build.xml

<?xml version="1.0"?>

<!--

==========================================================================

This build script requires Ant 1.6.2+. You can download Ant at
http://jakarta.apache.org/ant/index.html.

To use the (default) test target you will need to add a jar to the ant lib
directory for junit - see the Ant manual.

Tetrad IV is currently (2005/1/15) using Sun's JDK 1.5.0+.

To use this build script, assuming you've downloaded and unzipped the source
code archive (how else could you see this?), installed the JDK correctly,
installed Ant correctly, setting the JAVA_HOME and ANT_HOME environment
variables and adding the java bin and Ant bin directories to your PATH, it
should be sufficient to cd to the tetrad directory and type "ant" to compile
the project. "ant ejar" will build an executable jar for the project, which
will be deposited in build/upload. Typing "ant docs" will build the javadocs
for the project. (If it doesn't, exclude some of the packages from the build.
Cygwin seems to have difficulty issuing the entire javadoc moves that ant
generates.) Typing "ant clean" will delete the build directory. Typing "ant lib"
will generate the library jar and library documentation.

All generated jars and zip files will be deposited into build/tetrad/upload.

If you're using an IDE to look at Tetrad code, please use /build/tetrad/classes
as your classes (output) directory for the IDE to synchronize Ant with the IDE.

To run all of the unit tests, first put the junit.jar (in lib/ant_jars) archive
into the ant lib directory and then type "ant test" from the tetrad directory.

Laboratory for Symbolic and Educational Computing
Department of Philosophy
Carnegie Mellon University
$Revision: 9552 $ $Date: 2014-03-29 13:18:09 -0400 (Sat, 29 Mar 2014) $

Joseph Ramsey, jdramsey@andrew.cmu.edu

==========================================================================
-->

<project default="compile" basedir=".">

    <!-- ================================================================ -->
    <!-- Initialization target                                            -->
    <!-- ================================================================ -->
    <target name="init">
        <tstamp>
            <format property="YEAR_MONTH_DAY" pattern="yyyy-MM-dd"/>
            <format property="YEAR" pattern="yyyy"/>
        </tstamp>
        <property name="Name" value="Tetrad"/>
        <property name="name" value="tetrad"/>

        <!--This creates a new property 'version' and reads the value in-->
        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <echo message="${Name} ${version} ${YEAR_MONTH_DAY}"/>

        <property file="ant2.properties"/>

        <property name="build.compiler" value="classic"/>
        <property name="debug" value="on"/>
        <property name="optimize" value="on"/>
        <property name="deprecation" value="off"/>
        <property name="verbose" value="off"/>

        <property name="src" value="./src"/>
        <property name="lib" value="./lib"/>
        <property name="project" value="./project_tetrad"/>
        <property name="docs" value="./docs"/>

        <property name="javahelp" value="./docs/javahelp"/>
        <property name="packages" value="edu.cmu.*"/>
        <property name="overview"
                  value="${src}/edu/cmu/tetradapp/overview.html"/>
        <property name="resources" value="${project}/resources"/>

        <property name="build" value="./build"/>
        <property name="build.dir" value="${build}/${name}"/>
        <property name="build.classes" value="${build.dir}/classes"/>
        <property name="build.docs" value="${build.dir}/docs"/>
        <property name="build.javadocs" value="${build.docs}/javadocs"/>

        <property name="build.model" value="${build.dir}/model_contents"/>
        <property name="build.ejar" value="${build.dir}/ejar_contents"/>
        <property name="dist" value="${build.dir}/dist"/>
        <property name="upload" value="${build.dir}/upload"/>
        <property name="junit_reports" value="./junit_reports"/>

        <property name="jdepend" value="${build.dir}/jdepend"/>

        <mkdir dir="${build}"/>
    </target>

    <!-- ================================================================ -->
    <!-- Cleans build directories.                                        -->
    <!-- ================================================================ -->
    <target name="clean" depends="init"
            description="Cleans build directories.">
        <delete dir="${build}"/>
        <delete dir="${junit_reports}"/>
    </target>

    <!-- ================================================================ -->
    <!-- Cleans build directories.                                        -->
    <!-- ================================================================ -->
    <target name="copyresources" depends="init"
            description="Copies necessary resources to the build directory.">
        <copy todir="${build.classes}/resources">
            <fileset dir="${resources}"/>
        </copy>
        <copy todir="${build.classes}/javahelp">
            <fileset dir="${javahelp}"/>
        </copy>
    </target>

