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ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
1 <project name="CDK" default="dist-all" basedir=".">
3d221c1 Added additional PDBReader tests.
yeldar authored
2
0e9e5ef Added version info to JavaDoc html output, and share this with the bu…
egonw authored
3 <property file="build.props"/>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
4
3a26de3 Made compilation with debug=on customizable.
egonw authored
5 <!-- compile options -->
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
6 <property name="build.sysclasspath" value="ignore" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
7 <property name="build.compiler" value="modern" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
8 <property name="debug" value="on" />
460ea79 Detect deprecated methods
egonw authored
9 <property name="deprecation" value="on" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
10 <property name="optimization" value="off" />
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
11 <property name="threadCount" value="4" />
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
12 <property name="parallel" value="false"/>
3a26de3 Made compilation with debug=on customizable.
egonw authored
13
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
14 <!-- patches to apply -->
15
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
16 <!-- directories -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
17 <property name="build" value="build" />
bd36ed1 Trial for new build system
egonw authored
18 <property name="build.src" value="${build}/src" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
19 <property name="sourcedist" value="sourcedist" />
20 <property name="dist" value="dist" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
21 <property name="doc" value="doc" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
22 <property name="src" value="src" />
23 <property name="lib" value="jar" />
9e95b7b Finished splitting devel from user jars
egonw authored
24 <property name="devellib" value="develjar" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
25 <property name="src.tests" value="${src}/test/org/openscience/cdk/test" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
26 <property name="reports.tests" value="reports" />
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
27 <property name="appjars.dir" value="${dist}/appjars" />
bd36ed1 Trial for new build system
egonw authored
28 <property name="metainf" value="${src}/META-INF" />
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" />
32 <property name="arg1" value="" />
33 <property name="arg2" value="" />
34 <property name="arg3" value="" />
35 <property name="arg4" value="" />
5c40bcf Removed the check for rJava as we don't strictly need it. Also added …
rajarshi authored
36
37 <property environment="env" />
38
6fb8043 Typo fixed
egonw authored
39 <!-- Include the ant-contrib goodies -->
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
40 <taskdef resource="net/sf/antcontrib/antlib.xml">
41 <classpath>
42 <pathelement location="${basedir}/develjar/ant-contrib-1.0b3.jar"/>
43 </classpath>
44 </taskdef>
45
b7ba930 Commented out the code to get the latest SV rev since we don't need i…
rajarshi authored
46 <!--
59d696c Added some code to obtain the current svn revision. Should be used to…
rajarshi authored
47 <shellscript shell="bash" outputproperty="svn.output">
48 svn info
49 </shellscript>
50 <propertyregex property="svn.rev" input="${svn.output}" regexp="Revision: ([0-9]*)" select="\1" />
b7ba930 Commented out the code to get the latest SV rev since we don't need i…
rajarshi authored
51 -->
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
52
5c40bcf Removed the check for rJava as we don't strictly need it. Also added …
rajarshi authored
53 <target id="info" name="info" depends="check">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
54 <!-- Gives information about the building process. -->
8f6d674 Fixed after breaking it earlier today
egonw authored
55 <echo message="Platform:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
56 <echo message=" OS: ${os.name}" />
57 <echo message=" Architecture: ${os.arch}" />
58 <echo message=" Version: ${os.version}" />
59 <echo message=" Mac OS/X found: ${isMacOsX}" />
8f6d674 Fixed after breaking it earlier today
egonw authored
60 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
61 <echo message="Java/Ant Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
62 <echo message=" Java version: ${java.version}" />
63 <echo message=" Java vendor: ${java.vendor}" />
64 <echo message=" Java dir: ${java.home}" />
65 <echo message=" Java ext dir: ${java.ext.dirs}" />
66 <echo message=" Ant version: ${ant.version}" />
67 <echo message=" ${ANT_HOME}: ${ant.home}" />
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
68 <echo message=" hasAnt17: ${hasAnt17}" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
69 <echo message="" />
70 <echo message="CDK Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
71 <echo message=" CDK version: ${version}" />
72 <echo message=" build.xml: $Id$" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
73 <echo message=" Junit found: ${junit.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
74 <echo message=" --- required libraries ---" />
75 <echo message=" Vecmath found: ${vecmath.present}" />
76 <echo message=" Log4j found: ${log4j.present}" />
77 <echo message=" JGraphT found: ${jgrapht.present}" />
c1c3a3b Removed outdated optional compile checks
egonw authored
78 <echo message=" --- distributed (but optional) libraries ---" />
7cd4ff8 Added R/SJava found to info target
egonw authored
79 <echo message=" CMLDOM found: ${cmllibs.present}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
80 <echo message=" --- optional libraries ---" />
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
81 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
82 <echo message="Compiling:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
83 <echo message=" for: ${build.compiler}" />
84 <echo message=" debug: ${debug}" />
85 <echo message=" deprecation: ${deprecation}" />
86 <echo message=" optimization: ${optimization}" />
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
87 <echo message=" parallel: ${parallel}" />
88 <echo message=" threads: ${threadCount}" />
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
89 <echo message="" />
90 <echo message="Available Targets" />
91 <echo message=" clean: Remove class files and any temporary files" />
92 <echo message=" dist-all: Compile all modules" />
93 <echo message=" dist-large: Create the comprehensive jar, with all modules" />
94 <echo message=" test-dist-all: Compile all test modules" />
95 <echo message="test-dist-large: Create a single jar file with all test modules" />
96 <echo message=" jarTestdata: Create the jar file with all test data. Used in testing" />
97 <echo message="" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
98 </target>
99
806fbfe Updated build script with some new tasks that will clean up the top l…
rajarshi authored
100 <!-- See what platform were on -->
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
101
8f6d674 Fixed after breaking it earlier today
egonw authored
102 <target id="checkPlatforms" name="checkPlatforms">
58405cf Fixed build.xml to allow compile of doclets on MacOS/X (closes #1001497)
egonw authored
103 <condition property="isMacOsX">
104 <and>
105 <os family="mac"/>
106 <os family="unix"/>
107 </and>
108 </condition>
109 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
110
8f6d674 Fixed after breaking it earlier today
egonw authored
111 <target id="check" name="check" depends="checkPlatforms">
cc68a07 Added detection of more third party libraries
egonw authored
112 <!-- Check wether Doclets are compiled and output is generated -->
113 <uptodate property="dotjavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
114 targetfile="${build}/core.javafiles">
cc68a07 Added detection of more third party libraries
egonw authored
115 <srcfiles dir="${src}" includes="**/*.java" />
116 </uptodate>
117 <condition property="dotjjfiles.uptodate">
118 <and>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
119 <uptodate property="NomParserJavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
120 targetfile="${src}/main/org/openscience/cdk/iupac/parser/NomParser.java">
121 <srcfiles dir="${src}/main/" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
cc68a07 Added detection of more third party libraries
egonw authored
122 </uptodate>
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
123 <uptodate property="SMARTSParserJJTJavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
124 targetfile="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.java">
125 <srcfiles dir="${src}/main/" includes="org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj" />
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
126 </uptodate>
cc68a07 Added detection of more third party libraries
egonw authored
127 </and>
128 </condition>
129
130 <!-- Checks which parts of CDK can be build. -->
131
132 <!-- test for optional jars -->
133 <available property="vecmath.present"
134 file="${lib}/vecmath1.2-1.14.jar"/>
135 <available property="log4j.present"
136 file="${lib}/log4j.jar"/>
137 <available property="jgrapht.present"
152e213 Updated for recent upgrades to Jumbo 5.2 and JGraphT 0.6.0
egonw authored
138 file="${lib}/jgrapht-0.6.0.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
139
140 <!-- test for optional jars -->
