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7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1 <project name="CDK" default="dist" 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" />
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" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
26 <property name="src.tests" value="${src}/org/openscience/cdk/test" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
27 <property name="reports.tests" value="reports" />
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
28 <property name="appjars.dir" value="${dist}/appjars" />
f7be51f Removed alternative core classes patch offering more detailed debug info
egonw authored
29
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
30 <!-- class to run for testing-->
31 <property name="testclass" value="CDKTests" />
9bcd183 Fixed default executed application
egonw authored
32 <property name="runclass" value="applications.FileConvertor" />
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
33 <property name="arg1" value="" />
34 <property name="arg2" value="" />
35 <property name="arg3" value="" />
36 <property name="arg4" value="" />
58425b9 Added use of properties to run target
steinbeck authored
37
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
38 <!-- CLASSPATH -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
39 <path id="project.class.path">
0c049c7 Further work on new build system: all packages compile, but target te…
egonw authored
40 <pathelement location="${java.ext.dirs}/rt.jar" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
41
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
42 <fileset dir="${lib}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
43 <include name="batik-awt-util.jar" />
44 <include name="batik-dom.jar" />
9bcb948 Updated Xerces and Batik libraries to current versions
egonw authored
45 <include name="batik-svggen.jar" />
327694a Uploaded two required batik libs, and new version of castor
egonw authored
46 <include name="batik-util.jar" />
47 <include name="batik-xml.jar" />
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
48 <include name="baysmith-io.jar" />
49 <include name="dadml.jar" />
50 <include name="gnujaxp.jar" />
51 <include name="junit.jar" />
52 <include name="log4j-core.jar" />
53 <include name="log4j.jar" />
54 <include name="mysql-2.0.4.jar" />
55 <include name="postgresql7.0-1.2.jar" />
56 <include name="printf.jar" />
57 <include name="vecmath1.2-1.14.jar" />
21491b7 Updated for new Xerces lib
egonw authored
58 <include name="xerces-2.6.2.jar" />
59 <include name="xmlApis-2.6.2.jar" />
8658001 Added libraries for XindiceReader
yz237 authored
60 <include name="xindice.jar" />
61 <include name="xmldb.jar" />
4ac3d10 Add patches to sourcedist
egonw authored
62 <include name="stmml.jar" />
327694a Uploaded two required batik libs, and new version of castor
egonw authored
63 <include name="castor-0.9.5-xml.jar" />
482731a Extended classpath to include cml stuff
shk3 authored
64 <include name="cmlAll.jar" />
65 <include name="base.jar" />
66 <include name="pmrlib.jar" />
7f7ea85 Have the experimental JME reader actually compile
egonw authored
67 <include name="jmolApis.jar" />
68 <include name="jmolIO.jar" />
5569297 Updated FileConvertor: all options are now implemented, and the app n…
egonw authored
69 <include name="commons-cli-1.0.jar" />
85d8c8c Renderer2D font can now be set (closes JCP RFE #901009)
egonw authored
70 <include name="jfontchooser.jar" />
0223082 Updated for new jar for SSSRFinder code
egonw authored
71 <include name="jgrapht-0.5.3.jar" />
4b4ddb1 Included the Jama jar file in the classpath
rajarshi authored
72 <include name="Jama-1.0.1.jar" />
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
73
74 <include name="antlr.jar" />
75 <include name="sjava-0.68.jar" />
d69d0c9 Modified to use the cdk.require tag to decide whether to include clas…
rajarshi authored
76 <include name="jas.jar" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
77 </fileset>
943daec Location of Java3D classes is now settable. If Java3D is not installe…
egonw authored
78 <fileset dir="${pathtojava3d}">
79 <include name="*.jar" />
80 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
81 </path>
82
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
83 <target id="info" name="info" depends="check">
84 <!-- Gives information about the building process. -->
8f6d674 Fixed after breaking it earlier today
egonw authored
85 <echo message="Platform:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
86 <echo message=" OS: ${os.name}" />
87 <echo message=" Architecture: ${os.arch}" />
88 <echo message=" Version: ${os.version}" />
89 <echo message=" Mac OS/X found: ${isMacOsX}" />
8f6d674 Fixed after breaking it earlier today
egonw authored
90 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
91 <echo message="Java/Ant Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
92 <echo message=" Java version: ${java.version}" />
93 <echo message=" Java vendor: ${java.vendor}" />
94 <echo message=" Java dir: ${java.home}" />
95 <echo message=" Java ext dir: ${java.ext.dirs}" />
96 <echo message=" Ant version: ${ant.version}" />
97 <echo message=" ${ANT_HOME}: ${ant.home}" />
98 <echo message=" hasAnt16: ${hasAnt16}" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
99 <echo message="" />
100 <echo message="CDK Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
101 <echo message=" CDK version: ${version}" />
102 <echo message=" build.xml: $Id$" />
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
103 <echo message=" Doclets found: ${docletsAreCompiled}" />
7cd4ff8 Added R/SJava found to info target
egonw authored
104 <echo message=" JOELib found: ${joelib.present}" />
105 <echo message=" CMLDOM found: ${cmllibs.present}" />
106 <echo message=" Java3D found: ${java3D.present}" />
107 <echo message=" Junit found: ${junit.present}" />
108 <echo message="R/SJava present: ${rispresent}"/>
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
109 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
110 <echo message="Compiling:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
111 <echo message=" for: ${build.compiler}" />
112 <echo message=" debug: ${debug}" />
113 <echo message=" deprecation: ${deprecation}" />
114 <echo message=" optimization: ${optimization}" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
115 </target>
116
8f6d674 Fixed after breaking it earlier today
egonw authored
117 <target id="checkPlatforms" name="checkPlatforms">
58405cf Fixed build.xml to allow compile of doclets on MacOS/X (closes #1001497)
egonw authored
118 <condition property="isMacOsX">
119 <and>
120 <os family="mac"/>
121 <os family="unix"/>
122 </and>
123 </condition>
124 </target>
125
8f6d674 Fixed after breaking it earlier today
egonw authored
126 <target id="check" name="check" depends="checkPlatforms">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
127 <!-- Checks which parts of CDK can be build. -->
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
128 <condition property="docletsAreCompiled">
129 <and>
130 <available classname="MakeJavaFilesFilesDoclet" classpath="${doc}/javadoc"/>
131 <available classname="MakeCDKSetFilesDoclet" classpath="${doc}/javadoc"/>
132 </and>
133 </condition>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
134 <available classname="joelib.molecule.JOEAtom"
135 classpath="${lib}/libio/joelib.jar"
136 property="joelib.present"/>
137 <available file="${lib}/cmlAll.jar"
138 property="cmllibs.present"/>
139 <available classname="javax.media.j3d.Canvas3D"
140 classpathref="project.class.path"
141 property="java3D.present"/>
142 <available classname="junit.framework.TestCase"
143 classpath="${ant.home}/lib/junit.jar"
144 property="junit.present"/>
145 <condition property="hasAnt16">
146 <contains string="${ant.version}" substring="1.6"/>
147 </condition>
148 <condition property="isJava13">
149 <contains string="${java.version}" substring="1.3"/>
150 </condition>
151 <condition property="isJava14">
152 <contains string="${java.version}" substring="1.4"/>
153 </condition>
154 <condition property="isJava14+">
155 <or>
156 <contains string="${java.version}" substring="1.4"/>
157 <contains string="${java.version}" substring="1.5"/>
158 </or>