    <!-- ================================================================ -->
    <!-- Switch to use play configuration. (Recopies resources.)          -->
    <!-- ================================================================ -->
    <target name="configuration-play" depends="init"
            description="Prepares to use play configuration.">
        <delete file="${resources}/configuration.xml"/>
        <copy tofile="${resources}/configuration.xml"
              file="${resources}/configuration-play.xml">
        </copy>
        <copy todir="${build.classes}/resources">
            <fileset dir="${resources}"/>
        </copy>
        <copy todir="${build.classes}/javahelp">
            <fileset dir="${javahelp}"/>
        </copy>
        <copy todir="${build.classes}/resources">
            <fileset dir="${resources}"/>
        </copy>
        <copy todir="${build.classes}/javahelp">
            <fileset dir="${javahelp}"/>
        </copy>
    </target>

    <!-- ================================================================ -->
    <!-- Switch to use post configuration. (Recopies resources.)          -->
    <!-- ================================================================ -->
    <target name="configuration-post" depends="init"
            description="Prepares to use post configuration.">
        <delete file="${resources}/configuration.xml"/>
        <copy tofile="${resources}/configuration.xml"
              file="${resources}/configuration-post.xml">
        </copy>
        <copy todir="${build.classes}/resources">
            <fileset dir="${resources}"/>
        </copy>
        <copy todir="${build.classes}/javahelp">
            <fileset dir="${javahelp}"/>
        </copy>
        <copy todir="${build.classes}/resources">
            <fileset dir="${resources}"/>
        </copy>
        <copy todir="${build.classes}/javahelp">
            <fileset dir="${javahelp}"/>
        </copy>
    </target>

    <!-- ================================================================ -->
    <!-- Compiles the source directory                                    -->
    <!-- ================================================================ -->
    <target name="compile" depends="copyresources"
            description="Compiles the source directory.">

        <mkdir dir="${build.classes}"/>
        <javac srcdir="${src}"
               destdir="${build.classes}"
               debug="${debug}"
               source="1.6"
               deprecation="${deprecation}"
               excludes="**/package.html"
               compiler="modern"
               fork="true"
               memoryinitialsize="500m"
               memorymaximumsize="6000m">

            <!--Note the exclusion of tetradproj-->
            <!--<exclude name="**/tetradproj/**"/>-->
            <exclude name="**/scales/**"/>
            <exclude name="**/causality/**"/>
            <exclude name="**/causalityApp/**"/>
            <exclude name="**/command/**"/>
            <exclude name="**/oli/**"/>
            <exclude name="**/tetradproj/**"/>
            <classpath>
                <fileset dir="${lib}/tetrad">
                    <include name="colt.jar"/>
                    <include name="commons-collections-3.1.jar"/>
                    <include name="commons-math3-3.2.jar"/>
                    <include name="concurrent.jar"/>
                    <include name="f2jutil.jar"/>
                    <include name="Jama-1.0.2.jar"/>
                    <include name="jdepend.jar"/>
                    <include name="jdom.jar"/>
                    <include name="jh.jar"/>
                    <include name="junit.jar"/>
                    <include name="jxl.jar"/>
                    <include name="mrjtoolkitstubs.jar"/>
                    <include name="lsec_common.jar"/>
                    <include name="mtj.jar"/>
                    <include name="opt77.jar"/>
                    <include name="pal-1.5.1.jar"/>
                    <include name="xerbla.jar"/>
                    <include name="xom-1.1.jar"/>
                    <include name="jdom.jar"/>
                    <include name="superactivity-5.6.jar"/>
                </fileset>
            </classpath>
        </javac>
    </target>

    <!-- ================================================================ -->
    <!-- Creates the executable jar file                                  -->
    <!-- ================================================================ -->
    <target name="unsignedejar" depends="compile"
            description="Creates an executable jar file.">
        <loadfile srcfile="${project}/resources/version" property="version"/>

