Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Newer
Older
100644 1249 lines (1165 sloc) 67.127 kB
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" />
7406c2b Made the code Java 5 compilable.
dmak authored
8 <property name="compile.target.version" value="1.5"/>
3a26de3 Made compilation with debug=on customizable.
egonw authored
9 <property name="debug" value="on" />
460ea79 Detect deprecated methods
egonw authored
10 <property name="deprecation" value="on" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
11 <property name="optimization" value="off" />
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
12 <property name="threadCount" value="4" />
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
13 <property name="parallel" value="false"/>
3a26de3 Made compilation with debug=on customizable.
egonw authored
14
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
15 <!-- patches to apply -->
16
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
17 <!-- directories -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
18 <property name="build" value="build" />
bd36ed1 Trial for new build system
egonw authored
19 <property name="build.src" value="${build}/src" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
20 <property name="sourcedist" value="sourcedist" />
21 <property name="dist" value="dist" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
22 <property name="doc" value="doc" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
23 <property name="src" value="src" />
24 <property name="lib" value="jar" />
9e95b7b Finished splitting devel from user jars
egonw authored
25 <property name="devellib" value="develjar" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
26 <property name="src.tests" value="${src}/test/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="${dist}/appjars" />
bd36ed1 Trial for new build system
egonw authored
29 <property name="metainf" value="${src}/META-INF" />
f7be51f Removed alternative core classes patch offering more detailed debug info
egonw authored
30
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar whi…
egonw authored
31 <!-- class to run for testing-->
32 <property name="testclass" value="CDKTests" />
33 <property name="arg1" value="" />
34 <property name="arg2" value="" />
35 <property name="arg3" value="" />
36 <property name="arg4" value="" />
5c40bcf Removed the check for rJava as we don't strictly need it. Also added …
rajarshi authored
37
38 <property environment="env" />
39
6fb8043 Typo fixed
egonw authored
40 <!-- Include the ant-contrib goodies -->
a8b313e @egonw Added ant task to calculate JavaNCSS code statistics
egonw authored
41 <taskdef name="javancss" classname="javancss.JavancssAntTask">
42 <classpath>
43 <pathelement location="${basedir}/develjar/javacc.jar"/>
44 <pathelement location="${basedir}/develjar/javancss.jar"/>
45 <pathelement location="${basedir}/develjar/ccl.jar"/>
46 <pathelement location="${basedir}/develjar/jhbasic.jar"/>
47 </classpath>
48 </taskdef>
49 <!-- Include the JavaNCSS goodies -->
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
50 <taskdef resource="net/sf/antcontrib/antlib.xml">
51 <classpath>
52 <pathelement location="${basedir}/develjar/ant-contrib-1.0b3.jar"/>
53 </classpath>
54 </taskdef>
55
b7ba930 Commented out the code to get the latest SV rev since we don't need i…
rajarshi authored
56 <!--
59d696c Added some code to obtain the current svn revision. Should be used to…
rajarshi authored
57 <shellscript shell="bash" outputproperty="svn.output">
58 svn info
59 </shellscript>
60 <propertyregex property="svn.rev" input="${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
61 -->
10a9acb Updated build script to include the ant contrib tasks
rajarshi authored
62
5c40bcf Removed the check for rJava as we don't strictly need it. Also added …
rajarshi authored
63 <target id="info" name="info" depends="check">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
64 <!-- Gives information about the building process. -->
8f6d674 Fixed after breaking it earlier today
egonw authored
65 <echo message="Platform:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
66 <echo message=" OS: ${os.name}" />
67 <echo message=" Architecture: ${os.arch}" />
68 <echo message=" Version: ${os.version}" />
69 <echo message=" Mac OS/X found: ${isMacOsX}" />
8f6d674 Fixed after breaking it earlier today
egonw authored
70 <echo message="" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
71 <echo message="Java/Ant Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
72 <echo message=" Java version: ${java.version}" />
73 <echo message=" Java vendor: ${java.vendor}" />
74 <echo message=" Java dir: ${java.home}" />
75 <echo message=" Java ext dir: ${java.ext.dirs}" />
76 <echo message=" Ant version: ${ant.version}" />
77 <echo message=" ${ANT_HOME}: ${ant.home}" />
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
78 <echo message=" hasAnt17: ${hasAnt17}" />
679cde7 Third attempt to fix the Mac OS/X compile problem (and extended info …
egonw authored
79 <echo message="" />
80 <echo message="CDK Environment:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
81 <echo message=" CDK version: ${version}" />
82 <echo message=" build.xml: $Id$" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
83 <echo message=" Junit found: ${junit.present}" />
cc68a07 Added detection of more third party libraries
egonw authored
84 <echo message=" --- required libraries ---" />
85 <echo message=" Vecmath found: ${vecmath.present}" />
86 <echo message=" Log4j found: ${log4j.present}" />
87 <echo message=" JGraphT found: ${jgrapht.present}" />
c1c3a3b Removed outdated optional compile checks
egonw authored
88 <echo message=" --- distributed (but optional) libraries ---" />
7cd4ff8 Added R/SJava found to info target
egonw authored
89 <echo message=" CMLDOM found: ${cmllibs.present}" />
5a470af Added detection of Jmol, and added comments on optionality of libs
egonw authored
90 <echo message=" --- optional libraries ---" />
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
91 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
92 <echo message="Compiling:" />
7cd4ff8 Added R/SJava found to info target
egonw authored
93 <echo message=" for: ${build.compiler}" />
7406c2b Made the code Java 5 compilable.
dmak authored
94 <echo message=" target: ${compile.target.version}" />
7cd4ff8 Added R/SJava found to info target
egonw authored
95 <echo message=" debug: ${debug}" />
96 <echo message=" deprecation: ${deprecation}" />
97 <echo message=" optimization: ${optimization}" />
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
98 <echo message=" parallel: ${parallel}" />
99 <echo message=" threads: ${threadCount}" />
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
100 <echo message="" />
101 <echo message="Available Targets" />
102 <echo message=" clean: Remove class files and any temporary files" />
103 <echo message=" dist-all: Compile all modules" />
7406c2b Made the code Java 5 compilable.