159 </condition>
160 <condition property="isJava15">
161 <contains string="${java.version}" substring="1.5"/>
162 </condition>
163 <uptodate property="dotjavafiles.uptodate"
164 targetfile="${src}/core.javafiles">
165 <srcfiles dir="${src}" includes="**/*.java" />
166 </uptodate>
167 <condition property="dotjjfiles.uptodate">
168 <and>
169 <uptodate property="NomParserJavafiles.uptodate"
170 targetfile="${src}/org/openscience/cdk/iupac/parser/NomParser.java">
171 <srcfiles dir="${src}" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
172 </uptodate>
173 <uptodate property="SMARTSParserJavafiles.uptodate"
174 targetfile="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.java">
175 <srcfiles dir="${src}" includes="org/openscience/cdk/smiles/smarts/SMARTSParser.jj" />
176 </uptodate>
177 </and>
178 </condition>
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/" />
e55ee94 Added another dir to look, though the R tests still fail
egonw authored
188 <available file="/usr/local/lib/R/site-library/SJava/" />
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
189 </or>
190 </and>
191 </condition>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
192 </target>
193
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
194
d2ed020 Reworked dependencies
egonw authored
195 <target id="init" name="init" depends="check, setupBuildDir"/>
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
196 <target id="customize" name="customize" depends="javacc"/>
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
197
198 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
199 <tstamp />
200 <mkdir dir="${build}" />
201 <mkdir dir="${sourcedist}" />
202 <mkdir dir="${dist}" />
203 <mkdir dir="${reports.tests}" />
204 </target>
205
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
206 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
207 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
208 <fileset dir="." includes="**/*~" />
209 <fileset dir="." includes="*.tar.gz" />
210 <fileset dir="." includes="*.zip" />
211 <fileset dir="${src}" includes="*.classes" />
df95df5 Don't delete the *.javafiles from CVS
egonw authored
212 <fileset dir="${src}" includes="*.javafiles">
213 <exclude name="jmol*.javafiles" />
214 </fileset>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
215 <!-- remove java files generated with JavaCC -->
216 <fileset dir="${src}/org/openscience/cdk/smiles/smarts" includes="*.java" />
217 <fileset dir="${src}/org/openscience/cdk/iupac/parser" includes="*.java">
218 <!-- the next are from CVS -->
219 <exclude name="AttachedGroup.java" />
220 <exclude name="MoleculeBuilder.java" />
221 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
222 </delete>
223
224 <delete dir="${build}" />
225 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
226 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
227 <delete dir="${reports.tests}" />
228 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
229
6d246fd Fixed detection of class binaries of Doclets required to compile the CDK
egonw authored
230 <target name="compileDoclet" id="compileDoclet" depends="check" unless="docletsAreCompiled">
231 <echo>Compiling doclets in doc/javadoc that are required for compiling CDK...</echo>
232 <antcall target="compileDoclet.MacOSX"/>
233 <antcall target="compileDoclet.Other" />
234 </target>
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
235
236 <target name="compileDoclet.MacOSX" id="compileDoclet.MacOSX" if="isMacOsX">
237 <javac srcdir="doc/javadoc/source" destdir="doc/javadoc"
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
238 includes="MakeJavaFilesFilesDoclet.java, MakeCDKSetFilesDoclet.java" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
239 </target>
240
241 <target name="compileDoclet.Other" id="compileDoclet.Other" unless="isMacOsX">
ca98ea5 Refactored build process (closes #883519)
egonw authored
242 <javac srcdir="doc/javadoc/source" destdir="doc/javadoc"
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
243 includes="MakeJavaFilesFilesDoclet.java, MakeCDKSetFilesDoclet.java">
ca98ea5 Refactored build process (closes #883519)
egonw authored
244 <classpath>
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
245 <fileset dir="${java.ext.dirs}">
246 <include name="tools.jar" />
247 </fileset>
248 <fileset dir="${java.ext.dirs}/../../../lib">
249 <include name="tools.jar" />
5a62197 Fixed compileDoclet target
egonw authored
250 </fileset>
ca98ea5 Refactored build process (closes #883519)
egonw authored
251 </classpath>
252 </javac>
253 </target>
254
2583a62 Added better output about missing src/*.javafiles
egonw authored
255 <target name="runDoclet" id="runDoclet" depends="reallyRunDoclet, failIfNoDocletResults"/>
256
257 <target name="checkDocletResults">
258 <condition property="dotjavafiles.uptodate">
259 <and>
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
260 <available file="${src}/data.javafiles" />
2583a62 Added better output about missing src/*.javafiles
egonw authored
261 <available file="${src}/core.javafiles" />
262 <available file="${src}/standard.javafiles" />
263 <available file="${src}/extra.javafiles" />
264 <available file="${src}/io.javafiles" />
265 </and>
266 </condition>
267 </target>
268
269 <target name="failIfNoDocletResults" depends="checkDocletResults" unless="dotjavafiles.uptodate">
270 <fail>
271 There seems to be a problem with building the cdk/src/*.javafiles.
fa91151 A better error message: in most cases source code errors cause the pr…
egonw authored
272 Often this is caused by malformed java source code, so please check the output
273 of the reallyRunDoclet target (ant reallyRunDoclet).
274
275 If there is no reported source code error, please report this to
276 cdk-devel@lists.sf.net and send the output of
2583a62 Added better output about missing src/*.javafiles
egonw authored
277 this command: ant -v info runDoclet.
278 </fail>
279 </target>
280
281 <target name="reallyRunDoclet" depends="compileDoclet" unless="dotjavafiles.uptodate">
ca98ea5 Refactored build process (closes #883519)
egonw authored
282 <javadoc private="false" public="true">
283 <classpath refid="project.class.path" />
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
284 <classpath>
285 <fileset dir="${lib}/libio">
286 <include name="*.jar" />
287 </fileset>
288 </classpath>
289
ca98ea5 Refactored build process (closes #883519)
egonw authored
290 <doclet name="MakeJavaFilesFilesDoclet" path="${doc}/javadoc"/>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
291
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
292 <packageset dir="${src}">
ca98ea5 Refactored build process (closes #883519)
egonw authored
293 <include name="org/openscience/cdk/**"/>
294 </packageset>
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
295
ca98ea5 Refactored build process (closes #883519)
egonw authored
296 </javadoc>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
297 <javadoc private="false" public="true">
298 <classpath refid="project.class.path" />
299 <classpath>
300 <fileset dir="${lib}/libio">
301 <include name="*.jar" />
302 </fileset>
303 </classpath>
304
305 <doclet name="MakeCDKSetFilesDoclet" path="${doc}/javadoc"/>
306
307 <packageset dir="${src}">
308 <include name="org/openscience/cdk/**"/>
309 </packageset>
310
311 </javadoc>
0bbfc90 Removed Viewer application. Use JChemPaint (jchempaint.sf.net) or Jmo…
egonw authored
312 <move todir="${src}" failonerror="true">
ca98ea5 Refactored build process (closes #883519)
egonw authored
313 <fileset dir=".">
314 <include name="*.javafiles"/>
0c049c7 Further work on new build system: all packages compile, but target te…
egonw authored
315 <include name="*.classes"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
316 <include name="*.set"/>
46a17d2 Clean entity lists
egonw authored
317 <include name="*.entitylist"/>
ca98ea5 Refactored build process (closes #883519)
egonw authored
318 </fileset>
319 </move>
320 </target>
321
1449de7 Added test to see if *.javafiles are up to date
egonw authored
322 <target name="compile.init" id="compile.init"
323 depends="init, customize, compileDoclet, runDoclet"/>
324
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
325 <target id="compile" name="compile"
326 description="Compiles the CDK."
