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build.xml
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build.xml
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<project name="CDK" default="dist-all" basedir=".">
<property file="build.props"/>
<!-- compile options -->
<property name="build.sysclasspath" value="ignore" />
<property name="build.compiler" value="modern" />
<property name="debug" value="on" />
<property name="deprecation" value="on" />
<property name="optimization" value="off" />
<property name="threadCount" value="4" />
<property name="parallel" value="false"/>
<!-- patches to apply -->
<!-- directories -->
<property name="build" value="build" />
<property name="build.src" value="${build}/src" />
<property name="sourcedist" value="sourcedist" />
<property name="dist" value="dist" />
<property name="doc" value="doc" />
<property name="src" value="src" />
<property name="lib" value="jar" />
<property name="devellib" value="develjar" />
<property name="src.tests" value="${src}/test/org/openscience/cdk/test" />
<property name="reports.tests" value="reports" />
<property name="appjars.dir" value="${dist}/appjars" />
<property name="metainf" value="${src}/META-INF" />
<!-- class to run for testing-->
<property name="testclass" value="CDKTests" />
<property name="arg1" value="" />
<property name="arg2" value="" />
<property name="arg3" value="" />
<property name="arg4" value="" />
<property environment="env" />
<!-- Include the ant-contrib goodies -->
<taskdef name="javancss" classname="javancss.JavancssAntTask">
<classpath>
<pathelement location="${basedir}/develjar/javacc.jar"/>
<pathelement location="${basedir}/develjar/javancss.jar"/>
<pathelement location="${basedir}/develjar/ccl.jar"/>
<pathelement location="${basedir}/develjar/jhbasic.jar"/>
</classpath>
</taskdef>
<!-- Include the JavaNCSS goodies -->
<taskdef resource="net/sf/antcontrib/antlib.xml">
<classpath>
<pathelement location="${basedir}/develjar/ant-contrib-1.0b3.jar"/>
</classpath>
</taskdef>
<!--
<shellscript shell="bash" outputproperty="svn.output">
svn info
</shellscript>
<propertyregex property="svn.rev" input="${svn.output}" regexp="Revision: ([0-9]*)" select="\1" />
-->
<target id="info" name="info" depends="check">
<!-- Gives information about the building process. -->
<echo message="Platform:" />
<echo message=" OS: ${os.name}" />
<echo message=" Architecture: ${os.arch}" />
<echo message=" Version: ${os.version}" />
<echo message=" Mac OS/X found: ${isMacOsX}" />
<echo message="" />
<echo message="Java/Ant Environment:" />
<echo message=" Java version: ${java.version}" />
<echo message=" Java vendor: ${java.vendor}" />
<echo message=" Java dir: ${java.home}" />
<echo message=" Java ext dir: ${java.ext.dirs}" />
<echo message=" Ant version: ${ant.version}" />
<echo message=" ${ANT_HOME}: ${ant.home}" />
<echo message=" hasAnt17: ${hasAnt17}" />
<echo message="" />
<echo message="CDK Environment:" />
<echo message=" CDK version: ${version}" />
<echo message=" build.xml: $Id$" />
<echo message=" Junit found: ${junit.present}" />
<echo message=" --- required libraries ---" />
<echo message=" Vecmath found: ${vecmath.present}" />
<echo message=" Log4j found: ${log4j.present}" />
<echo message=" JGraphT found: ${jgrapht.present}" />
<echo message=" --- distributed (but optional) libraries ---" />
<echo message=" CMLDOM found: ${cmllibs.present}" />
<echo message=" --- optional libraries ---" />
<echo message="" />
<echo message="Compiling:" />
<echo message=" for: ${build.compiler}" />
<echo message=" debug: ${debug}" />
<echo message=" deprecation: ${deprecation}" />
<echo message=" optimization: ${optimization}" />
<echo message=" parallel: ${parallel}" />
<echo message=" threads: ${threadCount}" />
<echo message="" />
<echo message="Available Targets" />
<echo message=" clean: Remove class files and any temporary files" />
<echo message=" dist-all: Compile all modules" />
<echo message=" dist-large: Create the comprehensive jar, with all modules" />
<echo message=" test-dist-all: Compile all test modules" />
<echo message="test-dist-large: Create a single jar file with all test modules" />
<echo message=" jarTestdata: Create the jar file with all test data. Used in testing" />
<echo message="" />
</target>
<!-- See what platform were on -->
<target id="checkPlatforms" name="checkPlatforms">
<condition property="isMacOsX">
<and>
<os family="mac"/>