141 <condition property="cmllibs.present">
142 <or>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
143 <available file="${lib}/jumbo-with-fix-by-jonalv.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
144 </or>
145 </condition>
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
146
143fb1d OK, we're not using junit.framework.TestCase anymore, so don't look f…
egonw authored
147 <condition property="junit.present">
148 <or>
149 <available file="${ant.home}/lib/junit.jar"/>
150 <available file="${devellib}/junit-4.5.jar"/>
151 </or>
152 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
153
154 <!-- test Ant version -->
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
155 <condition property="hasAnt17">
95f0b04 Updated build script to indicate that ant 1.7.1 or better is required
rajarshi authored
156 <contains string="${ant.version}" substring="1.7.1"/>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
157 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
158
159 <!-- test Java version -->
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
160 <condition property="isJava13">
161 <contains string="${java.version}" substring="1.3"/>
162 </condition>
163 <condition property="isJava14">
164 <contains string="${java.version}" substring="1.4"/>
165 </condition>
866bc72 CML is now available for Java1.5 too
egonw authored
166 <condition property="isJava15">
167 <contains string="${java.version}" substring="1.5"/>
168 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
169 <condition property="isJava16">
170 <contains string="${java.version}" substring="1.6."/>
171 </condition>
3f17ad0 Added detection of Java 1.7
egonw authored
172 <condition property="isJava17">
173 <contains string="${java.version}" substring="1.7."/>
174 </condition>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
175 <condition property="isJava14+">
176 <or>
177 <contains string="${java.version}" substring="1.4"/>
178 <contains string="${java.version}" substring="1.5"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
179 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
180 <contains string="${java.version}" substring="1.7"/>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
181 </or>
182 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
183 <condition property="isJava15+">
184 <or>
185 <contains string="${java.version}" substring="1.5"/>
186 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
187 <contains string="${java.version}" substring="1.7"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
188 </or>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
189 </condition>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
190 <condition property="isNotJava15+">
191 <not>
192 <or>
193 <contains string="${java.version}" substring="1.5"/>
194 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
195 <contains string="${java.version}" substring="1.7"/>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
196 </or>
197 </not>
198 </condition>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
199 <fail if="isNotJava15+" message="This CDK release requires Java5 or better."/>
95f0b04 Updated build script to indicate that ant 1.7.1 or better is required
rajarshi authored
200 <fail unless="hasAnt17" message="This CDK release requires Ant 1.7.1 or better."/>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
201 </target>
202
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
203
d2ed020 Reworked dependencies
egonw authored
204 <target id="init" name="init" depends="check, setupBuildDir"/>
4302fbf Updated for Jumbo50 transition.
egonw authored
205 <target id="customize" name="customize" depends="javacc"/>
866bc72 CML is now available for Java1.5 too
egonw authored
206
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
207 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
208 <tstamp />
209 <mkdir dir="${build}" />
210 <mkdir dir="${sourcedist}" />
211 <mkdir dir="${dist}" />
212 <mkdir dir="${reports.tests}" />
213 </target>
214
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
215 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
216 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
217 <fileset dir="." includes="**/*~" />
218 <fileset dir="." includes="*.tar.gz" />
219 <fileset dir="." includes="*.zip" />
06ee5d1 Modified the clean target to remove .rda files generated during testi…
rajarshi authored
220 <fileset dir="." includes="*.rda" />
bfe0e17 Build interfaces before data
egonw authored
221 <fileset dir="${src}" includes="*.entitylist" />
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
222 <!-- remove java files generated with JavaCC -->
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
223 <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts" includes="*.java">
51e5934 Added missing autogenerated SMARTS file to the clean task (closes #18…
egonw authored
224 <exclude name="SMARTSQueryTool.java" />
225 </fileset>
226 <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
227 includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
228 <fileset dir="${src}/main/org/openscience/cdk/iupac/parser" includes="*.java">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
229 <!-- the next are from CVS -->
230 <exclude name="AttachedGroup.java" />
231 <exclude name="MoleculeBuilder.java" />
232 </fileset>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
233 <fileset dir="${src}/main/">
31994c5 Fixed deleting the doclet class files
egonw authored
234 <include name="net/sf/cdk/tools/*.class" />
2b81a22 Fixed a problem with deleting the doclet classes
egonw authored
235 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
236 </delete>
237
238 <delete dir="${build}" />
239 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
240 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
241 <delete dir="${reports.tests}" />
242 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
243
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
244 <target name="runDoclet" id="runDoclet" depends="check, customize">
245 <echo>Not skipping doclet run...</echo>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
246 <mkdir dir="${build}" />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
247 <javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
248 srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
249 debug="${debug}" deprecation="${deprecation}"/>
250 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
20a1056 Fixed a patch from the branch that got lost in the branch merge
egonw authored
251 <arg value="${src}/META-INF"/>
252 <arg value="${src}/main"/>
253 <arg value="${build}"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
254 </java>
255 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
20a1056 Fixed a patch from the branch that got lost in the branch merge
egonw authored
256 <arg value="${src}/META-INF"/>
257 <arg value="${src}/test"/>
258 <arg value="${build}"/>
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
259 </java>
ca98ea5 Refactored build process (closes #883519)
egonw authored
260 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
261
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
262 <target id="compile-needed-test" name="compile-needed-test">
263 <uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
264 <srcfiles dir="${src}/main/">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
265 <includesfile name="${build}/${module}.javafiles"/>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
266 </srcfiles>
267 </uptodate>
268 </target>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
269
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
270 <target id="compile-init" name="compile-init"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
271 depends="init, check, runDoclet"/>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
272
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
273 <target id="compile-module" name="compile-module"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
274 depends="check, dist.init, compile-needed-test"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
275 unless="module-uptodate">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
276
1366ba3 Removed use of source parameter, by making use of ant-contrib's <if>
egonw authored
277 <if>
278 <matches string="${module}" pattern="^test"/>
279 <then>
280 <property name="source" value="src/test"/>
281 </then>
282 <else>
283 <property name="source" value="src/main"/>
284 </else>
285 </if>
286
6153fc1 Report from which source tree files are copied
egonw authored
287 <echo message="Compiling classes for CDK's ${module} module from ${source}..." />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
288
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
289 <!-- check for availability for meta info files -->
290 <available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
291 <available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
c094513 Make sure the .set files end up in the right jars
egonw authored
292 <available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
293 <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
294 <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
295 <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
296 <available file="${metainf}/${module}.autogenerated" property="module.autogenerated.present"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
297
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
298 <!-- be somewhat informative -->
