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ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
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 bu…
egonw authored
3 <property file="build.props"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
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" />
11
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
12 <!-- patches to apply -->
13
320baea Removed more traces of Java3D
egonw authored
14 <!-- where to find some libraries -->
3a26de3 Made compilation with debug=on customizable.
egonw authored
15 <property name="pathtojoelib" value="../../JoeLib/joelib/" />
16
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
17
3a26de3 Made compilation with debug=on customizable.
egonw authored
18 <!-- directories -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
19 <property name="build" value="build" />
bd36ed1 Trial for new build system
egonw authored
20 <property name="build.src" value="${build}/src" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
21 <property name="sourcedist" value="sourcedist" />
22 <property name="dist" value="dist" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
23 <property name="doc" value="doc" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
24 <property name="src" value="src" />
25 <property name="lib" value="jar" />
9e95b7b Finished splitting devel from user jars
egonw authored
26 <property name="devellib" value="develjar" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
27 <property name="src.tests" value="${src}/org/openscience/cdk/test" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
28 <property name="reports.tests" value="reports" />
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
29 <property name="appjars.dir" value="${dist}/appjars" />
bd36ed1 Trial for new build system
egonw authored
30 <property name="metainf" value="${src}/META-INF" />
f7be51f Removed alternative core classes patch offering more detailed debug info
egonw authored
31
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
32 <!-- class to run for testing-->
33 <property name="testclass" value="CDKTests" />
9bcd183 Fixed default executed application
egonw authored
34 <property name="runclass" value="applications.FileConvertor" />
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
35 <property name="arg1" value="" />
36 <property name="arg2" value="" />
37 <property name="arg3" value="" />
38 <property name="arg4" value="" />
5c40bcf Removed the check for rJava as we don't strictly need it. Also added …
rajarshi authored
39
40 <property environment="env" />
41
42 <target id="info" name="info" depends="check">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
43 <!-- Gives information about the building process. -->
8f6d674 Fixed after breaking it earlier today
egonw authored
44 <echo message="Platform:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
45 <echo message=" OS: ${os.name}" />
46 <echo message=" Architecture: ${os.arch}" />
47 <echo message=" Version: ${os.version}" />
48 <echo message=" Mac OS/X found: ${isMacOsX}" />
8f6d674 Fixed after breaking it earlier today
egonw authored
49 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
50 <echo message="Java/Ant Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
51 <echo message=" Java version: ${java.version}" />
52 <echo message=" Java vendor: ${java.vendor}" />
53 <echo message=" Java dir: ${java.home}" />
54 <echo message=" Java ext dir: ${java.ext.dirs}" />
55 <echo message=" Ant version: ${ant.version}" />
56 <echo message=" ${ANT_HOME}: ${ant.home}" />
57 <echo message=" hasAnt16: ${hasAnt16}" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
58 <echo message="" />
c1e01f8 Added support for gjdoc
egonw authored
59 <echo message="JavaDoc Environment:" />
60 <echo message=" SUN JavaDoc: ${sunJavaDoc}" />
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
61 <echo message=" SUN JavaDoc 6: ${sunJavaDoc6}" />
c1e01f8 Added support for gjdoc
egonw authored
62 <echo message=" gjdoc JavaDoc: ${gjdocJavaDoc}" />
63 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
64 <echo message="CDK Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
65 <echo message=" CDK version: ${version}" />
66 <echo message=" build.xml: $Id$" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
67 <echo message=" Junit found: ${junit.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
68 <echo message=" --- required libraries ---" />
69 <echo message=" Vecmath found: ${vecmath.present}" />
70 <echo message=" Log4j found: ${log4j.present}" />
71 <echo message=" JGraphT found: ${jgrapht.present}" />
c1c3a3b Removed outdated optional compile checks
egonw authored
72 <echo message=" --- distributed (but optional) libraries ---" />
cc68a07 Added detection of more third party libraries
egonw authored
73 <echo message=" Batik found: ${batik.present}" />
7cd4ff8 Added R/SJava found to info target
egonw authored
74 <echo message=" CMLDOM found: ${cmllibs.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
75 <echo message=" DADML found: ${dadml.present}" />
76 <echo message=" JAI found: ${jai.present}" />
77 <echo message=" XIndice found: ${xindice.present}"/>
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
78 <echo message=" --- optional libraries ---" />
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
79 <echo message=" Jmol found: ${jmol.present}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
80 <echo message=" JOELib found: ${joelib.present}" />
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
81 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
82 <echo message="Compiling:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
83 <echo message=" for: ${build.compiler}" />
84 <echo message=" debug: ${debug}" />
85 <echo message=" deprecation: ${deprecation}" />