d2ed020 Reworked dependencies
egonw authored
327 depends="compile-core, compile-standard, compile-extra, compile-io,
6dc5408 Added stuff for qsar module
egonw authored
328 compile-render, compile-render-with-java3d, compile-libio,
4d7781d Split out builder3D stuff into separate module
egonw authored
329 compile-qsar, compile-builder3d">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
330 </target>
331
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
332 <target id="compile-all" name="compile-all" depends="compile, compile-experimental, compile-apps"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
333 description="Compiles the CDK, including experimental classes.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
334 </target>
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
335
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not…
egonw authored
336 <target id="compile-libio" name="compile-libio" depends="dist-standard,
337 compile-libio-joelib, compile-libio-cml" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
338
339 <target name="dont-compile-libio-joelib" unless="joelib.present">
340 <echo message="Not compiling libio for JOELib, jar/libio/joelib.jar is not present" />
341 </target>
342
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not…
egonw authored
343 <target name="dont-compile-libio-cml" unless="cmllibs.present">
344 <echo message="Not compiling libio for CMLDOM, jar/cmlAll.jar is not present" />
345 </target>
346
347 <target name="compile-libio-joelib" if="joelib.present" depends="dont-compile-libio-joelib">
bd7054c Don't try to build libio if lib jars are not available
egonw authored
348 <!-- Task to build the libio classes for JOELib. -->
349 <echo message="Compiling libio for JOELib" />
7ce93c7 Added cdk.Atom <-> joelib.molecule.JOEAtom Convertor procedure.
egonw authored
350
bd7054c Don't try to build libio if lib jars are not available
egonw authored
351 <javac destdir="${build}" optimize="${optimization}"
352 debug="${debug}" deprecation="${deprecation}">
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
353 <src path="${src}/org/openscience/cdk/libio/joelib" />
354 <src path="${src}/org/openscience/cdk/test/libio/joelib" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
355
356 <classpath refid="project.class.path" />
357 <classpath>
358 <fileset dir="${lib}/libio">
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
359 <include name="joelib.jar" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
360 </fileset>
361 </classpath>
362 </javac>
363 </target>
7ce93c7 Added cdk.Atom <-> joelib.molecule.JOEAtom Convertor procedure.
egonw authored
364
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not…
egonw authored
365 <target name="compile-libio-cml" if="cmllibs.present" depends="dont-compile-libio-cml">
366 <!-- Task to build the libio classes for CMLDOM. -->
367 <echo message="Compiling libio for CMLDOM" />
368
369 <javac destdir="${build}" optimize="${optimization}"
370 debug="${debug}" deprecation="${deprecation}">
371 <src path="${src}/org/openscience/cdk/libio/cml" />
372
373 <classpath refid="project.class.path" />
374 <classpath>
375 <fileset dir="${lib}">
376 <include name="base.jar" />
377 <include name="cmlAll.jar" />
378 <include name="pmrlib.jar" />
379 </fileset>
380 </classpath>
381 </javac>
382 </target>
383
4b8b4e6 Added shell variant of test.bat
egonw authored
384 <target id="compile-apps" name="compile-apps"
0bbfc90 Removed Viewer application. Use JChemPaint (jchempaint.sf.net) or Jmo…
egonw authored
385 depends="dist-libio, dist-experimental, dist-render-with-java3d">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
386 <!-- Task to build the applications classes. Some require extra
387 jars, like those in ${lib}/libio -->
388 <echo message="Compiling classes defined in ${src}/applications.javafiles." />
38401bd Put applications in separate jar.
egonw authored
389
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
390 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
391 debug="${debug}" deprecation="${deprecation}">
392 <includesfile name="${src}/applications.javafiles"/>
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
393 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
394 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
9247f2e Don't compile the SMARTS parser and the SubstructureSearcher
egonw authored
395 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
396 <classpath refid="project.class.path" />
397 <classpath>
398 <fileset dir="${dist}/jar">
399 <include name="cdk-core.jar" />
400 <include name="cdk-standard.jar" />
401 <include name="cdk-render.jar" />
402 <include name="cdk-io.jar" />
403 <include name="cdk-extra.jar" />
404 <include name="cdk-libio.jar" />
405 <include name="cdk-experimental.jar" />
406 </fileset>
407 </classpath>
408 <classpath>
409 <fileset dir="${lib}/libio">
410 <include name="*.jar" />
411 </fileset>
412 </classpath>
413 </javac>
38401bd Put applications in separate jar.
egonw authored
414 </target>
415
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
416 <target id="compile-data" name="compile-data" depends="compile.init">
417 <echo message="Compiling classes for cdk-data module." />
418
419 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
420 debug="${debug}" deprecation="${deprecation}">
421 <classpath refid="project.class.path" />
422 <includesfile name="${src}/data.javafiles"/>
423 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
424 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
425 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
426 </javac>
427 </target>
428
d2ed020 Reworked dependencies
egonw authored
429 <target id="compile-core" name="compile-core" depends="compile.init">
36b733d Adding cdk-standard module.
egonw authored
430 <echo message="Compiling classes for cdk-core module." />
20ba54a Simplifying the build proces.
egonw authored
431
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
432 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
433 debug="${debug}" deprecation="${deprecation}">
20ba54a Simplifying the build proces.
egonw authored
434 <classpath refid="project.class.path" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
435 <includesfile name="${src}/core.javafiles"/>
436 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
437 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
438 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
20ba54a Simplifying the build proces.
egonw authored
439 </javac>
440 </target>
441
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
442 <target id="compile-standard" name="compile-standard" depends="dist-core">
36b733d Adding cdk-standard module.
egonw authored
443 <echo message="Compiling classes for cdk-standard module." />
444
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
445 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
446 debug="${debug}" deprecation="${deprecation}">
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
447 <includesfile name="${src}/standard.javafiles"/>
448 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
449 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
36b733d Adding cdk-standard module.
egonw authored
450 <classpath>
451 <fileset dir="${lib}">
db10183 Moving general code out of ShelX reader.
egonw authored
452 <include name="vecmath1.2-1.14.jar" />
015e9b3 Fixed bug #649013.
egonw authored
453 <include name="log4j-core.jar" />
454 <include name="log4j.jar" />
4c55e18 Added missing jar files required for cdk-standard
egonw authored
455 <include name="gnujaxp.jar" />
9bcb948 Updated Xerces and Batik libraries to current versions
egonw authored
456 <include name="xerces-2.5.0.jar" />
0223082 Updated for new jar for SSSRFinder code
egonw authored
457 <include name="jgrapht-0.5.3.jar" />
36b733d Adding cdk-standard module.