dmak authored
104 <echo message=" test-all: Performs a full JUnit test for all modules" />
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
105 <echo message=" dist-large: Create the comprehensive jar, with all modules" />
106 <echo message=" test-dist-all: Compile all test modules" />
107 <echo message="test-dist-large: Create a single jar file with all test modules" />
108 <echo message=" jarTestdata: Create the jar file with all test data. Used in testing" />
109 <echo message="" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
110 </target>
111
806fbfe Updated build script with some new tasks that will clean up the top l…
rajarshi authored
112 <!-- See what platform were on -->
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
113
8f6d674 Fixed after breaking it earlier today
egonw authored
114 <target id="checkPlatforms" name="checkPlatforms">
58405cf Fixed build.xml to allow compile of doclets on MacOS/X (closes #1001497)
egonw authored
115 <condition property="isMacOsX">
116 <and>
117 <os family="mac"/>
118 <os family="unix"/>
119 </and>
120 </condition>
121 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
122
8f6d674 Fixed after breaking it earlier today
egonw authored
123 <target id="check" name="check" depends="checkPlatforms">
cc68a07 Added detection of more third party libraries
egonw authored
124 <!-- Check wether Doclets are compiled and output is generated -->
125 <uptodate property="dotjavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
126 targetfile="${build}/core.javafiles">
cc68a07 Added detection of more third party libraries
egonw authored
127 <srcfiles dir="${src}" includes="**/*.java" />
128 </uptodate>
129 <condition property="dotjjfiles.uptodate">
130 <and>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
131 <uptodate property="NomParserJavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
132 targetfile="${src}/main/org/openscience/cdk/iupac/parser/NomParser.java">
133 <srcfiles dir="${src}/main/" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
cc68a07 Added detection of more third party libraries
egonw authored
134 </uptodate>
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
135 <uptodate property="SMARTSParserJJTJavafiles.uptodate"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
136 targetfile="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.java">
137 <srcfiles dir="${src}/main/" includes="org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj" />
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
138 </uptodate>
cc68a07 Added detection of more third party libraries
egonw authored
139 </and>
140 </condition>
141
142 <!-- Checks which parts of CDK can be build. -->
143
144 <!-- test for optional jars -->
145 <available property="vecmath.present"
146 file="${lib}/vecmath1.2-1.14.jar"/>
147 <available property="log4j.present"
148 file="${lib}/log4j.jar"/>
149 <available property="jgrapht.present"
152e213 Updated for recent upgrades to Jumbo 5.2 and JGraphT 0.6.0
egonw authored
150 file="${lib}/jgrapht-0.6.0.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
151
152 <!-- test for optional jars -->
153 <condition property="cmllibs.present">
154 <or>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
155 <available file="${lib}/jumbo-with-fix-by-jonalv.jar"/>
cc68a07 Added detection of more third party libraries
egonw authored
156 </or>
157 </condition>
6415c45 Added some text to the info target to list useful targets. Also pdate…
rajarshi authored
158
143fb1d OK, we're not using junit.framework.TestCase anymore, so don't look f…
egonw authored
159 <condition property="junit.present">
160 <or>
161 <available file="${ant.home}/lib/junit.jar"/>
41075f3 @egonw Fixed JUnit version
egonw authored
162 <available file="${devellib}/junit-4.10.jar"/>
143fb1d OK, we're not using junit.framework.TestCase anymore, so don't look f…
egonw authored
163 </or>
164 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
165
166 <!-- test Ant version -->
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
167 <condition property="hasAnt17">
4398cc4 Ant has a release 1.8 that should be accepted in build.xml
Mark Rynbeek authored
168 <or>
95f0b04 Updated build script to indicate that ant 1.7.1 or better is required
rajarshi authored
169 <contains string="${ant.version}" substring="1.7.1"/>
4398cc4 Ant has a release 1.8 that should be accepted in build.xml
Mark Rynbeek authored
170 <contains string="${ant.version}" substring="1.8"/>
171 </or>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
172 </condition>
cc68a07 Added detection of more third party libraries
egonw authored
173
4398cc4 Ant has a release 1.8 that should be accepted in build.xml
Mark Rynbeek authored
174
cc68a07 Added detection of more third party libraries
egonw authored
175 <!-- test Java version -->
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
176 <condition property="isJava13">
177 <contains string="${java.version}" substring="1.3"/>
178 </condition>
179 <condition property="isJava14">
180 <contains string="${java.version}" substring="1.4"/>
181 </condition>
866bc72 CML is now available for Java1.5 too
egonw authored
182 <condition property="isJava15">
183 <contains string="${java.version}" substring="1.5"/>
184 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
185 <condition property="isJava16">
186 <contains string="${java.version}" substring="1.6."/>
187 </condition>
3f17ad0 Added detection of Java 1.7
egonw authored
188 <condition property="isJava17">
189 <contains string="${java.version}" substring="1.7."/>
190 </condition>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
191 <condition property="isJava14+">
192 <or>
193 <contains string="${java.version}" substring="1.4"/>
194 <contains string="${java.version}" substring="1.5"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
195 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
196 <contains string="${java.version}" substring="1.7"/>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
197 </or>
198 </condition>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
199 <condition property="isJava15+">
200 <or>
201 <contains string="${java.version}" substring="1.5"/>
202 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
203 <contains string="${java.version}" substring="1.7"/>
c77a2ac Should now work with the Sun Java 1.6.0 beta2
egonw authored
204 </or>
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
205 </condition>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
206 <condition property="isNotJava15+">
207 <not>
208 <or>
209 <contains string="${java.version}" substring="1.5"/>
210 <contains string="${java.version}" substring="1.6"/>
3f17ad0 Added detection of Java 1.7
egonw authored
211 <contains string="${java.version}" substring="1.7"/>
b836e8e Some tweaks and now CDK compiles with 1.6 too
egonw authored
212 </or>
213 </not>
214 </condition>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
215 <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
216 <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
217 </target>
218
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
219
d2ed020 Reworked dependencies
egonw authored
220 <target id="init" name="init" depends="check, setupBuildDir"/>
4302fbf Updated for Jumbo50 transition.
egonw authored
221 <target id="customize" name="customize" depends="javacc"/>
866bc72 CML is now available for Java1.5 too
egonw authored
222
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
223 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
224 <tstamp />
225 <mkdir dir="${build}" />
226 <mkdir dir="${sourcedist}" />
227 <mkdir dir="${dist}" />
228 <mkdir dir="${reports.tests}" />
229 </target>
230
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
231 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
232 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
233 <fileset dir="." includes="**/*~" />
234 <fileset dir="." includes="*.tar.gz" />
235 <fileset dir="." includes="*.zip" />
06ee5d1 Modified the clean target to remove .rda files generated during testi…
rajarshi authored
236 <fileset dir="." includes="*.rda" />
bfe0e17 Build interfaces before data
egonw authored
237 <fileset dir="${src}" includes="*.entitylist" />
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
238 <!-- remove java files generated with JavaCC -->
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
239 <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts" includes="*.java">
51e5934 Added missing autogenerated SMARTS file to the clean task (closes #18…
egonw authored
240 <exclude name="SMARTSQueryTool.java" />
241 </fileset>
242 <fileset dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
243 includes="SMARTSParser*.java,SMARTSParser.jj,JJT*,ParseException.java,SimpleCharStream.java,Token*.java" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
244 <fileset dir="${src}/main/org/openscience/cdk/iupac/parser" includes="*.java">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
245 <!-- the next are from CVS -->
246 <exclude name="AttachedGroup.java" />
247 <exclude name="MoleculeBuilder.java" />
248 </fileset>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
249 <fileset dir="${src}/main/">
31994c5 Fixed deleting the doclet class files
egonw authored
250 <include name="net/sf/cdk/tools/*.class" />
2b81a22 Fixed a problem with deleting the doclet classes
egonw authored
251 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
252 </delete>
253
254 <delete dir="${build}" />
255 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
256 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
257 <delete dir="${reports.tests}" />
258 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
259
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
260 <target name="runDoclet" id="runDoclet" depends="check, customize">
261 <echo>Not skipping doclet run...</echo>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
262 <mkdir dir="${build}" />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
263 <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
264 srcdir="${src}/main/" destdir="${build}" optimize="${optimization}"
7406c2b Made the code Java 5 compilable.