86 <echo message=" optimization: ${optimization}" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
87 </target>
88
8f6d674 Fixed after breaking it earlier today
egonw authored
89 <target id="checkPlatforms" name="checkPlatforms">
58405cf Fixed build.xml to allow compile of doclets on MacOS/X (closes #1001497)
egonw authored
90 <condition property="isMacOsX">
91 <and>
92 <os family="mac"/>
93 <os family="unix"/>
94 </and>
95 </condition>
96 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
97
8f6d674 Fixed after breaking it earlier today
egonw authored
98 <target id="check" name="check" depends="checkPlatforms">
cc68a07 Added detection of more third party libraries
egonw authored
99 <!-- Check wether Doclets are compiled and output is generated -->
100 <uptodate property="dotjavafiles.uptodate"
101 targetfile="${src}/core.javafiles">
102 <srcfiles dir="${src}" includes="**/*.java" />
103 </uptodate>
104 <condition property="dotjjfiles.uptodate">
105 <and>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
106 <uptodate property="NomParserJavafiles.uptodate"
cc68a07 Added detection of more third party libraries
egonw authored
107 targetfile="${src}/org/openscience/cdk/iupac/parser/NomParser.java">
108 <srcfiles dir="${src}" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
109 </uptodate>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
110 <uptodate property="SMARTSParserJavafiles.uptodate"
cc68a07 Added detection of more third party libraries
egonw authored
111 targetfile="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.java">
112 <srcfiles dir="${src}" includes="org/openscience/cdk/smiles/smarts/SMARTSParser.jj" />
113 </uptodate>
114 </and>
115 </condition>
116
117 <!-- Checks which parts of CDK can be build. -->
118
119 <!-- test for optional jars -->
120 <available property="vecmath.present"
121 file="${lib}/vecmath1.2-1.14.jar"/>
122 <available property="log4j.present"
123 file="${lib}/log4j.jar"/>
124 <available property="jgrapht.present"
152e213 Updated for recent upgrades to Jumbo 5.2 and JGraphT 0.6.0
egonw authored
125 file="${lib}/jgrapht-0.6.0.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
126
127 <!-- test for optional jars -->
128 <condition property="batik.present">
129 <and>
130 <available file="${lib}/batik-awt-util.jar"/>
131 <available file="${lib}/batik-dom.jar"/>
132 <available file="${lib}/batik-svggen.jar"/>
133 <available file="${lib}/batik-util.jar"/>
134 <available file="${lib}/batik-xml.jar"/>
135 </and>
136 </condition>
137 <condition property="cmllibs.present">
138 <or>
152e213 Updated for recent upgrades to Jumbo 5.2 and JGraphT 0.6.0
egonw authored
139 <available file="${lib}/jumbo52.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
140 </or>
141 </condition>
142 <available property="dadml.present"
143 file="${lib}/dadml.jar"/>
144 <condition property="jai.present">
145 <and>
146 <available file="${lib}/jai_codec.jar"/>
147 <available file="${lib}/jai_core.jar"/>
148 </and>
149 </condition>
150 <available property="joelib.present"
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
151 classname="joelib.molecule.JOEAtom"
cc68a07 Added detection of more third party libraries
egonw authored
152 classpath="${lib}/libio/joelib.jar"/>
153 <available property="jmol.present"
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
154 classname="org.jmol.api.JmolAdapter"
cc68a07 Added detection of more third party libraries
egonw authored
155 classpath="${lib}/jmolApis.jar"/>
156 <available property="junit.present"
157 classname="junit.framework.TestCase"
158 classpath="${ant.home}/lib/junit.jar"/>
159 <condition property="xindice.present">
160 <and>
161 <available file="${lib}/xindice.jar"/>
162 <available file="${lib}/xmldb.jar"/>
163 </and>
164 </condition>
165
166 <!-- test Ant version -->
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
167 <condition property="hasAnt16">
168 <contains string="${ant.version}" substring="1.6"/>
169 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
170
171 <!-- test Java version -->
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
172 <condition property="isJava13">
173 <contains string="${java.version}" substring="1.3"/>
174 </condition>
175 <condition property="isJava14">
176 <contains string="${java.version}" substring="1.4"/>
177 </condition>
866bc72 CML is now available for Java1.5 too
egonw authored
178 <condition property="isJava15">
179 <contains string="${java.version}" substring="1.5"/>
180 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
181 <condition property="isJava16">
182 <contains string="${java.version}" substring="1.6."/>
183 </condition>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
184 <condition property="isJava14+">
185 <or>
186 <contains string="${java.version}" substring="1.4"/>
187 <contains string="${java.version}" substring="1.5"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
188 <contains string="${java.version}" substring="1.6"/>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
189 </or>
190 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
191 <condition property="isJava15+">
192 <or>
193 <contains string="${java.version}" substring="1.5"/>
194 <contains string="${java.version}" substring="1.6"/>
195 </or>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
196 </condition>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
197 <condition property="isNotJava15+">
198 <not>
199 <or>
200 <contains string="${java.version}" substring="1.5"/>
201 <contains string="${java.version}" substring="1.6"/>
202 </or>
203 </not>
204 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
205
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
206 </target>
207
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
208
d2ed020 Reworked dependencies
egonw authored
209 <target id="init" name="init" depends="check, setupBuildDir"/>
4302fbf Updated for Jumbo50 transition.
