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ea39d29 More dependency clean up... A lot is working now, but the cyclic depende...
egonw authored
1 <project name="CDK" default="dist-all" basedir=".">
3d221c1 Added additional PDBReader tests.
yeldar authored
2
0e9e5ef Added version info to JavaDoc html output, and share this with the build...
egonw authored
3 <property file="build.props"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
4
3a26de3 Made compilation with debug=on customizable.
egonw authored
5 <!-- compile options -->
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
6 <property name="build.sysclasspath" value="ignore" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
7 <property name="build.compiler" value="modern" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
8 <property name="debug" value="on" />
460ea79 Detect deprecated methods
egonw authored
9 <property name="deprecation" value="on" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
10 <property name="optimization" value="off" />
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
11 <property name="threadCount" value="4" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
12
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
13 <!-- patches to apply -->
14
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
15 <!-- directories -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
16 <property name="build" value="build" />
bd36ed1 Trial for new build system
egonw authored
17 <property name="build.src" value="${build}/src" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
18 <property name="sourcedist" value="sourcedist" />
19 <property name="dist" value="dist" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
20 <property name="doc" value="doc" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
21 <property name="src" value="src" />
22 <property name="lib" value="jar" />
9e95b7b Finished splitting devel from user jars
egonw authored
23 <property name="devellib" value="develjar" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
24 <property name="src.tests" value="${src}/test/org/openscience/cdk/test" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
25 <property name="reports.tests" value="reports" />
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
26 <property name="appjars.dir" value="${dist}/appjars" />
bd36ed1 Trial for new build system
egonw authored
27 <property name="metainf" value="${src}/META-INF" />
f7be51f Removed alternative core classes patch offering more detailed debug info
egonw authored
28
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar which ...
egonw authored
29 <!-- class to run for testing-->
30 <property name="testclass" value="CDKTests" />
31 <property name="arg1" value="" />
32 <property name="arg2" value="" />
33 <property name="arg3" value="" />
34 <property name="arg4" value="" />
5c40bcf Removed the check for rJava as we don't strictly need it. Also added a p...
rajarshi authored
35
36 <property environment="env" />
37
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
38
39 <!-- Inlcude the ant-contrib goodies -->
40 <taskdef resource="net/sf/antcontrib/antlib.xml">
41 <classpath>
42 <pathelement location="${basedir}/develjar/ant-contrib-1.0b3.jar"/>
43 </classpath>
44 </taskdef>
45
46
47
5c40bcf Removed the check for rJava as we don't strictly need it. Also added a p...
rajarshi authored
48 <target id="info" name="info" depends="check">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
49 <!-- Gives information about the building process. -->
8f6d674 Fixed after breaking it earlier today
egonw authored
50 <echo message="Platform:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
51 <echo message=" OS: ${os.name}" />
52 <echo message=" Architecture: ${os.arch}" />
53 <echo message=" Version: ${os.version}" />
54 <echo message=" Mac OS/X found: ${isMacOsX}" />
8f6d674 Fixed after breaking it earlier today
egonw authored
55 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info fee...
egonw authored
56 <echo message="Java/Ant Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
57 <echo message=" Java version: ${java.version}" />
58 <echo message=" Java vendor: ${java.vendor}" />
59 <echo message=" Java dir: ${java.home}" />
60 <echo message=" Java ext dir: ${java.ext.dirs}" />
61 <echo message=" Ant version: ${ant.version}" />
62 <echo message=" ${ANT_HOME}: ${ant.home}" />
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
63 <echo message=" hasAnt17: ${hasAnt17}" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info fee...
egonw authored
64 <echo message="" />
65 <echo message="CDK Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
66 <echo message=" CDK version: ${version}" />
67 <echo message=" build.xml: $Id$" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
68 <echo message=" Junit found: ${junit.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
69 <echo message=" --- required libraries ---" />
70 <echo message=" Vecmath found: ${vecmath.present}" />
71 <echo message=" Log4j found: ${log4j.present}" />
72 <echo message=" JGraphT found: ${jgrapht.present}" />
c1c3a3b Removed outdated optional compile checks
egonw authored
73 <echo message=" --- distributed (but optional) libraries ---" />
7cd4ff8 Added R/SJava found to info target
egonw authored
74 <echo message=" CMLDOM found: ${cmllibs.present}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
75 <echo message=" --- optional libraries ---" />
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
76 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
77 <echo message="Compiling:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
78 <echo message=" for: ${build.compiler}" />
79 <echo message=" debug: ${debug}" />
80 <echo message=" deprecation: ${deprecation}" />
81 <echo message=" optimization: ${optimization}" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
82 </target>
83
8f6d674 Fixed after breaking it earlier today
egonw authored
84 <target id="checkPlatforms" name="checkPlatforms">
58405cf Fixed build.xml to allow compile of doclets on MacOS/X (closes #1001497)
egonw authored
85 <condition property="isMacOsX">
86 <and>
87 <os family="mac"/>
88 <os family="unix"/>
89 </and>
90 </condition>
91 </target>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
92
8f6d674 Fixed after breaking it earlier today
egonw authored
93 <target id="check" name="check" depends="checkPlatforms">
cc68a07 Added detection of more third party libraries
egonw authored
94 <!-- Check wether Doclets are compiled and output is generated -->
95 <uptodate property="dotjavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
96 targetfile="${build}/core.javafiles">
cc68a07 Added detection of more third party libraries
egonw authored
97 <srcfiles dir="${src}" includes="**/*.java" />
98 </uptodate>
99 <condition property="dotjjfiles.uptodate">
100 <and>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
101 <uptodate property="NomParserJavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
102 targetfile="${src}/main/org/openscience/cdk/iupac/parser/NomParser.java">
103 <srcfiles dir="${src}/main/" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
cc68a07 Added detection of more third party libraries
egonw authored
104 </uptodate>
65b6106 Added compatibility with ant1.7. Added building process for JJTree imple...
djiao authored
105 <uptodate property="SMARTSParserJJTJavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
106 targetfile="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.java">
107 <srcfiles dir="${src}/main/" includes="org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj" />
65b6106 Added compatibility with ant1.7. Added building process for JJTree imple...
djiao authored
108 </uptodate>
cc68a07 Added detection of more third party libraries
egonw authored
109 </and>
110 </condition>
111
112 <!-- Checks which parts of CDK can be build. -->
113
114 <!-- test for optional jars -->
115 <available property="vecmath.present"
116 file="${lib}/vecmath1.2-1.14.jar"/>
117 <available property="log4j.present"
118 file="${lib}/log4j.jar"/>
119 <available property="jgrapht.present"
152e213 Updated for recent upgrades to Jumbo 5.2 and JGraphT 0.6.0
egonw authored
120 file="${lib}/jgrapht-0.6.0.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
121
122 <!-- test for optional jars -->
123 <condition property="cmllibs.present">
124 <or>
6fa97cb replaced jumbo-5.4.2-b1 with jumbo-5.4.2-b2
drzz authored
125 <available file="${lib}/jumbo-5.4.2-b2.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
126 </or>
127 </condition>
128 <available property="junit.present"
129 classname="junit.framework.TestCase"
130 classpath="${ant.home}/lib/junit.jar"/>
131
132 <!-- test Ant version -->
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
133 <condition property="hasAnt17">
65b6106 Added compatibility with ant1.7. Added building process for JJTree imple...