299 <echo message="Datafiles defined: ${module.datafiles.present}"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
300 <echo message="Extra files defined: ${module.extrafiles.present}"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
301 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
302 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
303 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
304 <echo message="Autogenerated files specified: ${module.autogenerated.present}"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
305
bd36ed1 Trial for new build system
egonw authored
306 <!-- normally javac compiles not just the given files, but also missing
307 classes that are in the same src/ directory. By making a copy first,
308 we explicitely make it impossible to compile files that are not
309 marked for a specific module -->
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
310 <mkdir dir="${build.src}/${module}"/>
311 <mkdir dir="${build}/${module}"/>
312 <copy todir="${build.src}/${module}">
365a4d7 Fix to use the proper source folder, now passed via a target argument
egonw authored
313 <fileset dir="${source}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
314 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
315 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
316 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
317 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
318 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
319
320 <includesfile name="${build}/${module}.javafiles"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
321 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
bd36ed1 Trial for new build system
egonw authored
322 </fileset>
323 </copy>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
324
bd36ed1 Trial for new build system
egonw authored
325 <!-- ok, now that we have a copy, compile this copy -->
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
326 <javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
e531e6e Java5 List<IAtom> like constructs in the interfaces. trunk/cdk/ now o…
egonw authored
327 debug="${debug}" deprecation="${deprecation}" target="1.5" source="1.5">
bd36ed1 Trial for new build system
egonw authored
328 <classpath>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
329 <fileset dir="${lib}" >
330 <exclude name="**/*" unless="module.libdepends.present" />
331 <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
bd36ed1 Trial for new build system
egonw authored
332 </fileset>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
333 <fileset dir="${devellib}">
334 <exclude name="**/*" unless="module.devellibdepends.present" />
335 <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
336 </fileset>
bd36ed1 Trial for new build system
egonw authored
337 <fileset dir="${dist}/jar">
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
338 <exclude name="**/*" unless="module.cdkdepends.present" />
339 <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
bd36ed1 Trial for new build system
egonw authored
340 </fileset>
341 </classpath>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
342
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
343 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
344 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
345 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
346 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
347 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
348
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
349 <includesfile name="${build}/${module}.javafiles"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
350 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
bd36ed1 Trial for new build system
egonw authored
351 </javac>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
352
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
353 <!-- create a autogenerated.classes file, if applicable, so that these files can be included in the jar -->
f1360a2 Cleaned up handling of presence/absence of autogenerated files, so no…
rajarshi authored
354 <if>
355 <istrue value="${module.autogenerated.present}"/>
356 <then>
357 <copy file="${metainf}/${module}.autogenerated" tofile="${build}/${module}.autogenerated.classes"
358 failonerror="false"/>
359 <replace dir="${build}" token=".java" value="*.class">
360 <include name="*.autogenerated.classes"/>
361 </replace>
362 </then>
363 </if>
364
365
bd36ed1 Trial for new build system
egonw authored
366 <!-- and then jar things up into the module jar -->
367 <jar jarfile="${dist}/jar/cdk-${module}.jar">
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
368 <fileset dir="${build}/${module}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
369 <includesfile name="${build}/${module}.classes" />
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
370 <includesfile name="${build}/${module}.autogenerated.classes" if="module.autogenerated.present"/>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
371 <excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
372 <!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
373 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
374 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
375 <excludesfile name="${build}/ant1.6.classes" unless="hasAnt17"/>
bd36ed1 Trial for new build system
egonw authored
376 </fileset>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
377 <fileset dir="${build}">
bd36ed1 Trial for new build system
egonw authored
378 <include name="${module}.javafiles" />
379 </fileset>
174804f Fixed root location of .datafiles content
egonw authored
380 <fileset dir="${source}">
141cf36 Fixed problem with including data files in the module jars
egonw authored
381 <exclude name="**/*" unless="module.datafiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
382 <includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
383 </fileset>
7a673b7 Point to the correct root folder for datafiles and extrafiles
egonw authored
384 <fileset dir="${src}">
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
385 <exclude name="**/*" unless="module.extrafiles.present"/>
386 <includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
387 </fileset>
c8f144a Point to correct .set location.
egonw authored
388 <fileset dir="${build}">
c094513 Make sure the .set files end up in the right jars
egonw authored
389 <exclude name="**/*" unless="module.buildfiles.present"/>
c8f144a Point to correct .set location.
egonw authored
390 <includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
c094513 Make sure the .set files end up in the right jars
egonw authored
391 </fileset>
bd36ed1 Trial for new build system
egonw authored
392 </jar>
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
393
394 <!-- clean up afterwards -->
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
395 <delete dir="${build.src}/${module}"/>
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
396 <delete dir="${build}/${module}"/>
bd36ed1 Trial for new build system
egonw authored
397 </target>
398
6dc5408 Added stuff for qsar module
egonw authored
399 <!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
400 <target id="javacc" name="javacc" depends="init, check" if="hasAnt17" unless="dotjjfiles.uptodate">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
401 <echo message="Compiling Ant 1.6 depending classes." />
cd49d3a A bit of comment
egonw authored
402 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
403 <delete>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
404 <fileset id="javacc-generated"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
405 dir="${src}/main/org/openscience/cdk/iupac/parser/"
cd49d3a A bit of comment
egonw authored
406 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
407 </delete>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
408 <javacc target="${src}/main/org/openscience/cdk/iupac/parser/NomParser.jj"
409 outputdirectory="${src}/main/org/openscience/cdk/iupac/parser/"
d9680ff Removed compilation steps for the old SMARTS parser
rajarshi authored
410 javacchome="${lib}"/>
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
411 <delete>
412 <fileset id="javacc-generated"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
413 dir="${src}/main/org/openscience/cdk/smiles/smarts/parser/"
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
414 includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java"/>
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
415 </delete>
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
416 <jjtree target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt"
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
417 javacchome="${lib}"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
418 outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
419 <javacc target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj"
420 javacchome="${lib}"
421 outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
422
423 <!-- OK, we now need to do some replacements such as
424 adding cdk.module tags and changing access modes
425 -->
426 <replace file="${src}/main/org/openscience/cdk/smiles/smarts/parser/JJTSMARTSParserState.java"
427 token="class JJTSMARTSParserState {" value="public class JJTSMARTSParserState {" />
428 <replace dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
429 excludes="AST*.java,SMARTSParser.jjt,SMARTSParser.jj,*Node.java"
430 token="package org.openscience.cdk.smiles.smarts.parser;" summary="true" >
431 <replacevalue>package org.openscience.cdk.smiles.smarts.parser;