egonw authored
210 <target id="customize" name="customize" depends="javacc"/>
866bc72 CML is now available for Java1.5 too
egonw authored
211
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
212 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
213 <tstamp />
214 <mkdir dir="${build}" />
215 <mkdir dir="${sourcedist}" />
216 <mkdir dir="${dist}" />
217 <mkdir dir="${reports.tests}" />
218 </target>
219
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
220 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
221 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
222 <fileset dir="." includes="**/*~" />
223 <fileset dir="." includes="*.tar.gz" />
224 <fileset dir="." includes="*.zip" />
06ee5d1 Modified the clean target to remove .rda files generated during testi…
rajarshi authored
225 <fileset dir="." includes="*.rda" />
bfe0e17 Build interfaces before data
egonw authored
226 <fileset dir="${src}" includes="*.entitylist" />
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
227 <!-- remove java files generated with JavaCC -->
228 <fileset dir="${src}/org/openscience/cdk/smiles/smarts" includes="*.java" />
229 <fileset dir="${src}/org/openscience/cdk/iupac/parser" includes="*.java">
230 <!-- the next are from CVS -->
231 <exclude name="AttachedGroup.java" />
232 <exclude name="MoleculeBuilder.java" />
233 </fileset>
2b81a22 Fixed a problem with deleting the doclet classes
egonw authored
234 <fileset dir="${doc}">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
235 <include name="javadoc/net/sf/cdk/tools/*.class" />
2b81a22 Fixed a problem with deleting the doclet classes
egonw authored
236 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
237 </delete>
238
239 <delete dir="${build}" />
240 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
241 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
242 <delete dir="${reports.tests}" />
243 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
244
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
245 <target name="runDoclet" id="runDoclet" depends="check, customize">
246 <echo>Not skipping doclet run...</echo>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
247 <mkdir dir="${build}" />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
248 <javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
249 srcdir="${src}" destdir="${build}" optimize="${optimization}"
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
250 debug="${debug}" deprecation="${deprecation}"/>
251 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
252 <arg value="${src}"/>
253 <arg value="${build}"/>
254 </java>
ca98ea5 Refactored build process (closes #883519)
egonw authored
255 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
256
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
257 <target id="compile-needed-test" name="compile-needed-test">
258 <uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
259 <srcfiles dir="${src}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
260 <includesfile name="${build}/${module}.javafiles"/>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
261 </srcfiles>
262 </uptodate>
263 </target>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
264
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
265 <target id="compile-init" name="compile-init"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
266 depends="init, check, runDoclet"/>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
267
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
268 <target id="compile-module" name="compile-module"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
269 depends="check, dist.init, compile-needed-test"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
270 unless="module-uptodate">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
271
bd36ed1 Trial for new build system
egonw authored
272 <echo message="Compiling classes for CDK's ${module} module." />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
273
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
274 <!-- check for availability for meta info files -->
275 <available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
276 <available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
c094513 Make sure the .set files end up in the right jars
egonw authored
277 <available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
278 <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
279 <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
280 <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
281
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
282 <!-- be somewhat informative -->
283 <echo message="Datafiles defined: ${module.datafiles.present}"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
284 <echo message="Extra files defined: ${module.extrafiles.present}"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
285 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
286 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
287 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
288
bd36ed1 Trial for new build system
egonw authored
289 <!-- normally javac compiles not just the given files, but also missing
290 classes that are in the same src/ directory. By making a copy first,
291 we explicitely make it impossible to compile files that are not
292 marked for a specific module -->
25a9f0d Fixed syntax
egonw authored
293 <delete dir="${build.src}"/>
bd36ed1 Trial for new build system
egonw authored
294 <mkdir dir="${build.src}"/>
295 <copy todir="${build.src}">
296 <fileset dir="${src}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
297 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
298 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
299 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
300 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
301 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt16"/>
302 <excludesfile name="${build}/jai.javafiles" unless="jai.present"/>
303 <excludesfile name="${build}/dadml.javafiles" unless="dadml.present"/>
304 <excludesfile name="${build}/xindice.javafiles" unless="xindice.present"/>
305
306 <includesfile name="${build}/${module}.javafiles"/>
bd36ed1 Trial for new build system
egonw authored
307 </fileset>
308 </copy>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
309
bd36ed1 Trial for new build system
egonw authored
310 <!-- ok, now that we have a copy, compile this copy -->
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
311 <javac srcdir="${build.src}" destdir="${build}" optimize="${optimization}"
03a7837 merge with jcp21
shk3 authored
312 debug="${debug}" deprecation="${deprecation}" target="1.3" source="1.3">
bd36ed1 Trial for new build system
egonw authored
313 <classpath>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
314 <fileset dir="${lib}" >
315 <exclude name="**/*" unless="module.libdepends.present" />
316 <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
bd36ed1 Trial for new build system
egonw authored
317 </fileset>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
318 <fileset dir="${devellib}">
319 <exclude name="**/*" unless="module.devellibdepends.present" />
320 <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
321 </fileset>
bd36ed1 Trial for new build system
egonw authored
322 <fileset dir="${dist}/jar">
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
323 <exclude name="**/*" unless="module.cdkdepends.present" />
324 <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
bd36ed1 Trial for new build system
egonw authored
325 </fileset>
326 </classpath>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
327
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
328 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
329 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
330 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
331 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
332 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt16"/>
333 <excludesfile name="${build}/jai.javafiles" unless="jai.present"/>
334 <excludesfile name="${build}/dadml.javafiles" unless="dadml.present"/>
335 <excludesfile name="${build}/xindice.javafiles" unless="xindice.present"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
336
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
337 <includesfile name="${build}/${module}.javafiles"/>
bd36ed1 Trial for new build system
egonw authored
338 </javac>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
339
bd36ed1 Trial for new build system
egonw authored
340 <!-- and then jar things up into the module jar -->
341 <jar jarfile="${dist}/jar/cdk-${module}.jar">
342 <fileset dir="${build}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
343 <includesfile name="${build}/${module}.classes" />
344 <excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
345 <!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
346 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
347 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
348 <excludesfile name="${build}/ant1.6.classes" unless="hasAnt16"/>
349 <excludesfile name="${build}/jai.javafiles" unless="jai.present"/>
350 <excludesfile name="${build}/dadml.javafiles" unless="dadml.present"/>
351 <excludesfile name="${build}/xindice.javafiles" unless="xindice.present"/>
bd36ed1 Trial for new build system
egonw authored
352 </fileset>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
353 <fileset dir="${build}">
bd36ed1 Trial for new build system
egonw authored
354 <include name="${module}.javafiles" />
355 </fileset>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
356 <fileset dir="${src}">
141cf36 Fixed problem with including data files in the module jars
egonw authored
357 <exclude name="**/*" unless="module.datafiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
358 <includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
359 </fileset>
ddebad1 Modified to match new dir struct
egonw authored
360 <fileset dir="${src}">
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
361 <exclude name="**/*" unless="module.extrafiles.present"/>
362 <includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
363 </fileset>
c8f144a Point to correct .set location.
egonw authored
364 <fileset dir="${build}">
c094513 Make sure the .set files end up in the right jars
egonw authored
365 <exclude name="**/*" unless="module.buildfiles.present"/>
c8f144a Point to correct .set location.