egonw authored
458 </fileset>
459 <fileset dir="${dist}/jar">
460 <include name="cdk-core.jar" />
461 </fileset>
462 </classpath>
463 </javac>
464 </target>
465
a34eb22 More @cdkPackage completed: cdk-io now also compiles with kaffe
egonw authored
466 <target id="compile-io" name="compile-io" depends="init, dist-core, dist-standard">
36b733d Adding cdk-standard module.
egonw authored
467 <echo message="Compiling classes for cdk-io module." />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
468
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
469 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
470 debug="${debug}" deprecation="${deprecation}">
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
471 <includesfile name="${src}/io.javafiles"/>
472 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
473 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
474 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
475 <classpath refid="project.class.path" />
476 <classpath>
477 <fileset dir="${dist}/jar">
478 <include name="cdk-core.jar" />
36b733d Adding cdk-standard module.
egonw authored
479 <include name="cdk-standard.jar" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
480 </fileset>
481 </classpath>
482 </javac>
483 </target>
484
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
485 <target id="compile-render" name="compile-render" depends="init, dist-core, dist-standard">
8095921 Added rendering of wedged bonds.
egonw authored
486 <echo message="Compiling classes for cdk-render module." />
487
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
488 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
94396d9 More @cdkPackage completed: cdk-render now also compiles with kaffe
egonw authored
489 debug="${debug}" deprecation="${deprecation}"
490 includesfile="${src}/render.javafiles">
8095921 Added rendering of wedged bonds.
egonw authored
491
492 <classpath refid="project.class.path" />
493 <classpath>
494 <fileset dir="${dist}/jar">
495 <include name="cdk-core.jar" />
496 <include name="cdk-standard.jar" />
497 </fileset>
498 </classpath>
499 </javac>
500 </target>
1dd9647 Added IUPAC name parser
stomkinson authored
501
6dc5408 Added stuff for qsar module
egonw authored
502 <target id="compile-qsar" name="compile-qsar" depends="compile.init">
503 <echo message="Compiling classes for cdk-qsar module." />
504
505 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
506 debug="${debug}" deprecation="${deprecation}">
507 <classpath refid="project.class.path" />
508 <includesfile name="${src}/qsar.javafiles"/>
509 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
510 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
511 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
d69d0c9 Modified to use the cdk.require tag to decide whether to include clas…
rajarshi authored
512 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
6dc5408 Added stuff for qsar module
egonw authored
513 </javac>
514 </target>
515
4d7781d Split out builder3D stuff into separate module
egonw authored
516 <target id="compile-builder3d" name="compile-builder3d" depends="compile.init">
517 <echo message="Compiling classes for cdk-builder3d module." />
518
519 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
520 debug="${debug}" deprecation="${deprecation}">
521 <classpath refid="project.class.path" />
522 <includesfile name="${src}/builder3d.javafiles"/>
523 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
524 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
525 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
4d7781d Split out builder3D stuff into separate module
egonw authored
526 </javac>
527 </target>
528
6dc5408 Added stuff for qsar module
egonw authored
529 <!-- 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
530 <target id="javacc" name="javacc" depends="init, check" if="hasAnt16" unless="dotjjfiles.uptodate">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
531 <echo message="Compiling Ant 1.6 depending classes." />
cd49d3a A bit of comment
egonw authored
532 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
533 <delete>
534 <fileset id="javacc-generated"
cd49d3a A bit of comment
egonw authored
535 dir="${src}/org/openscience/cdk/iupac/parser/"
536 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
537 </delete>
538 <javacc target="${src}/org/openscience/cdk/iupac/parser/NomParser.jj"
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
539 outputdirectory="${src}/org/openscience/cdk/iupac/parser/"
1dd9647 Added IUPAC name parser
stomkinson authored
540 javacchome="${lib}"/>
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
541 <delete>
542 <fileset id="javacc-generated"
543 dir="${src}/org/openscience/cdk/smiles/smarts/"
544 includes="*.java"/>
545 </delete>
546 <javacc target="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.jj"
547 outputdirectory="${src}/org/openscience/cdk/smiles/smarts/"
548 javacchome="${lib}"/>
1dd9647 Added IUPAC name parser
stomkinson authored
549 </target>
8095921 Added rendering of wedged bonds.
egonw authored
550
d2ed020 Reworked dependencies
egonw authored
551 <target id="compile-extra" name="compile-extra" depends="dist-standard, dist-io, dist-render">
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
552 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
553 debug="${debug}" deprecation="${deprecation}">
554 <includesfile name="${src}/extra.javafiles"/>
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
555 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
556 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
557 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
558
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
559 <classpath refid="project.class.path" />
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
560 <classpath>
561 <fileset dir="${dist}/jar">
562 <include name="cdk-core.jar" />
563 <include name="cdk-standard.jar" />
0386767 More @cdkPackage completed for test classes
egonw authored
564 <include name="cdk-render.jar" />
565 <include name="cdk-io.jar" />
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
566 </fileset>
567 </classpath>
9f4ce4f Added patch for RFC #20
egonw authored
568 </javac>
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
569 </target>
f095e4e Fixed dist.extra target. Not all classes were added to the jar: it did
egonw authored
570
0386767 More @cdkPackage completed for test classes
egonw authored
571 <target id="compile-experimental" name="compile-experimental"
572 depends="dist-extra">
573 <echo message="Compiling classes for cdk-experimental module." />
0ef4af6 Added cdk-experimental package
egonw authored
574
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
575 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
576 debug="${debug}" deprecation="${deprecation}">
577 <includesfile name="${src}/experimental.javafiles"/>
578 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
579 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
580 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
0386767 More @cdkPackage completed for test classes
egonw authored
581 <classpath refid="project.class.path" />
582 <classpath>
583 <fileset dir="${dist}/jar">
584 <include name="cdk-core.jar" />
585 <include name="cdk-standard.jar" />
586 <include name="cdk-render.jar" />
587 <include name="cdk-io.jar" />
588 <include name="cdk-extra.jar" />
589 </fileset>
590 </classpath>
591 </javac>
0ef4af6 Added cdk-experimental package
egonw authored
592 </target>
593
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
594 <target id="compile-test" name="compile-test"
595 depends="dist-all">
0386767 More @cdkPackage completed for test classes
egonw authored
596 <!-- Task to build the test classes. -->
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
597 <javac srcdir="${src}"
0386767 More @cdkPackage completed for test classes
egonw authored
598 destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
599 debug="${debug}" deprecation="${deprecation}">
600 <includesfile name="${src}/test.javafiles"/>
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
601 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
602 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
603 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
d69d0c9 Modified to use the cdk.require tag to decide whether to include clas…
rajarshi authored
604 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
605
0386767 More @cdkPackage completed for test classes
egonw authored
606 <classpath refid="project.class.path" />
607 <classpath>
608 <fileset dir="${dist}/jar">
609 <include name="cdk-core.jar" />
610 <include name="cdk-standard.jar" />
611 <include name="cdk-render.jar" />
612 <include name="cdk-io.jar" />
613 <include name="cdk-extra.jar" />
614 <include name="cdk-libio.jar" />
615 <include name="cdk-experimental.jar" />
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
616 <include name="cdk-apps.jar" />
0386767 More @cdkPackage completed for test classes
egonw authored
617 </fileset>
618 </classpath>
619 </javac>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
620 </target>
621
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
622
623 <target name="compile-render-with-java3d"
624 depends="dont-compile-render-with-java3d, do-compile-render-with-java3d"/>
625
626 <target name="dont-compile-render-with-java3d" depends="compile-render"
627 unless="java3D.present">
628 <echo message="Cannot compile Java3D based viewer classes. Java3D is not present" />
629 </target>
630
631 <target name="do-compile-render-with-java3d" depends="compile-render"
632 if="java3D.present">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
633 <mkdir dir="${build}" />
634
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
635 <javac srcdir="${src}"
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
636 destdir="${build}" optimize="${optimization}"
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
637 debug="${debug}" deprecation="${deprecation}"
26336c0 Fixed build.xml for proper reference to java3d.javafiles (thanks to G…
egonw authored
638 includesfile="${src}/java3d.javafiles">
aa6535c Don't compile java source files in ${sourcedist} with java3D too.