dmak authored
265 debug="${debug}" deprecation="${deprecation}" source="${compile.target.version}" target="${compile.target.version}"/>
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
266 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
20a1056 Fixed a patch from the branch that got lost in the branch merge
egonw authored
267 <arg value="${src}/META-INF"/>
268 <arg value="${src}/main"/>
269 <arg value="${build}"/>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
270 </java>
271 <java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
20a1056 Fixed a patch from the branch that got lost in the branch merge
egonw authored
272 <arg value="${src}/META-INF"/>
273 <arg value="${src}/test"/>
274 <arg value="${build}"/>
07f21f7 New preprocessing build system: no longer uses JavaDoc, but a small c…
egonw authored
275 </java>
ca98ea5 Refactored build process (closes #883519)
egonw authored
276 </target>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
277
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
278 <target id="compile-needed-test" name="compile-needed-test">
85e02cd Fixed check for up to dateness of test jars
egonw authored
279 <if>
280 <matches string="${module}" pattern="^test"/>
281 <then>
282 <property name="source" value="src/test"/>
283 </then>
284 <else>
285 <property name="source" value="src/main"/>
286 </else>
287 </if>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
288 <uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
85e02cd Fixed check for up to dateness of test jars
egonw authored
289 <srcfiles dir="${source}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
290 <includesfile name="${build}/${module}.javafiles"/>
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
291 </srcfiles>
292 </uptodate>
293 </target>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
294
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
295 <target id="compile-init" name="compile-init"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
296 depends="init, check, runDoclet"/>
9012143 Reworked dependencies a bit, fixing the -DskipDoclet option
egonw authored
297
ae661aa @egonw Added a QA target
egonw authored
298 <target id="qa-module" name="qa-module"
a1e1f1b @egonw Added JavaDoc testing to the QA task; removed module-uptodate which c…
egonw authored
299 depends="check, dist.init">
ae661aa @egonw Added a QA target
egonw authored
300 <echo message="Running QA for CDK's ${module} module" />
301
302 <antcall target="test-module">
303 <param name="module" value="${module}"/>
304 </antcall>
305
03ef86b @egonw Ensure the OpenJavaDocCheck plugins are compiled
egonw authored
306 <ant antfile="javadoc.xml" target="compileDocTests"/>
a1e1f1b @egonw Added JavaDoc testing to the QA task; removed module-uptodate which c…
egonw authored
307 <ant antfile="javadoc.xml" target="ojdcheck-module">
308 <property name="module" value="${module}"/>
309 </ant>
ae661aa @egonw Added a QA target
egonw authored
310 <ant antfile="pmd.xml" target="test-module">
311 <property name="pmd.test" value="custom"/>
312 <property name="module" value="${module}"/>
313 <property name="lib" value="develjar" />
314 </ant>
315 <ant antfile="pmd-unused.xml" target="test-module">
316 <property name="pmd.test" value="custom"/>
317 <property name="module" value="${module}"/>
318 <property name="lib" value="develjar" />
319 </ant>
320 <ant antfile="pmd-migrating.xml" target="test-module">
321 <property name="pmd.test" value="migrating"/>
322 <property name="module" value="${module}"/>
323 <property name="lib" value="develjar" />
324 </ant>
325 </target>
326
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
327 <target id="compile-module" name="compile-module"
b0f7700 Checks are really needed a bit more often to ensure that some variabl…
egonw authored
328 depends="check, dist.init, compile-needed-test"
aa26775 Ok, ant clean test works again. With 300-ish problems, but it runs :)
egonw authored
329 unless="module-uptodate">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
330
1366ba3 Removed use of source parameter, by making use of ant-contrib's <if>
egonw authored
331 <if>
332 <matches string="${module}" pattern="^test"/>
333 <then>
334 <property name="source" value="src/test"/>
335 </then>
336 <else>
337 <property name="source" value="src/main"/>
338 </else>
339 </if>
340
6153fc1 Report from which source tree files are copied
egonw authored
341 <echo message="Compiling classes for CDK's ${module} module from ${source}..." />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
342
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
343 <!-- check for availability for meta info files -->
344 <available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
345 <available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
c094513 Make sure the .set files end up in the right jars
egonw authored
346 <available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
347 <available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
348 <available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
349 <available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
350 <available file="${metainf}/${module}.autogenerated" property="module.autogenerated.present"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
351
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
352 <!-- be somewhat informative -->
353 <echo message="Datafiles defined: ${module.datafiles.present}"/>
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
354 <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
355 <echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
356 <echo message="Library dependencies defined: ${module.libdepends.present}"/>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
357 <echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
358 <echo message="Autogenerated files specified: ${module.autogenerated.present}"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
359
bd36ed1 Trial for new build system
egonw authored
360 <!-- normally javac compiles not just the given files, but also missing
361 classes that are in the same src/ directory. By making a copy first,
362 we explicitely make it impossible to compile files that are not
363 marked for a specific module -->
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
364 <mkdir dir="${build.src}/${module}"/>
365 <mkdir dir="${build}/${module}"/>
366 <copy todir="${build.src}/${module}">
365a4d7 Fix to use the proper source folder, now passed via a target argument
egonw authored
367 <fileset dir="${source}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
368 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
369 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
370 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
371 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
372 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
373
374 <includesfile name="${build}/${module}.javafiles"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
375 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
bd36ed1 Trial for new build system
egonw authored
376 </fileset>
377 </copy>
5a2bc65 @egonw Introduced a helper class with info about the CDK library: the versio…
egonw authored
378 <copy todir="${build}" file="build.props" />
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
379
bd36ed1 Trial for new build system
egonw authored
380 <!-- ok, now that we have a copy, compile this copy -->
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
381 <javac srcdir="${build.src}/${module}" destdir="${build}/${module}" optimize="${optimization}"
7406c2b Made the code Java 5 compilable.
dmak authored
382 debug="${debug}" deprecation="${deprecation}" source="${compile.target.version}" target="${compile.target.version}">
bd36ed1 Trial for new build system
egonw authored
383 <classpath>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
384 <fileset dir="${lib}" >
385 <exclude name="**/*" unless="module.libdepends.present" />
386 <includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
bd36ed1 Trial for new build system
egonw authored
387 </fileset>
ea39d29 More dependency clean up... A lot is working now, but the cyclic depe…
egonw authored
388 <fileset dir="${devellib}">
389 <exclude name="**/*" unless="module.devellibdepends.present" />
390 <includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
391 </fileset>
bd36ed1 Trial for new build system
egonw authored
392 <fileset dir="${dist}/jar">
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
393 <exclude name="**/*" unless="module.cdkdepends.present" />
394 <includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
bd36ed1 Trial for new build system
egonw authored
395 </fileset>
396 </classpath>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
397
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
398 <excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
399 <!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
400 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
401 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
402 <excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt17"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
403
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
404 <includesfile name="${build}/${module}.javafiles"/>
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
405 <includesfile name="${metainf}/${module}.autogenerated" if="module.autogenerated.present"/>
bd36ed1 Trial for new build system
egonw authored
406 </javac>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
407
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
408 <!-- create a autogenerated.classes file, if applicable, so that these files can be included in the jar -->
f1360a2 Cleaned up handling of presence/absence of autogenerated files, so no…
rajarshi authored
409 <if>
410 <istrue value="${module.autogenerated.present}"/>
411 <then>
412 <copy file="${metainf}/${module}.autogenerated" tofile="${build}/${module}.autogenerated.classes"
413 failonerror="false"/>
414 <replace dir="${build}" token=".java" value="*.class">
415 <include name="*.autogenerated.classes"/>
416 </replace>
417 </then>
418 </if>
419
420
bd36ed1 Trial for new build system
egonw authored
421 <!-- and then jar things up into the module jar -->
422 <jar jarfile="${dist}/jar/cdk-${module}.jar">
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
423 <fileset dir="${build}/${module}">
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
424 <includesfile name="${build}/${module}.classes" />
0863077 Added infrastructure for putting autogenerated files in a non-extra m…
egonw authored
425 <includesfile name="${build}/${module}.autogenerated.classes" if="module.autogenerated.present"/>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
426 <excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
427 <!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
428 <!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
429 <excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15"/>
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
430 <excludesfile name="${build}/ant1.6.classes" unless="hasAnt17"/>
bd36ed1 Trial for new build system
egonw authored
431 </fileset>
54a21b6 The .javafiles now get created in build/ instead of src/
egonw authored
432 <fileset dir="${build}">
bd36ed1 Trial for new build system
egonw authored
433 <include name="${module}.javafiles" />
434 </fileset>
174804f Fixed root location of .datafiles content
egonw authored
435 <fileset dir="${source}">
141cf36 Fixed problem with including data files in the module jars
egonw authored
436 <exclude name="**/*" unless="module.datafiles.present"/>
666b237 Ok, next step... getting extra and apps to the new system; lot's of u…
egonw authored
437 <includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
438 </fileset>
7a673b7 Point to the correct root folder for datafiles and extrafiles
egonw authored
439 <fileset dir="${src}">
cd4dbe5 Added hook for extra files outside the src/ directory, solving the re…
egonw authored
440 <exclude name="**/*" unless="module.extrafiles.present"/>
441 <includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
442 </fileset>
c8f144a Point to correct .set location.