egonw authored
366 <includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
c094513 Make sure the .set files end up in the right jars
egonw authored
367 </fileset>
bd36ed1 Trial for new build system
egonw authored
368 </jar>
369 </target>
370
6dc5408 Added stuff for qsar module
egonw authored
371 <!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
62f2673 Don't delete everything in cdk.iupac.parser
egonw authored
372 <target id="javacc" name="javacc" depends="init, check" if="hasAnt16" unless="dotjjfiles.uptodate">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
373 <echo message="Compiling Ant 1.6 depending classes." />
cd49d3a A bit of comment
egonw authored
374 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
375 <delete>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
376 <fileset id="javacc-generated"
377 dir="${src}/org/openscience/cdk/iupac/parser/"
cd49d3a A bit of comment
egonw authored
378 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
379 </delete>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
380 <javacc target="${src}/org/openscience/cdk/iupac/parser/NomParser.jj"
381 outputdirectory="${src}/org/openscience/cdk/iupac/parser/"
1dd9647 Added IUPAC name parser
stomkinson authored
382 javacchome="${lib}"/>
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
383 <delete>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
384 <fileset id="javacc-generated"
385 dir="${src}/org/openscience/cdk/smiles/smarts/"
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
386 includes="*.java"/>
387 </delete>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
388 <javacc target="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.jj"
389 outputdirectory="${src}/org/openscience/cdk/smiles/smarts/"
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
390 javacchome="${lib}"/>
1dd9647 Added IUPAC name parser
stomkinson authored
391 </target>
8095921 Added rendering of wedged bonds.
egonw authored
392
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
393 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
394 <mkdir dir="${dist}/jar" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
395 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
396
90bb227 Added missing 'check' dependency
egonw authored
397 <target id="dist-joelib" name="dist-joelib" depends="check, nocompile-joelib, compile-joelib"/>
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
398 <target id="nocompile-joelib" name="nocompile-joelib" unless="${joelib.present}">
399 <echo message="JOELib is not found. Removed depending functionality. JOELib can be downloaded from http://joelib.sf.net/."/>
400 </target>
401 <target id="compile-joelib" name="compile-joelib" if="${joelib.present}">
402 <antcall target="compile-module"><param name="module" value="libio-joelib"/></antcall>
403 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
404
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
405 <target id="dist-jmol" name="dist-jmol" depends="nocompile-jmol, compile-jmol"/>
406 <target id="nocompile-jmol" name="nocompile-jmol" unless="${jmol.present}">
407 <echo message="Jmol is not found. Removed depending functionality. Jmol can be downloaded from http://www.jmol.org/."/>
408 </target>
409 <target id="compile-jmol" name="compile-jmol" if="${jmol.present}">
410 <antcall target="compile-module"><param name="module" value="io-jmol"/></antcall>
411 </target>
412
413 <target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
414 <target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
415 <echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
416 </target>
417 <target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
418 <antcall target="compile-module"><param name="module" value="java3d"/></antcall>
419 </target>
420
421 <target id="dist-optional" name="dist-optional" depends="dist-all"
422 description="Compile CDK modules that require optional libraries">
423 <antcall target="dist-java3d"/>
424 <antcall target="dist-jmol"/>
425 <antcall target="dist-joelib"/>
426 </target>
fe65a98 Fixed dependencies
egonw authored
427
428 <target id="dist-all" name="dist-all" description="dist-all">
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
429 <antcall target="compile-init"/>
bfe0e17 Build interfaces before data
egonw authored
430 <antcall target="compile-module"><param name="module" value="interfaces"/></antcall>
c378f2b Synched indentation
egonw authored
431 <antcall target="compile-module"><param name="module" value="core"/></antcall>
676c95b Cleaned up more of the build file
egonw authored
432 <antcall target="compile-module"><param name="module" value="standard"/></antcall>
ffb300f Updated dependencies for new sdg and control modules
egonw authored
433 <antcall target="compile-module"><param name="module" value="render"/></antcall>
434 <antcall target="compile-module"><param name="module" value="io"/></antcall>
435 <antcall target="compile-module"><param name="module" value="valencycheck"/></antcall>
436 <antcall target="compile-module"><param name="module" value="sdg"/></antcall>
437 <antcall target="compile-module"><param name="module" value="control"/></antcall>
d5e83b5 Made CDK build system aware of the new data-debug module.
egonw authored
438 <antcall target="compile-module"><param name="module" value="data"/></antcall>
7269de8 OK, added test suite for NoNotify classes
egonw authored
439 <antcall target="compile-module"><param name="module" value="datadebug"/></antcall>
440 <antcall target="compile-module"><param name="module" value="nonotify"/></antcall>
206145b Added a new module 'pdb' with a new class PDBAtom; PDB fields are now…
egonw authored
441 <antcall target="compile-module"><param name="module" value="pdb"/></antcall>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
442 <antcall target="compile-module"><param name="module" value="extra"/></antcall>
6e91a8e Created the test-smiles module
egonw authored
443 <antcall target="compile-module"><param name="module" value="smiles"/></antcall>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
444 <antcall target="compile-module"><param name="module" value="libio-cml"/></antcall>
e8cbc78 Attempting to get libioweka to work: no '-' in module names, if you w…
egonw authored
445 <antcall target="compile-module"><param name="module" value="libioweka"/></antcall>
6d4627d Fixed a dependency problem
egonw authored
446 <antcall target="compile-module"><param name="module" value="libio-openbabel"/></antcall>
29687ca Added a CML Customizer interface which reduces the CDK module depende…
egonw authored
447 <antcall target="compile-module"><param name="module" value="pdb-cml"/></antcall>
3bdf862 clear the conflicts between charges and reactions
miguelrojasch authored
448 <antcall target="compile-module"><param name="module" value="reaction"/></antcall>
449 <antcall target="compile-module"><param name="module" value="charges"/></antcall>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
450 <antcall target="compile-module"><param name="module" value="qsar"/></antcall>
29687ca Added a CML Customizer interface which reduces the CDK module depende…
egonw authored
451 <antcall target="compile-module"><param name="module" value="qsar-cml"/></antcall>
6270665 Some build fixes
egonw authored
452 <antcall target="compile-module"><param name="module" value="qsar-pdb"/></antcall>
f86e117 Created the smiles module
egonw authored
453 <antcall target="compile-module"><param name="module" value="forcefield"/></antcall>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
454 <antcall target="compile-module"><param name="module" value="builder3d"/></antcall>
3e84ce7 Setup a SVG module
egonw authored
455 <antcall target="compile-module"><param name="module" value="svg"/></antcall>
9ebdc29 Fixed build order.
