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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" />
efe8fe5 Added hansel jars. Forgot to upload this yesterday.
egonw authored
49 <include name="bcel-5.1.jar" />
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
50 <include name="dadml.jar" />
51 <include name="gnujaxp.jar" />
efe8fe5 Added hansel jars. Forgot to upload this yesterday.
egonw authored
52 <include name="hansel-1.02.jar" />
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
53 <include name="junit.jar" />
54 <include name="log4j-core.jar" />
55 <include name="log4j.jar" />
56 <include name="mysql-2.0.4.jar" />
57 <include name="postgresql7.0-1.2.jar" />
58 <include name="printf.jar" />
59 <include name="vecmath1.2-1.14.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="${src}/org/openscience/cdk/libio/joelib" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
354
355 <classpath refid="project.class.path" />
356 <classpath>
357 <fileset dir="${lib}/libio">
6dc1be4 Less complaining when running MakeJavaFilesFilesDoclet
egonw authored
358 <include name="joelib.jar" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
359 </fileset>
360 </classpath>
361 </javac>
362 </target>
7ce93c7 Added cdk.Atom <-> joelib.molecule.JOEAtom Convertor procedure.
egonw authored
363
a3a9e3f Fixed a dependency
egonw authored
364 <target name="compile-libio-cml" if="cmllibs.present" depends="dont-compile-libio-cml, dist-extra">
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not…
egonw authored
365 <!-- Task to build the libio classes for CMLDOM. -->
366 <echo message="Compiling libio for CMLDOM" />
367
368 <javac destdir="${build}" optimize="${optimization}"
369 debug="${debug}" deprecation="${deprecation}">
370 <src path="${src}/org/openscience/cdk/libio/cml" />
371
372 <classpath refid="project.class.path" />
373 <classpath>
374 <fileset dir="${lib}">
375 <include name="base.jar" />
376 <include name="cmlAll.jar" />
377 <include name="pmrlib.jar" />
378 </fileset>
379 </classpath>
380 </javac>
381 </target>
382
4b8b4e6 Added shell variant of test.bat
egonw authored
383 <target id="compile-apps" name="compile-apps"
0bbfc90 Removed Viewer application. Use JChemPaint (jchempaint.sf.net) or Jmo…
egonw authored
384 depends="dist-libio, dist-experimental, dist-render-with-java3d">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
385 <!-- Task to build the applications classes. Some require extra
386 jars, like those in ${lib}/libio -->
387 <echo message="Compiling classes defined in ${src}/applications.javafiles." />
38401bd Put applications in separate jar.
egonw authored
388
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
389 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
390 debug="${debug}" deprecation="${deprecation}">
391 <includesfile name="${src}/applications.javafiles"/>
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
392 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
393 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
9247f2e Don't compile the SMARTS parser and the SubstructureSearcher
egonw authored
394 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
395 <classpath refid="project.class.path" />
396 <classpath>
397 <fileset dir="${dist}/jar">
398 <include name="cdk-core.jar" />
399 <include name="cdk-standard.jar" />
400 <include name="cdk-render.jar" />
401 <include name="cdk-io.jar" />
402 <include name="cdk-extra.jar" />
403 <include name="cdk-libio.jar" />
404 <include name="cdk-experimental.jar" />
405 </fileset>
406 </classpath>
407 <classpath>
408 <fileset dir="${lib}/libio">
409 <include name="*.jar" />
410 </fileset>
411 </classpath>
412 </javac>
38401bd Put applications in separate jar.
egonw authored
413 </target>
414
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
415 <target id="compile-data" name="compile-data" depends="compile.init">
416 <echo message="Compiling classes for cdk-data module." />
417
418 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
419 debug="${debug}" deprecation="${deprecation}">
420 <classpath refid="project.class.path" />
421 <includesfile name="${src}/data.javafiles"/>
422 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
423 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
424 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
425 </javac>
426 </target>
427
d2ed020 Reworked dependencies
egonw authored
428 <target id="compile-core" name="compile-core" depends="compile.init">
36b733d Adding cdk-standard module.
egonw authored
429 <echo message="Compiling classes for cdk-core module." />
20ba54a Simplifying the build proces.
egonw authored
430
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
431 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
432 debug="${debug}" deprecation="${deprecation}">
20ba54a Simplifying the build proces.
egonw authored
433 <classpath refid="project.class.path" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
434 <includesfile name="${src}/core.javafiles"/>
435 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
436 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
437 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
20ba54a Simplifying the build proces.
egonw authored
438 </javac>
439 </target>
440
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
441 <target id="compile-standard" name="compile-standard" depends="dist-core">
36b733d Adding cdk-standard module.
egonw authored
442 <echo message="Compiling classes for cdk-standard module." />
443
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
444 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
445 debug="${debug}" deprecation="${deprecation}">
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
446 <includesfile name="${src}/standard.javafiles"/>
447 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
448 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
36b733d Adding cdk-standard module.
egonw authored
449 <classpath>
450 <fileset dir="${lib}">
db10183 Moving general code out of ShelX reader.
