Upgrade java3d dependency - we previously used 1.5.2 then switch to 1…

….3.1 but this had an API difference that users depended on.
cdk · Aug 26, 2015 · 40c1007 · 40c1007
1 parent dfd18ef
commit 40c1007
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Showing 54 changed files with 55 additions and 58 deletions.
diff --git a/base/data/pom.xml b/base/data/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-data</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/base/datadebug/pom.xml b/base/datadebug/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-datadebug</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/base/interfaces/pom.xml b/base/interfaces/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-interfaces</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/base/isomorphism/pom.xml b/base/isomorphism/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-isomorphism</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/base/silent/pom.xml b/base/silent/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-silent</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/base/standard/pom.xml b/base/standard/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-standard</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/base/test-interfaces/pom.xml b/base/test-interfaces/pom.xml
@@ -31,7 +31,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/base/test-standard/pom.xml b/base/test-standard/pom.xml
@@ -26,7 +26,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/base/test-valencycheck/pom.xml b/base/test-valencycheck/pom.xml
@@ -26,7 +26,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/base/test/pom.xml b/base/test/pom.xml
@@ -25,7 +25,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/descriptor/cip/pom.xml b/descriptor/cip/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-cip</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/fingerprint/pom.xml b/descriptor/fingerprint/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-fingerprint</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/ionpot/pom.xml b/descriptor/ionpot/pom.xml
@@ -36,7 +36,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/descriptor/qsar/pom.xml b/descriptor/qsar/pom.xml
@@ -19,7 +19,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/qsaratomic/pom.xml b/descriptor/qsaratomic/pom.xml
@@ -19,7 +19,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/qsarbond/pom.xml b/descriptor/qsarbond/pom.xml
@@ -19,7 +19,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/qsarcml/pom.xml b/descriptor/qsarcml/pom.xml
@@ -35,7 +35,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/descriptor/qsarionpot/pom.xml b/descriptor/qsarionpot/pom.xml
@@ -25,7 +25,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/descriptor/qsarmolecular/pom.xml b/descriptor/qsarmolecular/pom.xml
@@ -19,7 +19,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/qsarprotein/pom.xml b/descriptor/qsarprotein/pom.xml
@@ -19,7 +19,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/descriptor/signature/pom.xml b/descriptor/signature/pom.xml
@@ -43,7 +43,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/display/render/pom.xml b/display/render/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-render</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/display/renderawt/pom.xml b/display/renderawt/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-renderawt</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/display/renderbasic/pom.xml b/display/renderbasic/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-renderbasic</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/display/renderextra/pom.xml b/display/renderextra/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-renderextra</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/misc/control/pom.xml b/misc/control/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-control</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/misc/diff/pom.xml b/misc/diff/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-diff</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/misc/extra/pom.xml b/misc/extra/pom.xml
@@ -18,7 +18,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/misc/log4j/pom.xml b/misc/log4j/pom.xml
@@ -30,7 +30,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/misc/test-extra/pom.xml b/misc/test-extra/pom.xml
@@ -48,7 +48,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/pom.xml b/pom.xml
@@ -403,9 +403,9 @@
                 <version>1.9.5</version>
             </dependency>
             <dependency>
-                <groupId>java3d</groupId>
+                <groupId>javax.vecmath</groupId>
                 <artifactId>vecmath</artifactId>
-                <version>1.3.1</version>
+                <version>1.5.2</version>
             </dependency>
             <dependency>
                 <groupId>gov.nist.math</groupId>
@@ -546,9 +546,6 @@
                     <rulesets>
                         <ruleset>/pmd/custom.xml</ruleset>
                     </rulesets>
-                    <excludes>
-                        <exclude>**/smsd/*.java</exclude>
-                    </excludes>
                     <excludeRoots>
                         <excludeRoot>${basedir}/target/generated-sources/javacc</excludeRoot>
                     </excludeRoots>

diff --git a/storage/inchi/pom.xml b/storage/inchi/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-inchi</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/storage/io/pom.xml b/storage/io/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-io</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/storage/ioformats/pom.xml b/storage/ioformats/pom.xml
@@ -41,7 +41,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/storage/iordf/pom.xml b/storage/iordf/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-iordf</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/storage/libiocml/pom.xml b/storage/libiocml/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-libiocml</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/storage/libiomd/pom.xml b/storage/libiomd/pom.xml
@@ -35,7 +35,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/storage/pdb/pom.xml b/storage/pdb/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-pdb</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/storage/pdbcml/pom.xml b/storage/pdbcml/pom.xml
@@ -35,7 +35,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
             <scope>test</scope>
         </dependency>

diff --git a/storage/smiles/pom.xml b/storage/smiles/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-smiles</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/tool/builder3d/pom.xml b/tool/builder3d/pom.xml
@@ -19,7 +19,7 @@
             <artifactId>jama</artifactId>
         </dependency>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/tool/builder3dtools/pom.xml b/tool/builder3dtools/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-builder3dtools</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>

diff --git a/tool/charges/pom.xml b/tool/charges/pom.xml
@@ -15,7 +15,7 @@
     <name>cdk-charges</name>
     <dependencies>
         <dependency>
-            <groupId>java3d</groupId>
+            <groupId>javax.vecmath</groupId>
             <artifactId>vecmath</artifactId>
         </dependency>
         <dependency>