<os family="unix"/>
</and>
</condition>
</target>
<target id="check" name="check" depends="checkPlatforms">
<!-- Check wether Doclets are compiled and output is generated -->
<uptodate property="dotjavafiles.uptodate"
targetfile="${build}/core.javafiles">
<srcfiles dir="${src}" includes="**/*.java" />
</uptodate>
<condition property="dotjjfiles.uptodate">
<and>
<uptodate property="NomParserJavafiles.uptodate"
targetfile="${src}/main/org/openscience/cdk/iupac/parser/NomParser.java">
<srcfiles dir="${src}/main/" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
</uptodate>
<uptodate property="SMARTSParserJJTJavafiles.uptodate"
targetfile="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.java">
<srcfiles dir="${src}/main/" includes="org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj" />
</uptodate>
</and>
</condition>
<!-- Checks which parts of CDK can be build. -->
<!-- test for optional jars -->
<available property="vecmath.present"
file="${lib}/vecmath1.2-1.14.jar"/>
<available property="log4j.present"
file="${lib}/log4j.jar"/>
<available property="jgrapht.present"
file="${lib}/jgrapht-0.6.0.jar"/>
<!-- test for optional jars -->
<condition property="cmllibs.present">
<or>
<available file="${lib}/jumbo-with-fix-by-jonalv.jar"/>
</or>
</condition>
<condition property="junit.present">
<or>
<available file="${ant.home}/lib/junit.jar"/>
<available file="${devellib}/junit-4.5.jar"/>
</or>
</condition>
<!-- test Ant version -->
<condition property="hasAnt17">
<or>
<contains string="${ant.version}" substring="1.7.1"/>
<contains string="${ant.version}" substring="1.8"/>
</or>
</condition>
<!-- test Java version -->
<condition property="isJava13">
<contains string="${java.version}" substring="1.3"/>
</condition>
<condition property="isJava14">
<contains string="${java.version}" substring="1.4"/>
</condition>
<condition property="isJava15">
<contains string="${java.version}" substring="1.5"/>
</condition>
<condition property="isJava16">
<contains string="${java.version}" substring="1.6."/>
</condition>
<condition property="isJava17">
<contains string="${java.version}" substring="1.7."/>
</condition>
<condition property="isJava14+">
<or>
<contains string="${java.version}" substring="1.4"/>
<contains string="${java.version}" substring="1.5"/>
<contains string="${java.version}" substring="1.6"/>
<contains string="${java.version}" substring="1.7"/>
</or>
</condition>
<condition property="isJava15+">
<or>
<contains string="${java.version}" substring="1.5"/>
<contains string="${java.version}" substring="1.6"/>
<contains string="${java.version}" substring="1.7"/>
</or>
</condition>
<condition property="isNotJava15+">
<not>
<or>
<contains string="${java.version}" substring="1.5"/>
<contains string="${java.version}" substring="1.6"/>
<contains string="${java.version}" substring="1.7"/>
</or>
</not>
</condition>
<fail if="isNotJava15+" message="This CDK release requires Java5 or better."/>
<fail unless="hasAnt17" message="This CDK release requires Ant 1.7.1 or better."/>
</target>
<target id="init" name="init" depends="check, setupBuildDir"/>
<target id="customize" name="customize" depends="javacc"/>
<target id="setupBuildDir" name="setupBuildDir">
<tstamp />
<mkdir dir="${build}" />
<mkdir dir="${sourcedist}" />
<mkdir dir="${dist}" />
<mkdir dir="${reports.tests}" />
</target>
<target id="clean" name="clean" description="Removes autogenerated files.">
<delete>
<fileset dir="." includes="**/*~" />
<fileset dir="." includes="*.tar.gz" />
<fileset dir="." includes="*.zip" />
<fileset dir="." includes="*.rda" />
<fileset dir="${src}" includes="*.entitylist" />
<!-- remove java files generated with JavaCC -->
<fileset dir="${src}/main/org/openscience/cdk/smiles/smarts" includes="*.java">
<exclude name="SMARTSQueryTool.java" />
</fileset>
<fileset dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java" />
<fileset dir="${src}/main/org/openscience/cdk/iupac/parser" includes="*.java">
<!-- the next are from CVS -->
<exclude name="AttachedGroup.java" />
<exclude name="MoleculeBuilder.java" />
</fileset>
<fileset dir="${src}/main/">
<include name="net/sf/cdk/tools/*.class" />
</fileset>
</delete>
<delete dir="${build}" />
<delete dir="${sourcedist}" />
<delete dir="${dist}" />
<delete dir="${reports.tests}" />
</target>
<target name="runDoclet" id="runDoclet" depends="check, customize">
<echo>Not skipping doclet run...</echo>
<mkdir dir="${build}" />
<javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
debug="${debug}" deprecation="${deprecation}" source="1.5"/>
<java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
<arg value="${src}/META-INF"/>
<arg value="${src}/main"/>
<arg value="${build}"/>
</java>
<java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
<arg value="${src}/META-INF"/>
<arg value="${src}/test"/>
<arg value="${build}"/>
</java>
</target>
<target id="compile-needed-test" name="compile-needed-test">
<if>
<matches string="${module}" pattern="^test"/>
<then>
<property name="source" value="src/test"/>
</then>
<else>
<property name="source" value="src/main"/>
</else>
</if>
<uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
<srcfiles dir="${source}">
<includesfile name="${build}/${module}.javafiles"/>
</srcfiles>
</uptodate>
</target>
<target id="compile-init" name="compile-init"
depends="init, check, runDoclet"/>
<target id="qa-module" name="qa-module"
depends="check, dist.init, compile-needed-test"
unless="module-uptodate">
<echo message="Running QA for CDK's ${module} module" />
<antcall target="test-module">
<param name="module" value="${module}"/>
</antcall>
<ant antfile="pmd.xml" target="test-module">
<property name="pmd.test" value="custom"/>
<property name="module" value="${module}"/>
<property name="lib" value="develjar" />
</ant>
<ant antfile="pmd-unused.xml" target="test-module">
<property name="pmd.test" value="custom"/>
<property name="module" value="${module}"/>
<property name="lib" value="develjar" />
</ant>
<ant antfile="pmd-migrating.xml" target="test-module">
<property name="pmd.test" value="migrating"/>
<property name="module" value="${module}"/>
<property name="lib" value="develjar" />
</ant>
</target>
<target id="compile-module" name="compile-module"
depends="check, dist.init, compile-needed-test"
unless="module-uptodate">
<if>
<matches string="${module}" pattern="^test"/>
<then>
<property name="source" value="src/test"/>
</then>
<else>
<property name="source" value="src/main"/>
</else>
</if>
<echo message="Compiling classes for CDK's ${module} module from ${source}..." />
<!-- check for availability for meta info files -->
<available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
<available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
<available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
<available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
<available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
<available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
<available file="${metainf}/${module}.autogenerated" property="module.autogenerated.present"/>
<!-- be somewhat informative -->
<echo message="Datafiles defined: ${module.datafiles.present}"/>
<echo message="Extra files defined: ${module.extrafiles.present}"/>
<echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
<echo message="Library dependencies defined: ${module.libdepends.present}"/>
<echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
<echo message="Autogenerated files specified: ${module.autogenerated.present}"/>
<!-- normally javac compiles not just the given files, but also missing
classes that are in the same src/ directory. By making a copy first,
we explicitely make it impossible to compile files that are not
marked for a specific module -->
<mkdir dir="${build.src}/${module}"/>
<mkdir dir="${build}/${module}"/>
<copy todir="${build.src}/${module}">
<fileset dir="${source}">
<excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
<!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
<!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
<excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
<excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
<includesfile name="${build}/${module}.javafiles"/>
<includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
</fileset>
</copy>
<!-- ok, now that we have a copy, compile this copy -->
<javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5">
<classpath>
<fileset dir="${lib}" >
<exclude name="**/*" unless="module.libdepends.present" />
<includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
</fileset>
<fileset dir="${devellib}">
<exclude name="**/*" unless="module.devellibdepends.present" />
<includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
</fileset>
<fileset dir="${dist}/jar">
<exclude name="**/*" unless="module.cdkdepends.present" />
<includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