egonw authored
639
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
640 <classpath refid="project.class.path" />
641 </javac>
642 </target>
643
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
644 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
645 <mkdir dir="${dist}/jar" />
646
647 <!-- copy data files -->
648
649 <mkdir dir="${build}/org/openscience/cdk/config/data" />
650 <mkdir dir="${build}/org/openscience/cdk/io/cml/data" />
651 <mkdir dir="${build}/org/openscience/cdk/dict/data" />
652 <mkdir dir="${build}/org/openscience/cdk/iupac/generator/data" />
653 <mkdir dir="${build}/org/openscience/cdk/qsar/model/R/data" />
654
655 <copy
656 file="${src}/org/openscience/cdk/config/data/isotopes.xml"
657 tofile="${build}/org/openscience/cdk/config/data/isotopes.xml" />
658 <copy todir="${build}/org/openscience/cdk/config/data/">
659 <fileset dir="${src}/org/openscience/cdk/config/data/" includes="*_atomtypes.xml"/>
660 <fileset dir="${src}/org/openscience/cdk/config/data/" includes="jmol_atomtypes.txt"/>
661 </copy>
662 <copy
663 file="${src}/org/openscience/cdk/config/data/log4j.properties"
664 tofile="${build}/org/openscience/cdk/config/data/log4j.properties" />
665 <copy
666 file="${src}/org/openscience/cdk/io/cml/data/cml1_0.dtd"
667 tofile="${build}/org/openscience/cdk/io/cml/data/cml1_0.dtd" />
668 <copy
669 file="${src}/org/openscience/cdk/io/cml/data/cml1_0_1.dtd"
670 tofile="${build}/org/openscience/cdk/io/cml/data/cml1_0_1.dtd" />
671
672 <copy
673 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
674 tofile="${build}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
675
676 <copy todir="${build}/org/openscience/cdk/dict/data/">
677 <fileset dir="${src}/org/openscience/cdk/dict/data/" includes="*.xml"/>
678 </copy>
679
680 <copy todir="${build}/org/openscience/cdk/qsar/model/data/">
681 <fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
682 </copy>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
683 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
684
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
685 <target id="dist-data" name="dist-data" depends="compile-data, dist.init">
686 <jar jarfile="${dist}/jar/cdk-data.jar">
687 <fileset dir="${build}">
688 <includesfile name="${src}/data.classes" />
689 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
690 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
691 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
692 </fileset>
693 <fileset dir="${src}">
694 <include name="data.javafiles" />
695 </fileset>
696 </jar>
697 </target>
698
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
699 <target id="dist-core" name="dist-core" depends="compile-core, dist.init">
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
700 <jar jarfile="${dist}/jar/cdk-core.jar">
701 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
702 <includesfile name="${src}/core.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
703 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
704 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
705 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
706 </fileset>
efe917b The core module classes are now checked for coverage of JUnit testing
egonw authored
707 <fileset dir="${src}">
708 <include name="core.javafiles" />
709 </fileset>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
710 </jar>
711 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
712
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
713 <target id="dist-extra" name="dist-extra" depends="dist-core, compile-extra">
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
714 <jar jarfile="${dist}/jar/cdk-extra.jar">
715 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
716 <includesfile name="${src}/extra.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
717 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
718 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
719 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
720 </fileset>
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
721 <fileset dir="${build}">
2679b69 Added missing dictionaries to cdk-extra.jar
egonw authored
722 <include name="org/openscience/cdk/dict/data/*.xml" />
723 </fileset>
0ef4af6 Added cdk-experimental package
egonw authored
724 </jar>
725 </target>
726
727 <target id="dist-experimental" name="dist-experimental" depends="compile-experimental, dist.init">
728 <jar jarfile="${dist}/jar/cdk-experimental.jar">
729 <fileset dir="${build}">
730 <includesfile name="${src}/experimental.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
731 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
732 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
733 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
734 </fileset>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
735 </jar>
736 </target>
737
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
738 <target id="dist-apps" name="dist-apps" depends="compile-apps">
4ae9e15 Compile PublicJmol when doing compile-libio.
egonw authored
739 <jar jarfile="${dist}/jar/cdk-apps.jar" manifest="${src}/cdk-apps.manifest">
38401bd Put applications in separate jar.
egonw authored
740 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
741 <includesfile name="${src}/applications.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
742 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
743 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
744 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
38401bd Put applications in separate jar.
egonw authored
745 </fileset>
746 </jar>
747 </target>
748
df42e11 Fixed a few dependencies for the test target
egonw authored
749 <target id="dist-test" name="dist-test" depends="compile-test">
2c7c43d Fixed loading of files in JUnit IO tests: now using get resource.
egonw authored
750 <jar jarfile="${dist}/jar/cdk-test.jar">
751 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
752 <includesfile name="${src}/test.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
753 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
754 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
755 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
eb3206c Exclude r-project classes from jar too, which ensures that the R depe…
egonw authored
756 <excludesfile name="${src}/r-project.classes" unless="rispresent"/>
2c7c43d Fixed loading of files in JUnit IO tests: now using get resource.
egonw authored
757 </fileset>
758 <fileset dir=".">
759 <include name="data/**" />
760 </fileset>
761 </jar>
762 </target>
763
0386767 More @cdkPackage completed for test classes
egonw authored
764 <target id="dist-libio" name="dist-libio" depends="compile-libio" unless="libio.present">
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
765 <jar jarfile="${dist}/jar/cdk-libio.jar">
766 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
767 <includesfile name="${src}/libio.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
768 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
769 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
770 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
4ae9e15 Compile PublicJmol when doing compile-libio.
egonw authored
771 </fileset>
772 <fileset dir="${build}">
773 <include name="org/openscience/jmol/**" />
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
774 </fileset>
775 </jar>
776 </target>
777
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
778 <target id="dist-io" name="dist-io" depends="compile-io">
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
779 <jar jarfile="${dist}/jar/cdk-io.jar">
780 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
781 <includesfile name="${src}/io.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
782 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
783 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
784 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
2b0ab15 Make sure the CML DTDs are in the cdk-io.jar again
egonw authored
785 <include name="org/openscience/cdk/io/cml/data/**" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
786 </fileset>
787 </jar>
788 </target>
789
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
790 <target id="dist-render" name="dist-render" depends="compile-render">
8095921 Added rendering of wedged bonds.
egonw authored
791 <jar jarfile="${dist}/jar/cdk-render.jar">
792 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
793 <includesfile name="${src}/render.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
794 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
795 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
796 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
8095921 Added rendering of wedged bonds.
egonw authored
797 </fileset>
798 </jar>
799 </target>
800
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
801 <target id="dist-render-with-java3d" name="dist-render-with-java3d" depends="compile-render-with-java3d"
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
802 if="java3D.present">
803 <jar jarfile="${dist}/jar/cdk-render.jar">
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
804 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
805 <includesfile name="${src}/render.classes" />
26336c0 Fixed build.xml for proper reference to java3d.javafiles (thanks to G…
egonw authored
806 <includesfile name="${src}/java3d.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
807 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
808 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
809 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
810 </fileset>
811 </jar>
812 </target>
813
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
814 <target id="dist-standard" name="dist-standard" depends="compile-standard, dist.init">
36b733d Adding cdk-standard module.