djiao authored
134 <contains string="${ant.version}" substring="1.7"/>
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
135 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
136
137 <!-- test Java version -->
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
138 <condition property="isJava13">
139 <contains string="${java.version}" substring="1.3"/>
140 </condition>
141 <condition property="isJava14">
142 <contains string="${java.version}" substring="1.4"/>
143 </condition>
866bc72 CML is now available for Java1.5 too
egonw authored
144 <condition property="isJava15">
145 <contains string="${java.version}" substring="1.5"/>
146 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
147 <condition property="isJava16">
148 <contains string="${java.version}" substring="1.6."/>
149 </condition>
3f17ad0 Added detection of Java 1.7
egonw authored
150 <condition property="isJava17">
151 <contains string="${java.version}" substring="1.7."/>
152 </condition>
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
153 <condition property="isJava14+">
154 <or>
155 <contains string="${java.version}" substring="1.4"/>
156 <contains string="${java.version}" substring="1.5"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
157 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
158 <contains string="${java.version}" substring="1.7"/>
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
159 </or>
160 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
161 <condition property="isJava15+">
162 <or>
163 <contains string="${java.version}" substring="1.5"/>
164 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
165 <contains string="${java.version}" substring="1.7"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
166 </or>
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
167 </condition>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
168 <condition property="isNotJava15+">
169 <not>
170 <or>
171 <contains string="${java.version}" substring="1.5"/>
172 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
173 <contains string="${java.version}" substring="1.7"/>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
174 </or>
175 </not>
176 </condition>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
177 <fail if="isNotJava15+" message="This CDK release requires Java5 or better."/>
178 <fail unless="hasAnt17" message="This CDK release requires Ant 1.7 or better."/>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
179 </target>
180
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
181
d2ed020 Reworked dependencies
egonw authored
182 <target id="init" name="init" depends="check, setupBuildDir"/>
4302fbf Updated for Jumbo50 transition.
egonw authored
183 <target id="customize" name="customize" depends="javacc"/>
866bc72 CML is now available for Java1.5 too
egonw authored
184
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
185 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
186 <tstamp />
187 <mkdir dir="${build}" />
188 <mkdir dir="${sourcedist}" />
189 <mkdir dir="${dist}" />
190 <mkdir dir="${reports.tests}" />
191 </target>
192
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
193 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
194 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
195 <fileset dir="." includes="**/*~" />
196 <fileset dir="." includes="*.tar.gz" />
197 <fileset dir="." includes="*.zip" />
06ee5d1 Modified the clean target to remove .rda files generated during testing ...
rajarshi authored
198 <fileset dir="." includes="*.rda" />
bfe0e17 Build interfaces before data
egonw authored
199 <fileset dir="${src}" includes="*.entitylist" />
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
200 <!-- remove java files generated with JavaCC -->
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
201 <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts" includes="*.java">
51e5934 Added missing autogenerated SMARTS file to the clean task (closes #18948...
egonw authored
202 <exclude name="SMARTSQueryTool.java" />
203 </fileset>
204 <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the tree...
rajarshi authored
205 includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
206 <fileset dir="${src}/main/org/openscience/cdk/iupac/parser" includes="*.java">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
207 <!-- the next are from CVS -->
208 <exclude name="AttachedGroup.java" />
209 <exclude name="MoleculeBuilder.java" />
210 </fileset>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
211 <fileset dir="${src}/main/">
31994c5 Fixed deleting the doclet class files
egonw authored
212 <include name="net/sf/cdk/tools/*.class" />
2b81a22 Fixed a problem with deleting the doclet classes
egonw authored
213 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
214 </delete>
215
216 <delete dir="${build}" />
217 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
218 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
219 <delete dir="${reports.tests}" />
220 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
221
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small cust...
egonw authored
222 <target name="runDoclet" id="runDoclet" depends="check, customize">
223 <echo>Not skipping doclet run...</echo>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
224 <mkdir dir="${build}" />
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
225 <javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
226 srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small cust...
egonw authored
227 debug="${debug}" deprecation="${deprecation}"/>
228 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
20a1056 Fixed a patch from the branch that got lost in the branch merge
egonw authored
229 <arg value="${src}/META-INF"/>
230 <arg value="${src}/main"/>
231 <arg value="${build}"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
232 </java>
233 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
20a1056 Fixed a patch from the branch that got lost in the branch merge
egonw authored
234 <arg value="${src}/META-INF"/>
235 <arg value="${src}/test"/>
236 <arg value="${build}"/>
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small cust...
egonw authored
237 </java>
ca98ea5 Refactored build process (closes #883519)
egonw authored
238 </target>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
239
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
240 <target id="compile-needed-test" name="compile-needed-test">
241 <uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
242 <srcfiles dir="${src}/main/">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
243 <includesfile name="${build}/${module}.javafiles"/>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
244 </srcfiles>
245 </uptodate>
246 </target>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
247
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
248 <target id="compile-init" name="compile-init"
b0f7700 Checks are really needed a bit more often to ensure that some variable a...
egonw authored
249 depends="init, check, runDoclet"/>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
250
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
251 <target id="compile-module" name="compile-module"
b0f7700 Checks are really needed a bit more often to ensure that some variable a...
egonw authored
252 depends="check, dist.init, compile-needed-test"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
253 unless="module-uptodate">
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
254
6153fc1 Report from which source tree files are copied
egonw authored
255 <echo message="Compiling classes for CDK's ${module} module from ${source}..." />
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
256
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
egonw authored
257 <!-- check for availability for meta info files -->
258 <available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the remai...
egonw authored
259 <available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
c094513 Make sure the .set files end up in the right jars
egonw authored
260 <available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
egonw authored
261 <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
262 <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depende...
egonw authored
263 <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra modu...
egonw authored
264 <available file="${metainf}/${module}.autogenerated" property="module.autogenerated.present"/>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
265
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
egonw authored
266 <!-- be somewhat informative -->
267 <echo message="Datafiles defined: ${module.datafiles.present}"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the remai...
egonw authored
268 <echo message="Extra files defined: ${module.extrafiles.present}"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
egonw authored
269 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
270 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depende...
egonw authored
271 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra modu...
egonw authored
272 <echo message="Autogenerated files specified: ${module.autogenerated.present}"/>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
273
bd36ed1 Trial for new build system
egonw authored
274 <!-- normally javac compiles not just the given files, but also missing
275 classes that are in the same src/ directory. By making a copy first,
276 we explicitely make it impossible to compile files that are not
277 marked for a specific module -->
b868e9e Put source and class in module dependent build/ dirs, allowing compiling...
egonw authored
278 <mkdir dir="${build.src}/${module}"/>
279 <mkdir dir="${build}/${module}"/>
280 <copy todir="${build.src}/${module}">
365a4d7 Fix to use the proper source folder, now passed via a target argument
egonw authored
281 <fileset dir="${source}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
282 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
283 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
284 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
285 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
286 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
287
288 <includesfile name="${build}/${module}.javafiles"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra modu...
egonw authored
289 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
bd36ed1 Trial for new build system
egonw authored
290 </fileset>
291 </copy>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
292
bd36ed1 Trial for new build system
egonw authored
293 <!-- ok, now that we have a copy, compile this copy -->
b868e9e Put source and class in module dependent build/ dirs, allowing compiling...
egonw authored
294 <javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
e531e6e Java5 List<IAtom> like constructs in the interfaces. trunk/cdk/ now offi...
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295 debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5">
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296 <classpath>
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
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297 <fileset dir="${lib}" >
298 <exclude name="**/*" unless="module.libdepends.present" />
299 <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
bd36ed1 Trial for new build system
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300 </fileset>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depende...
egonw authored
301 <fileset dir="${devellib}">
302 <exclude name="**/*" unless="module.devellibdepends.present" />
303 <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
304 </fileset>
bd36ed1 Trial for new build system
egonw authored
305 <fileset dir="${dist}/jar">
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
egonw authored
306 <exclude name="**/*" unless="module.cdkdepends.present" />
307 <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
bd36ed1 Trial for new build system
egonw authored
308 </fileset>
309 </classpath>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
310
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
311 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
312 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
313 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
314 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
315 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
dece975 Fixed the build script to properly incldue the control module and its li...
