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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
3a26de3 Made compilation with debug=on customizable.
egonw authored
14 <!-- where to find Java3D -->
15 <property name="pathtojava3d" value="" />
16 <property name="pathtojoelib" value="../../JoeLib/joelib/" />
17
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
18
3a26de3 Made compilation with debug=on customizable.
egonw authored
19 <!-- directories -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
20 <property name="build" value="build" />
bd36ed1 Trial for new build system
egonw authored
21 <property name="build.src" value="${build}/src" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
22 <property name="sourcedist" value="sourcedist" />
23 <property name="dist" value="dist" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
24 <property name="doc" value="doc" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
25 <property name="src" value="src" />
26 <property name="lib" value="jar" />
9e95b7b Finished splitting devel from user jars
egonw authored
27 <property name="devellib" value="develjar" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
28 <property name="src.tests" value="${src}/org/openscience/cdk/test" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
29 <property name="reports.tests" value="reports" />
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
30 <property name="appjars.dir" value="${dist}/appjars" />
bd36ed1 Trial for new build system
egonw authored
31 <property name="metainf" value="${src}/META-INF" />
f7be51f Removed alternative core classes patch offering more detailed debug info
egonw authored
32
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
33 <!-- class to run for testing-->
34 <property name="testclass" value="CDKTests" />
9bcd183 Fixed default executed application
egonw authored
35 <property name="runclass" value="applications.FileConvertor" />
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
36 <property name="arg1" value="" />
37 <property name="arg2" value="" />
38 <property name="arg3" value="" />
39 <property name="arg4" value="" />
58425b9 Added use of properties to run target
steinbeck authored
40
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
41 <target id="info" name="info" depends="check">
42 <!-- Gives information about the building process. -->
8f6d674 Fixed after breaking it earlier today
egonw authored
43 <echo message="Platform:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
44 <echo message=" OS: ${os.name}" />
45 <echo message=" Architecture: ${os.arch}" />
46 <echo message=" Version: ${os.version}" />
47 <echo message=" Mac OS/X found: ${isMacOsX}" />
8f6d674 Fixed after breaking it earlier today
egonw authored
48 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
49 <echo message="Java/Ant Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
50 <echo message=" Java version: ${java.version}" />
51 <echo message=" Java vendor: ${java.vendor}" />
52 <echo message=" Java dir: ${java.home}" />
53 <echo message=" Java ext dir: ${java.ext.dirs}" />
54 <echo message=" Ant version: ${ant.version}" />
55 <echo message=" ${ANT_HOME}: ${ant.home}" />
56 <echo message=" hasAnt16: ${hasAnt16}" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
57 <echo message="" />
c1e01f8 Added support for gjdoc
egonw authored
58 <echo message="JavaDoc Environment:" />
59 <echo message=" SUN JavaDoc: ${sunJavaDoc}" />
60 <echo message=" gjdoc JavaDoc: ${gjdocJavaDoc}" />
61 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
62 <echo message="CDK Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
63 <echo message=" CDK version: ${version}" />
64 <echo message=" build.xml: $Id$" />
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
65 <echo message=" Doclets found: ${docletsAreCompiled}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
66 <echo message=" Junit found: ${junit.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
67 <echo message=" --- required libraries ---" />
68 <echo message=" Vecmath found: ${vecmath.present}" />
69 <echo message=" Log4j found: ${log4j.present}" />
70 <echo message=" JGraphT found: ${jgrapht.present}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
71 <echo message=" --- distributed libraries ---" />
cc68a07 Added detection of more third party libraries
egonw authored
72 <echo message=" Batik found: ${batik.present}" />
7cd4ff8 Added R/SJava found to info target
egonw authored
73 <echo message=" CMLDOM found: ${cmllibs.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
74 <echo message=" DADML found: ${dadml.present}" />
75 <echo message=" GNU JAXP found: ${gnujaxp.present}" />
76 <echo message=" JAI found: ${jai.present}" />
77 <echo message=" JavaHelp found: ${javahelp.present}" />
78 <echo message=" XIndice found: ${xindice.present}"/>
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
79 <echo message=" --- optional libraries ---" />
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
80 <echo message=" Jmol found: ${jmol.present}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
81 <echo message=" JOELib found: ${joelib.present}" />
7cd4ff8 Added R/SJava found to info target
egonw authored
82 <echo message=" Java3D found: ${java3D.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
83 <echo message=" R/SJava found: ${rispresent}"/>
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
84 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
85 <echo message="Compiling:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
86 <echo message=" for: ${build.compiler}" />
87 <echo message=" debug: ${debug}" />
88 <echo message=" deprecation: ${deprecation}" />
89 <echo message=" optimization: ${optimization}" />
eb01480 Added skipDoclet option: try ant -DskipDoclet info runDoclet
egonw authored
90 <echo message=" skipDoclet: ${doSkipDoclet}" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
91 </target>
92
8f6d674 Fixed after breaking it earlier today
egonw authored
93 <target id="checkPlatforms" name="checkPlatforms">
58405cf Fixed build.xml to allow compile of doclets on MacOS/X (closes #1001497)
egonw authored
94 <condition property="isMacOsX">
95 <and>
96 <os family="mac"/>
97 <os family="unix"/>
98 </and>
99 </condition>
100 </target>
101
8f6d674 Fixed after breaking it earlier today