egonw authored
815 <jar jarfile="${dist}/jar/cdk-standard.jar">
816 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
817 <includesfile name="${src}/standard.classes" />
95c12c2 Added config files to cdk-standard module.
egonw authored
818 <include name="org/openscience/cdk/config/**" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
819 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
820 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
821 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
36b733d Adding cdk-standard module.
egonw authored
822 </fileset>
823 </jar>
824 </target>
825
6dc5408 Added stuff for qsar module
egonw authored
826 <target id="dist-qsar" name="dist-qsar" depends="compile-qsar, dist.init">
827 <jar jarfile="${dist}/jar/cdk-qsar.jar">
828 <fileset dir="${build}">
829 <includesfile name="${src}/qsar.classes" />
830 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
831 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
832 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
eb3206c Exclude r-project classes from jar too, which ensures that the R depe…
egonw authored
833 <excludesfile name="${src}/r-project.classes" unless="rispresent"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
834 </fileset>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
835 <fileset dir="${build}">
836 <include name="org/openscience/cdk/qsar/model/data/*.R" if="rispresent"/>
837 </fileset>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
838 <fileset dir="${src}">
839 <include name="qsar-descriptors.set"/>
840 </fileset>
6dc5408 Added stuff for qsar module
egonw authored
841 </jar>
842 </target>
843
4d7781d Split out builder3D stuff into separate module
egonw authored
844 <target id="dist-builder3d" name="dist-builder3d" depends="compile-builder3d, dist.init">
845 <jar jarfile="${dist}/jar/cdk-builder3d.jar">
846 <fileset dir="${build}">
847 <includesfile name="${src}/builder3d.classes" />
848 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
849 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
850 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
851 </fileset>
852 <fileset dir="data/templates">
853 <include name="ringTemplateFingerprints.txt"/>
854 <include name="ringTemplateStructures.sdf"/>
855 </fileset>
856 </jar>
857 </target>
858
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
859 <target id="dist-large" name="dist-large" depends="compile-all, dist.init, libjars"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
860 description="Builds on big jar file for the CDK, including experimental classes.">
c5110c1 The build.xml now builds cdk-$version.jar instead of cdk-all.jar
egonw authored
861 <jar jarfile="${dist}/jar/cdk-${version}.jar">
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
862 <manifest>
863 <attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
864 <section name="org.openscience.cdk">
865 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
866 <attribute name="Specification-Version" value="1.0"/>
867 <attribute name="Specification-Vendor" value="The CDK Project"/>
868 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
869 <attribute name="Implementation-Version" value="${version}"/>
870 <attribute name="Implementation-Vendor" value="The CDK Project"/>
871 </section>
872 </manifest>
555ce1a Fixed build.xml to properly generate a self-containing cdk-all.jar re…
egonw authored
873 <fileset dir="${build}">
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
874 <include name="org/openscience/cdk/**" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
875 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
876 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
877 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
878 </fileset>
555ce1a Fixed build.xml to properly generate a self-containing cdk-all.jar re…
egonw authored
879 <fileset dir=".">
880 <include name="CHANGELOG" />
881 <include name="README" />
882 <include name="BUGS" />
883 </fileset>
884 <fileset dir="${doc}">
885 <include name="lgpl.license" />
886 </fileset>
887 <fileset dir="packages/tar/cdk">
888 <include name="AUTHORS" />
889 </fileset>
4d7781d Split out builder3D stuff into separate module
egonw authored
890 <fileset dir="${src}"> <!-- from qsar module -->
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
891 <include name="qsar-descriptors.set"/>
892 </fileset>
4d7781d Split out builder3D stuff into separate module
egonw authored
893 <fileset dir="data/templates"> <!-- from builder3d module -->
894 <include name="ringTemplateFingerprints.txt"/>
895 <include name="ringTemplateStructures.sdf"/>
896 </fileset>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
897 <fileset dir="${appjars.dir}" includes="**/*.class"/>
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
898 </jar>
899 </target>
900
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
901 <target name="check.libjars" id="check.libjars">
902 <uptodate property="libjars.uptodate" targetfile="${appjars.dir}">
903 <srcfiles dir="${lib}" includes="base.jar"/>
904 <srcfiles dir="${lib}" includes="batik-dom.jar"/>
905 <srcfiles dir="${lib}" includes="batik-awt-util.jar"/>
906 <srcfiles dir="${lib}" includes="batik-svggen.jar"/>
907 <srcfiles dir="${lib}" includes="batik-util.jar"/>
908 <srcfiles dir="${lib}" includes="batik-xml.jar"/>
909 <srcfiles dir="${lib}" includes="castor-0.9.5-xml.jar"/>
910 <srcfiles dir="${lib}" includes="cmlAll.jar"/>
911 <srcfiles dir="${lib}" includes="commons-cli-1.0.jar"/>
912 <srcfiles dir="${lib}" includes="dadml.jar"/>
913 <srcfiles dir="${lib}" includes="gnujaxp.jar"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
914 <srcfiles dir="${lib}" includes="Jama-1.0.1.jar"/>
ca29169 Added missing library to unpack for dist-large
egonw authored
915 <srcfiles dir="${lib}" includes="jgrapht-0.5.3.jar"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
916 <srcfiles dir="${lib}" includes="jmolApis.jar"/>
917 <srcfiles dir="${lib}" includes="jmolIO.jar"/>
918 <srcfiles dir="${lib}" includes="junit.jar"/>
919 <srcfiles dir="${lib}" includes="log4j-core.jar"/>
920 <srcfiles dir="${lib}" includes="log4j.jar"/>
921 <srcfiles dir="${lib}" includes="mysql-2.0.4.jar"/>
922 <srcfiles dir="${lib}" includes="pmrlib.jar"/>
923 <srcfiles dir="${lib}" includes="postgresql7.0-1.2.jar"/>
924 <srcfiles dir="${lib}" includes="printf.jar"/>
925 <srcfiles dir="${lib}" includes="stmml.jar"/>
926 <srcfiles dir="${lib}" includes="vecmath1.2-1.14.jar"/>
927 <srcfiles dir="${lib}" includes="xerces-2.6.2.jar"/>
928 <srcfiles dir="${lib}" includes="xindice.jar"/>
929 <srcfiles dir="${lib}" includes="xmlApis-2.6.2.jar"/>
930 <srcfiles dir="${lib}" includes="xmldb.jar"/>
931 </uptodate>
932 </target>
933
934 <target name="libjars" id="libjars" depends="check.libjars" unless="libjars.uptodate">
935 <mkdir dir="${appjars.dir}"/>
936 <unjar dest="${appjars.dir}" src="${lib}/base.jar"/>
937 <unjar dest="${appjars.dir}" src="${lib}/batik-dom.jar"/>
938 <unjar dest="${appjars.dir}" src="${lib}/batik-awt-util.jar"/>
939 <unjar dest="${appjars.dir}" src="${lib}/batik-svggen.jar"/>
940 <unjar dest="${appjars.dir}" src="${lib}/batik-util.jar"/>
941 <unjar dest="${appjars.dir}" src="${lib}/batik-xml.jar"/>
942 <unjar dest="${appjars.dir}" src="${lib}/castor-0.9.5-xml.jar"/>
943 <unjar dest="${appjars.dir}" src="${lib}/cmlAll.jar"/>
944 <unjar dest="${appjars.dir}" src="${lib}/commons-cli-1.0.jar"/>
945 <unjar dest="${appjars.dir}" src="${lib}/dadml.jar"/>
946 <unjar dest="${appjars.dir}" src="${lib}/gnujaxp.jar"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