432
433 /**
434 *
435 * @cdk.module smarts
436 */</replacevalue>
437 </replace>
1dd9647 Added IUPAC name parser
stomkinson authored
438 </target>
8095921 Added rendering of wedged bonds.
egonw authored
439
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
440 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
441 <mkdir dir="${dist}/jar" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
442 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
443
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
444 <target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
445 <target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
446 <echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
447 </target>
448 <target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
449 <antcall target="compile-module"><param name="module" value="java3d"/></antcall>
450 </target>
451
452 <target id="dist-optional" name="dist-optional" depends="dist-all"
453 description="Compile CDK modules that require optional libraries">
454 <antcall target="dist-java3d"/>
455 </target>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
456
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
457 <target id="dist-all" name="dist-all" description="dist-all">
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
458 <antcall target="compile-init"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
459 <foreach target="compile-module" param="module"
460 parallel="${parallel}" maxthreads="${threadCount}"
461 list="interfaces"/>
462 <foreach target="compile-module" param="module"
463 parallel="${parallel}" maxthreads="${threadCount}"
464 list="core"/>
465 <foreach target="compile-module" param="module"
466 parallel="${parallel}" maxthreads="${threadCount}"
467 list="data,dict,diff,qm,standard"/>
468 <foreach target="compile-module" param="module" trim="yes"
469 parallel="${parallel}" maxthreads="${threadCount}"
470 list="datadebug,nonotify,isomorphism,atomtype,render,valencycheck,
471 formula"/>
472 <foreach target="compile-module" param="module"
473 parallel="${parallel}" maxthreads="${threadCount}"
474 list="io,structgen"/>
475 <foreach target="compile-module" param="module"
476 parallel="${parallel}" maxthreads="${threadCount}"
d1e1fd7 Cleaned up build order, for changed dependencies
egonw authored
477 list="pdb,smiles,sdg,inchi,libiocml"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
478 <foreach target="compile-module" param="module"
479 parallel="${parallel}" maxthreads="${threadCount}"
d1e1fd7 Cleaned up build order, for changed dependencies
egonw authored
480 list="control,extra,reaction,pdbcml,libiomd"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
481 <foreach target="compile-module" param="module"
482 parallel="${parallel}" maxthreads="${threadCount}"
d1e1fd7 Cleaned up build order, for changed dependencies
egonw authored
483 list="charges,smarts"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
484 <foreach target="compile-module" param="module"
485 parallel="${parallel}" maxthreads="${threadCount}"
d1e1fd7 Cleaned up build order, for changed dependencies
egonw authored
486 list="qm,qsar,ionpot,fingerprint,pcore"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
487 <foreach target="compile-module" param="module"
488 parallel="${parallel}" maxthreads="${threadCount}"
489 list="qsaratomic,qsarbond,qsarprotein,qsarcml,qsarmolecular"/>
490 <foreach target="compile-module" param="module"
491 parallel="${parallel}" maxthreads="${threadCount}"
492 list="forcefield,qsarionpot"/>
493 <foreach target="compile-module" param="module"
494 parallel="${parallel}" maxthreads="${threadCount}"
495 list="builder3d,builder3dtools"/>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
496 </target>
fe65a98 Fixed dependencies
egonw authored
497
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
498 <target id="test-dist-all" name="test-dist-all" description="test-dist-all">
499 <antcall target="compile-init"/>
500 <foreach target="compile-module" param="module"
501 parallel="${parallel}" maxthreads="${threadCount}"
502 list="test"/>
503 <foreach target="compile-module" param="module" trim="true"
504 parallel="${parallel}" maxthreads="${threadCount}"
acfb5b5 Setting up implementation independent unit testing if IChemObject cla…
egonw authored
505 list="test-interfaces,test-libiocml,test-qsar,test-io,test-core,
506 test-valencycheck,test-smarts,test-standard,test-reaction,
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
507 test-pcore,test-sdg,test-forcefield,test-fingerprint,
508 test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict,
acfb5b5 Setting up implementation independent unit testing if IChemObject cla…
egonw authored
509 test-diff,test-charges,test-inchi,test-formula,
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
510 test-render"/>
511 <foreach target="compile-module" param="module" trim="true"
512 parallel="${parallel}" maxthreads="${threadCount}"
acfb5b5 Setting up implementation independent unit testing if IChemObject cla…
egonw authored
513 list="test-data,test-qsaratomic,test-qsarbond,
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
514 test-pdb,test-smiles,test-extra,test-atomtype,
515 test-structgen"/>
3678aaa Add missing trim attrib, fixing whitespace mess up
egonw authored
516 <foreach target="compile-module" param="module" trim="true"
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
517 parallel="${parallel}" maxthreads="${threadCount}"
acfb5b5 Setting up implementation independent unit testing if IChemObject cla…
egonw authored
518 list="test-qsarmolecular,test-builder3d,test-datadebug,
519 test-nonotify"/>
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
520 <foreach target="compile-module" param="module"
521 parallel="${parallel}" maxthreads="${threadCount}"
522 list="test-qsarprotein,test-qsarionpot"/>
523 </target>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
524
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now ja…
egonw authored
525 <target id="jarTestdata" name="jarTestdata" description="Creates jar files with test data.">
526 <mkdir dir="${dist}/jar"/>
527 <jar jarfile="${dist}/jar/cdk-testdata.jar">
f280f3f Updated for src/data -> src/test/data move
egonw authored
528 <fileset dir="${src}/test">
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now ja…
egonw authored
529 <include name="data/**/*" />
530 </fileset>
531 </jar>
532 </target>
533
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
534 <target id="dist-large" name="dist-large" depends="dist-all"
52638d6 Removed the experimental module: classes that are experimental should…
egonw authored
535 description="Builds one big jar file for the CDK, including third-party libraries.">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
536
c660505 Reworked dist-large target
egonw authored
537 <!-- first unjar the CDK and other jars we need -->
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
538 <mkdir dir="${appjars.dir}"/>
c660505 Reworked dist-large target
egonw authored
539 <unjar dest="${appjars.dir}">
540 <fileset dir="${lib}">
afac743 Set up the atomtype module
egonw authored
541 <includesfile name="${metainf}/atomtype.libdepends"/>
c660505 Reworked dist-large target
egonw authored
542 <includesfile name="${metainf}/builder3d.libdepends"/>
161b318 Put the helper tool into a separate module, to solve dependency issues.