egonw authored
102 <target id="check" name="check" depends="checkPlatforms">
cc68a07 Added detection of more third party libraries
egonw authored
103 <!-- Check wether Doclets are compiled and output is generated -->
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
104 <condition property="docletsAreCompiled">
105 <and>
efbfe43 Fixed 'doclets-are-compiled' detection
egonw authored
106 <available classname="net.sf.cdk.tools.MakeJavaFilesFilesDoclet" classpath="${doc}/javadoc"/>
107 <available classname="net.sf.cdk.tools.MakeCDKSetFilesDoclet" classpath="${doc}/javadoc"/>
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
108 </and>
109 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
110 <uptodate property="dotjavafiles.uptodate"
111 targetfile="${src}/core.javafiles">
112 <srcfiles dir="${src}" includes="**/*.java" />
113 </uptodate>
114 <condition property="dotjjfiles.uptodate">
115 <and>
116 <uptodate property="NomParserJavafiles.uptodate"
117 targetfile="${src}/org/openscience/cdk/iupac/parser/NomParser.java">
118 <srcfiles dir="${src}" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
119 </uptodate>
120 <uptodate property="SMARTSParserJavafiles.uptodate"
121 targetfile="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.java">
122 <srcfiles dir="${src}" includes="org/openscience/cdk/smiles/smarts/SMARTSParser.jj" />
123 </uptodate>
124 </and>
125 </condition>
126 <condition property="doSkipDoclet">
127 <equals arg1="${skipDoclet}" arg2="true"/>
128 </condition>
129
130 <!-- Checks which parts of CDK can be build. -->
131
132 <!-- test for optional jars -->
133 <available property="vecmath.present"
134 file="${lib}/vecmath1.2-1.14.jar"/>
135 <available property="log4j.present"
136 file="${lib}/log4j.jar"/>
137 <available property="jgrapht.present"
138 file="${lib}/jgrapht-0.5.3.jar"/>
139 <available property="gnujaxp.present"
140 file="${lib}/gnujaxp.jar"/>
141
142 <!-- test for optional jars -->
143 <condition property="batik.present">
144 <and>
145 <available file="${lib}/batik-awt-util.jar"/>
146 <available file="${lib}/batik-dom.jar"/>
147 <available file="${lib}/batik-svggen.jar"/>
148 <available file="${lib}/batik-util.jar"/>
149 <available file="${lib}/batik-xml.jar"/>
150 </and>
151 </condition>
152 <condition property="cmllibs.present">
153 <or>
154 <available file="${lib}/jumbo50.jar"/>
155 <available file="${lib}/jumbo51.jar"/>
156 </or>
157 </condition>
158 <available property="dadml.present"
159 file="${lib}/dadml.jar"/>
160 <condition property="jai.present">
161 <and>
162 <available file="${lib}/jai_codec.jar"/>
163 <available file="${lib}/jai_core.jar"/>
164 </and>
165 </condition>
166 <available property="java3D.present"
167 classname="javax.media.j3d.Canvas3D"/>
168 <available property="javahelp.present"
169 file="${lib}/jh.jar"/>
170 <available property="joelib.present"
171 classname="joelib.molecule.JOEAtom"
172 classpath="${lib}/libio/joelib.jar"/>
173 <available property="jmol.present"
174 classname="org.jmol.api.JmolAdapter"
175 classpath="${lib}/jmolApis.jar"/>
176 <available property="junit.present"
177 classname="junit.framework.TestCase"
178 classpath="${ant.home}/lib/junit.jar"/>
179 <condition property="rispresent">
180 <and>
181 <or>
182 <available file="/usr/bin/R" />
183 <available file="/usr/local/bin/R"/>
184 </or>
185 <or>
186 <available file="/usr/lib/R/library/SJava/" />
187 <available file="/usr/local/lib/R/library/SJava/" />
188 <available file="/usr/local/lib/R/site-library/SJava/" />
189 </or>
190 </and>
191 </condition>
192 <condition property="xindice.present">
193 <and>
194 <available file="${lib}/xindice.jar"/>
195 <available file="${lib}/xmldb.jar"/>
196 </and>
197 </condition>
198
199 <!-- test Ant version -->
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
200 <condition property="hasAnt16">
201 <contains string="${ant.version}" substring="1.6"/>
202 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
203
204 <!-- test Java version -->
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
205 <condition property="isJava13">
206 <contains string="${java.version}" substring="1.3"/>
207 </condition>
208 <condition property="isJava14">
209 <contains string="${java.version}" substring="1.4"/>
210 </condition>
866bc72 CML is now available for Java1.5 too
egonw authored
211 <condition property="isJava15">
212 <contains string="${java.version}" substring="1.5"/>
213 </condition>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
214 <condition property="isJava14+">
215 <or>
216 <contains string="${java.version}" substring="1.4"/>
217 <contains string="${java.version}" substring="1.5"/>
218 </or>
219 </condition>
220 <condition property="isJava15">
221 <contains string="${java.version}" substring="1.5"/>
222 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
223
224 <!-- testing which JavaDoc is present -->
b23a50f Hopefully fixed Rajarshi's problem
egonw authored
225 <condition property="sunJavaDocInExt">
c1e01f8 Added support for gjdoc
egonw authored
226 <or>
227 <available file="${java.ext.dirs}/tools.jar" />
b23a50f Hopefully fixed Rajarshi's problem
egonw authored
228 </or>
229 </condition>
230 <condition property="sunJavaDocInLib">
231 <or>
232 <available file="${java.home}/lib/tools.jar" />
f2b2a90 Applied Rajarshi's patch: gcj+gjdoc still works
egonw authored
233 <available file="${java.home}/../lib/tools.jar" />
c1e01f8 Added support for gjdoc
egonw authored
234 </or>
235 </condition>
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
236 <condition property="sunJavaDoc">
237 <or>
238 <available file="${java.ext.dirs}/tools.jar" />
278e9e1 Missed a ../lib case for the sun JavaDoc problem. Fixed
rajarshi authored
239 <available file="${java.home}/../lib/tools.jar" />
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
240 </or>
241 </condition>
c1e01f8 Added support for gjdoc
egonw authored
242 <condition property="gjdocJavaDoc">
243 <available file="/usr/share/java/gnu-classpath-tools-gjdoc.jar" />
244 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
245
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
246 </target>
247
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
248
d2ed020 Reworked dependencies
egonw authored
249 <target id="init" name="init" depends="check, setupBuildDir"/>
4302fbf Updated for Jumbo50 transition.