        <copy todir="${build.ejar}">
            <fileset dir="${build.classes}"/>
        </copy>
        <unjar src="lib/tetrad/colt.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-collections-3.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-math3-3.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/concurrent.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/f2jutil.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/Jama-1.0.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jdepend.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jdom.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jh.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/junit.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jxl.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/mrjtoolkitstubs.jar" dest="${build.ejar}"/>
        <!--<unjar src="${lib}/lsec_common.jar" dest="${build.ejar}"/>-->
        <unjar src="lib/tetrad/mtj.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/opt77.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/pal-1.5.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xerbla.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xom-1.1.jar" dest="${build.ejar}"/>

        <delete dir="${upload}"/>
        <mkdir dir="${upload}"/>
        <jar jarfile="${upload}/${name}-${version}.jar"
             excludes="META-INF/MANIFEST.MF"
             basedir="${build.ejar}"
             manifest="${project}/manifest.mf"/>

        <copy file="project_tetrad/tetrad-template.jnlp"
              tofile="${upload}/tetrad-${version}.jnlp"/>
        <replace file="${upload}/tetrad-${version}.jnlp"
                 token="##VERSION##" value="${version}"/>

        <copy file="project_tetrad/exercisebuilder-template.jnlp"
              tofile="${upload}/exercisebuilder-${version}.jnlp"/>
        <replace file="${upload}/exercisebuilder-${version}.jnlp"
                 token="##VERSION##" value="${version}"/>
    </target>

    <target name="unsignedejar-experimental" depends="compile"
            description="Creates an executable jar file.">
        <loadfile srcfile="${project}/resources/version" property="version"/>

        <copy todir="${build.ejar}">
            <fileset dir="${build.classes}"/>
        </copy>
        <unjar src="lib/tetrad/colt.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-collections-3.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-math3-3.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/concurrent.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/f2jutil.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/Jama-1.0.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jdepend.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jdom.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jh.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/junit.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jxl.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/mrjtoolkitstubs.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/lsec_common.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/mtj.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/opt77.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/pal-1.5.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xerbla.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xom-1.1.jar" dest="${build.ejar}"/>

        <delete dir="${upload}"/>
        <mkdir dir="${upload}"/>
        <jar jarfile="${upload}/${name}-${version}-experimental.jar"
             excludes="META-INF/MANIFEST.MF"
             basedir="${build.ejar}"
             manifest="project_tetrad/manifest.mf"/>

        <copy file="project_tetrad/tetrad-template.jnlp"
              tofile="${upload}/tetrad-${version}-experimental.jnlp"/>
        <replace file="${upload}/tetrad-${version}-experimental.jnlp"
                 token="##VERSION##" value="${version}-experimental"/>

        <copy file="project_tetrad/exercisebuilder-template.jnlp"
              tofile="${upload}/exercisebuilder-${version}-experimental.jnlp"/>
        <replace file="${upload}/exercisebuilder-${version}-experimental.jnlp"
                 token="##VERSION##" value="${version}-experimental"/>
    </target>

    <!-- ================================================================ -->
    <!-- Signs tetrad-devel.jar.                                         -->
    <!-- ================================================================ -->
    <target name="ejar" depends="unsignedejar"
            description="Creates an executable jar file.">
        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <input
                message="Storepass:"
                addproperty="storepass"
                />

        <signjar jar="${upload}/${name}-${version}.jar"
                 alias="carnegie mellon university - department of philosophy's comodo ca limited id"
                 keystore="${keystore}"
                 storepass="${storepass}"
                />
    </target>

    <target name="ejar-experimental" depends="unsignedejar-experimental"
            description="Creates an executable jar file.">
        <loadfile srcfile="${project}/resources/version" property="version"/>

        <input
                message="Storepass:"
                addproperty="storepass"
                />

        <signjar jar="${upload}/${name}-${version}-experimental.jar"
                 alias="carnegie mellon university - department of philosophy's comodo ca limited id"
                 keystore="${keystore}"
                 storepass="${storepass}"
                 verbose="true"/>
    </target>

    <target name="cmdjar" depends="clean,compile"
            description="Creates command-line jar file.">
        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <copy todir="${build.ejar}">
            <fileset dir="${build.classes}"/>
        </copy>

        <!--<unjar src="lib/tetrad/colt.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/commons-collections-3.1.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/commons-math3-3.2.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/Jama-1.0.2.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/f2jutil.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/jh.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/junit.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/jdepend.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/jxl.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/mrjtoolkitstubs.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/mtj.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/opt77.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/pal-1.5.1.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/xerbla.jar" dest="${build.ejar}"/>-->
        <!--<unjar src="lib/tetrad/xom-1.1.jar" dest="${build.ejar}"/>-->