egonw authored
451 <include name="vecmath1.2-1.14.jar" />
015e9b3 Fixed bug #649013.
egonw authored
452 <include name="log4j-core.jar" />
453 <include name="log4j.jar" />
4c55e18 Added missing jar files required for cdk-standard
egonw authored
454 <include name="gnujaxp.jar" />
9bcb948 Updated Xerces and Batik libraries to current versions
egonw authored
455 <include name="xerces-2.5.0.jar" />
0223082 Updated for new jar for SSSRFinder code
egonw authored
456 <include name="jgrapht-0.5.3.jar" />
36b733d Adding cdk-standard module.
egonw authored
457 </fileset>
458 <fileset dir="${dist}/jar">
459 <include name="cdk-core.jar" />
460 </fileset>
461 </classpath>
462 </javac>
463 </target>
464
a34eb22 More @cdkPackage completed: cdk-io now also compiles with kaffe
egonw authored
465 <target id="compile-io" name="compile-io" depends="init, dist-core, dist-standard">
36b733d Adding cdk-standard module.
egonw authored
466 <echo message="Compiling classes for cdk-io module." />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
467
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
468 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
469 debug="${debug}" deprecation="${deprecation}">
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
470 <includesfile name="${src}/io.javafiles"/>
471 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
472 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
473 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
474 <classpath refid="project.class.path" />
475 <classpath>
476 <fileset dir="${dist}/jar">
477 <include name="cdk-core.jar" />
36b733d Adding cdk-standard module.
egonw authored
478 <include name="cdk-standard.jar" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
479 </fileset>
480 </classpath>
481 </javac>
482 </target>
483
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
484 <target id="compile-render" name="compile-render" depends="init, dist-core, dist-standard">
8095921 Added rendering of wedged bonds.
egonw authored
485 <echo message="Compiling classes for cdk-render module." />
486
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
487 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
94396d9 More @cdkPackage completed: cdk-render now also compiles with kaffe
egonw authored
488 debug="${debug}" deprecation="${deprecation}"
489 includesfile="${src}/render.javafiles">
8095921 Added rendering of wedged bonds.
egonw authored
490
491 <classpath refid="project.class.path" />
492 <classpath>
493 <fileset dir="${dist}/jar">
494 <include name="cdk-core.jar" />
495 <include name="cdk-standard.jar" />
496 </fileset>
497 </classpath>
498 </javac>
499 </target>
1dd9647 Added IUPAC name parser
stomkinson authored
500
6dc5408 Added stuff for qsar module
egonw authored
501 <target id="compile-qsar" name="compile-qsar" depends="compile.init">
502 <echo message="Compiling classes for cdk-qsar module." />
503
504 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
505 debug="${debug}" deprecation="${deprecation}">
506 <classpath refid="project.class.path" />
507 <includesfile name="${src}/qsar.javafiles"/>
508 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
509 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
510 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
d69d0c9 Modified to use the cdk.require tag to decide whether to include clas…
rajarshi authored
511 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
6dc5408 Added stuff for qsar module
egonw authored
512 </javac>
513 </target>
514
4d7781d Split out builder3D stuff into separate module
egonw authored
515 <target id="compile-builder3d" name="compile-builder3d" depends="compile.init">
516 <echo message="Compiling classes for cdk-builder3d module." />
517
518 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
519 debug="${debug}" deprecation="${deprecation}">
520 <classpath refid="project.class.path" />
521 <includesfile name="${src}/builder3d.javafiles"/>
522 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
523 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
524 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
4d7781d Split out builder3D stuff into separate module
egonw authored
525 </javac>
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
d2ed020 Reworked dependencies
egonw authored
550 <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
551 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
552 debug="${debug}" deprecation="${deprecation}">
553 <includesfile name="${src}/extra.javafiles"/>
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
554 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
555 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
556 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
557
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
558 <classpath refid="project.class.path" />
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
559 <classpath>
560 <fileset dir="${dist}/jar">
561 <include name="cdk-core.jar" />
562 <include name="cdk-standard.jar" />
0386767 More @cdkPackage completed for test classes
egonw authored
563 <include name="cdk-render.jar" />
564 <include name="cdk-io.jar" />
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
565 </fileset>
566 </classpath>
9f4ce4f Added patch for RFC #20
egonw authored
567 </javac>
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
568 </target>
f095e4e Fixed dist.extra target. Not all classes were added to the jar: it did
egonw authored
569
0386767 More @cdkPackage completed for test classes
egonw authored
570 <target id="compile-experimental" name="compile-experimental"
571 depends="dist-extra">
572 <echo message="Compiling classes for cdk-experimental module." />
0ef4af6 Added cdk-experimental package
egonw authored
573
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
574 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
575 debug="${debug}" deprecation="${deprecation}">
576 <includesfile name="${src}/experimental.javafiles"/>
577 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
578 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
579 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
0386767 More @cdkPackage completed for test classes
egonw authored
580 <classpath refid="project.class.path" />
581 <classpath>
582 <fileset dir="${dist}/jar">
583 <include name="cdk-core.jar" />
584 <include name="cdk-standard.jar" />
585 <include name="cdk-render.jar" />
586 <include name="cdk-io.jar" />
587 <include name="cdk-extra.jar" />
588 </fileset>
589 </classpath>
590 </javac>
0ef4af6 Added cdk-experimental package
egonw authored
591 </target>
592
89db533 Fixed transition to use of dist-large for test targets
egonw authored
593 <target id="compile-test" name="compile-test" depends="dist-large">
0386767 More @cdkPackage completed for test classes
egonw authored
594 <!-- Task to build the test classes. -->
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
595 <javac srcdir="${src}"
0386767 More @cdkPackage completed for test classes
egonw authored
596 destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be gi…
egonw authored