egonw authored
443 <fileset dir="${build}">
c094513 Make sure the .set files end up in the right jars
egonw authored
444 <exclude name="**/*" unless="module.buildfiles.present"/>
c8f144a Point to correct .set location.
egonw authored
445 <includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
c094513 Make sure the .set files end up in the right jars
egonw authored
446 </fileset>
bd36ed1 Trial for new build system
egonw authored
447 </jar>
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
448
e33fba2 @PeterOdeus Added generation of java source jars
PeterOdeus authored
449 <jar jarfile="${dist}/jar/cdk-${module}-sources.jar">
450 <fileset dir="${build.src}/${module}">
451 <include name="**/*.java" />
452 </fileset>
453 </jar>
454
b868e9e Put source and class in module dependent build/ dirs, allowing compil…
egonw authored
455 <!-- clean up afterwards -->
45f683f @egonw New IChemObjectBuilder interface:
egonw authored
456 <!-- delete dir="${build.src}/${module}"/>
457 <delete dir="${build}/${module}"/ -->
bd36ed1 Trial for new build system
egonw authored
458 </target>
459
6dc5408 Added stuff for qsar module
egonw authored
460 <!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
cf9ad35 Ant1.7 is required because we now use JUnit4
egonw authored
461 <target id="javacc" name="javacc" depends="init, check" if="hasAnt17" unless="dotjjfiles.uptodate">
5ad21a8 Fixed building CDK with Ant 1.5.x
egonw authored
462 <echo message="Compiling Ant 1.6 depending classes." />
cd49d3a A bit of comment
egonw authored
463 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
464 <delete>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
465 <fileset id="javacc-generated"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
466 dir="${src}/main/org/openscience/cdk/iupac/parser/"
cd49d3a A bit of comment
egonw authored
467 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
468 </delete>
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
469 <javacc target="${src}/main/org/openscience/cdk/iupac/parser/NomParser.jj"
470 outputdirectory="${src}/main/org/openscience/cdk/iupac/parser/"
d9680ff Removed compilation steps for the old SMARTS parser
rajarshi authored
471 javacchome="${lib}"/>
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
472 <delete>
473 <fileset id="javacc-generated"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
474 dir="${src}/main/org/openscience/cdk/smiles/smarts/parser/"
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
475 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
476 </delete>
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
477 <jjtree target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt"
65b6106 Added compatibility with ant1.7. Added building process for JJTree im…
djiao authored
478 javacchome="${lib}"
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
479 outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
52a1568 Added ant tasks to correctly generate the SMARTS jj parser from the t…
rajarshi authored
480 <javacc target="${src}/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jj"
481 javacchome="${lib}"
482 outputdirectory="${src}/main/org/openscience/cdk/smiles/smarts/parser/"/>
483
484 <!-- OK, we now need to do some replacements such as
485 adding cdk.module tags and changing access modes
486 -->
487 <replace dir="${src}/main/org/openscience/cdk/smiles/smarts/parser"
488 excludes="AST*.java,SMARTSParser.jjt,SMARTSParser.jj,*Node.java"
489 token="package org.openscience.cdk.smiles.smarts.parser;" summary="true" >
490 <replacevalue>package org.openscience.cdk.smiles.smarts.parser;
491
492 /**
493 *
494 * @cdk.module smarts
495 */</replacevalue>
496 </replace>
1dd9647 Added IUPAC name parser
stomkinson authored
497 </target>
8095921 Added rendering of wedged bonds.
egonw authored
498
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
499 <target id="dist.init" name="dist.init">
246601c Added a test to check for the presence of R and thus prevent compilat…
rajarshi authored
500 <mkdir dir="${dist}/jar" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
501 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
502
81cab20 Added Ant target for compiling 'optional' modules
egonw authored
503 <target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
504 <target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
505 <echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
506 </target>
507 <target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
508 <antcall target="compile-module"><param name="module" value="java3d"/></antcall>
509 </target>
510
511 <target id="dist-optional" name="dist-optional" depends="dist-all"
512 description="Compile CDK modules that require optional libraries">
513 <antcall target="dist-java3d"/>
514 </target>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
515
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
516 <target id="dist-all" name="dist-all" description="dist-all">
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
517 <antcall target="compile-init"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
518 <foreach target="compile-module" param="module"
519 parallel="${parallel}" maxthreads="${threadCount}"
e05831b Moved the two annotation classes into a separate module
egonw authored
520 list="interfaces,annotation"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
521 <foreach target="compile-module" param="module"
522 parallel="${parallel}" maxthreads="${threadCount}"
40c5e92 Introduced a ioformats module (along with test-ioformats), which can …
egonw authored
523 list="core,ioformats"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
524 <foreach target="compile-module" param="module"
525 parallel="${parallel}" maxthreads="${threadCount}"
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
526 list="silent,data,dict,diff,qm,standard,log4j"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
527 <foreach target="compile-module" param="module" trim="yes"
528 parallel="${parallel}" maxthreads="${threadCount}"
51af326 @egonw Removed the nonotify module (replaced by silent)
egonw authored
529 list="datadebug,isomorphism,atomtype,render,valencycheck,
751488b @egonw Set up a CIP module.
egonw authored
530 formula,cip"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
531 <foreach target="compile-module" param="module"
532 parallel="${parallel}" maxthreads="${threadCount}"
533 list="io,structgen"/>
534 <foreach target="compile-module" param="module"
535 parallel="${parallel}" maxthreads="${threadCount}"
110f4c1 @egonw Setting up the new renderbasic module.
egonw authored
536 list="renderbasic"/>
537 <foreach target="compile-module" param="module"
538 parallel="${parallel}" maxthreads="${threadCount}"
8a4a98b @egonw Upgraded to the final JNI-InChI 0.7:
egonw authored
539 list="pdb,smiles,sdg,inchi,libiocml"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
540 <foreach target="compile-module" param="module"
541 parallel="${parallel}" maxthreads="${threadCount}"
646c37b @egonw Made qsarmolecular independent from data, by creating a new fragment …
egonw authored
542 list="control,extra,fragment,reaction,pdbcml,libiomd"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
543 <foreach target="compile-module" param="module"
544 parallel="${parallel}" maxthreads="${threadCount}"
7d5fc9d @egonw The smsd module now depends on the signature module
egonw authored
545 list="charges,smarts,signature"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
546 <foreach target="compile-module" param="module"
547 parallel="${parallel}" maxthreads="${threadCount}"
68d21b7 Create tautomers based on InChI
mrynbeek authored
548 list="qm,qsar,ionpot,fingerprint,pcore,smsd,tautomer"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
549 <foreach target="compile-module" param="module"
550 parallel="${parallel}" maxthreads="${threadCount}"
f1ca34b @egonw Render AWT module which allows rendering of the abstract rendering el…
egonw authored
551 list="renderawt"/>
552 <foreach target="compile-module" param="module"
553 parallel="${parallel}" maxthreads="${threadCount}"
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
554 list="qsaratomic,qsarbond,qsarprotein,qsarcml,qsarmolecular"/>
555 <foreach target="compile-module" param="module"
556 parallel="${parallel}" maxthreads="${threadCount}"
6c86f91 @egonw Added missing entry for compiling the iordf module
egonw authored
557 list="forcefield,qsarionpot,iordf"/>
a4d6392 Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
558 <foreach target="compile-module" param="module"
559 parallel="${parallel}" maxthreads="${threadCount}"
560 list="builder3d,builder3dtools"/>
4ecbc9a Added a task for parallelized compiling the CDK libs
egonw authored
561 </target>
fe65a98 Fixed dependencies
egonw authored
562
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
563 <target id="test-dist-all" name="test-dist-all" description="test-dist-all">
564 <antcall target="compile-init"/>
565 <foreach target="compile-module" param="module"
566 parallel="${parallel}" maxthreads="${threadCount}"
567 list="test"/>
568 <foreach target="compile-module" param="module" trim="true"
569 parallel="${parallel}" maxthreads="${threadCount}"
acfb5b5 Setting up implementation independent unit testing if IChemObject cla…
egonw authored
570 list="test-interfaces,test-libiocml,test-qsar,test-io,test-core,
571 test-valencycheck,test-smarts,test-standard,test-reaction,
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
572 test-pcore,test-sdg,test-forcefield,test-fingerprint,
573 test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict,
8a4a98b @egonw Upgraded to the final JNI-InChI 0.7:
egonw authored
574 test-diff,test-charges,test-inchi,test-formula,
751488b @egonw Set up a CIP module.