        <unjar src="lib/tetrad/colt.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-collections-3.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-math3-3.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/concurrent.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/f2jutil.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/Jama-1.0.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jdepend.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jdom.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jh.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/junit.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jxl.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/mrjtoolkitstubs.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/lsec_common.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/mtj.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/opt77.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/pal-1.5.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xerbla.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xom-1.1.jar" dest="${build.ejar}"/>

        <delete dir="${upload}"/>
        <mkdir dir="${upload}"/>
        <jar jarfile="${upload}/${name}cmd-${version}.jar"
             excludes="META-INF/MANIFEST.MF"
             basedir="${build.ejar}"
             manifest="project_tetrad/cmdmanifest.mf"/>
    </target>

    <!-- =================================================================== -->
    <!-- Runs JUnit tests (does not build ejar first)                        -->
    <!-- =================================================================== -->
    <target name="test" depends="compile"
            description="Runs all JUnit tests. Prefix for JUnit test classes is 'Test'.">
        <echo message="Look in the 'junit_reports' directory for JUnit reports."/>
        <mkdir dir="${junit_reports}"/>
        <junit printsummary="off" haltonerror="yes" fork="yes" maxmemory="50M">
            <formatter type="plain"/>
            <classpath>
                <pathelement location="${build.classes}"/>
                <fileset dir="${lib}">
                    <include name="*.jar"/>
                </fileset>
            </classpath>
            <batchtest fork="no" todir="${junit_reports}">
                <fileset dir="${src}">
                    <include name="**/Test*.java"/>
                    <!--<exclude name="**/tetradproj/**"/>-->
                    <exclude name="**/TestType.java"/>
                </fileset>
            </batchtest>
        </junit>
    </target>

    <!-- =================================================================== -->
    <!-- Runs identifiability tests (does not build ejar first)                        -->
    <!-- =================================================================== -->
    <target name="testIdentifiability" depends="compile"
            description="Runs identifiability tests.">
        <echo message="Runs identifiability tests."/>
        <mkdir dir="${junit_reports}"/>
        <junit printsummary="off" haltonerror="yes" fork="yes" maxmemory="50M">
            <formatter type="plain"/>
            <classpath>
                <pathelement location="${build.classes}"/>
                <fileset dir="${lib}">
                    <include name="*.jar"/>
                </fileset>
            </classpath>
            <batchtest fork="no" todir="${junit_reports}">
                <fileset dir="${src}">
                    <include name="**/TestIdentifiability.java"/>
                </fileset>
            </batchtest>
        </junit>
    </target>

    <!-- ================================================================ -->
    <!-- Makes the javadocs and puts all the docs into a single directory.-->
    <!-- ================================================================ -->
    <target name="docs" depends="init"
            description="Creates documentation, including javadocs.">
        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <mkdir dir="${build.docs}"/>
        <mkdir dir="${build.javadocs}"/>
        <mkdir dir="${upload}"/>

        <loadfile srcfile="COPYRIGHT" property="copyright"/>

        <javadoc packagenames="${packages}"
                 destdir="${build.javadocs}"
                 author="true"
                 version="true"
                 verbose="false"
                 use="true"
                 noindex="false"
                 source="1.5"
                 windowtitle="${Name} ${version} Javadocs"
                 doctitle="${Name} ${version}"
                 overview="${overview}"
                 bottom="${copyright}">
            <classpath>
                <fileset dir="${lib}">
                    <include name="*.jar"/>
                </fileset>
            </classpath>
            <fileset dir="${src}">
                <include name="**/*.java"/>
                <exclude name="**/Test*.java"/>
            </fileset>
        </javadoc>
        <copy todir="${build.docs}">
            <fileset dir="${docs}"/>
        </copy>

        <mkdir dir="${upload}"/>
        <zip zipfile="${upload}/tetraddocs-${version}.zip"
             basedir="${build.dir}/docs"/>
    </target>