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316
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
317 <includesfile name="${build}/${module}.javafiles"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra modu...
egonw authored
318 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
bd36ed1 Trial for new build system
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319 </javac>
dece975 Fixed the build script to properly incldue the control module and its li...
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320
0863077 Added infrastructure for putting autogenerated files in a non-extra modu...
egonw authored
321 <!-- create a autogenerated.classes file, if applicable, so that these files can be included in the jar -->
f1360a2 Cleaned up handling of presence/absence of autogenerated files, so no mo...
rajarshi authored
322 <if>
323 <istrue value="${module.autogenerated.present}"/>
324 <then>
325 <copy file="${metainf}/${module}.autogenerated" tofile="${build}/${module}.autogenerated.classes"
326 failonerror="false"/>
327 <replace dir="${build}" token=".java" value="*.class">
328 <include name="*.autogenerated.classes"/>
329 </replace>
330 </then>
331 </if>
332
333
bd36ed1 Trial for new build system
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334 <!-- and then jar things up into the module jar -->
335 <jar jarfile="${dist}/jar/cdk-${module}.jar">
b868e9e Put source and class in module dependent build/ dirs, allowing compiling...
egonw authored
336 <fileset dir="${build}/${module}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
337 <includesfile name="${build}/${module}.classes" />
0863077 Added infrastructure for putting autogenerated files in a non-extra modu...
egonw authored
338 <includesfile name="${build}/${module}.autogenerated.classes" if="module.autogenerated.present"/>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
339 <excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
340 <!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
341 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
342 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
343 <excludesfile name="${build}/ant1.6.classes" unless="hasAnt17"/>
bd36ed1 Trial for new build system
egonw authored
344 </fileset>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
345 <fileset dir="${build}">
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346 <include name="${module}.javafiles" />
347 </fileset>
174804f Fixed root location of .datafiles content
egonw authored
348 <fileset dir="${source}">
141cf36 Fixed problem with including data files in the module jars
egonw authored
349 <exclude name="**/*" unless="module.datafiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of unre...
egonw authored
350 <includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
351 </fileset>
7a673b7 Point to the correct root folder for datafiles and extrafiles
egonw authored
352 <fileset dir="${src}">
cd4dbe5 Added hook for extra files outside the src/ directory, solving the remai...
egonw authored
353 <exclude name="**/*" unless="module.extrafiles.present"/>
354 <includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
355 </fileset>
c8f144a Point to correct .set location.
egonw authored
356 <fileset dir="${build}">
c094513 Make sure the .set files end up in the right jars
egonw authored
357 <exclude name="**/*" unless="module.buildfiles.present"/>
c8f144a Point to correct .set location.
egonw authored
358 <includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
c094513 Make sure the .set files end up in the right jars
egonw authored
359 </fileset>
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360 </jar>
b868e9e Put source and class in module dependent build/ dirs, allowing compiling...
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361
362 <!-- clean up afterwards -->
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
363 <delete dir="${build.src}/${module}"/>
b868e9e Put source and class in module dependent build/ dirs, allowing compiling...
egonw authored
364 <delete dir="${build}/${module}"/>
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365 </target>
366
6dc5408 Added stuff for qsar module
egonw authored
367 <!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
368 <target id="javacc" name="javacc" depends="init, check" if="hasAnt17" unless="dotjjfiles.uptodate">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
369 <echo message="Compiling Ant 1.6 depending classes." />
cd49d3a A bit of comment
egonw authored
370 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
371 <delete>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
372 <fileset id="javacc-generated"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
373 dir="${src}/main/org/openscience/cdk/iupac/parser/"
cd49d3a A bit of comment
egonw authored
374 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
375 </delete>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
376 <javacc target="${src}/main/org/openscience/cdk/iupac/parser/NomParser.jj"
377 outputdirectory="${src}/main/org/openscience/cdk/iupac/parser/"
d9680ff Removed compilation steps for the old SMARTS parser
rajarshi authored
378 javacchome="${lib}"/>
65b6106 Added compatibility with ant1.7. Added building process for JJTree imple...
djiao authored
379 <delete>
380 <fileset id="javacc-generated"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
381 dir="${src}/main/org/openscience/cdk/smiles/smarts/parser/"
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the tree...
rajarshi authored
382 includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java"/>
65b6106 Added compatibility with ant1.7. Added building process for JJTree imple...
djiao authored
383 </delete>
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the tree...
rajarshi authored
384 <jjtree target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt"
65b6106 Added compatibility with ant1.7. Added building process for JJTree imple...
djiao authored
385 javacchome="${lib}"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
386 outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the tree...
rajarshi authored
387 <javacc target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj"
388 javacchome="${lib}"
389 outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
390
391 <!-- OK, we now need to do some replacements such as
392 adding cdk.module tags and changing access modes
393 -->
394 <replace file="${src}/main/org/openscience/cdk/smiles/smarts/parser/JJTSMARTSParserState.java"
395 token="class JJTSMARTSParserState {" value="public class JJTSMARTSParserState {" />
396 <replace dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
397 excludes="AST*.java,SMARTSParser.jjt,SMARTSParser.jj,*Node.java"
398 token="package org.openscience.cdk.smiles.smarts.parser;" summary="true" >
399 <replacevalue>package org.openscience.cdk.smiles.smarts.parser;
400
401 /**
402 *
403 * @cdk.module smarts
404 */</replacevalue>
405 </replace>
1dd9647 Added IUPAC name parser
stomkinson authored
406 </target>
8095921 Added rendering of wedged bonds.
egonw authored
407
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
408 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilation...
rajarshi authored
409 <mkdir dir="${dist}/jar" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
410 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
411
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
412 <target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
413 <target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
414 <echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
415 </target>
416 <target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
417 <antcall target="compile-module"><param name="module" value="java3d"/></antcall>
418 </target>
419
420 <target id="dist-optional" name="dist-optional" depends="dist-all"
421 description="Compile CDK modules that require optional libraries">
422 <antcall target="dist-java3d"/>
423 </target>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
424
425 <target id="parallel-all" name="parallel-all" description="dist-all in parallel mode">
426 <sequential>
427 <antcall target="compile-init"/>
428 <antcall target="compile-module"><param name="module" value="interfaces"/><param name="source" value="${src}/main"/></antcall>
429 <antcall target="compile-module"><param name="module" value="core"/><param name="source" value="${src}/main"/></antcall>
430 <parallel>
431 <antcall target="compile-module"><param name="module" value="data"/><param name="source" value="${src}/main"/></antcall>
432 <antcall target="compile-module"><param name="module" value="atomtype"/><param name="source" value="${src}/main"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
433 <antcall target="compile-module"><param name="module" value="dict"/><param name="source" value="${src}/main"/></antcall>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
434 <antcall target="compile-module"><param name="module" value="diff"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
435 </parallel>
436 <parallel>
437 <antcall target="compile-module"><param name="module" value="datadebug"/><param name="source" value="${src}/main"/></antcall>
438 <antcall target="compile-module"><param name="module" value="nonotify"/><param name="source" value="${src}/main"/></antcall>
439 <antcall target="compile-module"><param name="module" value="standard"/><param name="source" value="${src}/main"/></antcall>
440 <antcall target="compile-module"><param name="module" value="isomorphism"/><param name="source" value="${src}/main"/></antcall>
441 </parallel>
442 <parallel>
443 <antcall target="compile-module"><param name="module" value="io"/><param name="source" value="${src}/main"/></antcall>
444 <antcall target="compile-module"><param name="module" value="render"/><param name="source" value="${src}/main"/></antcall>
6f3c77f Some more dependency cleanup: now we have one sequential compile step le...