597 debug="${debug}" deprecation="${deprecation}">
598 <includesfile name="${src}/test.javafiles"/>
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
599 <excludesfile name="${src}/java1.4+.javafiles" if="isJava13"/>
600 <excludesfile name="${src}/java1.4.javafiles" unless="isJava14"/>
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
601 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
d69d0c9 Modified to use the cdk.require tag to decide whether to include clas…
rajarshi authored
602 <excludesfile name="${src}/r-project.javafiles" unless="rispresent"/>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
603
0386767 More @cdkPackage completed for test classes
egonw authored
604 <classpath refid="project.class.path" />
605 <classpath>
89db533 Fixed transition to use of dist-large for test targets
egonw authored
606 <pathelement location="${dist}/jar/cdk-${version}.jar" />
0386767 More @cdkPackage completed for test classes
egonw authored
607 </classpath>
608 </javac>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
609 </target>
610
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
611
612 <target name="compile-render-with-java3d"
613 depends="dont-compile-render-with-java3d, do-compile-render-with-java3d"/>
614
615 <target name="dont-compile-render-with-java3d" depends="compile-render"
616 unless="java3D.present">
617 <echo message="Cannot compile Java3D based viewer classes. Java3D is not present" />
618 </target>
619
620 <target name="do-compile-render-with-java3d" depends="compile-render"
621 if="java3D.present">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
622 <mkdir dir="${build}" />
623
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
624 <javac srcdir="${src}"
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
625 destdir="${build}" optimize="${optimization}"
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
626 debug="${debug}" deprecation="${deprecation}"
26336c0 Fixed build.xml for proper reference to java3d.javafiles (thanks to G…
egonw authored
627 includesfile="${src}/java3d.javafiles">
aa6535c Don't compile java source files in ${sourcedist} with java3D too.
egonw authored
628
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
629 <classpath refid="project.class.path" />
630 </javac>
631 </target>
632
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
633 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
634 <mkdir dir="${dist}/jar" />
635
636 <!-- copy data files -->
637
638 <mkdir dir="${build}/org/openscience/cdk/config/data" />
639 <mkdir dir="${build}/org/openscience/cdk/io/cml/data" />
640 <mkdir dir="${build}/org/openscience/cdk/dict/data" />
641 <mkdir dir="${build}/org/openscience/cdk/iupac/generator/data" />
642 <mkdir dir="${build}/org/openscience/cdk/qsar/model/R/data" />
643
644 <copy
645 file="${src}/org/openscience/cdk/config/data/isotopes.xml"
646 tofile="${build}/org/openscience/cdk/config/data/isotopes.xml" />
647 <copy todir="${build}/org/openscience/cdk/config/data/">
648 <fileset dir="${src}/org/openscience/cdk/config/data/" includes="*_atomtypes.xml"/>
649 <fileset dir="${src}/org/openscience/cdk/config/data/" includes="jmol_atomtypes.txt"/>
650 </copy>
651 <copy
652 file="${src}/org/openscience/cdk/config/data/log4j.properties"
653 tofile="${build}/org/openscience/cdk/config/data/log4j.properties" />
654 <copy
655 file="${src}/org/openscience/cdk/io/cml/data/cml1_0.dtd"
656 tofile="${build}/org/openscience/cdk/io/cml/data/cml1_0.dtd" />
657 <copy
658 file="${src}/org/openscience/cdk/io/cml/data/cml1_0_1.dtd"
659 tofile="${build}/org/openscience/cdk/io/cml/data/cml1_0_1.dtd" />
660
661 <copy
662 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
663 tofile="${build}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
664
665 <copy todir="${build}/org/openscience/cdk/dict/data/">
666 <fileset dir="${src}/org/openscience/cdk/dict/data/" includes="*.xml"/>
667 </copy>
668
669 <copy todir="${build}/org/openscience/cdk/qsar/model/data/">
670 <fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
671 </copy>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
672 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
673
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
674 <target id="dist-data" name="dist-data" depends="compile-data, dist.init">
675 <jar jarfile="${dist}/jar/cdk-data.jar">
676 <fileset dir="${build}">
677 <includesfile name="${src}/data.classes" />
678 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
679 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
680 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
681 </fileset>
682 <fileset dir="${src}">
683 <include name="data.javafiles" />
684 </fileset>
685 </jar>
686 </target>
687
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
688 <target id="dist-core" name="dist-core" depends="compile-core, dist.init">
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
689 <jar jarfile="${dist}/jar/cdk-core.jar">
690 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
691 <includesfile name="${src}/core.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
692 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
693 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
694 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
695 </fileset>
efe917b The core module classes are now checked for coverage of JUnit testing
egonw authored
696 <fileset dir="${src}">
697 <include name="core.javafiles" />
698 </fileset>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
699 </jar>
700 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
701
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
702 <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
703 <jar jarfile="${dist}/jar/cdk-extra.jar">
704 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
705 <includesfile name="${src}/extra.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
706 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
707 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
708 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
709 </fileset>
026da28 Removed last trace of patch system: compile errors in IDE tools work …
egonw authored
710 <fileset dir="${build}">
2679b69 Added missing dictionaries to cdk-extra.jar
egonw authored
711 <include name="org/openscience/cdk/dict/data/*.xml" />
712 </fileset>
0ef4af6 Added cdk-experimental package
egonw authored
713 </jar>
714 </target>
715
716 <target id="dist-experimental" name="dist-experimental" depends="compile-experimental, dist.init">
717 <jar jarfile="${dist}/jar/cdk-experimental.jar">
718 <fileset dir="${build}">
719 <includesfile name="${src}/experimental.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
720 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
721 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
722 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
723 </fileset>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
724 </jar>
725 </target>
726
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
727 <target id="dist-apps" name="dist-apps" depends="compile-apps">
4ae9e15 Compile PublicJmol when doing compile-libio.