egonw authored
250 <target id="customize" name="customize" depends="javacc"/>
866bc72 CML is now available for Java1.5 too
egonw authored
251
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
252 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
253 <tstamp />
254 <mkdir dir="${build}" />
255 <mkdir dir="${sourcedist}" />
256 <mkdir dir="${dist}" />
257 <mkdir dir="${reports.tests}" />
258 </target>
259
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
260 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
261 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
262 <fileset dir="." includes="**/*~" />
263 <fileset dir="." includes="*.tar.gz" />
264 <fileset dir="." includes="*.zip" />
06ee5d1 Modified the clean target to remove .rda files generated during testi…
rajarshi authored
265 <fileset dir="." includes="*.rda" />
24af772 Delete autogenerated .javafiles in clean target
egonw authored
266 <fileset dir="${src}" includes="*.classes" />
df95df5 Don't delete the *.javafiles from CVS
egonw authored
267 <fileset dir="${src}" includes="*.javafiles">
268 <exclude name="jmol*.javafiles" />
269 </fileset>
bfe0e17 Build interfaces before data
egonw authored
270 <fileset dir="${src}" includes="*.entitylist" />
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
271 <!-- remove java files generated with JavaCC -->
272 <fileset dir="${src}/org/openscience/cdk/smiles/smarts" includes="*.java" />
273 <fileset dir="${src}/org/openscience/cdk/iupac/parser" includes="*.java">
274 <!-- the next are from CVS -->
275 <exclude name="AttachedGroup.java" />
276 <exclude name="MoleculeBuilder.java" />
277 </fileset>
2b81a22 Fixed a problem with deleting the doclet classes
egonw authored
278 <fileset dir="${doc}">
279 <include name="javadoc/net/sf/cdk/tools/*.class" />
280 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
281 </delete>
282
283 <delete dir="${build}" />
284 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
285 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
286 <delete dir="${reports.tests}" />
287 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
288
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
289 <target name="compileDoclet" id="compileDoclet" depends="check" unless="docletsAreCompiled">
290 <echo>Compiling doclets in doc/javadoc that are required for compiling CDK...</echo>
291 <antcall target="compileDoclet.MacOSX"/>
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
292 <antcall target="compileDoclet.gjDoc" />
293 <antcall target="compileDoclet.sunJavaDoc" />
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
294 </target>
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
295
296 <target name="compileDoclet.MacOSX" id="compileDoclet.MacOSX" if="isMacOsX">
297 <javac srcdir="doc/javadoc/source" destdir="doc/javadoc"
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
298 includes="MakeJavaFilesFilesDoclet.java, MakeCDKSetFilesDoclet.java" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
299 </target>
300
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
301 <target name="compileDoclet.sunJavaDoc" id="compileDoclet.sunJavaDoc" if="sunJavaDoc" unless="isMacOsX">
ca98ea5 Refactored build process (closes #883519)
egonw authored
302 <javac srcdir="doc/javadoc/source" destdir="doc/javadoc"
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
303 includes="MakeJavaFilesFilesDoclet.java, MakeCDKSetFilesDoclet.java">
ca98ea5 Refactored build process (closes #883519)
egonw authored
304 <classpath>
c1e01f8 Added support for gjdoc
egonw authored
305 <fileset dir="${java.ext.dirs}">
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
306 <include name="tools.jar" if="sunJavaDocInExt"/>
b23a50f Hopefully fixed Rajarshi's problem
egonw authored
307 </fileset>
308 <fileset dir="${java.home}/lib">
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
309 <include name="tools.jar" if="sunJavaDocInLib"/>
c1e01f8 Added support for gjdoc
egonw authored
310 </fileset>
b534185 More fixes: ../lib in both required places, and commented out java1.4…
egonw authored
311 <fileset dir="${java.home}/../lib">
312 <include name="tools.jar" if="sunJavaDocInLib"/>
313 </fileset>
ca98ea5 Refactored build process (closes #883519)
egonw authored
314 </classpath>
315 </javac>
316 </target>
317
c7c3815 Another attempt for get the doclets compiled properly on gjdoc *and* …
egonw authored
318 <target name="compileDoclet.gjDoc" id="compileDoclet.gjDoc" if="gjdocJavaDoc">
319 <javac srcdir="doc/javadoc/source" destdir="doc/javadoc"
320 includes="MakeJavaFilesFilesDoclet.java, MakeCDKSetFilesDoclet.java">
321 <classpath>
322 <fileset dir="/usr/share/java">
323 <include name="com-sun-javadoc.jar" if="gjdocJavaDoc"/>
324 </fileset>
325 </classpath>
326 </javac>
327 </target>
328
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
329 <target name="runDoclet" id="runDoclet"
330 depends="check, customize" unless="doSkipDoclet">
331 <echo>Not skipping doclet run...</echo>
332 <antcall target="reallyRunDoclet"/>
333 <antcall target="failIfNoDocletResults"/>
334 </target>
2583a62 Added better output about missing src/*.javafiles
egonw authored
335
676c95b Cleaned up more of the build file
egonw authored
336 <target name="checkDocletResults" id="checkDocletResults">
2583a62 Added better output about missing src/*.javafiles
egonw authored
337 <condition property="dotjavafiles.uptodate">
338 <and>
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
339 <available file="${src}/data.javafiles" />
2583a62 Added better output about missing src/*.javafiles
egonw authored
340 <available file="${src}/core.javafiles" />
341 <available file="${src}/standard.javafiles" />
342 <available file="${src}/extra.javafiles" />
343 <available file="${src}/io.javafiles" />
344 </and>
345 </condition>
346 </target>
347
676c95b Cleaned up more of the build file
egonw authored
348 <target name="failIfNoDocletResults" id="failIfNoDocletResults" depends="checkDocletResults" unless="dotjavafiles.uptodate">
2583a62 Added better output about missing src/*.javafiles
egonw authored
349 <fail>
350 There seems to be a problem with building the cdk/src/*.javafiles.
fa91151 A better error message: in most cases source code errors cause the pr…
egonw authored
351 Often this is caused by malformed java source code, so please check the output
352 of the reallyRunDoclet target (ant reallyRunDoclet).
353
354 If there is no reported source code error, please report this to
355 cdk-devel@lists.sf.net and send the output of
2583a62 Added better output about missing src/*.javafiles
egonw authored
356 this command: ant -v info runDoclet.
357 </fail>
358 </target>
359
676c95b Cleaned up more of the build file
egonw authored
360 <target name="reallyRunDoclet" id="reallyRunDoclet" depends="compileDoclet" unless="dotjavafiles.uptodate">
3ec097a Modified the reallyRunDoclet task so that it considers all classes (p…
rajarshi authored
361 <javadoc private="true" maxmemory="128m">
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
362 <classpath>
6e42787 Moved render and io to new system
egonw authored
363 <fileset dir="${lib}">
364 <include name="*.jar" />
42ca7fe Don't include class format 49.0 depending jars if not running Java 1.5.
egonw authored
365 <!-- some jars require some Java version -->
366 <exclude name="jumbo50.jar" unless="isJava15"/>
6e42787 Moved render and io to new system
egonw authored
367 </fileset>
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
368 <fileset dir="${lib}/libio">
369 <include name="*.jar" />
370 </fileset>
b1187d4 The devel libs are needed when running the doclets too
egonw authored
371 <fileset dir="${devellib}">
372 <include name="*.jar" />
373 </fileset>
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
374 </classpath>
375
23408ac Put classes in a package (closes #1323761).
