    copyright="${TreeAnnotator_name} v${version}, ${copyright}, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard"
                    bundleid="dr.app.tools.treeannotator">
            <jarfileset dir="${Mac_package_dir}/lib">
                <include name="**/beast.jar"/>
            </jarfileset>
            <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
        </jarbundler>

        <echo message="Mac bundles created in: ${Mac_package_dir}"/>
        <echo message="Next (CI): codesign each .app, hdiutil create DMG, codesign DMG, notarytool, stapler."/>
    </target>


    <!-- ==============================================================
         embed-jvm macrodef
         Copies an external JDK into a single .app bundle's PlugIns
         directory and writes the JVMRuntime key into its Info.plist.

         universalJavaApplicationStub checks for JVMRuntime in the JavaX
         dict of Info.plist; when present it uses the bundled JDK instead
         of searching the system.

         cp -rp is used instead of ANT <copy> so that symlinks and
         execute bits inside the JDK tree are preserved exactly.
         ============================================================== -->
    <macrodef name="embed-jvm">
        <attribute name="appdir" description="Path to the .app bundle"/>
        <sequential>
            <mkdir dir="@{appdir}/Contents/PlugIns"/>

            <!-- Preserve symlinks and execute bits (required for a valid JDK) -->
            <exec executable="cp" failonerror="true">
                <arg value="-rp"/>
                <arg value="${jdk.bundle.dir}"/>
                <arg value="@{appdir}/Contents/PlugIns/"/>
            </exec>

            <!-- Point universalJavaApplicationStub at the bundled JVM -->
            <exec executable="/usr/libexec/PlistBuddy" failonerror="true">
                <arg value="-c"/>
                <arg value="Add :JavaX:JVMRuntime string ${jdk.plugin.name}"/>
                <arg value="@{appdir}/Contents/Info.plist"/>
            </exec>
        </sequential>
    </macrodef>


    <!-- ==============================================================
         package-mac-bundled-jvm
         Produces:  release/Mac/BEAST X v<version>/  — same staging dir
                    as package-mac but with a JDK embedded in each .app.

         Requires:
           -Djdk.bundle.dir=/path/to/jdk-21.jdk

         Note for CI signing:
           Apple requires each Mach-O binary inside the PlugIns JDK to be
           individually signed (codesign with the -deep flag covers it)
           before the outer .app is submitted for notarisation.
         ============================================================== -->
    <target name="package-mac-bundled-jvm" depends="package-mac"
            description="Create Mac .app bundles with embedded JDK (self-contained)">

        <fail unless="jdk.bundle.dir"
              message="Supply the JDK to embed via -Djdk.bundle.dir=/path/to/jdk.jdk"/>

        <!-- Derive the PlugIns subfolder name from the last path component -->
        <basename property="jdk.plugin.name" file="${jdk.bundle.dir}"/>

        <echo message="Embedding JDK '${jdk.plugin.name}' into .app bundles..."/>

        <embed-jvm appdir="${Mac_package_dir}/${BEAST_name} v${version}.app"/>
        <embed-jvm appdir="${Mac_package_dir}/${BEAUti_name} v${version}.app"/>
        <embed-jvm appdir="${Mac_package_dir}/${LogCombiner_name} v${version}.app"/>
        <embed-jvm appdir="${Mac_package_dir}/${TreeAnnotator_name} v${version}.app"/>

        <echo message="JDK '${jdk.plugin.name}' embedded into all four .app bundles."/>
        <echo message="Next (CI): codesign --deep each .app (PlugIns binaries are covered),"/>
        <echo message="           hdiutil create DMG, codesign DMG, notarytool, stapler."/>
    </target>


    <!-- ── Convenience target: build all three packages ────────── -->
    <target name="package-all"
            depends="package-linux, package-windows, package-mac"
            description="Build all three platform packages (macOS runner only)"/>

</project>