egonw authored
445 <antcall target="compile-module"><param name="module" value="valencycheck"/><param name="source" value="${src}/main"/></antcall>
e146a23 Updated for dependency cleanups
egonw authored
446 <antcall target="compile-module"><param name="module" value="formula"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
447 </parallel>
448 <parallel>
449 <antcall target="compile-module"><param name="module" value="pdb"/><param name="source" value="${src}/main"/></antcall>
450 <antcall target="compile-module"><param name="module" value="structgen"/><param name="source" value="${src}/main"/></antcall>
451 <antcall target="compile-module"><param name="module" value="extra"/><param name="source" value="${src}/main"/></antcall>
452 <antcall target="compile-module"><param name="module" value="sdg"/><param name="source" value="${src}/main"/></antcall>
453 <antcall target="compile-module"><param name="module" value="inchi"/><param name="source" value="${src}/main"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
454 <antcall target="compile-module"><param name="module" value="libiocml"/><param name="source" value="${src}/main"/></antcall>
e146a23 Updated for dependency cleanups
egonw authored
455 <antcall target="compile-module"><param name="module" value="smarts"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
456 </parallel>
457 <parallel>
458 <antcall target="compile-module"><param name="module" value="control"/><param name="source" value="${src}/main"/></antcall>
459 <antcall target="compile-module"><param name="module" value="smiles"/><param name="source" value="${src}/main"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
460 <antcall target="compile-module"><param name="module" value="reaction"/><param name="source" value="${src}/main"/></antcall>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
461 <antcall target="compile-module"><param name="module" value="pdbcml"/><param name="source" value="${src}/main"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
462 <antcall target="compile-module"><param name="module" value="libiomd"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
463 <antcall target="compile-module"><param name="module" value="pcore"/><param name="source" value="${src}/main"/></antcall>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
464 <antcall target="compile-module"><param name="module" value="fingerprint"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
465 </parallel>
e146a23 Updated for dependency cleanups
egonw authored
466 <antcall target="compile-module"><param name="module" value="charges"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
467 <parallel>
468 <antcall target="compile-module"><param name="module" value="qsar"/><param name="source" value="${src}/main"/></antcall>
e146a23 Updated for dependency cleanups
egonw authored
469 <antcall target="compile-module"><param name="module" value="ionpot"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
470 </parallel>
471 <parallel>
472 <antcall target="compile-module"><param name="module" value="qsaratomic"/><param name="source" value="${src}/main"/></antcall>
473 <antcall target="compile-module"><param name="module" value="qsarbond"/><param name="source" value="${src}/main"/></antcall>
474 <antcall target="compile-module"><param name="module" value="qsarprotein"/><param name="source" value="${src}/main"/></antcall>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
475 <antcall target="compile-module"><param name="module" value="qsarcml"/><param name="source" value="${src}/main"/></antcall>
e146a23 Updated for dependency cleanups
egonw authored
476 <antcall target="compile-module"><param name="module" value="qsarmolecular"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
477 </parallel>
478 <parallel>
479 <antcall target="compile-module"><param name="module" value="forcefield"/><param name="source" value="${src}/main"/></antcall>
e146a23 Updated for dependency cleanups
egonw authored
480 <antcall target="compile-module"><param name="module" value="qsarionpot"/><param name="source" value="${src}/main"/></antcall>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
481 </parallel>
482 <parallel>
483 <antcall target="compile-module"><param name="module" value="builder3d"/><param name="source" value="${src}/main"/></antcall>
484 <antcall target="compile-module"><param name="module" value="builder3dtools"/><param name="source" value="${src}/main"/></antcall>
485 </parallel>
486 </sequential>
487 </target>
fe65a98 Fixed dependencies
egonw authored
488
489 <target id="dist-all" name="dist-all" description="dist-all">
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
490 <antcall target="compile-init"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
491 <antcall target="compile-module"><param name="module" value="interfaces"/><param name="source" value="${src}/main"/></antcall>
492 <antcall target="compile-module"><param name="module" value="core"/><param name="source" value="${src}/main"/></antcall>
493 <antcall target="compile-module"><param name="module" value="atomtype"/><param name="source" value="${src}/main"/></antcall>
494 <antcall target="compile-module"><param name="module" value="standard"/><param name="source" value="${src}/main"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
495 <antcall target="compile-module"><param name="module" value="dict"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
496 <antcall target="compile-module"><param name="module" value="data"/><param name="source" value="${src}/main"/></antcall>
497 <antcall target="compile-module"><param name="module" value="render"/><param name="source" value="${src}/main"/></antcall>
498 <antcall target="compile-module"><param name="module" value="io"/><param name="source" value="${src}/main"/></antcall>
499 <antcall target="compile-module"><param name="module" value="valencycheck"/><param name="source" value="${src}/main"/></antcall>
500 <antcall target="compile-module"><param name="module" value="sdg"/><param name="source" value="${src}/main"/></antcall>
501 <antcall target="compile-module"><param name="module" value="control"/><param name="source" value="${src}/main"/></antcall>
502 <antcall target="compile-module"><param name="module" value="datadebug"/><param name="source" value="${src}/main"/></antcall>
503 <antcall target="compile-module"><param name="module" value="nonotify"/><param name="source" value="${src}/main"/></antcall>
504 <antcall target="compile-module"><param name="module" value="formula"/><param name="source" value="${src}/main"/></antcall>
505 <antcall target="compile-module"><param name="module" value="structgen"/><param name="source" value="${src}/main"/></antcall>
506 <antcall target="compile-module"><param name="module" value="pdb"/><param name="source" value="${src}/main"/></antcall>
75524f4 Set up a new module to get this code well tested
egonw authored
507 <antcall target="compile-module"><param name="module" value="isomorphism"/><param name="source" value="${src}/main"/></antcall>
f6848b6 Moved EState and MACCS fp's to the extra module and updated dependencies...
rajarshi authored
508 <antcall target="compile-module"><param name="module" value="smarts"/><param name="source" value="${src}/main"/></antcall>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
509 <antcall target="compile-module"><param name="module" value="fingerprint"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
510 <antcall target="compile-module"><param name="module" value="smiles"/><param name="source" value="${src}/main"/></antcall>
52638d6 Removed the experimental module: classes that are experimental should be...
egonw authored
511 <antcall target="compile-module"><param name="module" value="extra"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
512 <antcall target="compile-module"><param name="module" value="libiocml"/><param name="source" value="${src}/main"/></antcall>
513 <antcall target="compile-module"><param name="module" value="libiomd"/><param name="source" value="${src}/main"/></antcall>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
514 <antcall target="compile-module"><param name="module" value="pdbcml"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
515 <antcall target="compile-module"><param name="module" value="reaction"/><param name="source" value="${src}/main"/></antcall>
516 <antcall target="compile-module"><param name="module" value="charges"/><param name="source" value="${src}/main"/></antcall>
a5b2aef Merged from brunch to trunk: miguelrojasch-IP -> trunk/
miguelrojasch authored
517 <antcall target="compile-module"><param name="module" value="ionpot"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
518 <antcall target="compile-module"><param name="module" value="qsar"/><param name="source" value="${src}/main"/></antcall>
519 <antcall target="compile-module"><param name="module" value="qsaratomic"/><param name="source" value="${src}/main"/></antcall>
520 <antcall target="compile-module"><param name="module" value="qsarbond"/><param name="source" value="${src}/main"/></antcall>
521 <antcall target="compile-module"><param name="module" value="qsarmolecular"/><param name="source" value="${src}/main"/></antcall>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
522 <antcall target="compile-module"><param name="module" value="qsarionpot"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
523 <antcall target="compile-module"><param name="module" value="qsarprotein"/><param name="source" value="${src}/main"/></antcall>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
524 <antcall target="compile-module"><param name="module" value="qsarcml"/><param name="source" value="${src}/main"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
525 <antcall target="compile-module"><param name="module" value="forcefield"/><param name="source" value="${src}/main"/></antcall>
526 <antcall target="compile-module"><param name="module" value="builder3d"/><param name="source" value="${src}/main"/></antcall>
527 <antcall target="compile-module"><param name="module" value="builder3dtools"/><param name="source" value="${src}/main"/></antcall>
528 <antcall target="compile-module"><param name="module" value="pcore"/><param name="source" value="${src}/main"/></antcall>
ed41c5a The build.xml fix in r10230 uncovered many missing dependencies. This co...