egonw authored
728 <jar jarfile="${dist}/jar/cdk-apps.jar" manifest="${src}/cdk-apps.manifest">
38401bd Put applications in separate jar.
egonw authored
729 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
730 <includesfile name="${src}/applications.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
731 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
732 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
733 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
38401bd Put applications in separate jar.
egonw authored
734 </fileset>
735 </jar>
736 </target>
737
df42e11 Fixed a few dependencies for the test target
egonw authored
738 <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
739 <jar jarfile="${dist}/jar/cdk-test.jar">
740 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
741 <includesfile name="${src}/test.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
742 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
743 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
744 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
eb3206c Exclude r-project classes from jar too, which ensures that the R depe…
egonw authored
745 <excludesfile name="${src}/r-project.classes" unless="rispresent"/>
2c7c43d Fixed loading of files in JUnit IO tests: now using get resource.
egonw authored
746 </fileset>
747 <fileset dir=".">
748 <include name="data/**" />
749 </fileset>
89db533 Fixed transition to use of dist-large for test targets
egonw authored
750 <fileset dir="${src}">
751 <include name="data.javafiles"/>
752 <include name="core.javafiles"/>
753 </fileset>
2c7c43d Fixed loading of files in JUnit IO tests: now using get resource.
egonw authored
754 </jar>
755 </target>
756
0386767 More @cdkPackage completed for test classes
egonw authored
757 <target id="dist-libio" name="dist-libio" depends="compile-libio" unless="libio.present">
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
758 <jar jarfile="${dist}/jar/cdk-libio.jar">
759 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
760 <includesfile name="${src}/libio.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
761 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
762 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
763 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
4ae9e15 Compile PublicJmol when doing compile-libio.
egonw authored
764 </fileset>
765 <fileset dir="${build}">
766 <include name="org/openscience/jmol/**" />
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
767 </fileset>
768 </jar>
769 </target>
770
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
771 <target id="dist-io" name="dist-io" depends="compile-io">
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
772 <jar jarfile="${dist}/jar/cdk-io.jar">
773 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
774 <includesfile name="${src}/io.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
775 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
776 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
777 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
2b0ab15 Make sure the CML DTDs are in the cdk-io.jar again
egonw authored
778 <include name="org/openscience/cdk/io/cml/data/**" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
779 </fileset>
83278f7 ReaderFactory now uses the new CDK set io-formats instead of hardcodi…
egonw authored
780 <fileset dir="${src}">
781 <include name="io-formats.set"/>
782 </fileset>
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
783 </jar>
784 </target>
785
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
786 <target id="dist-render" name="dist-render" depends="compile-render">
8095921 Added rendering of wedged bonds.
egonw authored
787 <jar jarfile="${dist}/jar/cdk-render.jar">
788 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
789 <includesfile name="${src}/render.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
790 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
791 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
792 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
8095921 Added rendering of wedged bonds.
egonw authored
793 </fileset>
794 </jar>
795 </target>
796
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
797 <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
798 if="java3D.present">
799 <jar jarfile="${dist}/jar/cdk-render.jar">
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
800 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
801 <includesfile name="${src}/render.classes" />
26336c0 Fixed build.xml for proper reference to java3d.javafiles (thanks to G…
egonw authored
802 <includesfile name="${src}/java3d.classes" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
803 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
804 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
805 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
806 </fileset>
807 </jar>
808 </target>
809
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
810 <target id="dist-standard" name="dist-standard" depends="compile-standard, dist.init">
36b733d Adding cdk-standard module.
egonw authored
811 <jar jarfile="${dist}/jar/cdk-standard.jar">
812 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
813 <includesfile name="${src}/standard.classes" />
95c12c2 Added config files to cdk-standard module.