egonw authored
456 <antcall target="compile-module"><param name="module" value="experimental"/></antcall>
6270665 Some build fixes
egonw authored
457 <antcall target="compile-module"><param name="module" value="applications"/></antcall>
0bf100d Added InChI module to regular compile setup
egonw authored
458 <antcall target="compile-module"><param name="module" value="inchi"/></antcall>
38401bd Put applications in separate jar.
egonw authored
459 </target>
460
7511417 Fixed a dependency problem.
egonw authored
461 <target id="test-dist-all" name="test-dist-all" description="test-dist-all">
462 <antcall target="compile-init"/>
3f7319a First step in modularized testing
egonw authored
463 <antcall target="compile-module"><param name="module" value="test-core"/></antcall>
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
464 <antcall target="compile-module"><param name="module" value="test-standard"/></antcall>
0f12eb5 Made a test-data module
egonw authored
465 <antcall target="compile-module"><param name="module" value="test-data"/></antcall>
f05b101 Renamed module and made separate test module
egonw authored
466 <antcall target="compile-module"><param name="module" value="test-datadebug"/></antcall>
7269de8 OK, added test suite for NoNotify classes
egonw authored
467 <antcall target="compile-module"><param name="module" value="test-nonotify"/></antcall>
407c234 Made a test-io module
egonw authored
468 <antcall target="compile-module"><param name="module" value="test-io"/></antcall>
7511417 Fixed a dependency problem.
egonw authored
469 <antcall target="compile-module"><param name="module" value="test-extra"/></antcall>
6e91a8e Created the test-smiles module
egonw authored
470 <antcall target="compile-module"><param name="module" value="test-smiles"/></antcall>
e8cbc78 Attempting to get libioweka to work: no '-' in module names, if you w…
egonw authored
471 <antcall target="compile-module"><param name="module" value="test-libioweka"/></antcall>
39b2a26 new test-module: test-reaction
miguelrojasch authored
472 <antcall target="compile-module"><param name="module" value="test-reaction"/></antcall>
6e91a8e Created the test-smiles module
egonw authored
473 <antcall target="compile-module"><param name="module" value="test-forcefield"/></antcall>
865fa00 Setup a valencycheck module with our crappy 'find bond order' algorithms
egonw authored
474 <antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall>
908a364 Added missing build statement.
egonw authored
475 <antcall target="compile-module"><param name="module" value="test-experimental"/></antcall>
913abbb Setup test module for the pdb module
egonw authored
476 <antcall target="compile-module"><param name="module" value="test-qsar"/></antcall>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
477 <antcall target="compile-module"><param name="module" value="test-pdb"/></antcall>
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
478 <antcall target="compile-module"><param name="module" value="test-osjvmts"/></antcall>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
479 <antcall target="compile-module"><param name="module" value="test-inchi"/></antcall>
7511417 Fixed a dependency problem.
egonw authored
480 </target>
481
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
482 <target id="dist-large" name="dist-large" depends="dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
483 description="Builds on big jar file for the CDK, including experimental classes.">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
484
c660505 Reworked dist-large target
egonw authored
485 <!-- first unjar the CDK and other jars we need -->
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
486 <mkdir dir="${appjars.dir}"/>
c660505 Reworked dist-large target
egonw authored
487 <unjar dest="${appjars.dir}">
488 <fileset dir="${lib}">
489 <includesfile name="${metainf}/applications.libdepends"/>
490 <includesfile name="${metainf}/builder3d.libdepends"/>
3673f87 Added missing jar in dist-large target
egonw authored
491 <includesfile name="${metainf}/charges.libdepends"/>
c660505 Reworked dist-large target
egonw authored
492 <includesfile name="${metainf}/core.libdepends"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
493 <includesfile name="${metainf}/control.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
494 <includesfile name="${metainf}/datadebug.libdepends"/>
c660505 Reworked dist-large target
egonw authored
495 <includesfile name="${metainf}/data.libdepends"/>
496 <includesfile name="${metainf}/experimental.libdepends"/>
497 <includesfile name="${metainf}/extra.libdepends"/>
498 <includesfile name="${metainf}/io-jmol.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
499 <includesfile name="${metainf}/io.libdepends"/>
c660505 Reworked dist-large target
egonw authored
500 <includesfile name="${metainf}/libio-cml.libdepends"/>
e8cbc78 Attempting to get libioweka to work: no '-' in module names, if you w…
egonw authored
501 <includesfile name="${metainf}/libioweka.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
502 <includesfile name="${metainf}/nonotify.libdepends"/>
503 <includesfile name="${metainf}/pdb-cml.libdepends"/>
504 <includesfile name="${metainf}/pdb.libdepends"/>
c660505 Reworked dist-large target
egonw authored
505 <includesfile name="${metainf}/qsar.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
506 <includesfile name="${metainf}/qsar-cml.libdepends"/>
507 <includesfile name="${metainf}/qsar-pdb.libdepends"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
508 <includesfile name="${metainf}/reaction.libdepends"/>
c660505 Reworked dist-large target
egonw authored
509 <includesfile name="${metainf}/render.libdepends"/>
510 <includesfile name="${metainf}/standard.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
511 <includesfile name="${metainf}/svg.libdepends"/>
512 <includesfile name="${metainf}/valencycheck.libdepends"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