egonw authored
529 <antcall target="compile-module"><param name="module" value="inchi"/><param name="source" value="${src}/main"/></antcall>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
530 <antcall target="compile-module"><param name="module" value="diff"/><param name="source" value="${src}/main"/></antcall>
38401bd Put applications in separate jar.
egonw authored
531 </target>
532
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
533 <target id="test-parallel-all" name="test-parallel-all" description="test-dist-all in parallel mode">
534 <sequential>
535 <antcall target="compile-init"/>
536 <antcall target="compile-module"><param name="module" value="test"/><param name="source" value="${src}/test"/></antcall>
537 <parallel threadCount="${threadCount}">
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
538 <antcall target="compile-module"><param name="module" value="test-diff"/><param name="source" value="${src}/test"/></antcall>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
539 <antcall target="compile-module"><param name="module" value="test-core"/><param name="source" value="${src}/test"/></antcall>
540 <antcall target="compile-module"><param name="module" value="test-data"/><param name="source" value="${src}/test"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
541 <antcall target="compile-module"><param name="module" value="test-dict"/><param name="source" value="${src}/test"/></antcall>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
542 <antcall target="compile-module"><param name="module" value="test-qsar"/><param name="source" value="${src}/test"/></antcall>
543 <antcall target="compile-module"><param name="module" value="test-libiocml"/><param name="source" value="${src}/test"/></antcall>
544 <antcall target="compile-module"><param name="module" value="test-valencycheck"/><param name="source" value="${src}/test"/></antcall>
545 <antcall target="compile-module"><param name="module" value="test-pdb"/><param name="source" value="${src}/test"/></antcall>
546 <antcall target="compile-module"><param name="module" value="test-structgen"/><param name="source" value="${src}/test"/></antcall>
547 <antcall target="compile-module"><param name="module" value="test-charges"/><param name="source" value="${src}/test"/></antcall>
548 <antcall target="compile-module"><param name="module" value="test-smarts"/><param name="source" value="${src}/test"/></antcall>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
549 <antcall target="compile-module"><param name="module" value="test-fingerprint"/><param name="source" value="${src}/test"/></antcall>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
550 <antcall target="compile-module"><param name="module" value="test-builder3d"/><param name="source" value="${src}/test"/></antcall>
551 <antcall target="compile-module"><param name="module" value="test-reaction"/><param name="source" value="${src}/test"/></antcall>
552 <antcall target="compile-module"><param name="module" value="test-inchi"/><param name="source" value="${src}/test"/></antcall>
553 <antcall target="compile-module"><param name="module" value="test-pcore"/><param name="source" value="${src}/test"/></antcall>
554 <antcall target="compile-module"><param name="module" value="test-forcefield"/><param name="source" value="${src}/test"/></antcall>
555 <antcall target="compile-module"><param name="module" value="test-isomorphism"/><param name="source" value="${src}/test"/></antcall>
556 <antcall target="compile-module"><param name="module" value="test-formula"/><param name="source" value="${src}/test"/></antcall>
557 <antcall target="compile-module"><param name="module" value="test-libiomd"/><param name="source" value="${src}/test"/></antcall>
558 </parallel>
559 <parallel threadCount="${threadCount}">
560 <antcall target="compile-module"><param name="module" value="test-datadebug"/><param name="source" value="${src}/test"/></antcall>
561 <antcall target="compile-module"><param name="module" value="test-nonotify"/><param name="source" value="${src}/test"/></antcall>
562 <antcall target="compile-module"><param name="module" value="test-io"/><param name="source" value="${src}/test"/></antcall>
563 <antcall target="compile-module"><param name="module" value="test-standard"/><param name="source" value="${src}/test"/></antcall>
564 <antcall target="compile-module"><param name="module" value="test-qsarprotein"/><param name="source" value="${src}/test"/></antcall>
565 <antcall target="compile-module"><param name="module" value="test-qsaratomic"/><param name="source" value="${src}/test"/></antcall>
566 <antcall target="compile-module"><param name="module" value="test-smiles"/><param name="source" value="${src}/test"/></antcall>
567 <antcall target="compile-module"><param name="module" value="test-qsarbond"/><param name="source" value="${src}/test"/></antcall>
568 <antcall target="compile-module"><param name="module" value="test-atomtype"/><param name="source" value="${src}/test"/></antcall>
cb5b4ae Set up testing for the render module
egonw authored
569 <antcall target="compile-module"><param name="module" value="test-render"/><param name="source" value="${src}/test"/></antcall>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
570 </parallel>
52638d6 Removed the experimental module: classes that are experimental should be...
egonw authored
571 <antcall target="compile-module"><param name="module" value="test-extra"/><param name="source" value="${src}/test"/></antcall>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
572 <antcall target="compile-module"><param name="module" value="test-qsarmolecular"/><param name="source" value="${src}/test"/></antcall>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
573 <antcall target="compile-module"><param name="module" value="test-qsarionpot"/><param name="source" value="${src}/test"/></antcall>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
574 </sequential>
575 </target>
576
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now jared...
egonw authored
577 <target id="jarTestdata" name="jarTestdata" description="Creates jar files with test data.">
578 <mkdir dir="${dist}/jar"/>
579 <jar jarfile="${dist}/jar/cdk-testdata.jar">
f280f3f Updated for src/data -> src/test/data move
egonw authored
580 <fileset dir="${src}/test">
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now jared...
egonw authored
581 <include name="data/**/*" />
582 </fileset>
583 </jar>
584 </target>
585
7511417 Fixed a dependency problem.
egonw authored
586 <target id="test-dist-all" name="test-dist-all" description="test-dist-all">
587 <antcall target="compile-init"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
588 <antcall target="compile-module"><param name="module" value="test"/><param name="source" value="${src}/test"/></antcall>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
589 <antcall target="compile-module"><param name="module" value="test-diff"/><param name="source" value="${src}/test"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
590 <antcall target="compile-module"><param name="module" value="test-core"/><param name="source" value="${src}/test"/></antcall>
591 <antcall target="compile-module"><param name="module" value="test-atomtype"/><param name="source" value="${src}/test"/></antcall>
592 <antcall target="compile-module"><param name="module" value="test-standard"/><param name="source" value="${src}/test"/></antcall>
593 <antcall target="compile-module"><param name="module" value="test-data"/><param name="source" value="${src}/test"/></antcall>
c4d127b Introduced a dict module, to lower the number of deps on the extra modul...