egonw authored
543 <includesfile name="${metainf}/builder3dtools.libdepends"/>
3673f87 Added missing jar in dist-large target
egonw authored
544 <includesfile name="${metainf}/charges.libdepends"/>
c660505 Reworked dist-large target
egonw authored
545 <includesfile name="${metainf}/core.libdepends"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
546 <includesfile name="${metainf}/control.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
547 <includesfile name="${metainf}/datadebug.libdepends"/>
c660505 Reworked dist-large target
egonw authored
548 <includesfile name="${metainf}/data.libdepends"/>
549 <includesfile name="${metainf}/extra.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
550 <includesfile name="${metainf}/io.libdepends"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the modu…
egonw authored
551 <includesfile name="${metainf}/libiocml.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
552 <includesfile name="${metainf}/nonotify.libdepends"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
553 <includesfile name="${metainf}/pdbcml.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
554 <includesfile name="${metainf}/pdb.libdepends"/>
c660505 Reworked dist-large target
egonw authored
555 <includesfile name="${metainf}/qsar.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
556 <includesfile name="${metainf}/qsaratomic.libdepends"/>
557 <includesfile name="${metainf}/qsarbond.libdepends"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
558 <includesfile name="${metainf}/qsarmolecular.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
559 <includesfile name="${metainf}/qsarprotein.libdepends"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
560 <includesfile name="${metainf}/qsarcml.libdepends"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
561 <includesfile name="${metainf}/reaction.libdepends"/>
c660505 Reworked dist-large target
egonw authored
562 <includesfile name="${metainf}/render.libdepends"/>
563 <includesfile name="${metainf}/standard.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
564 <includesfile name="${metainf}/valencycheck.libdepends"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
565 <includesfile name="${metainf}/sdg.libdepends"/>
be50e2b Added new structgen module to dist-large.
egonw authored
566 <includesfile name="${metainf}/forcefield.libdepends"/>
0bf100d Added InChI module to regular compile setup
egonw authored
567 <includesfile name="${metainf}/inchi.libdepends"/>
cd11a7e Updated build script so that dist-large includes the smarts module
rajarshi authored
568 <includesfile name="${metainf}/smarts.libdepends"/>
71ce329 Updated build.xml to include the pcore module in the big jar file
rajarshi authored
569 <includesfile name="${metainf}/pcore.libdepends"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
570 <includesfile name="${metainf}/formula.libdepends"/>
ea8c273 Fixed dist-large generation: diff does not have any libdepends
egonw authored
571 <includesfile name="${metainf}/isomorphism.libdepends"/>
c660505 Reworked dist-large target
egonw authored
572 </fileset>
573 <fileset dir="${dist}/jar">
afac743 Set up the atomtype module
egonw authored
574 <include name="cdk-atomtype.jar"/>
c660505 Reworked dist-large target
egonw authored
575 <include name="cdk-builder3d.jar"/>
161b318 Put the helper tool into a separate module, to solve dependency issues.
egonw authored
576 <include name="cdk-builder3dtools.jar"/>
3673f87 Added missing jar in dist-large target
egonw authored
577 <include name="cdk-charges.jar"/>
c660505 Reworked dist-large target
egonw authored
578 <include name="cdk-core.jar"/>
0a739e8 Updted to include cdk-dict.jar in the big jar
rajarshi authored
579 <include name="cdk-dict.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
580 <include name="cdk-diff.jar"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
581 <include name="cdk-control.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
582 <include name="cdk-datadebug.jar"/>
c660505 Reworked dist-large target
egonw authored
583 <include name="cdk-data.jar"/>
584 <include name="cdk-extra.jar"/>
585 <include name="cdk-interfaces.jar"/>
586 <include name="cdk-io.jar"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the modu…
egonw authored
587 <include name="cdk-libiocml.jar"/>
8459c22 Included the libiomd module
egonw authored
588 <include name="cdk-libiomd.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
589 <include name="cdk-nonotify.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
590 <include name="cdk-pdbcml.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
591 <include name="cdk-pdb.jar"/>
c660505 Reworked dist-large target
egonw authored
592 <include name="cdk-qsar.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
593 <include name="cdk-qsaratomic.jar"/>
594 <include name="cdk-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
595 <include name="cdk-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
596 <include name="cdk-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
597 <include name="cdk-qsarprotein.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
598 <include name="cdk-qsarcml.jar"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
599 <include name="cdk-reaction.jar"/>
c660505 Reworked dist-large target
egonw authored
600 <include name="cdk-render.jar"/>
601 <include name="cdk-standard.jar"/>
be50e2b Added new structgen module to dist-large.
