Occupancy operator model

README.md

@@ -1 +1,41 @@
-# type-linked-time-trees
+# type-linked-time-trees
+
+## To Build This Package locally (recommended for developers)
+
+First you will need to make sure you have beast2, BeastFX, and beast-classic 
+cloned in the same directory as this repo. 
+
+Recommended file structure:
+```txt
+parent-dir
+|___beast2
+|___BeastFX
+|___beast-classic
+|___type-linked-time-trees
+```
+
+For convenience, here are the commands to clone these repos:
+```sh
+cd <parent-dir>
+git clone https://github.com/CompEvol/beast2.git
+git clone https://github.com/CompEvol/BeastFX.git
+git clone https://github.com/BEAST2-Dev/beast-classic.git
+git clone <this-repo>
+```
+
+Make sure you have `ant` installed. Set `JAVACMD` env variable to the path for the [JDK recommended for beast2 development](https://github.com/CompEvol/BeastFX/blob/master/DevGuideIntelliJ.md#azul-jdk-17). (See [here](https://www.beast2.org/package-development-guide/) for a general guide to Beast2 development.)
+
+Now, you can run these commands to build all necessary jar files and then 
+package files:
+
+```sh
+cd <parent-dir>/beast2
+ant build_jar_all_BEAST_NoJUnitTest
+cd ../BeastFX
+ant build_jar_all_BeastFX_NoJUnitTest
+cd ../beast-classic
+ant build_jar_all_BEAST_CLASSIC_NoJUnitTest
+cd ../type-linked-time-trees
+ant package
+```
+

build.xml

@@ -7,31 +7,38 @@
     </description>
     <!-- set global properties for this build -->
     <property name="TypeLinkedDir" location="../type-linked-time-trees/" />
-    <property name="beastClassicDir" location="../beast-classic"/>
     <property name="srcTypeLinked" location="src" />
     <property name="buildTypeLinked" location="build" />
-    <property name="libTypeLinked" location="lib" />
+<!--    <property name="libTypeLinked" location="lib" />-->
     <property name="release_dir" value="release" />
+    <property name="Package_dir" value="${release_dir}/package" />
     <property name="distTypeLinked" location="${buildTypeLinked}/dist" />
+    <property name="report" value="${buildTypeLinked}/junitreport"/>
+
+    <!--  folders for beast2  -->
     <property name="beast2path" location="../beast2" />
     <property name="libBeast2" location="${beast2path}/lib" />
     <property name="srcBeast2" location="${beast2path}/src" />
     <property name="beast2classpath" location="${beast2path}/build" />
+
+    <!-- beast classic -->
+    <property name="beastClassicDir" location="../beast-classic"/>
     <property name="libClassic" location="${beastClassicDir}/lib"/>
     <property name="srcClassic" location="${beastClassicDir}/src" />
     <property name="beastClassicClasspath" location="${beastClassicDir}/build" />
-    <property name="Package_dir" value="${release_dir}/package" />
-    <import file="${beast2path}/build.xml" />
-    <import file="${beastClassicDir}/build.xml"/>
-    <property name="main_class_BEAST" value="beast.app.BeastMCMC" />
-    <property name="report" value="${buildTypeLinked}/junitreport"/>
     <path id="classpath">
+        <pathelement path="${libBeast2}"/>
         <pathelement path="${buildTypeLinked}"/>
         <fileset dir="${libBeast2}" includes="junit-4.8.2.jar"/>
         <pathelement path="${beast2classpath}"/>
         <pathelement path="${beastClassicClasspath}"/>
         <fileset dir="${libBeast2}" includes="beagle.jar"/>
     </path>
+
+    <import file="${beast2path}/build.xml"/>
+    <import file="${beastClassicDir}/build.xml"/>
+    <property name="main_class_BEAST" value="beast.app.BeastMCMC" />
+
     <!-- start -->
     <target name="initTypeLinked">
         <echo message="${ant.project.name}: ${ant.file}" />
@@ -58,7 +65,7 @@
     </target>
 
     <!-- compile Java source code -->
-    <target name="compile-allTypeLinked" depends="initTypeLinked,compile-all">
+    <target name="compile-allTypeLinked" depends="initTypeLinked,compile-all,compile-allBEAST_CLASSIC">
         <!-- Capture the path as a delimited property using the refid attribute -->
         <property name="myclasspath" refid="classpath"/>
         <!-- Emit the property to the ant console -->