egonw authored
594 <antcall target="compile-module"><param name="module" value="test-dict"/><param name="source" value="${src}/test"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
595 <antcall target="compile-module"><param name="module" value="test-datadebug"/><param name="source" value="${src}/test"/></antcall>
596 <antcall target="compile-module"><param name="module" value="test-nonotify"/><param name="source" value="${src}/test"/></antcall>
597 <antcall target="compile-module"><param name="module" value="test-io"/><param name="source" value="${src}/test"/></antcall>
598 <antcall target="compile-module"><param name="module" value="test-structgen"/><param name="source" value="${src}/test"/></antcall>
e2a6ffe Set up a test module for 'isomorphism'
egonw authored
599 <antcall target="compile-module"><param name="module" value="test-isomorphism"/><param name="source" value="${src}/test"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
600 <antcall target="compile-module"><param name="module" value="test-extra"/><param name="source" value="${src}/test"/></antcall>
601 <antcall target="compile-module"><param name="module" value="test-smiles"/><param name="source" value="${src}/test"/></antcall>
602 <antcall target="compile-module"><param name="module" value="test-reaction"/><param name="source" value="${src}/test"/></antcall>
603 <antcall target="compile-module"><param name="module" value="test-builder3d"/><param name="source" value="${src}/test"/></antcall>
604 <antcall target="compile-module"><param name="module" value="test-forcefield"/><param name="source" value="${src}/test"/></antcall>
605 <antcall target="compile-module"><param name="module" value="test-valencycheck"/><param name="source" value="${src}/test"/></antcall>
606 <antcall target="compile-module"><param name="module" value="test-charges"/><param name="source" value="${src}/test"/></antcall>
a5b2aef Merged from brunch to trunk: miguelrojasch-IP -> trunk/
miguelrojasch authored
607 <antcall target="compile-module"><param name="module" value="test-ionpot"/><param name="source" value="${src}/test"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
608 <antcall target="compile-module"><param name="module" value="test-qsar"/><param name="source" value="${src}/test"/></antcall>
609 <antcall target="compile-module"><param name="module" value="test-qsaratomic"/><param name="source" value="${src}/test"/></antcall>
610 <antcall target="compile-module"><param name="module" value="test-qsarbond"/><param name="source" value="${src}/test"/></antcall>
611 <antcall target="compile-module"><param name="module" value="test-qsarmolecular"/><param name="source" value="${src}/test"/></antcall>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
612 <antcall target="compile-module"><param name="module" value="test-qsarionpot"/><param name="source" value="${src}/test"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
613 <antcall target="compile-module"><param name="module" value="test-qsarprotein"/><param name="source" value="${src}/test"/></antcall>
614 <antcall target="compile-module"><param name="module" value="test-pdb"/><param name="source" value="${src}/test"/></antcall>
615 <antcall target="compile-module"><param name="module" value="test-inchi"/><param name="source" value="${src}/test"/></antcall>
616 <antcall target="compile-module"><param name="module" value="test-libiomd"/><param name="source" value="${src}/test"/></antcall>
617 <antcall target="compile-module"><param name="module" value="test-libiocml"/><param name="source" value="${src}/test"/></antcall>
618 <antcall target="compile-module"><param name="module" value="test-smarts"/><param name="source" value="${src}/test"/></antcall>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
619 <antcall target="compile-module"><param name="module" value="test-fingerprint"/><param name="source" value="${src}/test"/></antcall>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
620 <antcall target="compile-module"><param name="module" value="test-pcore"/><param name="source" value="${src}/test"/></antcall>
621 <antcall target="compile-module"><param name="module" value="test-formula"/><param name="source" value="${src}/test"/></antcall>
cb5b4ae Set up testing for the render module
egonw authored
622 <antcall target="compile-module"><param name="module" value="test-render"/><param name="source" value="${src}/test"/></antcall>
2249f4b Completed adding of testing of the sdg module
egonw authored
623 <antcall target="compile-module"><param name="module" value="test-sdg"/><param name="source" value="${src}/test"/></antcall>
7511417 Fixed a dependency problem.
egonw authored
624 </target>
625
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
626 <target id="dist-large" name="dist-large" depends="dist-all"
52638d6 Removed the experimental module: classes that are experimental should be...
egonw authored
627 description="Builds one big jar file for the CDK, including third-party libraries.">
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
628
c660505 Reworked dist-large target
egonw authored
629 <!-- first unjar the CDK and other jars we need -->
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
630 <mkdir dir="${appjars.dir}"/>
c660505 Reworked dist-large target
egonw authored
631 <unjar dest="${appjars.dir}">
632 <fileset dir="${lib}">
afac743 Set up the atomtype module
egonw authored
633 <includesfile name="${metainf}/atomtype.libdepends"/>
c660505 Reworked dist-large target
egonw authored
634 <includesfile name="${metainf}/builder3d.libdepends"/>
161b318 Put the helper tool into a separate module, to solve dependency issues.
egonw authored
635 <includesfile name="${metainf}/builder3dtools.libdepends"/>
3673f87 Added missing jar in dist-large target
egonw authored
636 <includesfile name="${metainf}/charges.libdepends"/>
c660505 Reworked dist-large target
egonw authored
637 <includesfile name="${metainf}/core.libdepends"/>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
638 <includesfile name="${metainf}/control.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
639 <includesfile name="${metainf}/datadebug.libdepends"/>
c660505 Reworked dist-large target
egonw authored
640 <includesfile name="${metainf}/data.libdepends"/>
641 <includesfile name="${metainf}/extra.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
642 <includesfile name="${metainf}/io.libdepends"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the module ...
egonw authored
643 <includesfile name="${metainf}/libiocml.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
644 <includesfile name="${metainf}/nonotify.libdepends"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
645 <includesfile name="${metainf}/pdbcml.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
646 <includesfile name="${metainf}/pdb.libdepends"/>
c660505 Reworked dist-large target
egonw authored
647 <includesfile name="${metainf}/qsar.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
648 <includesfile name="${metainf}/qsaratomic.libdepends"/>
649 <includesfile name="${metainf}/qsarbond.libdepends"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecular ...
egonw authored
650 <includesfile name="${metainf}/qsarmolecular.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
651 <includesfile name="${metainf}/qsarprotein.libdepends"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
652 <includesfile name="${metainf}/qsarcml.libdepends"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
653 <includesfile name="${metainf}/reaction.libdepends"/>
c660505 Reworked dist-large target
egonw authored
654 <includesfile name="${metainf}/render.libdepends"/>
655 <includesfile name="${metainf}/standard.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
656 <includesfile name="${metainf}/valencycheck.libdepends"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
657 <includesfile name="${metainf}/sdg.libdepends"/>
be50e2b Added new structgen module to dist-large.
egonw authored
658 <includesfile name="${metainf}/forcefield.libdepends"/>
0bf100d Added InChI module to regular compile setup
egonw authored
659 <includesfile name="${metainf}/inchi.libdepends"/>
cd11a7e Updated build script so that dist-large includes the smarts module
rajarshi authored
660 <includesfile name="${metainf}/smarts.libdepends"/>
71ce329 Updated build.xml to include the pcore module in the big jar file
rajarshi authored
661 <includesfile name="${metainf}/pcore.libdepends"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
662 <includesfile name="${metainf}/formula.libdepends"/>
ea8c273 Fixed dist-large generation: diff does not have any libdepends
egonw authored
663 <includesfile name="${metainf}/isomorphism.libdepends"/>
c660505 Reworked dist-large target
egonw authored
664 </fileset>
665 <fileset dir="${dist}/jar">
afac743 Set up the atomtype module
egonw authored
666 <include name="cdk-atomtype.jar"/>
c660505 Reworked dist-large target
egonw authored
667 <include name="cdk-builder3d.jar"/>
161b318 Put the helper tool into a separate module, to solve dependency issues.