</fileset>
</classpath>
<excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
<!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
<!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
<excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
<excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
<includesfile name="${build}/${module}.javafiles"/>
<includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
</javac>
<!-- create a autogenerated.classes file, if applicable, so that these files can be included in the jar -->
<if>
<istrue value="${module.autogenerated.present}"/>
<then>
<copy file="${metainf}/${module}.autogenerated" tofile="${build}/${module}.autogenerated.classes"
failonerror="false"/>
<replace dir="${build}" token=".java" value="*.class">
<include name="*.autogenerated.classes"/>
</replace>
</then>
</if>
<!-- and then jar things up into the module jar -->
<jar jarfile="${dist}/jar/cdk-${module}.jar">
<fileset dir="${build}/${module}">
<includesfile name="${build}/${module}.classes" />
<includesfile name="${build}/${module}.autogenerated.classes" if="module.autogenerated.present"/>
<excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
<!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
<!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
<excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
<excludesfile name="${build}/ant1.6.classes" unless="hasAnt17"/>
</fileset>
<fileset dir="${build}">
<include name="${module}.javafiles" />
</fileset>
<fileset dir="${source}">
<exclude name="**/*" unless="module.datafiles.present"/>
<includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
</fileset>
<fileset dir="${src}">
<exclude name="**/*" unless="module.extrafiles.present"/>
<includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
</fileset>
<fileset dir="${build}">
<exclude name="**/*" unless="module.buildfiles.present"/>
<includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
</fileset>
</jar>
<jar jarfile="${dist}/jar/cdk-${module}-sources.jar">
<fileset dir="${build.src}/${module}">
<include name="**/*.java" />
</fileset>
</jar>
<!-- clean up afterwards -->
<delete dir="${build.src}/${module}"/>
<delete dir="${build}/${module}"/>
</target>
<!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
<target id="javacc" name="javacc" depends="init, check" if="hasAnt17" unless="dotjjfiles.uptodate">
<echo message="Compiling Ant 1.6 depending classes." />
<!-- the IUPAC name parser -->
<delete>
<fileset id="javacc-generated"
dir="${src}/main/org/openscience/cdk/iupac/parser/"
includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
</delete>
<javacc target="${src}/main/org/openscience/cdk/iupac/parser/NomParser.jj"
outputdirectory="${src}/main/org/openscience/cdk/iupac/parser/"
javacchome="${lib}"/>
<delete>
<fileset id="javacc-generated"
dir="${src}/main/org/openscience/cdk/smiles/smarts/parser/"
includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java"/>
</delete>
<jjtree target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt"
javacchome="${lib}"
outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
<javacc target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj"
javacchome="${lib}"
outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
<!-- OK, we now need to do some replacements such as
adding cdk.module tags and changing access modes
-->
<replace file="${src}/main/org/openscience/cdk/smiles/smarts/parser/JJTSMARTSParserState.java"
token="class JJTSMARTSParserState {" value="public class JJTSMARTSParserState {" />
<replace dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
excludes="AST*.java,SMARTSParser.jjt,SMARTSParser.jj,*Node.java"
token="package org.openscience.cdk.smiles.smarts.parser;" summary="true" >
<replacevalue>package org.openscience.cdk.smiles.smarts.parser;
/**
*
* @cdk.module smarts
*/</replacevalue>
</replace>
</target>
<target id="dist.init" name="dist.init">
<mkdir dir="${dist}/jar" />
</target>
<target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
<target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
<echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
</target>
<target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
<antcall target="compile-module"><param name="module" value="java3d"/></antcall>
</target>
<target id="dist-optional" name="dist-optional" depends="dist-all"
description="Compile CDK modules that require optional libraries">