egonw authored
814 <include name="org/openscience/cdk/config/**" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
815 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
816 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
817 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
36b733d Adding cdk-standard module.
egonw authored
818 </fileset>
819 </jar>
820 </target>
821
6dc5408 Added stuff for qsar module
egonw authored
822 <target id="dist-qsar" name="dist-qsar" depends="compile-qsar, dist.init">
823 <jar jarfile="${dist}/jar/cdk-qsar.jar">
824 <fileset dir="${build}">
825 <includesfile name="${src}/qsar.classes" />
826 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
827 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
828 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
eb3206c Exclude r-project classes from jar too, which ensures that the R depe…
egonw authored
829 <excludesfile name="${src}/r-project.classes" unless="rispresent"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
830 </fileset>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
831 <fileset dir="${build}">
832 <include name="org/openscience/cdk/qsar/model/data/*.R" if="rispresent"/>
833 </fileset>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
834 <fileset dir="${src}">
835 <include name="qsar-descriptors.set"/>
836 </fileset>
6dc5408 Added stuff for qsar module
egonw authored
837 </jar>
838 </target>
839
4d7781d Split out builder3D stuff into separate module
egonw authored
840 <target id="dist-builder3d" name="dist-builder3d" depends="compile-builder3d, dist.init">
841 <jar jarfile="${dist}/jar/cdk-builder3d.jar">
842 <fileset dir="${build}">
843 <includesfile name="${src}/builder3d.classes" />
844 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
845 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
846 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
847 </fileset>
848 <fileset dir="data/templates">
849 <include name="ringTemplateFingerprints.txt"/>
850 <include name="ringTemplateStructures.sdf"/>
851 </fileset>
852 </jar>
853 </target>
854
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
855 <target id="dist-large" name="dist-large" depends="compile-all, dist.init, libjars"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
856 description="Builds on big jar file for the CDK, including experimental classes.">
c5110c1 The build.xml now builds cdk-$version.jar instead of cdk-all.jar
egonw authored
857 <jar jarfile="${dist}/jar/cdk-${version}.jar">
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
858 <manifest>
859 <attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
860 <section name="org.openscience.cdk">
861 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
862 <attribute name="Specification-Version" value="1.0"/>
863 <attribute name="Specification-Vendor" value="The CDK Project"/>
864 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
865 <attribute name="Implementation-Version" value="${version}"/>
866 <attribute name="Implementation-Vendor" value="The CDK Project"/>
867 </section>
868 </manifest>
555ce1a Fixed build.xml to properly generate a self-containing cdk-all.jar re…
egonw authored
869 <fileset dir="${build}">
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
870 <include name="org/openscience/cdk/**" />
8cdb861 Extended build/test system to conditionally build/test non-Java5 stuf…
egonw authored
871 <excludesfile name="${src}/java1.4+.classes" if="isJava13"/>
872 <excludesfile name="${src}/java1.4.classes" unless="isJava14"/>
873 <excludesfile name="${src}/ant1.6.classes" unless="hasAnt16"/>
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
874 </fileset>
555ce1a Fixed build.xml to properly generate a self-containing cdk-all.jar re…
egonw authored
875 <fileset dir=".">
876 <include name="CHANGELOG" />
877 <include name="README" />
878 <include name="BUGS" />
879 </fileset>
880 <fileset dir="${doc}">
881 <include name="lgpl.license" />
882 </fileset>
883 <fileset dir="packages/tar/cdk">
884 <include name="AUTHORS" />
885 </fileset>
89db533 Fixed transition to use of dist-large for test targets
egonw authored
886 <fileset dir="${src}"> <!-- from io and qsar module -->
887 <include name="io-formats.set"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
888 <include name="qsar-descriptors.set"/>
889 </fileset>
4d7781d Split out builder3D stuff into separate module
egonw authored
890 <fileset dir="data/templates"> <!-- from builder3d module -->
891 <include name="ringTemplateFingerprints.txt"/>
892 <include name="ringTemplateStructures.sdf"/>
893 </fileset>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
894 <fileset dir="${appjars.dir}" includes="**/*.class"/>
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
895 </jar>
896 </target>
897
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