egonw authored
376 <doclet name="net.sf.cdk.tools.MakeJavaFilesFilesDoclet" path="${doc}/javadoc"/>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
377
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
378 <packageset dir="${src}">
ca98ea5 Refactored build process (closes #883519)
egonw authored
379 <include name="org/openscience/cdk/**"/>
380 </packageset>
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
381
ca98ea5 Refactored build process (closes #883519)
egonw authored
382 </javadoc>
3ec097a Modified the reallyRunDoclet task so that it considers all classes (p…
rajarshi authored
383 <javadoc private="true" maxmemory="128m">
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
384 <classpath>
6e42787 Moved render and io to new system
egonw authored
385 <fileset dir="${lib}">
386 <include name="*.jar" />
42ca7fe Don't include class format 49.0 depending jars if not running Java 1.5.
egonw authored
387 <!-- some jars require some Java version -->
388 <exclude name="jumbo50.jar" unless="isJava15"/>
6e42787 Moved render and io to new system
egonw authored
389 </fileset>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
390 <fileset dir="${lib}/libio">
391 <include name="*.jar" />
392 </fileset>
b1187d4 The devel libs are needed when running the doclets too
egonw authored
393 <fileset dir="${devellib}">
394 <include name="*.jar" />
395 </fileset>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
396 </classpath>
397
23408ac Put classes in a package (closes #1323761).
egonw authored
398 <doclet name="net.sf.cdk.tools.MakeCDKSetFilesDoclet" path="${doc}/javadoc"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
399
400 <packageset dir="${src}">
401 <include name="org/openscience/cdk/**"/>
402 </packageset>
403
404 </javadoc>
0bbfc90 Removed Viewer application. Use JChemPaint (jchempaint.sf.net) or Jmo…
egonw authored
405 <move todir="${src}" failonerror="true">
ca98ea5 Refactored build process (closes #883519)
egonw authored
406 <fileset dir=".">
407 <include name="*.javafiles"/>
0c049c7 Further work on new build system: all packages compile, but target te…
egonw authored
408 <include name="*.classes"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
409 <include name="*.set"/>
46a17d2 Clean entity lists
egonw authored
410 <include name="*.entitylist"/>
ca98ea5 Refactored build process (closes #883519)
egonw authored
411 </fileset>
412 </move>
413 </target>
414
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
415 <target id="compile-needed-test" name="compile-needed-test">
416 <uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
417 <srcfiles dir="${src}">
418 <includesfile name="${src}/${module}.javafiles"/>
419 </srcfiles>
420 </uptodate>
421 </target>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
422
423 <target id="compile-init" name="compile-init"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
424 depends="init, check, runDoclet"/>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
425
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
426 <target id="compile-module" name="compile-module"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
427 depends="check, dist.init, compile-needed-test"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
428 unless="module-uptodate">
429
bd36ed1 Trial for new build system
egonw authored
430 <echo message="Compiling classes for CDK's ${module} module." />
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
431
432 <!-- check for availability for meta info files -->
433 <available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
434 <available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
435 <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
436 <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
437 <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
bd36ed1 Trial for new build system
egonw authored
438
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
439 <!-- be somewhat informative -->
440 <echo message="Datafiles defined: ${module.datafiles.present}"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
441 <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
442 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
443 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
444 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
445
bd36ed1 Trial for new build system
egonw authored
446 <!-- normally javac compiles not just the given files, but also missing
447 classes that are in the same src/ directory. By making a copy first,
448 we explicitely make it impossible to compile files that are not
449 marked for a specific module -->
51ac13a Also delete .class files as they mess up CDK dependency cleanless too
egonw authored
450 <delete dir="${build}"/>
451 <mkdir dir="${build}"/>
bd36ed1 Trial for new build system
egonw authored
452 <mkdir dir="${build.src}"/>
453 <copy todir="${build.src}">
454 <fileset dir="${src}">
927c067 Don't copy files it cannot compile either, fixing another set of buil…
egonw authored
455 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
b534185 More fixes: ../lib in both required places, and commented out java1.4…
egonw authored
456 <!-- excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/ -->
6ceda47 Make sure to exclude java sources that depend on Java 1.5 if not comp…
egonw authored
457 <excludesfile name="${src}/java1.5.javafiles" unless="isJava15"/>
927c067 Don't copy files it cannot compile either, fixing another set of buil…
egonw authored
458 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
459 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
6e04e94 Conditionally compile JAI depending classes.
egonw authored
460 <excludesfile name="${src}/jai.javafiles" unless="jai.present"/>
5370376 Conditionally compile DADML depending classes.
egonw authored
461 <excludesfile name="${src}/dadml.javafiles" unless="dadml.present"/>
41cb46c Conditionally compile JavaHelp depending classes.
egonw authored
462 <excludesfile name="${src}/javahelp.javafiles" unless="javahelp.present"/>
cd7c194 Conditionally compile XIndice depending classes.
egonw authored
463 <excludesfile name="${src}/xindice.javafiles" unless="xindice.present"/>
927c067 Don't copy files it cannot compile either, fixing another set of buil…
egonw authored
464
bd36ed1 Trial for new build system
egonw authored
465 <includesfile name="${src}/${module}.javafiles"/>
466 </fileset>
467 </copy>
468
469 <!-- ok, now that we have a copy, compile this copy -->
470 <javac srcdir="${build.src}" destdir="${build}" optimize="${optimization}"
03a7837 merge with jcp21
shk3 authored
471 debug="${debug}" deprecation="${deprecation}" target="1.3" source="1.3">
bd36ed1 Trial for new build system
egonw authored
472 <classpath>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
473 <fileset dir="${lib}" >
474 <exclude name="**/*" unless="module.libdepends.present" />
475 <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
bd36ed1 Trial for new build system
egonw authored
476 </fileset>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
477 <fileset dir="${devellib}">
478 <exclude name="**/*" unless="module.devellibdepends.present" />
479 <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
480 </fileset>
bd36ed1 Trial for new build system
egonw authored
481 <fileset dir="${dist}/jar">
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
482 <exclude name="**/*" unless="module.cdkdepends.present" />
483 <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
bd36ed1 Trial for new build system
egonw authored
484 </fileset>
485 </classpath>
486
487 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
b534185 More fixes: ../lib in both required places, and commented out java1.4…
egonw authored
488 <!-- excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/ -->
6ceda47 Make sure to exclude java sources that depend on Java 1.5 if not comp…
egonw authored
489 <excludesfile name="${src}/java1.5.javafiles" unless="isJava15"/>
bd36ed1 Trial for new build system
egonw authored
490 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
676c95b Cleaned up more of the build file
egonw authored
491 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
5370376 Conditionally compile DADML depending classes.
egonw authored
492 <excludesfile name="${src}/jai.javafiles" unless="jai.present"/>
493 <excludesfile name="${src}/dadml.javafiles" unless="dadml.present"/>
41cb46c Conditionally compile JavaHelp depending classes.