513 <includesfile name="${metainf}/sdg.libdepends"/>
6270665 Some build fixes
egonw authored
514 <includesfile name="${metainf}/forcefield.libdepends"/>
0bf100d Added InChI module to regular compile setup
egonw authored
515 <includesfile name="${metainf}/inchi.libdepends"/>
c660505 Reworked dist-large target
egonw authored
516 </fileset>
517 <fileset dir="${dist}/jar">
518 <include name="cdk-applications.jar"/>
519 <include name="cdk-builder3d.jar"/>
3673f87 Added missing jar in dist-large target
egonw authored
520 <include name="cdk-charges.jar"/>
c660505 Reworked dist-large target
egonw authored
521 <include name="cdk-core.jar"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
522 <include name="cdk-control.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
523 <include name="cdk-datadebug.jar"/>
c660505 Reworked dist-large target
egonw authored
524 <include name="cdk-data.jar"/>
525 <include name="cdk-experimental.jar"/>
526 <include name="cdk-extra.jar"/>
527 <include name="cdk-interfaces.jar"/>
528 <include name="cdk-io.jar"/>
529 <include name="cdk-io-jmol.jar"/>
530 <include name="cdk-libio-cml.jar"/>
e8cbc78 Attempting to get libioweka to work: no '-' in module names, if you w…
egonw authored
531 <include name="cdk-libioweka.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
532 <include name="cdk-nonotify.jar"/>
533 <include name="cdk-pdb-cml.jar"/>
534 <include name="cdk-pdb.jar"/>
c660505 Reworked dist-large target
egonw authored
535 <include name="cdk-qsar.jar"/>
29687ca Added a CML Customizer interface which reduces the CDK module depende…
egonw authored
536 <include name="cdk-qsar-cml.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
537 <include name="cdk-qsar-pdb.jar"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
538 <include name="cdk-reaction.jar"/>
c660505 Reworked dist-large target
egonw authored
539 <include name="cdk-render.jar"/>
540 <include name="cdk-standard.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
541 <include name="cdk-svg.jar"/>
9c7431a Fixed stupid typo
egonw authored
542 <include name="cdk-valencycheck.jar"/>
f86e117 Created the smiles module
egonw authored
543 <include name="cdk-forcefield.jar"/>
544 <include name="cdk-smiles.jar"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
545 <include name="cdk-sdg.jar"/>
0bf100d Added InChI module to regular compile setup
egonw authored
546 <include name="cdk-inchi.jar"/>
c660505 Reworked dist-large target
egonw authored
547 </fileset>
548 </unjar>
9db2505 Added missing jars to dist-large target
egonw authored
549
c660505 Reworked dist-large target
egonw authored
550 <!-- then zip up things -->
41cd367 Modified the filename for the dist-large target to include the curren…
rajarshi authored
551 <tstamp>
552 <format property="TODAY_SVN" pattern="yyyyMMdd" locale="en" />
553 </tstamp>
554 <jar jarfile="${dist}/jar/cdk-svn-${TODAY_SVN}.jar">
c660505 Reworked dist-large target
egonw authored
555 <manifest>
556 <attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
557 <section name="org.openscience.cdk">
558 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
559 <attribute name="Specification-Version" value="1.0"/>
560 <attribute name="Specification-Vendor" value="The CDK Project"/>
561 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
562 <attribute name="Implementation-Version" value="${version}"/>
563 <attribute name="Implementation-Vendor" value="The CDK Project"/>
564 </section>
565 </manifest>
566 <fileset dir="${appjars.dir}">
567 <include name="**/*" />
568 </fileset>
569 </jar>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
570 </target>
571
8c06c63 Fixed inclusion of .javafiles, .classes, and .set files for easy buil…
egonw authored
572 <target id="sourcedist" name="sourcedist" depends="init, runDoclet"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
573 description="Builds the source packages.">
a0ba425 Updated sourcedist target so that it uses the current date for the fi…
rajarshi authored
574 <tstamp>
575 <format property="TODAY_SVN" pattern="yyyyMMdd" locale="en" />
576 </tstamp>
577 <property name="package" value="cdk-source-${TODAY_SVN}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
578 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
579 <copy todir="${sourcedist.dir}/${src}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
580 <fileset dir="${build}" includes="*.javafiles" />
581 <fileset dir="${build}" includes="*.classes" />
582 <fileset dir="${build}" includes="*.set" />
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
583 <fileset dir="${src}" includes="**/*.java" />
584 <fileset dir="${src}" includes="**/*.jj" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
585 <fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
586 </copy>
587 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
588 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
589 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
590 <fileset dir="." includes="javadoc.xml" />
591 <fileset dir="." includes="README" />
e99a32a Preparing for a release
egonw authored
592 <fileset dir="." includes="changelog*" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
593 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
594 <copy todir="${sourcedist.dir}/jar">
fbf19c3 The source releases contained unnecessary libraries
egonw authored
595 <fileset dir="jar">
596 <exclude name="libio/*.jar"/>
597 </fileset>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
598 </copy>
998ae6a Updated for current CVS.
egonw authored
599 <copy todir="${sourcedist.dir}/develjar">
600 <fileset dir="develjar">
601 <exclude name="pmd-1.8.jar"/>
602 <exclude name="doccheck.jar"/>
603 <exclude name="dbdoclet*.*"/>
604 </fileset>
605 </copy>
606 <copy todir="${sourcedist.dir}/src/data">
ddebad1 Modified to match new dir struct
egonw authored
607 <fileset dir="src/data" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
608 </copy>
998ae6a Updated for current CVS.