947 <unjar dest="${appjars.dir}" src="${lib}/Jama-1.0.1.jar"/>
ca29169 Added missing library to unpack for dist-large
egonw authored
948 <unjar dest="${appjars.dir}" src="${lib}/jgrapht-0.5.3.jar"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
949 <unjar dest="${appjars.dir}" src="${lib}/jmolApis.jar"/>
950 <unjar dest="${appjars.dir}" src="${lib}/jmolIO.jar"/>
951 <unjar dest="${appjars.dir}" src="${lib}/junit.jar"/>
952 <unjar dest="${appjars.dir}" src="${lib}/log4j-core.jar"/>
953 <unjar dest="${appjars.dir}" src="${lib}/log4j.jar"/>
954 <unjar dest="${appjars.dir}" src="${lib}/mysql-2.0.4.jar"/>
955 <unjar dest="${appjars.dir}" src="${lib}/pmrlib.jar"/>
956 <unjar dest="${appjars.dir}" src="${lib}/postgresql7.0-1.2.jar"/>
957 <unjar dest="${appjars.dir}" src="${lib}/printf.jar"/>
958 <unjar dest="${appjars.dir}" src="${lib}/stmml.jar"/>
959 <unjar dest="${appjars.dir}" src="${lib}/vecmath1.2-1.14.jar"/>
960 <unjar dest="${appjars.dir}" src="${lib}/xerces-2.6.2.jar"/>
961 <unjar dest="${appjars.dir}" src="${lib}/xindice.jar"/>
962 <unjar dest="${appjars.dir}" src="${lib}/xmlApis-2.6.2.jar"/>
963 <unjar dest="${appjars.dir}" src="${lib}/xmldb.jar"/>
964 </target>
965
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
966 <target id="dist-all" name="dist-all" depends="dist, dist-experimental, dist-apps"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
967 description="Builds the jar files for the CDK, including experimental classes."/>
53aff7c dist-all should also build cdk-experimental.jar, dist should not
egonw authored
968
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
969 <target id="dist" name="dist" depends="dist-data, dist-core, dist-standard,
90025c1 Added missing editor classes to cdk-render.jar when compiling with-ja…
egonw authored
970 dist-io, dist-render,
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
971 dist-extra, dist-libio,
6dc5408 Added stuff for qsar module
egonw authored
972 dist-render-with-java3d,
4d7781d Split out builder3D stuff into separate module
egonw authored
973 dist-qsar, dist-builder3d"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
974 description="Builds the jar files for the CDK."/>
ce6c169 Include config and data files in dist-with-java3d too.
egonw authored
975
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
976 <target id="sourcedist" name="sourcedist" depends="init"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
977 description="Builds the source packages.">
dccd7d0 Sourcedist making now also uses the defined version
egonw authored
978 <property name="package" value="cdk-source-${version}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
979 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
980 <copy todir="${sourcedist.dir}/${src}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
981 <fileset dir="${src}" includes="*.javafiles" />
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
982 <fileset dir="${src}" includes="**/*.java" />
983 <fileset dir="${src}" includes="**/*.jj" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
984 <fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
985 </copy>
986 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
987 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
988 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
989 <fileset dir="." includes="javadoc.xml" />
990 <fileset dir="." includes="README" />
991 <fileset dir="." includes="CHANGELOG" />
992 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
993 <copy todir="${sourcedist.dir}/jar">
fbf19c3 The source releases contained unnecessary libraries
egonw authored
994 <fileset dir="jar">
995 <exclude name="libio/*.jar"/>
996 <exclude name="pmd-1.8.jar"/>
997 <exclude name="xalan-2.0.1.jar"/>
998 <exclude name="doccheck.jar"/>
999 <exclude name="dbdoclet*.*"/>
1000 </fileset>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
1001 </copy>
1002 <copy todir="${sourcedist.dir}/data">
1003 <fileset dir="data" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1004 </copy>
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
1005 <copy tofile="${sourcedist.dir}/doc/javadoc/source//MakeJavaFilesFilesDoclet.java"
1006 file="doc/javadoc/source/MakeJavaFilesFilesDoclet.java"/>
7aa27da Make sure the config.data files get included in the source dist (clos…
egonw authored
1007 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
1008 <fileset dir="${src}/org/openscience/cdk/config/data/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
1009 includes="*" />
1010 </copy>
a289167 Minor tweak to get distribs working
egonw authored
1011 <copy
1012 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
1013 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
1014 <copy
1015 file="${src}/org/openscience/cdk/dict/data/chemical.xml"
1016 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
1017 <copy
1018 file="${src}/org/openscience/cdk/dict/data/elements.xml"
1019 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
e2623a3 Added some missing files to the sourcedist
egonw authored
1020 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
1021 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/">
1022 <fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
1023 </copy>
9496005 Added missing manifest
egonw authored
1024 <copy todir="${sourcedist.dir}/${src}/">
1025 <fileset dir="${src}/" includes="*.manifest" />
1026 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
1027 <mkdir dir="${sourcedist.dir}/doc/" />
1028 <copy todir="${sourcedist.dir}/doc/">
1029 <fileset dir="doc/" includes="lgpl.license" />
1030 </copy>
7447e16 Getting ready for release
egonw authored
1031 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
1032 <copy todir="${sourcedist.dir}/doc/javadoc">
1033 <fileset dir="doc/javadoc" includes="MakeJavaFilesFilesDoclet.class" />
1034 <fileset dir="doc/javadoc" includes="MakeCDKSetFilesDoclet.class" />
1035 </copy>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
1036 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
dccd7d0 Sourcedist making now also uses the defined version
egonw authored
1037 <gzip zipfile="${package}.tar.gz" src="cdk-source-${version}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
1038 <delete file="${package}.tar" />
1039 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1040 </target>
1041
cd012c0 Added posibility to just check the experimental classes
egonw authored
1042 <target id="test-all" name="test-all" depends="test, test-experimental"/>
1043
1044 <target id="test-experimental" name="test-experimental" depends="noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1045 description="Performs a full JUnit test for the CDK, including experimental classes.">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
1046 <mkdir dir="${reports.tests}"/>
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1047 <junit printsummary="yes" haltonfailure="yes" fork="yes">
1048 <classpath>
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
1049 <pathelement location="${dist}/jar/cdk-data.jar" />
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1050 <pathelement location="${dist}/jar/cdk-core.jar" />
1051 <pathelement location="${dist}/jar/cdk-standard.jar" />
1052 <pathelement location="${dist}/jar/cdk-io.jar" />
1053 <pathelement location="${dist}/jar/cdk-render.jar" />
1054 <pathelement location="${dist}/jar/cdk-extra.jar" />
1055 <pathelement location="${dist}/jar/cdk-apps.jar" />
1056 <pathelement location="${dist}/jar/cdk-test.jar" />