egonw authored
575 test-render,test-ioformats,test-log4j,test-cip"/>
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
576 <foreach target="compile-module" param="module" trim="true"
577 parallel="${parallel}" maxthreads="${threadCount}"
acfb5b5 Setting up implementation independent unit testing if IChemObject cla…
egonw authored
578 list="test-data,test-qsaratomic,test-qsarbond,
646c37b @egonw Made qsarmolecular independent from data, by creating a new fragment …
egonw authored
579 test-pdb,test-smiles,test-extra,test-fragment,test-atomtype,
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
580 test-structgen,test-iordf,test-silent"/>
3678aaa Add missing trim attrib, fixing whitespace mess up
egonw authored
581 <foreach target="compile-module" param="module" trim="true"
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
582 parallel="${parallel}" maxthreads="${threadCount}"
51af326 @egonw Removed the nonotify module (replaced by silent)
egonw authored
583 list="test-qsarmolecular,test-builder3d,test-datadebug"/>
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
584 <foreach target="compile-module" param="module"
585 parallel="${parallel}" maxthreads="${threadCount}"
68d21b7 Create tautomers based on InChI
mrynbeek authored
586 list="test-qsarprotein,test-qsarionpot,test-smsd,test-tautomer"/>
4ea7d48 @egonw Hooked the signature module into the CDK build system
egonw authored
587 <foreach target="compile-module" param="module"
588 parallel="${parallel}" maxthreads="${threadCount}"
589 list="test-signature"/>
110f4c1 @egonw Setting up the new renderbasic module.
egonw authored
590 <foreach target="compile-module" param="module"
591 parallel="${parallel}" maxthreads="${threadCount}"
592 list="test-renderbasic"/>
f1ca34b @egonw Render AWT module which allows rendering of the abstract rendering el…
egonw authored
593 <foreach target="compile-module" param="module"
594 parallel="${parallel}" maxthreads="${threadCount}"
595 list="test-renderawt"/>
b2a0eed Use ant-contrib's foreach, allowing code cleanup and making running i…
egonw authored
596 </target>
3eac543 Added a parallel task for compiling the test modules too now
egonw authored
597
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now ja…
egonw authored
598 <target id="jarTestdata" name="jarTestdata" description="Creates jar files with test data.">
599 <mkdir dir="${dist}/jar"/>
600 <jar jarfile="${dist}/jar/cdk-testdata.jar">
f280f3f Updated for src/data -> src/test/data move
egonw authored
601 <fileset dir="${src}/test">
a3a838d Solved way too large cdk-test-*.jar's: Test data (src/data) is now ja…
egonw authored
602 <include name="data/**/*" />
603 </fileset>
604 </jar>
605 </target>
606
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
607 <target id="dist-large" name="dist-large" depends="dist-all"
52638d6 Removed the experimental module: classes that are experimental should…
egonw authored
608 description="Builds one big jar file for the CDK, including third-party libraries.">
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
609
c660505 Reworked dist-large target
egonw authored
610 <!-- first unjar the CDK and other jars we need -->
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
611 <mkdir dir="${appjars.dir}"/>
c660505 Reworked dist-large target
egonw authored
612 <unjar dest="${appjars.dir}">
613 <fileset dir="${lib}">
614 <includesfile name="${metainf}/builder3d.libdepends"/>
161b318 Put the helper tool into a separate module, to solve dependency issues.
egonw authored
615 <includesfile name="${metainf}/builder3dtools.libdepends"/>
3673f87 Added missing jar in dist-large target
egonw authored
616 <includesfile name="${metainf}/charges.libdepends"/>
112f64d @egonw Moved the log4j.jar depending LoggingTool into a separate module
egonw authored
617 <includesfile name="${metainf}/log4j.libdepends"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
618 <includesfile name="${metainf}/control.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
619 <includesfile name="${metainf}/datadebug.libdepends"/>
c660505 Reworked dist-large target
egonw authored
620 <includesfile name="${metainf}/data.libdepends"/>
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
621 <includesfile name="${metainf}/silent.libdepends"/>
c660505 Reworked dist-large target
egonw authored
622 <includesfile name="${metainf}/extra.libdepends"/>
751488b @egonw Set up a CIP module.
egonw authored
623 <includesfile name="${metainf}/cip.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
624 <includesfile name="${metainf}/io.libdepends"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the modu…
egonw authored
625 <includesfile name="${metainf}/libiocml.libdepends"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
626 <includesfile name="${metainf}/pdbcml.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
627 <includesfile name="${metainf}/pdb.libdepends"/>
c660505 Reworked dist-large target
egonw authored
628 <includesfile name="${metainf}/qsar.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
629 <includesfile name="${metainf}/qsaratomic.libdepends"/>
630 <includesfile name="${metainf}/qsarbond.libdepends"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
631 <includesfile name="${metainf}/qsarmolecular.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
632 <includesfile name="${metainf}/qsarprotein.libdepends"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
633 <includesfile name="${metainf}/qsarcml.libdepends"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
634 <includesfile name="${metainf}/reaction.libdepends"/>
c660505 Reworked dist-large target
egonw authored
635 <includesfile name="${metainf}/render.libdepends"/>
191bbb3 @egonw Include renderbasic in the large jar dist
egonw authored
636 <includesfile name="${metainf}/renderbasic.libdepends"/>
d5f042f @rajarshi Updated build.xml to properly include AWT rendering classes in the la…
rajarshi authored
637 <includesfile name="${metainf}/renderawt.libdepends"/>
c660505 Reworked dist-large target
egonw authored
638 <includesfile name="${metainf}/standard.libdepends"/>
9db2505 Added missing jars to dist-large target
egonw authored
639 <includesfile name="${metainf}/valencycheck.libdepends"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
640 <includesfile name="${metainf}/sdg.libdepends"/>
be50e2b Added new structgen module to dist-large.
egonw authored
641 <includesfile name="${metainf}/forcefield.libdepends"/>
0bf100d Added InChI module to regular compile setup
egonw authored
642 <includesfile name="${metainf}/inchi.libdepends"/>
cd11a7e Updated build script so that dist-large includes the smarts module
rajarshi authored
643 <includesfile name="${metainf}/smarts.libdepends"/>
ee5e0a2 @rajarshi Minor fix to build.xml to ensure that SMSD code gets included in the …
rajarshi authored
644 <includesfile name="${metainf}/smsd.libdepends"/>
71ce329 Updated build.xml to include the pcore module in the big jar file
rajarshi authored
645 <includesfile name="${metainf}/pcore.libdepends"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
646 <includesfile name="${metainf}/formula.libdepends"/>
ea8c273 Fixed dist-large generation: diff does not have any libdepends
egonw authored
647 <includesfile name="${metainf}/isomorphism.libdepends"/>
e2c95ec @egonw Included the qm module in the dist-all (fixes #3002622)
egonw authored
648 <includesfile name="${metainf}/qm.libdepends"/>
2854df5 @egonw Added iordf to dist-large
egonw authored
649 <includesfile name="${metainf}/iordf.libdepends"/>
4ea7d48 @egonw Hooked the signature module into the CDK build system
egonw authored
650 <includesfile name="${metainf}/signature.libdepends"/>
c660505 Reworked dist-large target
egonw authored
651 </fileset>
652 <fileset dir="${dist}/jar">
2d74153 Updated for annotation and ioformats
egonw authored
653 <include name="cdk-annotation.jar"/>
654 <include name="cdk-ioformats.jar"/>
afac743 Set up the atomtype module
egonw authored
655 <include name="cdk-atomtype.jar"/>
c660505 Reworked dist-large target
egonw authored
656 <include name="cdk-builder3d.jar"/>
161b318 Put the helper tool into a separate module, to solve dependency issues.