egonw authored
494 <excludesfile name="${src}/javahelp.javafiles" unless="javahelp.present"/>
cd7c194 Conditionally compile XIndice depending classes.
egonw authored
495 <excludesfile name="${src}/xindice.javafiles" unless="xindice.present"/>
bd36ed1 Trial for new build system
egonw authored
496
497 <includesfile name="${src}/${module}.javafiles"/>
498 </javac>
499
500 <!-- and then jar things up into the module jar -->
501 <jar jarfile="${dist}/jar/cdk-${module}.jar">
502 <fileset dir="${build}">
503 <includesfile name="${src}/${module}.classes" />
504 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
b534185 More fixes: ../lib in both required places, and commented out java1.4…
egonw authored
505 <!-- excludesfile name="${src}/java1.4.classes" unless="isJava14"/ -->
6ceda47 Make sure to exclude java sources that depend on Java 1.5 if not comp…
egonw authored
506 <excludesfile name="${src}/java1.5.classes" unless="isJava15"/>
bd36ed1 Trial for new build system
egonw authored
507 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
5370376 Conditionally compile DADML depending classes.
egonw authored
508 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
509 <excludesfile name="${src}/jai.javafiles" unless="jai.present"/>
510 <excludesfile name="${src}/dadml.javafiles" unless="dadml.present"/>
41cb46c Conditionally compile JavaHelp depending classes.
egonw authored
511 <excludesfile name="${src}/javahelp.javafiles" unless="javahelp.present"/>
cd7c194 Conditionally compile XIndice depending classes.
egonw authored
512 <excludesfile name="${src}/xindice.javafiles" unless="xindice.present"/>
bd36ed1 Trial for new build system
egonw authored
513 </fileset>
514 <fileset dir="${src}">
515 <include name="${module}.javafiles" />
516 </fileset>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
517 <fileset dir="${src}">
141cf36 Fixed problem with including data files in the module jars
egonw authored
518 <exclude name="**/*" unless="module.datafiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
519 <includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
520 </fileset>
ddebad1 Modified to match new dir struct
egonw authored
521 <fileset dir="${src}">
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
522 <exclude name="**/*" unless="module.extrafiles.present"/>
523 <includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
524 </fileset>
bd36ed1 Trial for new build system
egonw authored
525 </jar>
526 </target>
527
6dc5408 Added stuff for qsar module
egonw authored
528 <!-- 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
529 <target id="javacc" name="javacc" depends="init, check" if="hasAnt16" unless="dotjjfiles.uptodate">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
530 <echo message="Compiling Ant 1.6 depending classes." />
cd49d3a A bit of comment
egonw authored
531 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
532 <delete>
533 <fileset id="javacc-generated"
cd49d3a A bit of comment
egonw authored
534 dir="${src}/org/openscience/cdk/iupac/parser/"
535 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
536 </delete>
537 <javacc target="${src}/org/openscience/cdk/iupac/parser/NomParser.jj"
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
538 outputdirectory="${src}/org/openscience/cdk/iupac/parser/"
1dd9647 Added IUPAC name parser
stomkinson authored
539 javacchome="${lib}"/>
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
540 <delete>
541 <fileset id="javacc-generated"
542 dir="${src}/org/openscience/cdk/smiles/smarts/"
543 includes="*.java"/>
544 </delete>
545 <javacc target="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.jj"
546 outputdirectory="${src}/org/openscience/cdk/smiles/smarts/"
547 javacchome="${lib}"/>
1dd9647 Added IUPAC name parser
stomkinson authored
548 </target>
8095921 Added rendering of wedged bonds.
egonw authored
549
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
550 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
551 <mkdir dir="${dist}/jar" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
552 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
553
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
554 <target id="dist-joelib" name="dist-joelib" depends="nocompile-joelib, compile-joelib"/>
555 <target id="nocompile-joelib" name="nocompile-joelib" unless="${joelib.present}">
556 <echo message="JOELib is not found. Removed depending functionality. JOELib can be downloaded from http://joelib.sf.net/."/>
557 </target>
558 <target id="compile-joelib" name="compile-joelib" if="${joelib.present}">
559 <antcall target="compile-module"><param name="module" value="libio-joelib"/></antcall>
560 </target>
561
562 <target id="dist-jmol" name="dist-jmol" depends="nocompile-jmol, compile-jmol"/>
563 <target id="nocompile-jmol" name="nocompile-jmol" unless="${jmol.present}">
564 <echo message="Jmol is not found. Removed depending functionality. Jmol can be downloaded from http://www.jmol.org/."/>
565 </target>
566 <target id="compile-jmol" name="compile-jmol" if="${jmol.present}">
567 <antcall target="compile-module"><param name="module" value="io-jmol"/></antcall>
568 </target>
569
570 <target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
571 <target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
572 <echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
573 </target>
574 <target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
575 <antcall target="compile-module"><param name="module" value="java3d"/></antcall>
576 </target>
577
578 <target id="dist-optional" name="dist-optional" depends="dist-all"
579 description="Compile CDK modules that require optional libraries">
580 <antcall target="dist-java3d"/>
581 <antcall target="dist-jmol"/>
582 <antcall target="dist-joelib"/>
583 </target>
584
585
586 <target id="dist-all" name="dist-all" description="dist-all">
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
587 <antcall target="compile-init"/>
bfe0e17 Build interfaces before data
egonw authored
588 <antcall target="compile-module"><param name="module" value="interfaces"/></antcall>
c378f2b Synched indentation
egonw authored
589 <antcall target="compile-module"><param name="module" value="core"/></antcall>
676c95b Cleaned up more of the build file
egonw authored
590 <antcall target="compile-module"><param name="module" value="standard"/></antcall>
d5e83b5 Made CDK build system aware of the new data-debug module.