egonw authored
602 <include name="cdk-structgen.jar"/>
9c7431a Fixed stupid typo
egonw authored
603 <include name="cdk-valencycheck.jar"/>
f86e117 Created the smiles module
egonw authored
604 <include name="cdk-forcefield.jar"/>
605 <include name="cdk-smiles.jar"/>
cd11a7e Updated build script so that dist-large includes the smarts module
rajarshi authored
606 <include name="cdk-smarts.jar"/>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
607 <include name="cdk-fingerprint.jar"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
608 <include name="cdk-sdg.jar"/>
0bf100d Added InChI module to regular compile setup
egonw authored
609 <include name="cdk-inchi.jar"/>
71ce329 Updated build.xml to include the pcore module in the big jar file
rajarshi authored
610 <include name="cdk-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
611 <include name="cdk-formula.jar"/>
2e98012 Added missing ionpot to dist-large
egonw authored
612 <include name="cdk-isomorphism.jar"/>
613 <include name="cdk-ionpot.jar"/>
c660505 Reworked dist-large target
egonw authored
614 </fileset>
615 </unjar>
9db2505 Added missing jars to dist-large target
egonw authored
616
c660505 Reworked dist-large target
egonw authored
617 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what…
rajarshi authored
618 <jar jarfile="${dist}/jar/cdk-${version}.jar">
c660505 Reworked dist-large target
egonw authored
619 <manifest>
620 <section name="org.openscience.cdk">
621 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
0fcda7c Copied command line utils to separate project
egonw authored
622 <attribute name="Specification-Version" value="1.2"/>
c660505 Reworked dist-large target
egonw authored
623 <attribute name="Specification-Vendor" value="The CDK Project"/>
624 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
625 <attribute name="Implementation-Version" value="${version}"/>
626 <attribute name="Implementation-Vendor" value="The CDK Project"/>
627 </section>
628 </manifest>
629 <fileset dir="${appjars.dir}">
630 <include name="**/*" />
631 </fileset>
632 </jar>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
633 </target>
634
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
635 <target id="dist-pure" name="dist-pure" depends="dist-all"
52638d6 Removed the experimental module: classes that are experimental should…
egonw authored
636 description="Builds one big jar file for the CDK, excluding third party libraries.">
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
637
638 <!-- first unjar the CDK and other jars we need -->
639 <mkdir dir="${appjars.dir}"/>
640 <unjar dest="${appjars.dir}">
641 <fileset dir="${dist}/jar">
642 <include name="cdk-builder3d.jar"/>
643 <include name="cdk-builder3dtools.jar"/>
644 <include name="cdk-charges.jar"/>
645 <include name="cdk-core.jar"/>
646 <include name="cdk-control.jar"/>
647 <include name="cdk-datadebug.jar"/>
648 <include name="cdk-data.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
649 <include name="cdk-diff.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
650 <include name="cdk-extra.jar"/>
651 <include name="cdk-interfaces.jar"/>
652 <include name="cdk-io.jar"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the modu…
egonw authored
653 <include name="cdk-libiocml.jar"/>
8459c22 Included the libiomd module
egonw authored
654 <include name="cdk-libiomd.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
655 <include name="cdk-nonotify.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
656 <include name="cdk-pdbcml.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
657 <include name="cdk-pdb.jar"/>
658 <include name="cdk-qsar.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
659 <include name="cdk-qsaratomic.jar"/>
660 <include name="cdk-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
661 <include name="cdk-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
662 <include name="cdk-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
663 <include name="cdk-qsarprotein.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
664 <include name="cdk-qsarcml.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
665 <include name="cdk-reaction.jar"/>
666 <include name="cdk-render.jar"/>
667 <include name="cdk-standard.jar"/>
668 <include name="cdk-structgen.jar"/>
669 <include name="cdk-valencycheck.jar"/>
670 <include name="cdk-forcefield.jar"/>
45c8c0c Added smarts to JUnit testing
egonw authored
671 <include name="cdk-smarts.jar"/>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
672 <include name="cdk-fingerprint.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
673 <include name="cdk-smiles.jar"/>
674 <include name="cdk-sdg.jar"/>
675 <include name="cdk-inchi.jar"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
676 <include name="cdk-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
677 <include name="cdk-formula.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
678 </fileset>
679 </unjar>
680
681 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what…
rajarshi authored
682 <jar jarfile="${dist}/jar/cdk-pure-${version}.jar">
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
683 <manifest>
684 <section name="org.openscience.cdk">
685 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
686 <attribute name="Specification-Version" value="1.0"/>
687 <attribute name="Specification-Vendor" value="The CDK Project"/>
688 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
689 <attribute name="Implementation-Version" value="${version}"/>
690 <attribute name="Implementation-Vendor" value="The CDK Project"/>
691 </section>
692 </manifest>
693 <fileset dir="${appjars.dir}">
694 <include name="**/*" />
695 </fileset>
696 </jar>
697 </target>
698
88311e5 Added target for a jar with all the test stuff
egonw authored
699 <target id="dist-test-large" name="dist-test-large" depends="test-dist-all"
700 description="Builds on big jar file for the CDK test classes.">
701
702 <!-- first unjar the CDK and other jars we need -->
703 <mkdir dir="${appjars.dir}"/>
704 <unjar dest="${appjars.dir}">
705 <fileset dir="${lib}">
706 <includesfile name="${metainf}/test-core.libdepends"/>
707 <includesfile name="${metainf}/test-data.libdepends"/>
708 <includesfile name="${metainf}/test-datadebug.libdepends"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
709 <includesfile name="${metainf}/test-diff.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
710 <includesfile name="${metainf}/test-extra.libdepends"/>
d31ee42 New module: test-builder3d
egonw authored
711 <includesfile name="${metainf}/test-builder3d.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
712 <includesfile name="${metainf}/test-forcefield.libdepends"/>
713 <includesfile name="${metainf}/test-inchi.libdepends"/>
714 <includesfile name="${metainf}/test-io.libdepends"/>
715 <includesfile name="${metainf}/test-nonotify.libdepends"/>
716 <includesfile name="${metainf}/test-pdb.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
717 <includesfile name="${metainf}/test-qsaratomic.libdepends"/>
718 <includesfile name="${metainf}/test-qsarbond.libdepends"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
719 <includesfile name="${metainf}/test-qsarmolecular.libdepends"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
720 <includesfile name="${metainf}/test-qsarionpot.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
721 <includesfile name="${metainf}/test-qsarprotein.libdepends"/>
722 <includesfile name="${metainf}/test-qsar.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
723 <includesfile name="${metainf}/test-reaction.libdepends"/>
45c8c0c Added smarts to JUnit testing
egonw authored
724 <includesfile name="${metainf}/test-smarts.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
725 <includesfile name="${metainf}/test-smiles.libdepends"/>
726 <includesfile name="${metainf}/test-standard.libdepends"/>
be50e2b Added new structgen module to dist-large.
egonw authored
727 <includesfile name="${metainf}/test-structgen.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
728 <includesfile name="${metainf}/test-valencycheck.libdepends"/>
cb52b54 Hooked in stuff for the charges module
egonw authored
729 <includesfile name="${metainf}/test-charges.libdepends"/>
8459c22 Included the libiomd module
egonw authored
730 <includesfile name="${metainf}/test-libiomd.libdepends"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
731 <includesfile name="${metainf}/test-pcore.libdepends"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
732 <includesfile name="${metainf}/test-formula.libdepends"/>
cb5b4ae Set up testing for the render module
egonw authored
733 <includesfile name="${metainf}/test-render.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
734 </fileset>
735 <fileset dir="${dist}/jar">
736 <include name="cdk-test-core.jar"/>
737 <include name="cdk-test-data.jar"/>
738 <include name="cdk-test-datadebug.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
739 <include name="cdk-test-diff.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
740 <include name="cdk-test-extra.jar"/>
d31ee42 New module: test-builder3d
egonw authored
741 <include name="cdk-test-builder3d.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
742 <include name="cdk-test-forcefield.jar"/>
743 <include name="cdk-test-inchi.jar"/>
744 <include name="cdk-test-io.jar"/>
745 <include name="cdk-test-nonotify.jar"/>
746 <include name="cdk-test-pdb.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
747 <include name="cdk-test-qsaratomic.jar"/>
748 <include name="cdk-test-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
749 <include name="cdk-test-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
750 <include name="cdk-test-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
751 <include name="cdk-test-qsarprotein.jar"/>
752 <include name="cdk-test-qsar.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
753 <include name="cdk-test-reaction.jar"/>
45c8c0c Added smarts to JUnit testing
egonw authored
754 <include name="cdk-test-smarts.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
755 <include name="cdk-test-smiles.jar"/>
756 <include name="cdk-test-standard.jar"/>
be50e2b Added new structgen module to dist-large.