egonw authored
657 <include name="cdk-builder3dtools.jar"/>
3673f87 Added missing jar in dist-large target
egonw authored
658 <include name="cdk-charges.jar"/>
c660505 Reworked dist-large target
egonw authored
659 <include name="cdk-core.jar"/>
751488b @egonw Set up a CIP module.
egonw authored
660 <include name="cdk-cip.jar"/>
112f64d @egonw Moved the log4j.jar depending LoggingTool into a separate module
egonw authored
661 <include name="cdk-log4j.jar"/>
0a739e8 Updted to include cdk-dict.jar in the big jar
rajarshi authored
662 <include name="cdk-dict.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
663 <include name="cdk-diff.jar"/>
dece975 Fixed the build script to properly incldue the control module and its…
rajarshi authored
664 <include name="cdk-control.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
665 <include name="cdk-datadebug.jar"/>
c660505 Reworked dist-large target
egonw authored
666 <include name="cdk-data.jar"/>
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
667 <include name="cdk-silent.jar"/>
c660505 Reworked dist-large target
egonw authored
668 <include name="cdk-extra.jar"/>
646c37b @egonw Made qsarmolecular independent from data, by creating a new fragment …
egonw authored
669 <include name="cdk-fragment.jar"/>
c660505 Reworked dist-large target
egonw authored
670 <include name="cdk-interfaces.jar"/>
671 <include name="cdk-io.jar"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the modu…
egonw authored
672 <include name="cdk-libiocml.jar"/>
8459c22 Included the libiomd module
egonw authored
673 <include name="cdk-libiomd.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
674 <include name="cdk-pdbcml.jar"/>
9db2505 Added missing jars to dist-large target
egonw authored
675 <include name="cdk-pdb.jar"/>
c660505 Reworked dist-large target
egonw authored
676 <include name="cdk-qsar.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
677 <include name="cdk-qsaratomic.jar"/>
678 <include name="cdk-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
679 <include name="cdk-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
680 <include name="cdk-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
681 <include name="cdk-qsarprotein.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
682 <include name="cdk-qsarcml.jar"/>
41766ae new reaction type class which contains reaction processes
miguelrojasch authored
683 <include name="cdk-reaction.jar"/>
c660505 Reworked dist-large target
egonw authored
684 <include name="cdk-render.jar"/>
191bbb3 @egonw Include renderbasic in the large jar dist
egonw authored
685 <include name="cdk-renderbasic.jar"/>
d5f042f @rajarshi Updated build.xml to properly include AWT rendering classes in the la…
rajarshi authored
686 <include name="cdk-renderawt.jar"/>
c660505 Reworked dist-large target
egonw authored
687 <include name="cdk-standard.jar"/>
be50e2b Added new structgen module to dist-large.
egonw authored
688 <include name="cdk-structgen.jar"/>
9c7431a Fixed stupid typo
egonw authored
689 <include name="cdk-valencycheck.jar"/>
f86e117 Created the smiles module
egonw authored
690 <include name="cdk-forcefield.jar"/>
691 <include name="cdk-smiles.jar"/>
cd11a7e Updated build script so that dist-large includes the smarts module
rajarshi authored
692 <include name="cdk-smarts.jar"/>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
693 <include name="cdk-fingerprint.jar"/>
41a8981 Created unit tests for cdk-inchi module
sea36 authored
694 <include name="cdk-sdg.jar"/>
0bf100d Added InChI module to regular compile setup
egonw authored
695 <include name="cdk-inchi.jar"/>
71ce329 Updated build.xml to include the pcore module in the big jar file
rajarshi authored
696 <include name="cdk-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
697 <include name="cdk-formula.jar"/>
2e98012 Added missing ionpot to dist-large
egonw authored
698 <include name="cdk-isomorphism.jar"/>
699 <include name="cdk-ionpot.jar"/>
ee5e0a2 @rajarshi Minor fix to build.xml to ensure that SMSD code gets included in the …
rajarshi authored
700 <include name="cdk-smsd.jar"/>
2854df5 @egonw Added iordf to dist-large
egonw authored
701 <include name="cdk-iordf.jar"/>
4ea7d48 @egonw Hooked the signature module into the CDK build system
egonw authored
702 <include name="cdk-signature.jar"/>
e2c95ec @egonw Included the qm module in the dist-all (fixes #3002622)
egonw authored
703 <include name="cdk-qm.jar"/>
68d21b7 Create tautomers based on InChI
mrynbeek authored
704 <include name="cdk-tautomer.jar"/>
c660505 Reworked dist-large target
egonw authored
705 </fileset>
706 </unjar>
9db2505 Added missing jars to dist-large target
egonw authored
707
c660505 Reworked dist-large target
egonw authored
708 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what…
rajarshi authored
709 <jar jarfile="${dist}/jar/cdk-${version}.jar">
c660505 Reworked dist-large target
egonw authored
710 <manifest>
711 <section name="org.openscience.cdk">
712 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
f9b5fe6 @egonw Bumped the Specification version to 1.4
egonw authored
713 <attribute name="Specification-Version" value="1.4"/>
c660505 Reworked dist-large target
egonw authored
714 <attribute name="Specification-Vendor" value="The CDK Project"/>
715 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
716 <attribute name="Implementation-Version" value="${version}"/>
717 <attribute name="Implementation-Vendor" value="The CDK Project"/>
7406c2b Made the code Java 5 compilable.
dmak authored
718 <attribute name="X-Compile-Target-JDK" value="${compile.target.version}"/>
c660505 Reworked dist-large target
egonw authored
719 </section>
720 </manifest>
721 <fileset dir="${appjars.dir}">
722 <include name="**/*" />
723 </fileset>
724 </jar>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -j…
egonw authored
725 </target>
726
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
727 <target id="dist-pure" name="dist-pure" depends="dist-all"
52638d6 Removed the experimental module: classes that are experimental should…
egonw authored
728 description="Builds one big jar file for the CDK, excluding third party libraries.">
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
729
730 <!-- first unjar the CDK and other jars we need -->
731 <mkdir dir="${appjars.dir}"/>
732 <unjar dest="${appjars.dir}">
733 <fileset dir="${dist}/jar">
2d74153 Updated for annotation and ioformats
egonw authored
734 <include name="cdk-annotation.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
735 <include name="cdk-builder3d.jar"/>
736 <include name="cdk-builder3dtools.jar"/>
737 <include name="cdk-charges.jar"/>
112f64d @egonw Moved the log4j.jar depending LoggingTool into a separate module
egonw authored
738 <include name="cdk-log4j.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
739 <include name="cdk-core.jar"/>
751488b @egonw Set up a CIP module.