egonw authored
591 <antcall target="compile-module"><param name="module" value="data"/></antcall>
7269de8 OK, added test suite for NoNotify classes
egonw authored
592 <antcall target="compile-module"><param name="module" value="datadebug"/></antcall>
593 <antcall target="compile-module"><param name="module" value="nonotify"/></antcall>
676c95b Cleaned up more of the build file
egonw authored
594 <antcall target="compile-module"><param name="module" value="render"/></antcall>
595 <antcall target="compile-module"><param name="module" value="io"/></antcall>
206145b Added a new module 'pdb' with a new class PDBAtom; PDB fields are now…
egonw authored
596 <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
597 <antcall target="compile-module"><param name="module" value="extra"/></antcall>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
598 <antcall target="compile-module"><param name="module" value="libio-cml"/></antcall>
29687ca Added a CML Customizer interface which reduces the CDK module depende…
egonw authored
599 <antcall target="compile-module"><param name="module" value="pdb-cml"/></antcall>
676c95b Cleaned up more of the build file
egonw authored
600 <antcall target="compile-module"><param name="module" value="experimental"/></antcall>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
601 <antcall target="compile-module"><param name="module" value="swing"/></antcall>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
602 <antcall target="compile-module"><param name="module" value="qsar"/></antcall>
29687ca Added a CML Customizer interface which reduces the CDK module depende…
egonw authored
603 <antcall target="compile-module"><param name="module" value="qsar-cml"/></antcall>
40e2447 Added the new qsar-pdb module to the build system, fixing another pro…
egonw authored
604 <antcall target="compile-module"><param name="module" value="qsar-pdb"/></antcall>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
605 <antcall target="compile-module"><param name="module" value="builder3d"/></antcall>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
606 <antcall target="compile-module"><param name="module" value="applications"/></antcall>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
607 <antcall target="compile-module"><param name="module" value="reaction"/></antcall>
38401bd Put applications in separate jar.
egonw authored
608 </target>
609
7511417 Fixed a dependency problem.
egonw authored
610 <target id="test-dist-all" name="test-dist-all" description="test-dist-all">
611 <antcall target="compile-init"/>
3f7319a First step in modularized testing
egonw authored
612 <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
613 <antcall target="compile-module"><param name="module" value="test-standard"/></antcall>
0f12eb5 Made a test-data module
egonw authored
614 <antcall target="compile-module"><param name="module" value="test-data"/></antcall>
f05b101 Renamed module and made separate test module
egonw authored
615 <antcall target="compile-module"><param name="module" value="test-datadebug"/></antcall>
7269de8 OK, added test suite for NoNotify classes
egonw authored
616 <antcall target="compile-module"><param name="module" value="test-nonotify"/></antcall>
407c234 Made a test-io module
egonw authored
617 <antcall target="compile-module"><param name="module" value="test-io"/></antcall>
7511417 Fixed a dependency problem.
egonw authored
618 <antcall target="compile-module"><param name="module" value="test-extra"/></antcall>
39b2a26 new test-module: test-reaction
miguelrojasch authored
619 <antcall target="compile-module"><param name="module" value="test-reaction"/></antcall>
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
620 <antcall target="compile-module"><param name="module" value="test-osjvmts"/></antcall>
7511417 Fixed a dependency problem.
egonw authored
621 </target>
622
623 <target id="dist-large" name="dist-large" depends="dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
624 description="Builds on big jar file for the CDK, including experimental classes.">
c660505 Reworked dist-large target
egonw authored
625
626 <!-- first unjar the CDK and other jars we need -->
627 <delete dir="${build}"/>
628 <mkdir dir="${build}"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
629 <mkdir dir="${appjars.dir}"/>
c660505 Reworked dist-large target
egonw authored
630 <unjar dest="${appjars.dir}">
631 <fileset dir="${lib}">
632 <includesfile name="${metainf}/applications.libdepends"/>
633 <includesfile name="${metainf}/builder3d.libdepends"/>
634 <includesfile name="${metainf}/core.libdepends"/>
635 <includesfile name="${metainf}/data.libdepends"/>
636 <includesfile name="${metainf}/experimental.libdepends"/>
637 <includesfile name="${metainf}/extra.libdepends"/>
638 <includesfile name="${metainf}/io.libdepends"/>
639 <includesfile name="${metainf}/io-jmol.libdepends"/>
640 <includesfile name="${metainf}/libio-cml.libdepends"/>
641 <includesfile name="${metainf}/qsar.libdepends"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
642 <includesfile name="${metainf}/reaction.libdepends"/>
c660505 Reworked dist-large target
egonw authored
643 <includesfile name="${metainf}/render.libdepends"/>
644 <includesfile name="${metainf}/standard.libdepends"/>
645 <includesfile name="${metainf}/swing.libdepends"/>
646 </fileset>
647 <fileset dir="${dist}/jar">
648 <include name="cdk-applications.jar"/>
649 <include name="cdk-builder3d.jar"/>
650 <include name="cdk-core.jar"/>
651 <include name="cdk-data.jar"/>
652 <include name="cdk-experimental.jar"/>
653 <include name="cdk-extra.jar"/>
654 <include name="cdk-interfaces.jar"/>
655 <include name="cdk-io.jar"/>
656 <include name="cdk-io-jmol.jar"/>
206145b Added a new module 'pdb' with a new class PDBAtom; PDB fields are now…
egonw authored
657 <include name="cdk-pdb.jar"/>
c660505 Reworked dist-large target
egonw authored
658 <include name="cdk-libio-cml.jar"/>
659 <include name="cdk-qsar.jar"/>
29687ca Added a CML Customizer interface which reduces the CDK module depende…
egonw authored
660 <include name="cdk-qsar-cml.jar"/>
661 <include name="cdk-pdb.jar"/>
662 <include name="cdk-pdb-cml.jar"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
663 <include name="cdk-reaction.jar"/>
c660505 Reworked dist-large target
egonw authored
664 <include name="cdk-render.jar"/>
665 <include name="cdk-standard.jar"/>
666 <include name="cdk-swing.jar"/>
667 </fileset>
668 </unjar>
669
670 <!-- then zip up things -->
671 <jar jarfile="${dist}/jar/cdk-${version}.jar">
672 <manifest>
673 <attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
674 <section name="org.openscience.cdk">
675 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
676 <attribute name="Specification-Version" value="1.0"/>
677 <attribute name="Specification-Vendor" value="The CDK Project"/>
678 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
679 <attribute name="Implementation-Version" value="${version}"/>
680 <attribute name="Implementation-Vendor" value="The CDK Project"/>
681 </section>
682 </manifest>
683 <fileset dir="${appjars.dir}">
684 <include name="**/*" />
685 </fileset>
686 </jar>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
687 </target>
688
8c06c63 Fixed inclusion of .javafiles, .classes, and .set files for easy buil…
egonw authored
689 <target id="sourcedist" name="sourcedist" depends="init, runDoclet"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
690 description="Builds the source packages.">
dccd7d0 Sourcedist making now also uses the defined version
egonw authored
691 <property name="package" value="cdk-source-${version}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
692 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
693 <copy todir="${sourcedist.dir}/${src}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
694 <fileset dir="${src}" includes="*.javafiles" />
ba078b3 Also include .classes file, otherwise I still won't compile :(
egonw authored
695 <fileset dir="${src}" includes="*.classes" />
8c06c63 Fixed inclusion of .javafiles, .classes, and .set files for easy buil…
egonw authored
696 <fileset dir="${src}" includes="*.set" />
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
697 <fileset dir="${src}" includes="**/*.java" />
698 <fileset dir="${src}" includes="**/*.jj" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
699 <fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
700 </copy>
701 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
702 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
703 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
704 <fileset dir="." includes="javadoc.xml" />
705 <fileset dir="." includes="README" />
706 <fileset dir="." includes="CHANGELOG" />
707 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
708 <copy todir="${sourcedist.dir}/jar">
fbf19c3 The source releases contained unnecessary libraries
egonw authored
709 <fileset dir="jar">
710 <exclude name="libio/*.jar"/>
711 <exclude name="pmd-1.8.jar"/>
712 <exclude name="xalan-2.0.1.jar"/>
713 <exclude name="doccheck.jar"/>
714 <exclude name="dbdoclet*.*"/>
715 </fileset>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
716 </copy>
998ae6a Updated for current CVS.