egonw authored
668 <include name="cdk-builder3dtools.jar"/>
3673f87 Added missing jar in dist-large target
egonw authored
669 <include name="cdk-charges.jar"/>
c660505 Reworked dist-large target
egonw authored
670 <include name="cdk-core.jar"/>
0a739e8 Updted to include cdk-dict.jar in the big jar
rajarshi authored
671 <include name="cdk-dict.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
672 <include name="cdk-diff.jar"/>
dece975 Fixed the build script to properly incldue the control module and its li...
rajarshi authored
673 <include name="cdk-control.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
674 <include name="cdk-datadebug.jar"/>
c660505 Reworked dist-large target
egonw authored
675 <include name="cdk-data.jar"/>
676 <include name="cdk-extra.jar"/>
677 <include name="cdk-interfaces.jar"/>
678 <include name="cdk-io.jar"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the module ...
egonw authored
679 <include name="cdk-libiocml.jar"/>
8459c22 Included the libiomd module
egonw authored
680 <include name="cdk-libiomd.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
681 <include name="cdk-nonotify.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
682 <include name="cdk-pdbcml.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
683 <include name="cdk-pdb.jar"/>
c660505 Reworked dist-large target
egonw authored
684 <include name="cdk-qsar.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
685 <include name="cdk-qsaratomic.jar"/>
686 <include name="cdk-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecular ...
egonw authored
687 <include name="cdk-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
688 <include name="cdk-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
689 <include name="cdk-qsarprotein.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
690 <include name="cdk-qsarcml.jar"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
691 <include name="cdk-reaction.jar"/>
c660505 Reworked dist-large target
egonw authored
692 <include name="cdk-render.jar"/>
693 <include name="cdk-standard.jar"/>
be50e2b Added new structgen module to dist-large.
egonw authored
694 <include name="cdk-structgen.jar"/>
9c7431a Fixed stupid typo
egonw authored
695 <include name="cdk-valencycheck.jar"/>
f86e117 Created the smiles module
egonw authored
696 <include name="cdk-forcefield.jar"/>
697 <include name="cdk-smiles.jar"/>
cd11a7e Updated build script so that dist-large includes the smarts module
rajarshi authored
698 <include name="cdk-smarts.jar"/>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
699 <include name="cdk-fingerprint.jar"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
700 <include name="cdk-sdg.jar"/>
0bf100d Added InChI module to regular compile setup
egonw authored
701 <include name="cdk-inchi.jar"/>
71ce329 Updated build.xml to include the pcore module in the big jar file
rajarshi authored
702 <include name="cdk-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
703 <include name="cdk-formula.jar"/>
2e98012 Added missing ionpot to dist-large
egonw authored
704 <include name="cdk-isomorphism.jar"/>
705 <include name="cdk-ionpot.jar"/>
c660505 Reworked dist-large target
egonw authored
706 </fileset>
707 </unjar>
9db2505 Added missing jars to dist-large target
egonw authored
708
c660505 Reworked dist-large target
egonw authored
709 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what ev...
rajarshi authored
710 <jar jarfile="${dist}/jar/cdk-${version}.jar">
c660505 Reworked dist-large target
egonw authored
711 <manifest>
712 <section name="org.openscience.cdk">
713 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
0fcda7c Copied command line utils to separate project
egonw authored
714 <attribute name="Specification-Version" value="1.2"/>
c660505 Reworked dist-large target
egonw authored
715 <attribute name="Specification-Vendor" value="The CDK Project"/>
716 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
717 <attribute name="Implementation-Version" value="${version}"/>
718 <attribute name="Implementation-Vendor" value="The CDK Project"/>
719 </section>
720 </manifest>
721 <fileset dir="${appjars.dir}">
722 <include name="**/*" />
723 </fileset>
724 </jar>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
725 </target>
726
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
727 <target id="dist-pure" name="dist-pure" depends="dist-all"
52638d6 Removed the experimental module: classes that are experimental should be...
egonw authored
728 description="Builds one big jar file for the CDK, excluding third party libraries.">
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
729
730 <!-- first unjar the CDK and other jars we need -->
731 <mkdir dir="${appjars.dir}"/>
732 <unjar dest="${appjars.dir}">
733 <fileset dir="${dist}/jar">
734 <include name="cdk-builder3d.jar"/>
735 <include name="cdk-builder3dtools.jar"/>
736 <include name="cdk-charges.jar"/>
737 <include name="cdk-core.jar"/>
738 <include name="cdk-control.jar"/>
739 <include name="cdk-datadebug.jar"/>
740 <include name="cdk-data.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
741 <include name="cdk-diff.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
742 <include name="cdk-extra.jar"/>
743 <include name="cdk-interfaces.jar"/>
744 <include name="cdk-io.jar"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the module ...
egonw authored
745 <include name="cdk-libiocml.jar"/>
8459c22 Included the libiomd module
egonw authored
746 <include name="cdk-libiomd.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
747 <include name="cdk-nonotify.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
748 <include name="cdk-pdbcml.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
749 <include name="cdk-pdb.jar"/>
750 <include name="cdk-qsar.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
751 <include name="cdk-qsaratomic.jar"/>
752 <include name="cdk-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecular ...
egonw authored
753 <include name="cdk-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
754 <include name="cdk-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
755 <include name="cdk-qsarprotein.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
756 <include name="cdk-qsarcml.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
757 <include name="cdk-reaction.jar"/>
758 <include name="cdk-render.jar"/>
759 <include name="cdk-standard.jar"/>
760 <include name="cdk-structgen.jar"/>
761 <include name="cdk-valencycheck.jar"/>
762 <include name="cdk-forcefield.jar"/>
45c8c0c Added smarts to JUnit testing
egonw authored
763 <include name="cdk-smarts.jar"/>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
764 <include name="cdk-fingerprint.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
765 <include name="cdk-smiles.jar"/>
766 <include name="cdk-sdg.jar"/>
767 <include name="cdk-inchi.jar"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
768 <include name="cdk-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
769 <include name="cdk-formula.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
770 </fileset>
771 </unjar>
772
773 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what ev...
rajarshi authored
774 <jar jarfile="${dist}/jar/cdk-pure-${version}.jar">
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
775 <manifest>
776 <section name="org.openscience.cdk">
777 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
778 <attribute name="Specification-Version" value="1.0"/>
779 <attribute name="Specification-Vendor" value="The CDK Project"/>
780 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
781 <attribute name="Implementation-Version" value="${version}"/>
782 <attribute name="Implementation-Vendor" value="The CDK Project"/>
783 </section>
784 </manifest>
785 <fileset dir="${appjars.dir}">
786 <include name="**/*" />
787 </fileset>
788 </jar>
789 </target>
790
88311e5 Added target for a jar with all the test stuff
egonw authored
791 <target id="dist-test-large" name="dist-test-large" depends="test-dist-all"
792 description="Builds on big jar file for the CDK test classes.">
793
794 <!-- first unjar the CDK and other jars we need -->
795 <mkdir dir="${appjars.dir}"/>
796 <unjar dest="${appjars.dir}">
797 <fileset dir="${lib}">
798 <includesfile name="${metainf}/test-core.libdepends"/>
799 <includesfile name="${metainf}/test-data.libdepends"/>
800 <includesfile name="${metainf}/test-datadebug.libdepends"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
801 <includesfile name="${metainf}/test-diff.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
802 <includesfile name="${metainf}/test-extra.libdepends"/>
d31ee42 New module: test-builder3d
egonw authored
803 <includesfile name="${metainf}/test-builder3d.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
804 <includesfile name="${metainf}/test-forcefield.libdepends"/>
805 <includesfile name="${metainf}/test-inchi.libdepends"/>
806 <includesfile name="${metainf}/test-io.libdepends"/>
807 <includesfile name="${metainf}/test-nonotify.libdepends"/>
808 <includesfile name="${metainf}/test-pdb.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
809 <includesfile name="${metainf}/test-qsaratomic.libdepends"/>
810 <includesfile name="${metainf}/test-qsarbond.libdepends"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecular ...