egonw authored
740 <include name="cdk-cip.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
741 <include name="cdk-control.jar"/>
742 <include name="cdk-datadebug.jar"/>
743 <include name="cdk-data.jar"/>
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
744 <include name="cdk-silent.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
745 <include name="cdk-diff.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
746 <include name="cdk-extra.jar"/>
646c37b @egonw Made qsarmolecular independent from data, by creating a new fragment …
egonw authored
747 <include name="cdk-fragment.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
748 <include name="cdk-interfaces.jar"/>
749 <include name="cdk-io.jar"/>
2d74153 Updated for annotation and ioformats
egonw authored
750 <include name="cdk-ioformats.jar"/>
7e20d83 Fixed libiocml module: remove '-' and added a test suite for the modu…
egonw authored
751 <include name="cdk-libiocml.jar"/>
8459c22 Included the libiomd module
egonw authored
752 <include name="cdk-libiomd.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
753 <include name="cdk-pdbcml.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
754 <include name="cdk-pdb.jar"/>
755 <include name="cdk-qsar.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
756 <include name="cdk-qsaratomic.jar"/>
757 <include name="cdk-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
758 <include name="cdk-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
759 <include name="cdk-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
760 <include name="cdk-qsarprotein.jar"/>
71667e6 Removed hyphens from the module names pdb_cml and qsar_pdb
egonw authored
761 <include name="cdk-qsarcml.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
762 <include name="cdk-reaction.jar"/>
763 <include name="cdk-render.jar"/>
d5f042f @rajarshi Updated build.xml to properly include AWT rendering classes in the la…
rajarshi authored
764 <include name="cdk-renderbasic.jar"/>
765 <include name="cdk-renderawt.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
766 <include name="cdk-standard.jar"/>
767 <include name="cdk-structgen.jar"/>
768 <include name="cdk-valencycheck.jar"/>
769 <include name="cdk-forcefield.jar"/>
45c8c0c Added smarts to JUnit testing
egonw authored
770 <include name="cdk-smarts.jar"/>
a97064c Created a fingerprint module, reducing deps on extra
egonw authored
771 <include name="cdk-fingerprint.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
772 <include name="cdk-smiles.jar"/>
773 <include name="cdk-sdg.jar"/>
774 <include name="cdk-inchi.jar"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
775 <include name="cdk-pcore.jar"/>
5eb312a Added missing jar to dist-pure: atomtype
egonw authored
776 <include name="cdk-formula.jar"/>
777 <include name="cdk-atomtype.jar"/>
4ea7d48 @egonw Hooked the signature module into the CDK build system
egonw authored
778 <include name="cdk-signature.jar"/>
68d21b7 Create tautomers based on InChI
mrynbeek authored
779 <include name="cdk-tautomer.jar"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
780 </fileset>
781 </unjar>
782
783 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what…
rajarshi authored
784 <jar jarfile="${dist}/jar/cdk-pure-${version}.jar">
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
785 <manifest>
786 <section name="org.openscience.cdk">
787 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
788 <attribute name="Specification-Version" value="1.0"/>
789 <attribute name="Specification-Vendor" value="The CDK Project"/>
790 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
791 <attribute name="Implementation-Version" value="${version}"/>
792 <attribute name="Implementation-Vendor" value="The CDK Project"/>
7406c2b Made the code Java 5 compilable.
dmak authored
793 <attribute name="X-Compile-Target-JDK" value="${compile.target.version}"/>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
794 </section>
795 </manifest>
796 <fileset dir="${appjars.dir}">
797 <include name="**/*" />
798 </fileset>
799 </jar>
800 </target>
801
f2080e1 @egonw But the test data should be added too
egonw authored
802 <target id="dist-test-large" name="dist-test-large" depends="test-dist-all, jarTestdata"
88311e5 Added target for a jar with all the test stuff
egonw authored
803 description="Builds on big jar file for the CDK test classes.">
804
805 <!-- first unjar the CDK and other jars we need -->
806 <mkdir dir="${appjars.dir}"/>
807 <unjar dest="${appjars.dir}">
808 <fileset dir="${lib}">
02fec4a @egonw Added the missing cdk-test.jar (patch by Jonty Lawson)
egonw authored
809 <includesfile name="${metainf}/test.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
810 <includesfile name="${metainf}/test-core.libdepends"/>
811 <includesfile name="${metainf}/test-data.libdepends"/>
812 <includesfile name="${metainf}/test-datadebug.libdepends"/>
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
813 <includesfile name="${metainf}/test-silent.libdepends"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
814 <includesfile name="${metainf}/test-diff.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
815 <includesfile name="${metainf}/test-extra.libdepends"/>
646c37b @egonw Made qsarmolecular independent from data, by creating a new fragment …
egonw authored
816 <includesfile name="${metainf}/test-fragment.libdepends"/>
d31ee42 New module: test-builder3d
egonw authored
817 <includesfile name="${metainf}/test-builder3d.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
818 <includesfile name="${metainf}/test-forcefield.libdepends"/>
819 <includesfile name="${metainf}/test-inchi.libdepends"/>
820 <includesfile name="${metainf}/test-io.libdepends"/>
821 <includesfile name="${metainf}/test-pdb.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
822 <includesfile name="${metainf}/test-qsaratomic.libdepends"/>
823 <includesfile name="${metainf}/test-qsarbond.libdepends"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
824 <includesfile name="${metainf}/test-qsarmolecular.libdepends"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
825 <includesfile name="${metainf}/test-qsarionpot.libdepends"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
826 <includesfile name="${metainf}/test-qsarprotein.libdepends"/>
827 <includesfile name="${metainf}/test-qsar.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
828 <includesfile name="${metainf}/test-reaction.libdepends"/>
45c8c0c Added smarts to JUnit testing
egonw authored
829 <includesfile name="${metainf}/test-smarts.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
830 <includesfile name="${metainf}/test-smiles.libdepends"/>
831 <includesfile name="${metainf}/test-standard.libdepends"/>
be50e2b Added new structgen module to dist-large.
egonw authored
832 <includesfile name="${metainf}/test-structgen.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
833 <includesfile name="${metainf}/test-valencycheck.libdepends"/>
cb52b54 Hooked in stuff for the charges module
egonw authored
834 <includesfile name="${metainf}/test-charges.libdepends"/>
8459c22 Included the libiomd module
egonw authored
835 <includesfile name="${metainf}/test-libiomd.libdepends"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
836 <includesfile name="${metainf}/test-pcore.libdepends"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
837 <includesfile name="${metainf}/test-formula.libdepends"/>
cb5b4ae Set up testing for the render module
egonw authored
838 <includesfile name="${metainf}/test-render.libdepends"/>
112f64d @egonw Moved the log4j.jar depending LoggingTool into a separate module
egonw authored
839 <includesfile name="${metainf}/test-log4j.libdepends"/>
4ea7d48 @egonw Hooked the signature module into the CDK build system
egonw authored
840 <includesfile name="${metainf}/test-signature.libdepends"/>
751488b @egonw Set up a CIP module.
egonw authored
841 <includesfile name="${metainf}/test-cip.libdepends"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
842 </fileset>
843 <fileset dir="${dist}/jar">
02fec4a @egonw Added the missing cdk-test.jar (patch by Jonty Lawson)
egonw authored
844 <include name="cdk-test.jar"/>
f2080e1 @egonw But the test data should be added too
egonw authored
845 <include name="cdk-testdata.jar"/>
2d74153 Updated for annotation and ioformats
egonw authored
846 <include name="cdk-test-annotation.jar"/>
847 <include name="cdk-test-ioformats.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
848 <include name="cdk-test-core.jar"/>
849 <include name="cdk-test-data.jar"/>
850 <include name="cdk-test-datadebug.jar"/>
78fb9c8 @egonw Implemented the silent module as a nonotify replacement, copied from …
egonw authored
851 <include name="cdk-test-silent.jar"/>
bcbcaa7 First draft on diffing IChemObject's.
egonw authored
852 <include name="cdk-test-diff.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
853 <include name="cdk-test-extra.jar"/>
646c37b @egonw Made qsarmolecular independent from data, by creating a new fragment …
egonw authored
854 <include name="cdk-test-fragment.jar"/>
d31ee42 New module: test-builder3d
egonw authored
855 <include name="cdk-test-builder3d.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
856 <include name="cdk-test-forcefield.jar"/>
857 <include name="cdk-test-inchi.jar"/>
858 <include name="cdk-test-io.jar"/>
859 <include name="cdk-test-pdb.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
860 <include name="cdk-test-qsaratomic.jar"/>
861 <include name="cdk-test-qsarbond.jar"/>
5b57bad Forgot to upload the changed build.xml to reflect the new qsarmolecul…
egonw authored
862 <include name="cdk-test-qsarmolecular.jar"/>
cf7d72f Ported patch from the egonw-cleanlibiocml branch: Created an qsarionp…
egonw authored
863 <include name="cdk-test-qsarionpot.jar"/>
03c62ba Set up the modules qsaratomic, qsarbond and qsarprotein
egonw authored
864 <include name="cdk-test-qsarprotein.jar"/>
865 <include name="cdk-test-qsar.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
866 <include name="cdk-test-reaction.jar"/>
45c8c0c Added smarts to JUnit testing
egonw authored
867 <include name="cdk-test-smarts.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
868 <include name="cdk-test-smiles.jar"/>
869 <include name="cdk-test-standard.jar"/>
be50e2b Added new structgen module to dist-large.