898 <target name="check.libjars" id="check.libjars">
899 <uptodate property="libjars.uptodate" targetfile="${appjars.dir}">
900 <srcfiles dir="${lib}" includes="base.jar"/>
901 <srcfiles dir="${lib}" includes="batik-dom.jar"/>
902 <srcfiles dir="${lib}" includes="batik-awt-util.jar"/>
903 <srcfiles dir="${lib}" includes="batik-svggen.jar"/>
904 <srcfiles dir="${lib}" includes="batik-util.jar"/>
905 <srcfiles dir="${lib}" includes="batik-xml.jar"/>
906 <srcfiles dir="${lib}" includes="castor-0.9.5-xml.jar"/>
907 <srcfiles dir="${lib}" includes="cmlAll.jar"/>
908 <srcfiles dir="${lib}" includes="commons-cli-1.0.jar"/>
909 <srcfiles dir="${lib}" includes="dadml.jar"/>
910 <srcfiles dir="${lib}" includes="gnujaxp.jar"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
911 <srcfiles dir="${lib}" includes="Jama-1.0.1.jar"/>
ca29169 Added missing library to unpack for dist-large
egonw authored
912 <srcfiles dir="${lib}" includes="jgrapht-0.5.3.jar"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
913 <srcfiles dir="${lib}" includes="jmolApis.jar"/>
914 <srcfiles dir="${lib}" includes="jmolIO.jar"/>
915 <srcfiles dir="${lib}" includes="junit.jar"/>
916 <srcfiles dir="${lib}" includes="log4j-core.jar"/>
917 <srcfiles dir="${lib}" includes="log4j.jar"/>
918 <srcfiles dir="${lib}" includes="mysql-2.0.4.jar"/>
919 <srcfiles dir="${lib}" includes="pmrlib.jar"/>
920 <srcfiles dir="${lib}" includes="postgresql7.0-1.2.jar"/>
921 <srcfiles dir="${lib}" includes="printf.jar"/>
922 <srcfiles dir="${lib}" includes="stmml.jar"/>
923 <srcfiles dir="${lib}" includes="vecmath1.2-1.14.jar"/>
924 <srcfiles dir="${lib}" includes="xindice.jar"/>
925 <srcfiles dir="${lib}" includes="xmldb.jar"/>
926 </uptodate>
927 </target>
928
929 <target name="libjars" id="libjars" depends="check.libjars" unless="libjars.uptodate">
930 <mkdir dir="${appjars.dir}"/>
931 <unjar dest="${appjars.dir}" src="${lib}/base.jar"/>
932 <unjar dest="${appjars.dir}" src="${lib}/batik-dom.jar"/>
933 <unjar dest="${appjars.dir}" src="${lib}/batik-awt-util.jar"/>
934 <unjar dest="${appjars.dir}" src="${lib}/batik-svggen.jar"/>
935 <unjar dest="${appjars.dir}" src="${lib}/batik-util.jar"/>
936 <unjar dest="${appjars.dir}" src="${lib}/batik-xml.jar"/>
937 <unjar dest="${appjars.dir}" src="${lib}/castor-0.9.5-xml.jar"/>
938 <unjar dest="${appjars.dir}" src="${lib}/cmlAll.jar"/>
939 <unjar dest="${appjars.dir}" src="${lib}/commons-cli-1.0.jar"/>
940 <unjar dest="${appjars.dir}" src="${lib}/dadml.jar"/>
941 <unjar dest="${appjars.dir}" src="${lib}/gnujaxp.jar"/>
da8d319 Implemented @cdk.set to define sets of certain types of classes, e.g.…
egonw authored
942 <unjar dest="${appjars.dir}" src="${lib}/Jama-1.0.1.jar"/>
ca29169 Added missing library to unpack for dist-large
egonw authored
943 <unjar dest="${appjars.dir}" src="${lib}/jgrapht-0.5.3.jar"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
944 <unjar dest="${appjars.dir}" src="${lib}/jmolApis.jar"/>
945 <unjar dest="${appjars.dir}" src="${lib}/jmolIO.jar"/>
946 <unjar dest="${appjars.dir}" src="${lib}/junit.jar"/>
947 <unjar dest="${appjars.dir}" src="${lib}/log4j-core.jar"/>
948 <unjar dest="${appjars.dir}" src="${lib}/log4j.jar"/>
949 <unjar dest="${appjars.dir}" src="${lib}/mysql-2.0.4.jar"/>
950 <unjar dest="${appjars.dir}" src="${lib}/pmrlib.jar"/>
951 <unjar dest="${appjars.dir}" src="${lib}/postgresql7.0-1.2.jar"/>
952 <unjar dest="${appjars.dir}" src="${lib}/printf.jar"/>
953 <unjar dest="${appjars.dir}" src="${lib}/stmml.jar"/>
954 <unjar dest="${appjars.dir}" src="${lib}/vecmath1.2-1.14.jar"/>
955 <unjar dest="${appjars.dir}" src="${lib}/xindice.jar"/>
956 <unjar dest="${appjars.dir}" src="${lib}/xmldb.jar"/>
957 </target>
958
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
959 <target id="dist-all" name="dist-all" depends="dist, dist-experimental, dist-apps"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
960 description="Builds the jar files for the CDK, including experimental classes."/>
53aff7c dist-all should also build cdk-experimental.jar, dist should not
egonw authored
961
3148e46 Moved the former core module classes to the data module, and the Logg…
egonw authored
962 <target id="dist" name="dist" depends="dist-data, dist-core, dist-standard,
90025c1 Added missing editor classes to cdk-render.jar when compiling with-ja…
egonw authored
963 dist-io, dist-render,
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
964 dist-extra, dist-libio,
6dc5408 Added stuff for qsar module
egonw authored
965 dist-render-with-java3d,
4d7781d Split out builder3D stuff into separate module
egonw authored
966 dist-qsar, dist-builder3d"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
967 description="Builds the jar files for the CDK."/>
ce6c169 Include config and data files in dist-with-java3d too.