    <!-- ================================================================ -->
    <!-- Creates javadocs for the library jar.                            -->
    <!-- ================================================================ -->
    <target name="libdocs" depends="init">
        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <javadoc
                sourcepath="${src}"
                destdir="${build.dir}/lib/docs/javadocs"
                author="true"
                version="true"
                verbose="false"
                use="true"
                noindex="false"
                source="1.5"
                windowtitle="${Name} ${version} API"
                doctitle="${Name} v. ${version}"
                overview="${overview}"
                bottom="Tetrad v. 4.2, Copyright &#169; ${YEAR}, Laboratory for Symbolic and Educational Computing, Philosophy Department, Carnegie Mellon University.  All rights reserved. For information contact Joe Ramsey, jdramsey@andrew.cmu.edu.">
            <classpath>
                <fileset dir="${lib}">
                    <include name="*.jar"/>
                </fileset>
            </classpath>
            <fileset dir="${src}">
                <include name="edu/cmu/tetrad/*.java"/>
                <exclude name="**/Test*.java"/>
            </fileset>
        </javadoc>
    </target>

    <!-- ================================================================ -->
    <!-- Creates the executable jar file                                  -->
    <!-- ================================================================ -->
    <target name="lib" depends="compile"
            description="Creates a library jar. This will require external jars for support.">
        <delete dir="${build.dir}/lib"/>
        <mkdir dir="${build.dir}/lib"/>
        <mkdir dir="${build.dir}/lib/classes"/>
        <mkdir dir="${build.dir}/lib/zipcontents"/>
        <mkdir dir="${build.dir}/lib/zipcontents/tetrad"/>

        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <javadoc
                sourcepath="${src}"
                packagenames="edu.cmu.tetrad.*"
                destdir="${build.dir}/lib/zipcontents/tetrad/doc"
                author="true"
                version="true"
                verbose="false"
                use="true"
                noindex="false"
                source="1.5"
                windowtitle="${Name} ${version} API"
                doctitle="${Name} v. ${version}"
                overview="${overview}"
                bottom="Tetrad v. 4.2, Copyright &#169; ${YEAR}, Laboratory for Symbolic and Educational Computing, Philosophy Department, Carnegie Mellon University.  All rights reserved. For information contact Joe Ramsey, jdramsey@andrew.cmu.edu.">
            <classpath>
                <fileset dir="${lib}">
                    <include name="*.jar"/>
                </fileset>
            </classpath>
            <fileset dir="${src}">
                <include name="edu/cmu/tetrad/*.java"/>
                <exclude name="**/Test*.java"/>
            </fileset>
        </javadoc>

        <copy todir="${build.dir}/lib/classes">
            <fileset dir="${build.classes}">
                <include name="edu/cmu/tetrad/**/"/>
                <!--<include name="**/tetradapp/**"/>-->
            </fileset>
        </copy>

        <unjar src="lib/tetrad/colt.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/commons-collections-3.1.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/commons-math3-3.2.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/junit.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/mtj.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/opt77.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/pal-1.5.1.jar" dest="${build.dir}/lib/classes"/>
        <unjar src="lib/tetrad/xom-1.1.jar" dest="${build.dir}/lib/classes"/>

        <!--<unjar src="${lib}/Jama-1.0.2.jar" dest="${build.dir}/lib/classes"/>-->
        <!--<unjar src="${lib}/f2jutil.jar" dest="${build.dir}/lib/classes"/>-->
        <!--<unjar src="${lib}/jh.jar" dest="${build.dir}/lib/classes"/>-->
        <!--<unjar src="${lib}/jdepend.jar" dest="${build.dir}/lib/classes"/>-->
        <!--<unjar src="${lib}/jxl.jar" dest="${build.dir}/lib/classes"/>-->
        <!--<unjar src="${lib}/mrjtoolkitstubs.jar" dest="${build.dir}/lib/classes"/>-->
        <!--<unjar src="${lib}/xerbla.jar" dest="${build.dir}/lib/classes"/>-->

        <mkdir dir="${upload}"/>
        <jar jarfile="${build.dir}/lib/zipcontents/tetrad/${name}.jar"
             basedir="${build.dir}/lib/classes"/>

        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <input
                message="SCP Login:"
                addproperty="storepass"
                />

        <signjar jar="${build.dir}/lib/zipcontents/tetrad/${name}.jar"
                 alias="${alias}"
                 keystore="${keystore}"
                 storepass="${storepass}"/>