<antcall target="dist-java3d"/>
</target>
<target id="dist-all" name="dist-all" description="dist-all">
<antcall target="compile-init"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="interfaces,annotation"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="core,ioformats"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="data,dict,diff,qm,standard,log4j"/>
<foreach target="compile-module" param="module" trim="yes"
parallel="${parallel}" maxthreads="${threadCount}"
list="datadebug,nonotify,isomorphism,atomtype,render,valencycheck,
formula"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="io,structgen"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="pdb,smiles,sdg,inchi,libiocml"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="control,extra,reaction,pdbcml,libiomd"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="charges,smarts"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="qm,qsar,ionpot,fingerprint,pcore"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="qsaratomic,qsarbond,qsarprotein,qsarcml,qsarmolecular"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="forcefield,qsarionpot"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="builder3d,builder3dtools"/>
</target>
<target id="test-dist-all" name="test-dist-all" description="test-dist-all">
<antcall target="compile-init"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="test"/>
<foreach target="compile-module" param="module" trim="true"
parallel="${parallel}" maxthreads="${threadCount}"
list="test-interfaces,test-libiocml,test-qsar,test-io,test-core,
test-valencycheck,test-smarts,test-standard,test-reaction,
test-pcore,test-sdg,test-forcefield,test-fingerprint,
test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict,
test-diff,test-charges,test-inchi,test-formula,
test-render,test-ioformats,test-log4j"/>
<foreach target="compile-module" param="module" trim="true"
parallel="${parallel}" maxthreads="${threadCount}"
list="test-data,test-qsaratomic,test-qsarbond,
test-pdb,test-smiles,test-extra,test-atomtype,
test-structgen"/>
<foreach target="compile-module" param="module" trim="true"
parallel="${parallel}" maxthreads="${threadCount}"
list="test-qsarmolecular,test-builder3d,test-datadebug,
test-nonotify"/>
<foreach target="compile-module" param="module"
parallel="${parallel}" maxthreads="${threadCount}"
list="test-qsarprotein,test-qsarionpot"/>
</target>
<target id="jarTestdata" name="jarTestdata" description="Creates jar files with test data.">
<mkdir dir="${dist}/jar"/>
<jar jarfile="${dist}/jar/cdk-testdata.jar">
<fileset dir="${src}/test">
<include name="data/**/*" />
</fileset>
</jar>
</target>
<target id="dist-large" name="dist-large" depends="dist-all"
description="Builds one big jar file for the CDK, including third-party libraries.">
<!-- first unjar the CDK and other jars we need -->
<mkdir dir="${appjars.dir}"/>
<unjar dest="${appjars.dir}">
<fileset dir="${lib}">
<includesfile name="${metainf}/builder3d.libdepends"/>
<includesfile name="${metainf}/builder3dtools.libdepends"/>
<includesfile name="${metainf}/charges.libdepends"/>
<includesfile name="${metainf}/log4j.libdepends"/>
<includesfile name="${metainf}/control.libdepends"/>
<includesfile name="${metainf}/datadebug.libdepends"/>
<includesfile name="${metainf}/data.libdepends"/>
<includesfile name="${metainf}/extra.libdepends"/>
<includesfile name="${metainf}/io.libdepends"/>
<includesfile name="${metainf}/libiocml.libdepends"/>
<includesfile name="${metainf}/nonotify.libdepends"/>
<includesfile name="${metainf}/pdbcml.libdepends"/>
<includesfile name="${metainf}/pdb.libdepends"/>
<includesfile name="${metainf}/qsar.libdepends"/>
<includesfile name="${metainf}/qsaratomic.libdepends"/>
<includesfile name="${metainf}/qsarbond.libdepends"/>
<includesfile name="${metainf}/qsarmolecular.libdepends"/>
<includesfile name="${metainf}/qsarprotein.libdepends"/>
<includesfile name="${metainf}/qsarcml.libdepends"/>
<includesfile name="${metainf}/reaction.libdepends"/>
<includesfile name="${metainf}/render.libdepends"/>
<includesfile name="${metainf}/standard.libdepends"/>
<includesfile name="${metainf}/valencycheck.libdepends"/>
<includesfile name="${metainf}/sdg.libdepends"/>
<includesfile name="${metainf}/forcefield.libdepends"/>
<includesfile name="${metainf}/inchi.libdepends"/>
<includesfile name="${metainf}/smarts.libdepends"/>
<includesfile name="${metainf}/pcore.libdepends"/>