egonw authored
968
e3792d4 Added description for sourcedist target, and target for putting all c…
egonw authored
969 <target id="sourcedist" name="sourcedist" depends="init"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
970 description="Builds the source packages.">
dccd7d0 Sourcedist making now also uses the defined version
egonw authored
971 <property name="package" value="cdk-source-${version}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
972 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
973 <copy todir="${sourcedist.dir}/${src}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
974 <fileset dir="${src}" includes="*.javafiles" />
ba078b3 Also include .classes file, otherwise I still won't compile :(
egonw authored
975 <fileset dir="${src}" includes="*.classes" />
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
976 <fileset dir="${src}" includes="**/*.java" />
977 <fileset dir="${src}" includes="**/*.jj" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
978 <fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
979 </copy>
980 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
981 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
982 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
983 <fileset dir="." includes="javadoc.xml" />
984 <fileset dir="." includes="README" />
985 <fileset dir="." includes="CHANGELOG" />
986 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
987 <copy todir="${sourcedist.dir}/jar">
fbf19c3 The source releases contained unnecessary libraries
egonw authored
988 <fileset dir="jar">
989 <exclude name="libio/*.jar"/>
990 <exclude name="pmd-1.8.jar"/>
991 <exclude name="xalan-2.0.1.jar"/>
992 <exclude name="doccheck.jar"/>
993 <exclude name="dbdoclet*.*"/>
994 </fileset>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
995 </copy>
996 <copy todir="${sourcedist.dir}/data">
997 <fileset dir="data" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
998 </copy>
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
999 <copy tofile="${sourcedist.dir}/doc/javadoc/source//MakeJavaFilesFilesDoclet.java"
1000 file="doc/javadoc/source/MakeJavaFilesFilesDoclet.java"/>
7aa27da Make sure the config.data files get included in the source dist (clos…
egonw authored
1001 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
1002 <fileset dir="${src}/org/openscience/cdk/config/data/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
1003 includes="*" />
1004 </copy>
a289167 Minor tweak to get distribs working
egonw authored
1005 <copy
1006 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
1007 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
1008 <copy
1009 file="${src}/org/openscience/cdk/dict/data/chemical.xml"
1010 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
1011 <copy
1012 file="${src}/org/openscience/cdk/dict/data/elements.xml"
1013 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
e2623a3 Added some missing files to the sourcedist
egonw authored
1014 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
1015 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/">
1016 <fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
1017 </copy>
9496005 Added missing manifest
egonw authored
1018 <copy todir="${sourcedist.dir}/${src}/">
1019 <fileset dir="${src}/" includes="*.manifest" />
1020 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
1021 <mkdir dir="${sourcedist.dir}/doc/" />
1022 <copy todir="${sourcedist.dir}/doc/">
1023 <fileset dir="doc/" includes="lgpl.license" />
1024 </copy>
7447e16 Getting ready for release
egonw authored
1025 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
1026 <copy todir="${sourcedist.dir}/doc/javadoc">
1027 <fileset dir="doc/javadoc" includes="MakeJavaFilesFilesDoclet.class" />
1028 <fileset dir="doc/javadoc" includes="MakeCDKSetFilesDoclet.class" />
1029 </copy>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
1030 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
dccd7d0 Sourcedist making now also uses the defined version
egonw authored
1031 <gzip zipfile="${package}.tar.gz" src="cdk-source-${version}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
1032 <delete file="${package}.tar" />
1033 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1034 </target>
1035
cd012c0 Added posibility to just check the experimental classes
egonw authored
1036 <target id="test-all" name="test-all" depends="test, test-experimental"/>
1037
f68c4b9 Tests now depends on dist-large
egonw authored
1038 <target id="test-experimental" name="test-experimental" depends="dist-large, noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1039 description="Performs a full JUnit test for the CDK, including experimental classes.">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
1040 <mkdir dir="${reports.tests}"/>
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1041 <junit printsummary="yes" haltonfailure="yes" fork="yes">
1042 <classpath>
f68c4b9 Tests now depends on dist-large
egonw authored
1043 <pathelement location="${dist}/jar/cdk-${version}.jar" />
89db533 Fixed transition to use of dist-large for test targets
egonw authored
1044 <pathelement location="${dist}/jar/cdk-test.jar" />
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1045 <fileset dir="${lib}">
1046 <include name="*.jar" />
1047 </fileset>
1048 <fileset dir="${lib}/libio">
1049 <include name="*.jar" />
1050 </fileset>
1051 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
1052 <test name="org.openscience.cdk.test.ExperimentalClassesTests"
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1053 haltonfailure="no"
1054 todir="${reports.tests}"
0c93d33 Put results of tests for experimental classes in result.experimental.…
egonw authored
1055 outfile="result.experimental">
60b89d5 Added test suite for cdk-experimental, and moved Association to exper…
egonw authored
1056 <formatter type="brief" />
1057 </test>
1058 </junit>
1059 </target>
1060
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
1061 <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
1062 <fail message="JUnit is not installed in Ant. Please copy cdk/jar/junit.jar to ${ant.home}/lib/."/>