egonw authored
757 <include name="cdk-test-structgen.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
758 <include name="cdk-test-valencycheck.jar"/>
cb52b54 Hooked in stuff for the charges module
egonw authored
759 <include name="cdk-test-charges.jar"/>
8459c22 Included the libiomd module
egonw authored
760 <include name="cdk-test-libiomd.jar"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
761 <include name="cdk-test-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
762 <include name="cdk-test-formula.jar"/>
cb5b4ae Set up testing for the render module
egonw authored
763 <include name="cdk-test-render.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
764 </fileset>
765 </unjar>
766
767 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what…
rajarshi authored
768 <jar jarfile="${dist}/jar/cdk-test-${version}.jar">
88311e5 Added target for a jar with all the test stuff
egonw authored
769 <manifest>
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
770 <attribute name="Main-Class" value="org.openscience.cdk.CDKTests"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
771 <section name="org.openscience.cdk">
772 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
0fcda7c Copied command line utils to separate project
egonw authored
773 <attribute name="Specification-Version" value="1.2"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
774 <attribute name="Specification-Vendor" value="The CDK Project"/>
775 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
776 <attribute name="Implementation-Version" value="${version}"/>
777 <attribute name="Implementation-Vendor" value="The CDK Project"/>
778 </section>
779 </manifest>
780 <fileset dir="${appjars.dir}">
781 <include name="**/*" />
782 </fileset>
783 </jar>
784 </target>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
785
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
786 <target id="sourcedist" name="sourcedist"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
787 description="Builds the source packages.">
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
788 <property name="package" value="cdk-src+libs-${version}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
789 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
790 <delete dir="${sourcedist.dir}"/>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
791 <copy todir="${sourcedist.dir}/${src}/main/">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
792 <fileset dir="${src}/main/" includes="**/*.java" />
793 <fileset dir="${src}/main/" includes="**/*.jj" />
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
794 <fileset dir="${src}/main/" includes="**/*.jjt" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
795 <fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
796 </copy>
797 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
798 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
799 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
800 <fileset dir="." includes="javadoc.xml" />
801 <fileset dir="." includes="README" />
e99a32a Preparing for a release
egonw authored
802 <fileset dir="." includes="changelog*" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
803 </copy>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
804 <copy todir="${sourcedist.dir}/jar">
805 <fileset dir="jar">
806 <exclude name="*.so"/>
807 <exclude name="*.dll"/>
808 <exclude name="jumbo-5.4.2-b2.jar"/>
809 </fileset>
810 </copy>
998ae6a Updated for current CVS.
egonw authored
811 <copy todir="${sourcedist.dir}/develjar">
812 <fileset dir="develjar">
813 <exclude name="pmd-1.8.jar"/>
814 <exclude name="doccheck.jar"/>
815 <exclude name="dbdoclet*.*"/>
816 </fileset>
817 </copy>
818 <copy todir="${sourcedist.dir}/src/META-INF">
819 <fileset dir="src/META-INF" />
820 </copy>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
821 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/config/data/">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
822 <fileset dir="${src}/main/org/openscience/cdk/config/data/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
823 includes="*" />
824 </copy>
a289167 Minor tweak to get distribs working
egonw authored
825 <copy
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
826 file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
827 tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
be06f71 Fixed building of sourcedist: removed elements.xml, included *.owl
egonw authored
828 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
829 <fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
830 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
831 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/"/>
832 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/">
833 <fileset dir="${src}/main/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
e2623a3 Added some missing files to the sourcedist
egonw authored
834 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
835 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
836 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
837 <fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
998ae6a Updated for current CVS.
egonw authored
838 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
839 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
840 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
841 <fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
00c2efc Added missing builder3d templates to sourcedist.
egonw authored
842 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
843 <mkdir dir="${sourcedist.dir}/doc/" />
844 <copy todir="${sourcedist.dir}/doc/">
845 <fileset dir="doc/" includes="lgpl.license" />
846 </copy>
7447e16 Getting ready for release
egonw authored
847 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
848 <!-- the below deteles are a workaround, because the above should not have copied
849 in the src/data and src/org/openscience/cdk/test dirs -->
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
850 <delete dir="${sourcedist.dir}/src/test/data"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
851
852 <!-- now package things up -->
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
853 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
a0ba425 Updated sourcedist target so that it uses the current date for the fi…
rajarshi authored
854 <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
855 <delete file="${package}.tar" />
856 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
998ae6a Updated for current CVS.
egonw authored
857 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
858
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
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859 <target id="puredist" name="puredist" depends="init, runDoclet"
860 description="Builds the source packages without third-party libaries.">
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
861 <property name="package" value="cdk-${version}"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
862 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
863 <delete dir="${sourcedist.dir}"/>
b0892e4 More updates to get the sourcedist working
egonw authored
864 <copy todir="${sourcedist.dir}/${src}/main">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
865 <fileset dir="${src}/main/" includes="**/*.java" />
866 <fileset dir="${src}/main/" includes="**/*.jj" />
b0892e4 More updates to get the sourcedist working
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867 <fileset dir="${src}/main/" includes="**/*.jjt" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
868 <fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
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869 </copy>
870 <copy todir="${sourcedist.dir}">
871 <fileset dir="." includes="build.props" />
872 <fileset dir="." includes="build.xml" />
873 <fileset dir="." includes="javadoc.xml" />
874 <fileset dir="." includes="README" />
875 <fileset dir="." includes="changelog*" />
876 </copy>
877 <copy todir="${sourcedist.dir}/src/META-INF">
878 <fileset dir="src/META-INF" />
879 </copy>
880 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
881 <fileset dir="${src}/main/org/openscience/cdk/config/data/"
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
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882 includes="*" />
883 </copy>
884 <copy
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
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885 file="${src}/main/org/openscience/cdk/dict/data/chemical.xml"
886 tofile="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/chemical.xml" />
b0892e4 More updates to get the sourcedist working
egonw authored
887 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/dict/data/">
888 <fileset dir="${src}/main/org/openscience/cdk/dict/data/" includes="*.owl"/>
889 </copy>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
890 <mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
891 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/qsar/model/data/">
892 <fileset dir="${src}/main/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
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893 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
894 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/"/>
895 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/forcefield/data/">
896 <fileset dir="${src}/main/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
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897 </copy>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
898 <mkdir dir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/"/>
899 <copy todir="${sourcedist.dir}/${src}/main/org/openscience/cdk/modeling/builder3d/data/">
900 <fileset dir="${src}/main/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
901 </copy>
902 <mkdir dir="${sourcedist.dir}/doc/" />
903 <copy todir="${sourcedist.dir}/doc/">
904 <fileset dir="doc/" includes="lgpl.license" />
905 </copy>
906 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
907 <!-- the below deteles are a workaround, because the above should not have copied
908 in the src/data and src/org/openscience/cdk/test dirs -->
909 <delete dir="${sourcedist.dir}/src/data"/>
b0892e4 More updates to get the sourcedist working
egonw authored
910 <delete dir="${sourcedist.dir}/src/test"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
911
912 <!-- now package things up -->
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
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913 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
914 <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
915 <delete file="${package}.tar" />
916 </target>
917
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
918 <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
0f66d81 Better solution for missing JUnit; does not require super cow powers
egonw authored
919 <fail message="JUnit is not installed in Ant. Please run ant with the option '-lib develjar/junit-4.3.1.jar'."/>
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_…
egonw authored
920 </target>
921
a68b440 Moved a redundant dependency.