<includesfile name="${metainf}/formula.libdepends"/>
<includesfile name="${metainf}/isomorphism.libdepends"/>
</fileset>
<fileset dir="${dist}/jar">
<include name="cdk-annotation.jar"/>
<include name="cdk-ioformats.jar"/>
<include name="cdk-atomtype.jar"/>
<include name="cdk-builder3d.jar"/>
<include name="cdk-builder3dtools.jar"/>
<include name="cdk-charges.jar"/>
<include name="cdk-core.jar"/>
<include name="cdk-log4j.jar"/>
<include name="cdk-dict.jar"/>
<include name="cdk-diff.jar"/>
<include name="cdk-control.jar"/>
<include name="cdk-datadebug.jar"/>
<include name="cdk-data.jar"/>
<include name="cdk-extra.jar"/>
<include name="cdk-interfaces.jar"/>
<include name="cdk-io.jar"/>
<include name="cdk-libiocml.jar"/>
<include name="cdk-libiomd.jar"/>
<include name="cdk-nonotify.jar"/>
<include name="cdk-pdbcml.jar"/>
<include name="cdk-pdb.jar"/>
<include name="cdk-qsar.jar"/>
<include name="cdk-qsaratomic.jar"/>
<include name="cdk-qsarbond.jar"/>
<include name="cdk-qsarmolecular.jar"/>
<include name="cdk-qsarionpot.jar"/>
<include name="cdk-qsarprotein.jar"/>
<include name="cdk-qsarcml.jar"/>
<include name="cdk-reaction.jar"/>
<include name="cdk-render.jar"/>
<include name="cdk-standard.jar"/>
<include name="cdk-structgen.jar"/>
<include name="cdk-valencycheck.jar"/>
<include name="cdk-forcefield.jar"/>
<include name="cdk-smiles.jar"/>
<include name="cdk-smarts.jar"/>
<include name="cdk-fingerprint.jar"/>
<include name="cdk-sdg.jar"/>
<include name="cdk-inchi.jar"/>
<include name="cdk-pcore.jar"/>
<include name="cdk-formula.jar"/>
<include name="cdk-isomorphism.jar"/>
<include name="cdk-ionpot.jar"/>
</fileset>
</unjar>
<!-- then zip up things -->
<jar jarfile="${dist}/jar/cdk-${version}.jar">
<manifest>
<section name="org.openscience.cdk">
<attribute name="Specification-Title" value="The Chemistry Development Kit"/>
<attribute name="Specification-Version" value="1.2"/>
<attribute name="Specification-Vendor" value="The CDK Project"/>
<attribute name="Implementation-Title" value="org.openscience.cdk"/>
<attribute name="Implementation-Version" value="${version}"/>
<attribute name="Implementation-Vendor" value="The CDK Project"/>
</section>
</manifest>
<fileset dir="${appjars.dir}">
<include name="**/*" />
</fileset>
</jar>
</target>
<target id="dist-pure" name="dist-pure" depends="dist-all"
description="Builds one big jar file for the CDK, excluding third party libraries.">
<!-- first unjar the CDK and other jars we need -->
<mkdir dir="${appjars.dir}"/>
<unjar dest="${appjars.dir}">
<fileset dir="${dist}/jar">
<include name="cdk-annotation.jar"/>
<include name="cdk-builder3d.jar"/>
<include name="cdk-builder3dtools.jar"/>
<include name="cdk-charges.jar"/>
<include name="cdk-log4j.jar"/>
<include name="cdk-core.jar"/>
<include name="cdk-control.jar"/>
<include name="cdk-datadebug.jar"/>
<include name="cdk-data.jar"/>
<include name="cdk-diff.jar"/>
<include name="cdk-extra.jar"/>
<include name="cdk-interfaces.jar"/>
<include name="cdk-io.jar"/>
<include name="cdk-ioformats.jar"/>
<include name="cdk-libiocml.jar"/>
<include name="cdk-libiomd.jar"/>
<include name="cdk-nonotify.jar"/>
<include name="cdk-pdbcml.jar"/>
<include name="cdk-pdb.jar"/>
<include name="cdk-qsar.jar"/>
<include name="cdk-qsaratomic.jar"/>
<include name="cdk-qsarbond.jar"/>
<include name="cdk-qsarmolecular.jar"/>
<include name="cdk-qsarionpot.jar"/>
<include name="cdk-qsarprotein.jar"/>
<include name="cdk-qsarcml.jar"/>
<include name="cdk-reaction.jar"/>
<include name="cdk-render.jar"/>
<include name="cdk-standard.jar"/>
<include name="cdk-structgen.jar"/>
<include name="cdk-valencycheck.jar"/>
<include name="cdk-forcefield.jar"/>
<include name="cdk-smarts.jar"/>
<include name="cdk-fingerprint.jar"/>
<include name="cdk-smiles.jar"/>
<include name="cdk-sdg.jar"/>
<include name="cdk-inchi.jar"/>
<include name="cdk-pcore.jar"/>
<include name="cdk-formula.jar"/>
<include name="cdk-atomtype.jar"/>
</fileset>
</unjar>
<!-- then zip up things -->
<jar jarfile="${dist}/jar/cdk-pure-${version}.jar">
<manifest>
<section name="org.openscience.cdk">
<attribute name="Specification-Title" value="The Chemistry Development Kit"/>
<attribute name="Specification-Version" value="1.0"/>
<attribute name="Specification-Vendor" value="The CDK Project"/>
<attribute name="Implementation-Title" value="org.openscience.cdk"/>
<attribute name="Implementation-Version" value="${version}"/>