egonw authored
870 <include name="cdk-test-structgen.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
871 <include name="cdk-test-valencycheck.jar"/>
cb52b54 Hooked in stuff for the charges module
egonw authored
872 <include name="cdk-test-charges.jar"/>
8459c22 Included the libiomd module
egonw authored
873 <include name="cdk-test-libiomd.jar"/>
9c15cf9 Updated scripts so that testing is performed on the pcore module
rajarshi authored
874 <include name="cdk-test-pcore.jar"/>
bf6d69c Applied the mf/ branch to trunk/
egonw authored
875 <include name="cdk-test-formula.jar"/>
cb5b4ae Set up testing for the render module
egonw authored
876 <include name="cdk-test-render.jar"/>
112f64d @egonw Moved the log4j.jar depending LoggingTool into a separate module
egonw authored
877 <include name="cdk-test-log4j.jar"/>
4ea7d48 @egonw Hooked the signature module into the CDK build system
egonw authored
878 <include name="cdk-test-signature.jar"/>
68d21b7 Create tautomers based on InChI
mrynbeek authored
879 <include name="cdk-test-cip.jar"/>
880 <include name="cdk-test-tautomer.jar"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
881 </fileset>
882 </unjar>
883
884 <!-- then zip up things -->
169e29a Updated build.xml to remove usage of a date stamp and rather use what…
rajarshi authored
885 <jar jarfile="${dist}/jar/cdk-test-${version}.jar">
88311e5 Added target for a jar with all the test stuff
egonw authored
886 <manifest>
0ed56fa Fixed with respect to cdk.test now being cdk (together with src/test)
egonw authored
887 <attribute name="Main-Class" value="org.openscience.cdk.CDKTests"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
888 <section name="org.openscience.cdk">
889 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
f9b5fe6 @egonw Bumped the Specification version to 1.4
egonw authored
890 <attribute name="Specification-Version" value="1.4"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
891 <attribute name="Specification-Vendor" value="The CDK Project"/>
892 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
893 <attribute name="Implementation-Version" value="${version}"/>
894 <attribute name="Implementation-Vendor" value="The CDK Project"/>
7406c2b Made the code Java 5 compilable.
dmak authored
895 <attribute name="X-Compile-Target-JDK" value="${compile.target.version}"/>
88311e5 Added target for a jar with all the test stuff
egonw authored
896 </section>
897 </manifest>
898 <fileset dir="${appjars.dir}">
899 <include name="**/*" />
900 </fileset>
901 </jar>
902 </target>
e423642 Added 'pure' variants of sourcedist and dist-large, for situations wh…
egonw authored
903
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
904 <target id="sourcedist" name="sourcedist"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
905 description="Builds the source packages.">
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
906 <property name="package" value="cdk-src+libs-${version}"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
907 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
908 <delete dir="${sourcedist.dir}"/>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
909 <copy todir="${sourcedist.dir}/${src}/main/">
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
910 <fileset dir="${src}/main/" includes="**/*.java" />
911 <fileset dir="${src}/main/" includes="**/*.jj" />
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
912 <fileset dir="${src}/main/" includes="**/*.jjt" />
7c5c872 Merged the branch egonw/maintest: sets up src/main and src/test for s…
egonw authored
913 <fileset dir="${src}/main/" includes="org/openscience/cdk/io/cml/data/**" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
914 </copy>
915 <copy todir="${sourcedist.dir}">
7447e16 Getting ready for release
egonw authored
916 <fileset dir="." includes="build.props" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
917 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
918 <fileset dir="." includes="javadoc.xml" />
919 <fileset dir="." includes="README" />
e99a32a Preparing for a release
egonw authored
920 <fileset dir="." includes="changelog*" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
921 </copy>
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
922 <copy todir="${sourcedist.dir}/jar">
923 <fileset dir="jar">
924 <exclude name="*.so"/>
925 <exclude name="*.dll"/>
926 <exclude name="jumbo-5.4.2-b2.jar"/>
927 </fileset>
928 </copy>
1cd2124 @egonw Added missing references file to the source dist (full and pure)
egonw authored
929 <copy todir="${sourcedist.dir}/doc/refs">
930 <fileset dir="doc/refs">
931 <include name="*.*"/>
932 </fileset>
933 </copy>
998ae6a Updated for current CVS.
egonw authored
934 <copy todir="${sourcedist.dir}/develjar">
935 <fileset dir="develjar">
936 <exclude name="pmd-1.8.jar"/>
937 <exclude name="dbdoclet*.*"/>
938 </fileset>
939 </copy>
940 <copy todir="${sourcedist.dir}/src/META-INF">
941 <fileset dir="src/META-INF" />
942 </copy>
68536e1 @egonw Changed how data files are copied: copy those specified in the src/ME…
egonw authored
943 <copy todir="${sourcedist.dir}/${src}/main/">
944 <fileset dir="${src}/main/" includesfile="${src}/META-INF/atomtype.datafiles" />
945 <fileset dir="${src}/main/" includesfile="${src}/META-INF/builder3d.datafiles" />
946 <fileset dir="${src}/main/" includesfile="${src}/META-INF/core.datafiles" />
947 <fileset dir="${src}/main/" includesfile="${src}/META-INF/dict.datafiles" />
948 <fileset dir="${src}/main/" includesfile="${src}/META-INF/extra.datafiles" />
949 <fileset dir="${src}/main/" includesfile="${src}/META-INF/fingerprint.datafiles" />
950 <fileset dir="${src}/main/" includesfile="${src}/META-INF/forcefield.datafiles" />
951 <fileset dir="${src}/main/" includesfile="${src}/META-INF/io.datafiles" />
952 <fileset dir="${src}/main/" includesfile="${src}/META-INF/log4j.datafiles" />
953 <fileset dir="${src}/main/" includesfile="${src}/META-INF/pdb.datafiles" />
954 <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsaratomic.datafiles" />
955 <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsar.datafiles" />
956 <fileset dir="${src}/main/" includesfile="${src}/META-INF/qsarmolecular.datafiles" />
957 <fileset dir="${src}/main/" includesfile="${src}/META-INF/sdg.datafiles" />
5bcd111 @egonw Copy the 2D templates into the source distribution
egonw authored
958 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
959 <mkdir dir="${sourcedist.dir}/doc/" />
960 <copy todir="${sourcedist.dir}/doc/">
961 <fileset dir="doc/" includes="lgpl.license" />
962 </copy>
7447e16 Getting ready for release
egonw authored
963 <mkdir dir="${sourcedist.dir}/doc/javadoc" />
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
964 <!-- the below deteles are a workaround, because the above should not have copied
965 in the src/data and src/org/openscience/cdk/test dirs -->
8da930e Fixing sourcedist building: fixes paths, smarts/*.jtt to include; rel…
egonw authored
966 <delete dir="${sourcedist.dir}/src/test/data"/>
218de5b Release Candidate 1 for the CDK: 0.99.1. Now on SourceForge! Happy bu…
egonw authored
967
968 <!-- now package things up -->
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
969 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
a0ba425 Updated sourcedist target so that it uses the current date for the fi…
rajarshi authored
970 <gzip zipfile="${package}.tar.gz" src="${package}.tar" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
971 <delete file="${package}.tar" />
972 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
998ae6a Updated for current CVS.
egonw authored
973 </target>
5e15181