egonw authored
922 <target id="test-module" name="test-module" depends="noJunit"
bd190c6 Finished transition to modularized testing
egonw authored
923 description="Performs a full JUnit test for the CDK."
924 if="junit.present">
925
926 <echo message="Testing classes for CDK's ${module} module." />
806fbfe Updated build script with some new tasks that will clean up the top l…
rajarshi authored
927
bd190c6 Finished transition to modularized testing
egonw authored
928 <!-- check for availability for meta info files -->
929 <available file="${metainf}/test-${module}.cdkdepends" property="module.cdkdepends.present"/>
930 <available file="${metainf}/test-${module}.libdepends" property="module.libdepends.present"/>
931 <available file="${metainf}/test-${module}.devellibdepends" property="module.devellibdepends.present"/>
932
933 <!-- be somewhat informative -->
934 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
935 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
936 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
937
938 <mkdir dir="${reports.tests}"/>
939 <junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="256m">
940 <classpath>
941 <fileset dir="${lib}" >
942 <exclude name="**/*" unless="module.libdepends.present" />
943 <includesfile name="${metainf}/test-${module}.libdepends" if="module.libdepends.present" />
944 </fileset>
945 <fileset dir="${devellib}">
946 <exclude name="**/*" unless="module.devellibdepends.present" />
947 <includesfile name="${metainf}/test-${module}.devellibdepends" if="module.devellibdepends.present" />
948 </fileset>
949 <fileset dir="${dist}/jar">
950 <exclude name="**/*" unless="module.cdkdepends.present" />
951 <includesfile name="${metainf}/test-${module}.cdkdepends" if="module.cdkdepends.present" />
952 <include name="cdk-test-${module}.jar" />
953 </fileset>
954 </classpath>
b9baedb Fixed location of test modules
egonw authored
955 <test name="org.openscience.cdk.modulesuites.M${module}Tests"
bd190c6 Finished transition to modularized testing
egonw authored
956 haltonfailure="no"
957 todir="${reports.tests}"
958 outfile="result-${module}">
959 <formatter type="brief" />
960 </test>
961 </junit>
806fbfe Updated build script with some new tasks that will clean up the top l…
rajarshi authored
962 </target>
bd190c6 Finished transition to modularized testing
egonw authored
963
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now ja…
egonw authored
964 <target id="test-all" name="test-all" depends="noJunit, dist-all, test-dist-all, jarTestdata"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
965 description="Performs a full JUnit test for the CDK."
966 if="junit.present">
f5c5f2f Added missing trim="true" attribute, fixing running test-all.
egonw authored
967 <foreach target="test-module" param="module" trim="true"
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
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968 list="core,data,datadebug,diff,nonotify,atomtype,standard,
969 io,builder3d,forcefield,valencycheck,charges,reaction,
970 smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond,
971 qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi,
972 structgen,libiomd,libiocml,formula,render,extra,sdg"/>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
973 </target>
3790797 Splitted tests which are supposed to fail from those which are suppos…
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974
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
975 <target id="limitations" name="limitations" depends="noJunit, dist-all"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
976 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
977 <junit printsummary="yes" haltonfailure="yes" fork="yes">
978 <classpath>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
979 <fileset dir="${dist}/jar">
980 <include name="cdk-*.jar" />
981 </fileset>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
982 <fileset dir="${lib}">
983 <include name="*.jar" />
984 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
985 <fileset dir="${devellib}">
986 <include name="*.jar" />
987 </fileset>
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
988 </classpath>
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
989 <test name="org.openscience.cdk.limitations.AlgorithmLimitations"
3790797 Splitted tests which are supposed to fail from those which are suppos…
egonw authored
990 haltonfailure="no"
991 todir="${reports.tests}"
992 outfile="limitations">
993 <formatter type="brief" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
994 </test>
995 </junit>
40c31d0 Fixed more dependency problems: ant clean test-all now works
egonw authored
996 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
997
6029346 Added missing dependencies
egonw authored
998 <target id="run-test" name="run-test" depends="dist-all,test-dist-all"
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
999 description="Runs one specific JUnit test suite (org.openscience.cdk.&lt;class>) as a standalone application with
1000 -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
1001 <echo message="Running test class: testclass=${testclass}"/>
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
1002 <java classname="org.openscience.cdk.${testclass}" fork="yes" maxmemory="512m">
3d88ed4 Turn on CDK debugging while running JUnit test
egonw authored
1003 <jvmarg value="-Dcdk.debugging=true"/>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
1004 <classpath>
bd397e8 Run test target should be working too now
egonw authored
1005 <fileset dir="${dist}/jar/">
1006 <include name="*.jar" />
1007 </fileset>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
1008 <fileset dir="${lib}">
1009 <include name="*.jar" />
1010 </fileset>
9e95b7b Finished splitting devel from user jars
egonw authored
1011 <fileset dir="${devellib}">
1012 <include name="*.jar" />
1013 </fileset>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSe…
egonw authored
1014 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
1015 </java>
bd397e8 Run test target should be working too now
egonw authored
1016 </target>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
1017
6029346 Added missing dependencies
egonw authored
1018 <target id="junit-test" name="junit-test" depends="dist-all,test-dist-all,noJunit"
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
1019 description="Runs one specific JUnit test suite (org.openscience.cdk.&lt;class>) with -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
1020 <echo message="JUnit tests class: testclass=${testclass}"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
1021 <junit printsummary="yes" haltonfailure="no" fork="yes">
79f7451 Switch debugging on in run-test target
steinbeck authored
1022 <jvmarg value="-Dcdk.debugging=true"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
1023 <jvmarg value="-Dcdk.debug.stdout=true"/>
1024 <classpath>
5b2a8d2 Reintroduced the junit-test target
egonw authored
1025 <fileset dir="${dist}/jar/">
1026 <include name<