egonw authored
717 <copy todir="${sourcedist.dir}/develjar">
718 <fileset dir="develjar">
719 <exclude name="pmd-1.8.jar"/>
720 <exclude name="doccheck.jar"/>
721 <exclude name="dbdoclet*.*"/>
722 </fileset>
723 </copy>
724 <copy todir="${sourcedist.dir}/src/data">
ddebad1 Modified to match new dir struct
egonw authored
725 <fileset dir="src/data" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
726 </copy>
998ae6a Updated for current CVS.
egonw authored
727 <copy todir="${sourcedist.dir}/src/META-INF">
728 <fileset dir="src/META-INF" />
729 </copy>
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
730 <copy tofile="${sourcedist.dir}/doc/javadoc/source//MakeJavaFilesFilesDoclet.java"
731 file="doc/javadoc/source/MakeJavaFilesFilesDoclet.java"/>
7aa27da Make sure the config.data files get included in the source dist (clos…
egonw authored
732 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
733 <fileset dir="${src}/org/openscience/cdk/config/data/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
734 includes="*" />
735 </copy>
a289167 Minor tweak to get distribs working
egonw authored
736 <copy
737 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
738 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
739 <copy
740 file="${src}/org/openscience/cdk/dict/data/chemical.xml"
741 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
742 <copy
743 file="${src}/org/openscience/cdk/dict/data/elements.xml"
744 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
e2623a3 Added some missing files to the sourcedist
egonw authored
745 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
746 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/">
747 <fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
748 </copy>
998ae6a Updated for current CVS.
egonw authored
749 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/"/>
750 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/">
b566a03 Fixed copying of .prm files.
egonw authored
751 <fileset dir="${src}/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
998ae6a Updated for current CVS.
egonw authored
752 </copy>
00c2efc Added missing builder3d templates to sourcedist.
egonw authored
753 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/"/>
754 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/">
755 <fileset dir="${src}/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
756 </copy>
9496005 Added missing manifest
egonw authored
757 <copy todir="${sourcedist.dir}/${src}/">
758 <fileset dir="${src}/" includes="*.manifest" />
759 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
760 <mkdir dir="${sourcedist.dir}/doc/" />
761 <copy todir="${sourcedist.dir}/doc/">
762 <fileset dir="doc/" includes="lgpl.license" />
763 </copy>
7447e16 Getting ready for release
egonw authored
764 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
765 <copy todir="${sourcedist.dir}/doc/javadoc">
766 <fileset dir="doc/javadoc" includes="MakeJavaFilesFilesDoclet.class" />
767 <fileset dir="doc/javadoc" includes="MakeCDKSetFilesDoclet.class" />
768 </copy>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
769 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
dccd7d0 Sourcedist making now also uses the defined version
egonw authored
770 <gzip zipfile="${package}.tar.gz" src="cdk-source-${version}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
771 <delete file="${package}.tar" />
772 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
998ae6a Updated for current CVS.
egonw authored
773 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
774
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
775 <target id="test-all" name="test-all" depends="test, test-experimental"/>
cd012c0 Added posibility to just check the experimental classes
egonw authored
776
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
777 <target id="test-experimental" name="test-experimental" depends="noJunit, dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
778 description="Performs a full JUnit test for the CDK, including experimental classes.">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
779 <mkdir dir="${reports.tests}"/>
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
780 <junit printsummary="yes" haltonfailure="yes" fork="yes">
781 <classpath>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
782 <fileset dir="${dist}/jar">
783 <include name="cdk-*.jar" />
784 </fileset>
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
785 <fileset dir="${lib}">
786 <include name="*.jar" />
787 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
788 <fileset dir="${devellib}">
789 <include name="*.jar" />
790 </fileset>
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
791 <fileset dir="${lib}/libio">
792 <include name="*.jar" />
793 </fileset>
794 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
795 <test name="org.openscience.cdk.test.ExperimentalClassesTests"
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
796 haltonfailure="no"
797 todir="${reports.tests}"
0c93d33 Put results of tests for experimental classes in result.experimental.…
egonw authored
798 outfile="result.experimental">
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
799 <formatter type="brief" />
800 </test>
801 </junit>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
802 </target>
39b2a26 new test-module: test-reaction
miguelrojasch authored
803
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
804
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
805 <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
32a84b3 Fixed location of junit.jar
egonw authored
806 <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
807 </target>
808
a68b440 Moved a redundant dependency.
egonw authored
809 <target id="test-module" name="test-module" depends="noJunit"
bd190c6 Finished transition to modularized testing
egonw authored
810 description="Performs a full JUnit test for the CDK."
811 if="junit.present">
812
813 <echo message="Testing classes for CDK's ${module} module." />
814
815 <!-- check for availability for meta info files -->
816 <available file="${metainf}/test-${module}.cdkdepends" property="module.cdkdepends.present"/>
817 <available file="${metainf}/test-${module}.libdepends" property="module.libdepends.present"/>
818 <available file="${metainf}/test-${module}.devellibdepends" property="module.devellibdepends.present"/>
819
820 <!-- be somewhat informative -->
821 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
822 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
823 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
824
825 <mkdir dir="${reports.tests}"/>
826 <junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="256m">
827 <classpath>
828 <fileset dir="${lib}" >
829 <exclude name="**/*" unless="module.libdepends.present" />
830 <includesfile name="${metainf}/test-${module}.libdepends" if="module.libdepends.present" />
831 </fileset>
832 <fileset dir="${devellib}">
833 <exclude name="**/*" unless="module.devellibdepends.present" />
834 <includesfile name="${metainf}/test-${module}.devellibdepends" if="module.devellibdepends.present" />
835 </fileset>
836 <fileset dir="${dist}/jar">
837 <exclude name="**/*" unless="module.cdkdepends.present" />
838 <includesfile name="${metainf}/test-${module}.cdkdepends" if="module.cdkdepends.present" />
839 <include name="cdk-test-${module}.jar" />
840 </fileset>
841 </classpath>
842 <test name="org.openscience.cdk.test.M${module}Tests"
843 haltonfailure="no"
844 todir="${reports.tests}"
845 outfile="result-${module}">
846 <formatter type="brief" />
847 </test>
848 </junit>
849 </target>
850
7511417 Fixed a dependency problem.
egonw authored
851 <target id="test" name="test" depends="noJunit, dist-all, test-dist-all"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
852 description="Performs a full JUnit test for the CDK."