<attribute name="Implementation-Vendor" value="The CDK Project"/>
</section>
</manifest>
<fileset dir="${appjars.dir}">
<include name="**/*" />
</fileset>
</jar>
</target>
<target id="dist-test-large" name="dist-test-large" depends="test-dist-all"
description="Builds on big jar file for the CDK test classes.">
<!-- first unjar the CDK and other jars we need -->
<mkdir dir="${appjars.dir}"/>
<unjar dest="${appjars.dir}">
<fileset dir="${lib}">
<includesfile name="${metainf}/test-core.libdepends"/>
<includesfile name="${metainf}/test-data.libdepends"/>
<includesfile name="${metainf}/test-datadebug.libdepends"/>
<includesfile name="${metainf}/test-diff.libdepends"/>
<includesfile name="${metainf}/test-extra.libdepends"/>
<includesfile name="${metainf}/test-builder3d.libdepends"/>
<includesfile name="${metainf}/test-forcefield.libdepends"/>
<includesfile name="${metainf}/test-inchi.libdepends"/>
<includesfile name="${metainf}/test-io.libdepends"/>
<includesfile name="${metainf}/test-nonotify.libdepends"/>
<includesfile name="${metainf}/test-pdb.libdepends"/>
<includesfile name="${metainf}/test-qsaratomic.libdepends"/>
<includesfile name="${metainf}/test-qsarbond.libdepends"/>
<includesfile name="${metainf}/test-qsarmolecular.libdepends"/>
<includesfile name="${metainf}/test-qsarionpot.libdepends"/>
<includesfile name="${metainf}/test-qsarprotein.libdepends"/>
<includesfile name="${metainf}/test-qsar.libdepends"/>
<includesfile name="${metainf}/test-reaction.libdepends"/>
<includesfile name="${metainf}/test-smarts.libdepends"/>
<includesfile name="${metainf}/test-smiles.libdepends"/>
<includesfile name="${metainf}/test-standard.libdepends"/>
<includesfile name="${metainf}/test-structgen.libdepends"/>
<includesfile name="${metainf}/test-valencycheck.libdepends"/>
<includesfile name="${metainf}/test-charges.libdepends"/>
<includesfile name="${metainf}/test-libiomd.libdepends"/>
<includesfile name="${metainf}/test-pcore.libdepends"/>
<includesfile name="${metainf}/test-formula.libdepends"/>
<includesfile name="${metainf}/test-render.libdepends"/>
<includesfile name="${metainf}/test-log4j.libdepends"/>
</fileset>
<fileset dir="${dist}/jar">
<include name="cdk-test-annotation.jar"/>
<include name="cdk-test-ioformats.jar"/>
<include name="cdk-test-core.jar"/>
<include name="cdk-test-data.jar"/>
<include name="cdk-test-datadebug.jar"/>
<include name="cdk-test-diff.jar"/>
<include name="cdk-test-extra.jar"/>
<include name="cdk-test-builder3d.jar"/>
<include name="cdk-test-forcefield.jar"/>
<include name="cdk-test-inchi.jar"/>
<include name="cdk-test-io.jar"/>
<include name="cdk-test-nonotify.jar"/>
<include name="cdk-test-pdb.jar"/>
<include name="cdk-test-qsaratomic.jar"/>
<include name="cdk-test-qsarbond.jar"/>
<include name="cdk-test-qsarmolecular.jar"/>
<include name="cdk-test-qsarionpot.jar"/>
<include name="cdk-test-qsarprotein.jar"/>
<include name="cdk-test-qsar.jar"/>
<include name="cdk-test-reaction.jar"/>
<include name="cdk-test-smarts.jar"/>
<include name="cdk-test-smiles.jar"/>
<include name="cdk-test-standard.jar"/>
<include name="cdk-test-structgen.jar"/>
<include name="cdk-test-valencycheck.jar"/>
<include name="cdk-test-charges.jar"/>
<include name="cdk-test-libiomd.jar"/>
<include name="cdk-test-pcore.jar"/>
<include name="cdk-test-formula.jar"/>
<include name="cdk-test-render.jar"/>
<include name="cdk-test-log4j.jar"/>
</fileset>
</unjar>
<!-- then zip up things -->
<jar jarfile="${dist}/jar/cdk-test-${version}.jar">
<manifest>
<attribute name="Main-Class" value="org.openscience.cdk.CDKTests"/>
<section name="org.openscience.cdk">
<attribute name="Specification-Title" value="The Chemistry Development Kit"/>
<attribute name="Specification-Version" value="1.2"/>
<attribute name="Specification-Vendor" value="The CDK Project"/>
<attribute name="Implementation-Title" value="org.openscience.cdk"/>
<attribute name="Implementation-Version" value="${version}"/>
<attribute name="Implementation-Vendor" value="The CDK Project"/>
</section>
</manifest>
<fileset dir="${appjars.dir}">
<include name="**/*" />
</fileset>
</jar>
</target>
<target id="sourcedist" name="sourcedist"
description="Builds the source packages.">
<property name="package" value="cdk-src+libs-${version}"/>
<property name="sourcedist.dir" value="${sourcedist}/${package}"/>
<delete dir="${sourcedist.dir}"/>
<copy todir="${sourcedist.dir}/${src}/main/">
<fileset dir="${src}/main/" includes="**/*.java" />