6dc5408 Added stuff for qsar module
egonw authored
1057 <pathelement location="${dist}/jar/cdk-qsar.jar" />
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1058 <pathelement location="${dist}/jar/cdk-libio.jar" />
1059 <pathelement location="${dist}/jar/cdk-experimental.jar" />
1060 <fileset dir="${lib}">
1061 <include name="*.jar" />
1062 </fileset>
1063 <fileset dir="${lib}/libio">
1064 <include name="*.jar" />
1065 </fileset>
1066 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
1067 <test name="org.openscience.cdk.test.ExperimentalClassesTests"
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1068 haltonfailure="no"
1069 todir="${reports.tests}"
0c93d33 Put results of tests for experimental classes in result.experimental.…
egonw authored
1070 outfile="result.experimental">
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1071 <formatter type="brief" />
1072 </test>
1073 </junit>
1074 </target>
1075
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
1076 <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
1077 <fail message="JUnit is not installed in Ant. Please copy cdk/jar/junit.jar to ${ant.home}/lib/."/>
1078 </target>
1079
1080 <target id="test" name="test" depends="dist-test, noJunit"
1081 description="Performs a full JUnit test for the CDK." if="junit.present">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
1082 <mkdir dir="${reports.tests}"/>
fbbfe4f Corrected JavaDoc errors in builder3d
chhoppe authored
1083 <junit printsummary="yes" haltonfailure="yes" fork="yes" maxmemory="256m">
9344d76 Fork testing, and removed reference to classpaths "." and "${java.cla…
egonw authored
1084 <classpath>
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
1085 <pathelement location="${dist}/jar/cdk-data.jar" />
9344d76 Fork testing, and removed reference to classpaths "." and "${java.cla…
egonw authored
1086 <pathelement location="${dist}/jar/cdk-core.jar" />
1087 <pathelement location="${dist}/jar/cdk-standard.jar" />
1088 <pathelement location="${dist}/jar/cdk-io.jar" />
1089 <pathelement location="${dist}/jar/cdk-render.jar" />
1090 <pathelement location="${dist}/jar/cdk-extra.jar" />
1091 <pathelement location="${dist}/jar/cdk-apps.jar" />
1092 <pathelement location="${dist}/jar/cdk-test.jar" />
1093 <pathelement location="${dist}/jar/cdk-libio.jar" />
6dc5408 Added stuff for qsar module
egonw authored
1094 <pathelement location="${dist}/jar/cdk-qsar.jar" />
4c961ee Added missing jar file
egonw authored
1095 <pathelement location="${dist}/jar/cdk-experimental.jar" />
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
1096 <pathelement location="${dist}/jar/cdk-builder3d.jar" />
9344d76 Fork testing, and removed reference to classpaths "." and "${java.cla…
egonw authored
1097 <fileset dir="${lib}">
1098 <include name="*.jar" />
1099 </fileset>
1100 <fileset dir="${lib}/libio">
1101 <include name="*.jar" />
1102 </fileset>
1103 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
1104 <test name="org.openscience.cdk.test.CDKTests"
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1105 haltonfailure="no"
1106 todir="${reports.tests}"
1107 outfile="result">
81258bd Added Ant task for doing Junit tests on the cdk-core and cdk-standard…
egonw authored
1108 <formatter type="brief" />
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
1109 </test>
1110 </junit>
1111 </target>
1112
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
1113 <target id="limitations" name="limitations" depends="dist-test, noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1114 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
1115 <junit printsummary="yes" haltonfailure="yes" fork="yes">
1116 <classpath>
1117 <pathelement location="${dist}/jar/cdk-core.jar" />
1118 <pathelement location="${dist}/jar/cdk-standard.jar" />
1119 <pathelement location="${dist}/jar/cdk-io.jar" />
1120 <pathelement location="${dist}/jar/cdk-render.jar" />
1121 <pathelement location="${dist}/jar/cdk-extra.jar" />
1122 <pathelement location="${dist}/jar/cdk-apps.jar" />
1123 <pathelement location="${dist}/jar/cdk-test.jar" />
1124 <pathelement location="${dist}/jar/cdk-libio.jar" />
1125 <fileset dir="${lib}">
1126 <include name="*.jar" />
1127 </fileset>
1128 <fileset dir="${lib}/libio">
1129 <include name="*.jar" />
1130 </fileset>
1131 </classpath>
1132 <test name="org.openscience.cdk.test.limitations.AlgorithmLimitations"
1133 haltonfailure="no"
1134 todir="${reports.tests}"
1135 outfile="limitations">
1136 <formatter type="brief" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1137 </test>
1138 </junit>
1139 </target>
1140
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1141 <target name="test-libio" depends="dist-libio">
1142 <java classname="org.openscience.cdk.test.libio.joelib.JOELibIOTest" fork="yes">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1143 <classpath>
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
1144 <pathelement location="${dist}/jar/cdk-core.jar" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1145 <pathelement location="${dist}/jar/cdk-extra.jar" />
1146 <pathelement location="${dist}/jar/cdk-libio.jar" />
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
1147 <pathelement path="${java.class.path}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1148 <pathelement location="." />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1149 <fileset dir="${lib}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1150 <include name="*.jar" />
1151 </fileset>
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1152 <fileset dir="${lib}/libio">
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
1153 <include name="*.jar" />
1154 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1155 </classpath>
1156 </java>
1157 </target>
1158
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1159 <target name="run-with-java3d"
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
1160 depends="dist-extra, dist-io, dist-extra, dist-render-with-java3d">
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1161 <java
1162 classname="org.openscience.cdk.test.OrbitalsRenderer3DTest"
1163 fork="yes">
1164 <arg value="data/reserpine.mol" />
1165
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1166 <classpath>
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1167 <pathelement location="${dist}/jar/cdk-core.jar" />
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
1168 <pathelement location="${dist}/jar/cdk-standard.jar" />
1169 <pathelement location="${dist}/jar/cdk-extra.jar" />
1170 <pathelement location="${dist}/jar/cdk-io.jar" />
1171 <pathelement location="${dist}/jar/cdk-render.jar" />
1172 <pathelement location="${dist}/jar/cdk-render-with-java3d.jar" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1173 <pathelement path="${java.class.path}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1174 <pathelement location="." />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1175 <fileset dir="${lib}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1176 <include name="*.jar" />
1177 </fileset>
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1178 <fileset dir="${pathto3djava}">
1179 <include name="*.jar" />
1180 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1181 </classpath>
1182 </java>
1183 </target>
1184
58425b9 Added use of properties to run target
steinbeck authored
1185 <target id="run-test" name="run-test" depends="dist-core, dist-extra, dist-test, dist-standard"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1186 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