853 if="junit.present">
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
854 <antcall target="test-module"><param name="module" value="core"/></antcall>
0f12eb5 Made a test-data module
egonw authored
855 <antcall target="test-module"><param name="module" value="data"/></antcall>
f05b101 Renamed module and made separate test module
egonw authored
856 <antcall target="test-module"><param name="module" value="datadebug"/></antcall>
7269de8 OK, added test suite for NoNotify classes
egonw authored
857 <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
858 <antcall target="test-module"><param name="module" value="standard"/></antcall>
407c234 Made a test-io module
egonw authored
859 <antcall target="test-module"><param name="module" value="io"/></antcall>
28b1d67 Mega patch: test-standard now exists, and tests for test-reaction can…
egonw authored
860 <antcall target="test-module"><param name="module" value="extra"/></antcall>
39b2a26 new test-module: test-reaction
miguelrojasch authored
861 <antcall target="test-module"><param name="module" value="reaction"/></antcall>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
862 </target>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
863
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
864 <target id="limitations" name="limitations" depends="noJunit, dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
865 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
866 <junit printsummary="yes" haltonfailure="yes" fork="yes">
867 <classpath>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
868 <fileset dir="${dist}/jar">
869 <include name="cdk-*.jar" />
870 </fileset>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
871 <fileset dir="${lib}">
872 <include name="*.jar" />
873 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
874 <fileset dir="${devellib}">
875 <include name="*.jar" />
876 </fileset>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
877 <fileset dir="${lib}/libio">
878 <include name="*.jar" />
879 </fileset>
880 </classpath>
881 <test name="org.openscience.cdk.test.limitations.AlgorithmLimitations"
882 haltonfailure="no"
883 todir="${reports.tests}"
884 outfile="limitations">
885 <formatter type="brief" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
886 </test>
887 </junit>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
888 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
889
bd397e8 Run test target should be working too now
egonw authored
890 <target id="run-test" name="run-test" depends="dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
891 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
892 <echo message="Running test class: testclass=${testclass}"/>
03a7837 merge with jcp21
shk3 authored
893 <java classname="org.openscience.cdk.test.${testclass}" fork="yes" maxmemory="512m">
3d88ed4 Turn on CDK debugging while running JUnit test
egonw authored
894 <jvmarg value="-Dcdk.debugging=true"/>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
895 <classpath>
bd397e8 Run test target should be working too now
egonw authored
896 <fileset dir="${dist}/jar/">
897 <include name="*.jar" />
898 </fileset>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
899 <fileset dir="${lib}">
900 <include name="*.jar" />
901 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
902 <fileset dir="${devellib}">
903 <include name="*.jar" />
904 </fileset>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
905 <fileset dir="${lib}/libio">
906 <include name="*.jar" />
907 </fileset>
908 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
909 </java>
bd397e8 Run test target should be working too now
egonw authored
910 </target>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
911
5b2a8d2 Reintroduced the junit-test target
egonw authored
912 <target id="junit-test" name="junit-test" depends="dist-all, noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
913 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
914 <echo message="JUnit tests class: testclass=${testclass}"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
915 <junit printsummary="yes" haltonfailure="no" fork="yes">
79f7451 Switch debugging on in run-test target
steinbeck authored
916 <jvmarg value="-Dcdk.debugging=true"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
917 <jvmarg value="-Dcdk.debug.stdout=true"/>
918 <classpath>
5b2a8d2 Reintroduced the junit-test target
egonw authored
919 <fileset dir="${dist}/jar/">
920 <include name="*.jar" />
921 </fileset>
58425b9 Added use of properties to run target
steinbeck authored
922 <pathelement path="${java.class.path}" />
923 <pathelement location="." />
924 <fileset dir="${lib}">
925 <include name="*.jar" />
926 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
927 <fileset dir="${devellib}">
928 <include name="*.jar" />
929 </fileset>
58425b9 Added use of properties to run target
steinbeck authored
930 <fileset dir="${lib}/libio">
931 <include name="*.jar" />
932 </fileset>
933 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
934 <test name="org.openscience.cdk.test.${testclass}"
935 haltonfailure="no"
936 todir="${reports.tests}"
937 outfile="result.${testclass}">
938 <formatter type="brief" />
939 </test>
940 </junit>
5b2a8d2 Reintroduced the junit-test target
egonw authored
941 </target>
58425b9 Added use of properties to run target
steinbeck authored
942
676c95b Cleaned up more of the build file
egonw authored
943 <target id="run" name="run" depends="dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
944 description="Runs an application (org.openscience.cdk.&lt;class>) with -Drunclass=&lt;class>.">
58425b9 Added use of properties to run target
steinbeck authored
945 <java classname="org.openscience.cdk.${runclass}" fork="yes" >
21cfa9b More documentation in AllRingsFinder and FingerPrinter on recent time…
steinbeck authored
946 <!--jvmarg value="-Dcdk.debugging=true"/>
947 <jvmarg value="-Dcdk.debug.stdout=true"/-->
5d724f3 Fix and test for bug 931608
steinbeck authored
948
949 <arg value="${arg1}" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
950 <arg value="${arg2}" />
951 <arg value="${arg3}" />
952 <arg value="${arg4}" />
ac448e9 Nothing happend here.
steinbeck authored
953 <classpath>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
954 <fileset dir="${dist}/jar">
955 <include name="*.jar" />
956 </fileset>
8095921 Added rendering of wedged bonds.
egonw authored
957 <fileset dir="${lib}">
958 <include name="*.jar" />
959 </fileset>
960 <fileset dir="${lib}/libio">
961 <include name="*.jar" />
962 </fileset>
963 </classpath>
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
964 </java>
965 </target>
966
c5eb7ec Added Ant build file.
egonw authored
967 </project>
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