<fileset dir="${src}/main/" includes="**/*.jj" />
<fileset dir="${src}/main/" includes="**/*.jjt" />
<fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
</copy>
<copy todir="${sourcedist.dir}">
<fileset dir="." includes="build.props" />
<fileset dir="." includes="build.xml" />
<fileset dir="." includes="javadoc.xml" />
<fileset dir="." includes="README" />
<fileset dir="." includes="changelog*" />
</copy>
<copy todir="${sourcedist.dir}/jar">
<fileset dir="jar">
<exclude name="*.so"/>
<exclude name="*.dll"/>
<exclude name="jumbo-5.4.2-b2.jar"/>
</fileset>
</copy>
<copy todir="${sourcedist.dir}/doc/refs">
<fileset dir="doc/refs">
<include name="*.*"/>
</fileset>
</copy>
<copy todir="${sourcedist.dir}/develjar">
<fileset dir="develjar">
<exclude name="pmd-1.8.jar"/>
<exclude name="doccheck.jar"/>
<exclude name="dbdoclet*.*"/>
</fileset>
</copy>
<copy todir="${sourcedist.dir}/src/META-INF">
<fileset dir="src/META-INF" />
</copy>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/config/data/">
<fileset dir="${src}/main/org/openscience/cdk/config/data/"
includes="*" />
</copy>
<copy
file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
<fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/">
<fileset dir="${src}/main/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
</copy>
<mkdir dir="${sourcedist.dir}/doc/" />
<copy todir="${sourcedist.dir}/doc/">
<fileset dir="doc/" includes="lgpl.license" />
</copy>
<mkdir dir="${sourcedist.dir}/doc/javadoc" />
<!-- the below deteles are a workaround, because the above should not have copied
in the src/data and src/org/openscience/cdk/test dirs -->
<delete dir="${sourcedist.dir}/src/test/data"/>
<!-- now package things up -->
<tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
<gzip zipfile="${package}.tar.gz" src="${package}.tar" />
<delete file="${package}.tar" />
<zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
</target>
<target id="puredist" name="puredist" depends="init, runDoclet"
description="Builds the source packages without third-party libaries.">
<property name="package" value="cdk-${version}"/>
<property name="sourcedist.dir" value="${sourcedist}/${package}"/>
<delete dir="${sourcedist.dir}"/>
<copy todir="${sourcedist.dir}/${src}/main">
<fileset dir="${src}/main/" includes="**/*.java" />
<fileset dir="${src}/main/" includes="**/*.jj" />
<fileset dir="${src}/main/" includes="**/*.jjt" />
<fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
</copy>
<copy todir="${sourcedist.dir}/doc/refs">
<fileset dir="doc/refs">
<include name="*.*"/>
</fileset>
</copy>
<copy todir="${sourcedist.dir}">
<fileset dir="." includes="build.props" />
<fileset dir="." includes="build.xml" />
<fileset dir="." includes="javadoc.xml" />
<fileset dir="." includes="README" />
<fileset dir="." includes="changelog*" />
</copy>
<copy todir="${sourcedist.dir}/src/META-INF">
<fileset dir="src/META-INF" />
</copy>
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
<fileset dir="${src}/main/org/openscience/cdk/config/data/"
includes="*" />
</copy>
<copy
file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
<fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/">
<fileset dir="${src}/main/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
</copy>
<mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
<copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
<fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
</copy>
<mkdir dir="${sourcedist.dir}/doc/" />
<copy todir="${sourcedist.dir}/doc/">
<fileset dir="doc/" includes="lgpl.license" />
</copy>
<mkdir dir="${sourcedist.dir}/doc/javadoc" />
<!-- the below deteles are a workaround, because the above should not have copied
in the src/data and src/org/openscience/cdk/test dirs -->
<delete dir="${sourcedist.dir}/src/data"/>
<delete dir="${sourcedist.dir}/src/test"/>
<!-- now package things up -->
<tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
<gzip zipfile="${package}.tar.gz" src="${package}.tar" />
<delete file="${package}.tar" />
</target>
<target id="noJunit" name="noJunit" depends="check" unless="junit.present">
<fail message="JUnit is not installed in Ant. Please run ant with the option '-lib develjar/junit-4.3.1.jar'."/>
</target>
<target id="test-module" name="test-module" depends="noJunit"
description="Performs a full JUnit test for the CDK."
if="junit.present">
<echo message="Testing classes for CDK's ${module} module." />