egonw authored
609 <copy todir="${sourcedist.dir}/src/META-INF">
610 <fileset dir="src/META-INF" />
611 </copy>
7aa27da Make sure the config.data files get included in the source dist (clos…
egonw authored
612 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
613 <fileset dir="${src}/org/openscience/cdk/config/data/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
614 includes="*" />
615 </copy>
a289167 Minor tweak to get distribs working
egonw authored
616 <copy
617 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
618 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
619 <copy
620 file="${src}/org/openscience/cdk/dict/data/chemical.xml"
621 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
622 <copy
a289167 Minor tweak to get distribs working
egonw authored
623 file="${src}/org/openscience/cdk/dict/data/elements.xml"
624 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
e2623a3 Added some missing files to the sourcedist
egonw authored
625 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
626 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/">
627 <fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
628 </copy>
998ae6a Updated for current CVS.
egonw authored
629 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/"/>
630 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/">
b566a03 Fixed copying of .prm files.
egonw authored
631 <fileset dir="${src}/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
998ae6a Updated for current CVS.
egonw authored
632 </copy>
00c2efc Added missing builder3d templates to sourcedist.
egonw authored
633 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/"/>
634 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/">
635 <fileset dir="${src}/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
636 </copy>
9496005 Added missing manifest
egonw authored
637 <copy todir="${sourcedist.dir}/${src}/">
638 <fileset dir="${src}/" includes="*.manifest" />
639 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
640 <mkdir dir="${sourcedist.dir}/doc/" />
641 <copy todir="${sourcedist.dir}/doc/">
642 <fileset dir="doc/" includes="lgpl.license" />
643 </copy>
7447e16 Getting ready for release
egonw authored
644 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
645 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
a0ba425 Updated sourcedist target so that it uses the current date for the fi…
rajarshi authored
646 <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
647 <delete file="${package}.tar" />
648 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
998ae6a Updated for current CVS.
egonw authored
649 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
650
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
651 <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
32a84b3 Fixed location of junit.jar
egonw authored
652 <fail message="JUnit is not installed in Ant. Please copy cdk/develjar/junit.jar to ${ant.home}/lib/."/>
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
653 </target>
654
a68b440 Moved a redundant dependency.
egonw authored
655 <target id="test-module" name="test-module" depends="noJunit"
bd190c6 Finished transition to modularized testing
egonw authored
656 description="Performs a full JUnit test for the CDK."
657 if="junit.present">
658
659 <echo message="Testing classes for CDK's ${module} module." />
660
661 <!-- check for availability for meta info files -->
662 <available file="${metainf}/test-${module}.cdkdepends" property="module.cdkdepends.present"/>
663 <available file="${metainf}/test-${module}.libdepends" property="module.libdepends.present"/>
664 <available file="${metainf}/test-${module}.devellibdepends" property="module.devellibdepends.present"/>
665
666 <!-- be somewhat informative -->
667 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
668 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
669 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
670
671 <mkdir dir="${reports.tests}"/>
672 <junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="256m">
673 <classpath>
674 <fileset dir="${lib}" >
675 <exclude name="**/*" unless="module.libdepends.present" />
676 <includesfile name="${metainf}/test-${module}.libdepends" if="module.libdepends.present" />
677 </fileset>
678 <fileset dir="${devellib}">
679 <exclude name="**/*" unless="module.devellibdepends.present" />
680 <includesfile name="${metainf}/test-${module}.devellibdepends" if="module.devellibdepends.present" />
681 </fileset>
682 <fileset dir="${dist}/jar">
683 <exclude name="**/*" unless="module.cdkdepends.present" />
684 <includesfile name="${metainf}/test-${module}.cdkdepends" if="module.cdkdepends.present" />
685 <include name="cdk-test-${module}.jar" />
686 </fileset>
687 </classpath>
688 <test name="org.openscience.cdk.test.M${module}Tests"
689 haltonfailure="no"
690 todir="${reports.tests}"
691 outfile="result-${module}">
692 <formatter type="brief" />
693 </test>
694 </junit>
695 </target>
696
e44e207 Removed special ant target for experimental module
egonw authored
697 <target id="test-all" name="test-all" depends="noJunit, dist-all, test-dist-all"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
698 description="Performs a full JUnit test for the CDK."