1063 </target>
1064
f68c4b9 Tests now depends on dist-large
egonw authored
1065 <target id="test" name="test" depends="dist-test, dist-large, noJunit"
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
1066 description="Performs a full JUnit test for the CDK." if="junit.present">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
1067 <mkdir dir="${reports.tests}"/>
fbbfe4f Corrected JavaDoc errors in builder3d
chhoppe authored
1068 <junit printsummary="yes" haltonfailure="yes" fork="yes" maxmemory="256m">
9344d76 Fork testing, and removed reference to classpaths "." and "${java.cla…
egonw authored
1069 <classpath>
f68c4b9 Tests now depends on dist-large
egonw authored
1070 <pathelement location="${dist}/jar/cdk-${version}.jar" />
89db533 Fixed transition to use of dist-large for test targets
egonw authored
1071 <pathelement location="${dist}/jar/cdk-test.jar" />
9344d76 Fork testing, and removed reference to classpaths "." and "${java.cla…
egonw authored
1072 <fileset dir="${lib}">
1073 <include name="*.jar" />
1074 </fileset>
1075 <fileset dir="${lib}/libio">
1076 <include name="*.jar" />
1077 </fileset>
1078 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
1079 <test name="org.openscience.cdk.test.CDKTests"
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1080 haltonfailure="no"
1081 todir="${reports.tests}"
1082 outfile="result">
81258bd Added Ant task for doing Junit tests on the cdk-core and cdk-standard…
egonw authored
1083 <formatter type="brief" />
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
1084 </test>
1085 </junit>
1086 </target>
1087
f68c4b9 Tests now depends on dist-large
egonw authored
1088 <target id="limitations" name="limitations" depends="dist-large, dist-test, noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1089 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
1090 <junit printsummary="yes" haltonfailure="yes" fork="yes">
1091 <classpath>
f68c4b9 Tests now depends on dist-large
egonw authored
1092 <pathelement location="${dist}/jar/cdk-${version}.jar" />
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
1093 <fileset dir="${lib}">
1094 <include name="*.jar" />
1095 </fileset>
1096 <fileset dir="${lib}/libio">
1097 <include name="*.jar" />
1098 </fileset>
1099 </classpath>
1100 <test name="org.openscience.cdk.test.limitations.AlgorithmLimitations"
1101 haltonfailure="no"
1102 todir="${reports.tests}"
1103 outfile="limitations">
1104 <formatter type="brief" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1105 </test>
1106 </junit>
1107 </target>
1108
89db533 Fixed transition to use of dist-large for test targets
egonw authored
1109 <target id="test-libio" name="test-libio" depends="dist-large, dist-libio">
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1110 <java classname="org.openscience.cdk.test.libio.joelib.JOELibIOTest" fork="yes">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1111 <classpath>
89db533 Fixed transition to use of dist-large for test targets
egonw authored
1112 <pathelement location="${dist}/jar/cdk-${version}.jar" />
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
1113 <pathelement path="${java.class.path}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1114 <pathelement location="." />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1115 <fileset dir="${lib}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1116 <include name="*.jar" />
1117 </fileset>
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1118 <fileset dir="${lib}/libio">
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
1119 <include name="*.jar" />
1120 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1121 </classpath>
1122 </java>
1123 </target>
1124
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1125 <target name="run-with-java3d"
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
1126 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
1127 <java
1128 classname="org.openscience.cdk.test.OrbitalsRenderer3DTest"
1129 fork="yes">
1130 <arg value="data/reserpine.mol" />
1131
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1132 <classpath>
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1133 <pathelement location="${dist}/jar/cdk-core.jar" />
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
1134 <pathelement location="${dist}/jar/cdk-standard.jar" />
1135 <pathelement location="${dist}/jar/cdk-extra.jar" />
1136 <pathelement location="${dist}/jar/cdk-io.jar" />
1137 <pathelement location="${dist}/jar/cdk-render.jar" />
1138 <pathelement location="${dist}/jar/cdk-render-with-java3d.jar" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1139 <pathelement path="${java.class.path}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1140 <pathelement location="." />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
1141 <fileset dir="${lib}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1142 <include name="*.jar" />
1143 </fileset>
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
1144 <fileset dir="${pathto3djava}">
1145 <include name="*.jar" />
1146 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
1147 </classpath>
1148 </java>
1149 </target>
1150
f68c4b9 Tests now depends on dist-large
egonw authored
1151 <target id="run-test" name="run-test" depends="dist-large, dist-test"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1152 description="Runs one specific JUnit test suite (org.openscience.cdk.test.&lt;class>) as a standalone application with -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
1153 <echo message="Running test class: testclass=${testclass}"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
1154 <java classname="org.openscience.cdk.test.${testclass}" fork="yes">
3d88ed4 Turn on CDK debugging while running JUnit test
egonw authored
1155 <jvmarg value="-Dcdk.debugging=true"/>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
1156 <classpath>
f68c4b9 Tests now depends on dist-large
egonw authored
1157 <pathelement location="${dist}/jar/cdk-${version}.jar" />
89db533 Fixed transition to use of dist-large for test targets
egonw authored
1158