egonw authored
811 <includesfile name="${metainf}/test-qsarmolecular.libdepends"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
812 <includesfile name="${metainf}/test-qsarionpot.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
813 <includesfile name="${metainf}/test-qsarprotein.libdepends"/>
814 <includesfile name="${metainf}/test-qsar.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
815 <includesfile name="${metainf}/test-reaction.libdepends"/>
45c8c0c Added smarts to JUnit testing
egonw authored
816 <includesfile name="${metainf}/test-smarts.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
817 <includesfile name="${metainf}/test-smiles.libdepends"/>
818 <includesfile name="${metainf}/test-standard.libdepends"/>
be50e2b Added new structgen module to dist-large.
egonw authored
819 <includesfile name="${metainf}/test-structgen.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
820 <includesfile name="${metainf}/test-valencycheck.libdepends"/>
cb52b54 Hooked in stuff for the charges module
egonw authored
821 <includesfile name="${metainf}/test-charges.libdepends"/>
8459c22 Included the libiomd module
egonw authored
822 <includesfile name="${metainf}/test-libiomd.libdepends"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
823 <includesfile name="${metainf}/test-pcore.libdepends"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
824 <includesfile name="${metainf}/test-formula.libdepends"/>
cb5b4ae Set up testing for the render module
egonw authored
825 <includesfile name="${metainf}/test-render.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
826 </fileset>
827 <fileset dir="${dist}/jar">
828 <include name="cdk-test-core.jar"/>
829 <include name="cdk-test-data.jar"/>
830 <include name="cdk-test-datadebug.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
831 <include name="cdk-test-diff.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
832 <include name="cdk-test-extra.jar"/>
d31ee42 New module: test-builder3d
egonw authored
833 <include name="cdk-test-builder3d.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
834 <include name="cdk-test-forcefield.jar"/>
835 <include name="cdk-test-inchi.jar"/>
836 <include name="cdk-test-io.jar"/>
837 <include name="cdk-test-nonotify.jar"/>
838 <include name="cdk-test-pdb.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
839 <include name="cdk-test-qsaratomic.jar"/>
840 <include name="cdk-test-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecular ...
egonw authored
841 <include name="cdk-test-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionpot ...
egonw authored
842 <include name="cdk-test-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
843 <include name="cdk-test-qsarprotein.jar"/>
844 <include name="cdk-test-qsar.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
845 <include name="cdk-test-reaction.jar"/>
45c8c0c Added smarts to JUnit testing
egonw authored
846 <include name="cdk-test-smarts.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
847 <include name="cdk-test-smiles.jar"/>
848 <include name="cdk-test-standard.jar"/>
be50e2b Added new structgen module to dist-large.
egonw authored
849 <include name="cdk-test-structgen.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
850 <include name="cdk-test-valencycheck.jar"/>
cb52b54 Hooked in stuff for the charges module
egonw authored
851 <include name="cdk-test-charges.jar"/>
8459c22 Included the libiomd module
egonw authored
852 <include name="cdk-test-libiomd.jar"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
853 <include name="cdk-test-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
854 <include name="cdk-test-formula.jar"/>
cb5b4ae Set up testing for the render module
egonw authored
855 <include name="cdk-test-render.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
856 </fileset>
857 </unjar>
858
859 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what ev...
rajarshi authored
860 <jar jarfile="${dist}/jar/cdk-test-${version}.jar">
88311e5 Added target for a jar with all the test stuff
egonw authored
861 <manifest>
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
862 <attribute name="Main-Class" value="org.openscience.cdk.CDKTests"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
863 <section name="org.openscience.cdk">
864 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
0fcda7c Copied command line utils to separate project
egonw authored
865 <attribute name="Specification-Version" value="1.2"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
866 <attribute name="Specification-Vendor" value="The CDK Project"/>
867 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
868 <attribute name="Implementation-Version" value="${version}"/>
869 <attribute name="Implementation-Vendor" value="The CDK Project"/>
870 </section>
871 </manifest>
872 <fileset dir="${appjars.dir}">
873 <include name="**/*" />
874 </fileset>
875 </jar>
876 </target>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations where...
egonw authored
877
8c06c63 Fixed inclusion of .javafiles, .classes, and .set files for easy buildin...
egonw authored
878 <target id="sourcedist" name="sourcedist" depends="init, runDoclet"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
879 description="Builds the source packages.">
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bug r...
egonw authored
880 <property name="package" value="cdk-src+libs-${version}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
881 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bug r...
egonw authored
882 <delete dir="${sourcedist.dir}"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
883 <copy todir="${sourcedist.dir}/${${src}/main/org/}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
884 <fileset dir="${build}" includes="*.javafiles" />
885 <fileset dir="${build}" includes="*.classes" />
886 <fileset dir="${build}" includes="*.set" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
887 <fileset dir="${src}/main/" includes="**/*.java" />
888 <fileset dir="${src}/main/" includes="**/*.jj" />
889 <fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
890 </copy>
891 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
892 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
893 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
894 <fileset dir="." includes="javadoc.xml" />
895 <fileset dir="." includes="README" />
e99a32a Preparing for a release
egonw authored
896 <fileset dir="." includes="changelog*" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
897 </copy>
998ae6a Updated for current CVS.
egonw authored
898 <copy todir="${sourcedist.dir}/develjar">
899 <fileset dir="develjar">
900 <exclude name="pmd-1.8.jar"/>
901 <exclude name="doccheck.jar"/>
902 <exclude name="dbdoclet*.*"/>
903 </fileset>
904 </copy>
905 <copy todir="${sourcedist.dir}/src/META-INF">
906 <fileset dir="src/META-INF" />
907 </copy>
7aa27da Make sure the config.data files get included in the source dist (closes ...
egonw authored
908 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
909 <fileset dir="${src}/main/org/openscience/cdk/config/data/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
910 includes="*" />
911 </copy>
a289167 Minor tweak to get distribs working
egonw authored
912 <copy
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
913 file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
914 tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
be06f71 Fixed building of sourcedist: removed elements.xml, included *.owl
egonw authored
915 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
916 <fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
917 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
918 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/"/>
919 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/">
920 <fileset dir="${src}/main/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
e2623a3 Added some missing files to the sourcedist
egonw authored
921 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
922 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
923 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
924 <fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
998ae6a Updated for current CVS.
egonw authored
925 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
926 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
927 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
928 <fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
00c2efc Added missing builder3d templates to sourcedist.
egonw authored
929 </copy>
9496005 Added missing manifest
egonw authored
930 <copy todir="${sourcedist.dir}/${src}/">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for spli...
egonw authored
931 <fileset dir="${src}/main/" includes="*.manifest" />
9496005 Added missing manifest
egonw authored
932 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
933 <mkdir dir="${sourcedist.dir}/doc/" />
934 <copy todir="${sourcedist.dir}/doc/">
935 <fileset dir="doc/" includes="lgpl.license" />
936 </copy>
7447e16 Getting ready for release
egonw authored
937 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bug r...
egonw authored
938 <!-- the below deteles are a workaround, because the above should not have copied
939 in the src/data and src/org/openscience/cdk/test dirs -->
940 <delete dir="${sourcedist.dir}/src/data"/>
941
942 <!-- now package things up -->
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
943 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
a0ba425 Updated sourcedist target so that it uses the current date for the final...
rajarshi authored
944 <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
945 <delete file="${package}.tar" />
946 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
998ae6a Updated for current CVS.
egonw authored
947 </target>
5e15181