699 if="junit.present">
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
700 <antcall target="test-module"><param name="module" value="core"/></antcall>
0f12eb5 Made a test-data module
egonw authored
701 <antcall target="test-module"><param name="module" value="data"/></antcall>
f05b101 Renamed module and made separate test module
egonw authored
702 <antcall target="test-module"><param name="module" value="datadebug"/></antcall>
7269de8 OK, added test suite for NoNotify classes
egonw authored
703 <antcall target="test-module"><param name="module" value="nonotify"/></antcall>
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
704 <antcall target="test-module"><param name="module" value="standard"/></antcall>
407c234 Made a test-io module
egonw authored
705 <antcall target="test-module"><param name="module" value="io"/></antcall>
6e91a8e Created the test-smiles module
egonw authored
706 <antcall target="test-module"><param name="module" value="forcefield"/></antcall>
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
707 <antcall target="test-module"><param name="module" value="extra"/></antcall>
865fa00 Setup a valencycheck module with our crappy 'find bond order' algorithms
egonw authored
708 <antcall target="test-module"><param name="module" value="valencycheck"/></antcall>
5df2c32 new package for weka libio. And tests
miguelrojasch authored
709 <antcall target="test-module"><param name="module" value="reaction"/></antcall>
cef30e4 added forgot class
miguelrojasch authored
710 <antcall target="test-module"><param name="module" value="libioweka"/></antcall>
6e91a8e Created the test-smiles module
egonw authored
711 <antcall target="test-module"><param name="module" value="smiles"/></antcall>
e44e207 Removed special ant target for experimental module
egonw authored
712 <antcall target="test-module"><param name="module" value="experimental"/></antcall>
1d5576d added new test-model:qsar
miguelrojasch authored
713 <antcall target="test-module"><param name="module" value="qsar"/></antcall>
913abbb Setup test module for the pdb module
egonw authored
714 <antcall target="test-module"><param name="module" value="pdb"/></antcall>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
715 <antcall target="test-module"><param name="module" value="inchi"/></antcall>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
716 </target>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
717
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
718 <target id="limitations" name="limitations" depends="noJunit, dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
719 description="Performs a JUnit tests that indicate limitations of certain CDK algorithms/classes.">
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
720 <junit printsummary="yes" haltonfailure="yes" fork="yes">
721 <classpath>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
722 <fileset dir="${dist}/jar">
723 <include name="cdk-*.jar" />
724 </fileset>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
725 <fileset dir="${lib}">
726 <include name="*.jar" />
727 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
728 <fileset dir="${devellib}">
729 <include name="*.jar" />
730 </fileset>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
731 <fileset dir="${lib}/libio">
732 <include name="*.jar" />
733 </fileset>
734 </classpath>
735 <test name="org.openscience.cdk.test.limitations.AlgorithmLimitations"
736 haltonfailure="no"
737 todir="${reports.tests}"
738 outfile="limitations">
739 <formatter type="brief" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
740 </test>
741 </junit>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
742 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
743
6029346 Added missing dependencies
egonw authored
744 <target id="run-test" name="run-test" depends="dist-all,test-dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
745 description="Runs one specific JUnit test suite (org.openscience.cdk.test.&lt;class>) as a standalone application with -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
746 <echo message="Running test class: testclass=${testclass}"/>
03a7837 merge with jcp21
shk3 authored
747 <java classname="org.openscience.cdk.test.${testclass}" fork="yes" maxmemory="512m">
3d88ed4 Turn on CDK debugging while running JUnit test
egonw authored
748 <jvmarg value="-Dcdk.debugging=true"/>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
749 <classpath>
bd397e8 Run test target should be working too now
egonw authored
750 <fileset dir="${dist}/jar/">
751 <include name="*.jar" />
752 </fileset>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
753 <fileset dir="${lib}">
754 <include name="*.jar" />
755 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
756 <fileset dir="${devellib}">
757 <include name="*.jar" />
758 </fileset>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
759 <fileset dir="${lib}/libio">
760 <include name="*.jar" />
761 </fileset>
762 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
763 </java>
bd397e8 Run test target should be working too now
egonw authored
764 </target>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
765
6029346 Added missing dependencies
egonw authored
766 <target id="junit-test" name="junit-test" depends="dist-all,test-dist-all,noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
767 description="Runs one specific JUnit test suite (org.openscience.cdk.test.&lt;class>) with -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
768 <echo message="JUnit tests class: testclass=${testclass}"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
769 <junit printsummary="yes" haltonfailure="no" fork="yes">
79f7451 Switch debugging on in run-test target
steinbeck authored
770 <jvmarg value="-Dcdk.debugging=true"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
771 <jvmarg value="-Dcdk.debug.stdout=true"/>
772 <classpath>
5b2a8d2 Reintroduced the junit-test target
egonw authored
773 <fileset dir="${dist}/jar/">
774 <include name="*.jar" />
775 </fileset>
58425b9 Added use of properties to run target
steinbeck authored
776 <pathelement path="${java.class.path}" />
777 <pathelement location="." />
778 <fileset dir="${lib}">
779 <include name="*.jar" />
780 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
781 <fileset dir="${devellib}">
782 <include name="*.jar" />
783 </fileset>
58425b9 Added use of properties to run target
steinbeck authored
784 <fileset dir="${lib}/libio">
785 <include name="*.jar" />
786 </fileset>
787 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
788 <test name="org.openscience.cdk.test.${testclass}"
789 haltonfailure="no"
790 todir="${reports.tests}"
791 outfile="result.${testclass}">
792 <formatter type="brief" />
793 </test>
794 </junit>
5b2a8d2 Reintroduced the junit-test target
egonw authored
795 </target>
58425b9 Added use of properties to run target
steinbeck authored
796
676c95b Cleaned up more of the build file
egonw authored
797 <target id="run" name="run" depends="dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
798 description="Runs an application (org.openscience.cdk.&lt;class>) with -Drunclass=&lt;class>.">
58425b9 Added use of properties to run target
steinbeck authored
799 <java classname="org.openscience.cdk.${runclass}" fork="yes" >
21cfa9b More documentation in AllRingsFinder and FingerPrinter on recent time…
steinbeck authored
800 <!--jvmarg value="-Dcdk.debugging=true"/>
801 <jvmarg value="-Dcdk.debug.stdout=true"/-->
5d724f3 Fix and test for bug 931608
steinbeck authored
802
803 <arg value="${arg1}" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
804 <arg value="${arg2}" />
805 <arg value="${arg3}" />
806 <arg value="${arg4}" />
ac448e9 Nothing happend here.
steinbeck authored
807 <classpath>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
808 <fileset dir="${dist}/jar">
809 <include name="*.jar" />
810 </fileset>
8095921 Added rendering of wedged bonds.
egonw authored
811 <fileset dir="${lib}">
812 <include name="*.jar" />
813 </fileset>
814 <fileset dir="${lib}/libio">
815 <include name="*.jar" />
816 </fileset>
817 </classpath>
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
818 </java>
819 </target>
820
c5eb7ec Added Ant build file.
egonw authored
821 </project>
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