        <mkdir dir="{build.dir}/lib/zipcontents/tetrad/lib"/>
        <copy todir="${build.dir}/lib/zipcontents/tetrad/lib">
            <fileset dir="./lib">
                <include name="colt.jar"/>
                <include name="commons-collections-3.1.jar"/>
                <include name="junit.jar"/>
                <include name="mtj.jar"/>
                <include name="opt77.jar"/>
                <include name="pal-1.4.jar"/>
                <include name="xom-1.1.jar"/>
            </fileset>
        </copy>

        <mkdir dir="${build.dir}/lib/zipcontents/tetrad/src"/>
        <copy todir="${build.dir}/lib/zipcontents/tetrad/src">
            <fileset dir="./src">
                <include name="edu/cmu/tetrad/**"/>
            </fileset>
        </copy>

        <!--<copy file="build.xml" todir="${build.dir}/lib/zipcontents/tetrad"/>-->
        <copy file="./COPYRIGHT" todir="${build.dir}/lib/zipcontents/tetrad"/>
        <copy file="./LICENSE" todir="${build.dir}/lib/zipcontents/tetrad"/>
        <copy file="./docs/notes/tetradlib_readme.txt" tofile="${build.dir}/lib/zipcontents/tetrad/README"/>
        <copy file="./lib.xml" tofile="${build.dir}/lib/zipcontents/tetrad/build.xml"/>

        <zip zipfile="${upload}/${name}lib-${version}.zip"
             basedir="${build.dir}/lib/zipcontents/"/>

    </target>


    <!-- ================================================================ -->
    <!-- Creates the jar file used by Causality Lab 2.0                   -->
    <!-- ================================================================ -->
    <target name="causalitylibcompile" depends="init"
            description="compile classes needed by causality lib">
        <mkdir dir="${build.dir}/causalitylib/classes"/>
        <javac
                destdir="${build.dir}/causalitylib/classes"
                debug="${debug}"
                verbose="${verbose}"
                optimize="${optimize}"
                source="1.5"
                deprecation="${deprecation}">
            <classpath>
                <fileset dir="${lib}">
                    <include name="*.jar"/>
                </fileset>
            </classpath>
            <src path="${src}"/>
            <include name="edu/cmu/tetrad/util/*.java"/>
            <include name="edu/cmu/tetrad/graph/*.java"/>
            <include name="edu/cmu/tetrad/coltData/*.java"/>
            <include name="edu/cmu/tetrad/bayes/*.java"/>
            <include name="edu/cmu/tetrad/sem/*.java"/>
            <include name="edu/cmu/tetrad/search/*.java"/>
            <exclude name="edu/cmu/tetrad/search/test/*.java"/>
            <include name="edu/cmu/tetrad/predict/*.java"/>

            <include name="edu/cmu/tetradapp/editor/*.java"/>
            <include name="edu/cmu/tetradapp/model/*.java"/>
            <include name="edu/cmu/tetradapp/workbench/*.java"/>
        </javac>

    </target>

    <!-- ================================================================ -->
    <!-- Creates the executable jar file                                  -->
    <!-- ================================================================ -->
    <target name="causalitylib" depends="causalitylibcompile"
            description="Creates an executable jar file.">

        <loadfile srcfile="project_tetrad/resources/version" property="version"/>

        <mkdir dir="${build.dir}/causalitylib/jarcontents"/>
        <copy todir="${build.dir}/causalitylib/jarcontents">
            <fileset dir="${build.dir}/causalitylib/classes"/>
        </copy>
        <unjar src="lib/tetrad/commons-collections-3.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/commons-math3-3.2.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/colt.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/jh.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/pal-1.5.1.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/mrjtoolkitstubs.jar" dest="${build.ejar}"/>
        <unjar src="lib/tetrad/xom-1.1.jar" dest="${build.ejar}"/>

        <mkdir dir="${upload}"/>
        <jar jarfile="${upload}/${name}causalitylib-${version}.jar"
             basedir="${build.dir}/causalitylib/jarcontents"/>
    </target>

    <target name="run" depends="unsignedejar" description="Runs Tetrad.">
        <java jar="${upload}/${name}-${version}.jar" fork="true"/>
    </target>

    <target name="explore_latent_ensemble_2" depends="unsignedejar" description="Runs Tetrad.">
        <java classpath="${upload}/${name}-${version}.jar"
              classname="edu.cmu.tetradproj.fmri.ExploreLatentEnsembleSearch2" fork="true"/>
    </target>

</project>