Author: mes
Date: 2011-03-10 12:39:22 -0800 (Thu, 10 Mar 2011)
New Revision: 24382
Modified:
cytoscape/trunk/acceptance-testing/pom.xml
cytoscape/trunk/application/pom.xml
cytoscape/trunk/archetypes/sample-plugin/pom.xml
cytoscape/trunk/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml
cytoscape/trunk/corelibs/ding/pom.xml
cytoscape/trunk/corelibs/docs/pom.xml
cytoscape/trunk/corelibs/fing/pom.xml
cytoscape/trunk/corelibs/geom.rtree/pom.xml
cytoscape/trunk/corelibs/geom.spacial/pom.xml
cytoscape/trunk/corelibs/graph.dynamic/pom.xml
cytoscape/trunk/corelibs/graph.fixed/pom.xml
cytoscape/trunk/corelibs/render.stateful/pom.xml
cytoscape/trunk/coreplugins/EquationFunctions/pom.xml
cytoscape/trunk/coreplugins/ManualLayout/pom.xml
cytoscape/trunk/coreplugins/PSI-MI/pom.xml
cytoscape/trunk/coreplugins/cPath2/pom.xml
cytoscape/trunk/coreplugins/pom.xml
cytoscape/trunk/distribution/pom.xml
cytoscape/trunk/javadoc/pom.xml
cytoscape/trunk/packaging/pom.xml
cytoscape/trunk/pom.xml
cytoscape/trunk/webstart/pom.xml
Log:
updates for maven 3
Modified: cytoscape/trunk/acceptance-testing/pom.xml
===================================================================
--- cytoscape/trunk/acceptance-testing/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/acceptance-testing/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -20,7 +20,7 @@
<dependency>
<groupId>cytoscape</groupId>
<artifactId>application</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>junit</groupId>
Modified: cytoscape/trunk/application/pom.xml
===================================================================
--- cytoscape/trunk/application/pom.xml 2011-03-10 20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/application/pom.xml 2011-03-10 20:39:22 UTC (rev 24382)
@@ -41,7 +41,7 @@
<artifactItem>
<groupId>cytoscape.corelibs</groupId>
<artifactId>docs</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<type>zip</type>
<classifier>javahelp</classifier>
<overWrite>true</overWrite>
@@ -75,6 +75,7 @@
<plugin>
<groupId>org.jvnet.jaxb2.maven2</groupId>
<artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.7.4</version>
<executions>
<execution>
<id>session</id>
@@ -156,6 +157,22 @@
</goals>
</execution>
</executions>
+ <!-- We need to specify this so that we can exclude fop,
+ otherwise we get duplicate XML libs, which cause
problems. -->
+ <dependencies>
+ <dependency>
+ <groupId>batik</groupId>
+ <artifactId>batik-rasterizer-ext</artifactId>
+ <version>1.6-1</version>
+ <scope>compile</scope>
+ <exclusions>
+ <exclusion>
+ <artifactId>fop</artifactId>
+ <groupId>fop</groupId>
+ </exclusion>
+ </exclusions>
+ </dependency>
+ </dependencies>
</plugin>
</plugins>
</build>
@@ -190,108 +207,100 @@
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Maven 2 Repository</name>
- <url>http://download.java.net/maven/2
- </url>
+ <url>http://download.java.net/maven/2</url>
</pluginRepository>
- <pluginRepository>
- <id>maven-repository.dev.java.net</id>
- <name>Java.net Maven 1 Repository (legacy)</name>
- <url>http://download.java.net/maven/1
- </url>
- <layout>legacy</layout>
- </pluginRepository>
</pluginRepositories>
<dependencies>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-dynamic</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-fixed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>giny</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-immed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-stateful</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-export</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>fing</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>phoebe-dnd</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-spacial</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-rtree</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>undo-support</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>equations</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>task</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>ding</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>obo</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>commons-cli-1-x-cytocape-custom</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>docs</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>javahelp</classifier>
<type>zip</type>
</dependency>
Modified: cytoscape/trunk/archetypes/sample-plugin/pom.xml
===================================================================
--- cytoscape/trunk/archetypes/sample-plugin/pom.xml 2011-03-10 20:10:31 UTC
(rev 24381)
+++ cytoscape/trunk/archetypes/sample-plugin/pom.xml 2011-03-10 20:39:22 UTC
(rev 24382)
@@ -23,6 +23,7 @@
</extensions>
<plugins>
<plugin>
+ <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-archetype-plugin</artifactId>
<version>2.0-alpha-5</version>
<extensions>true</extensions>
@@ -36,6 +37,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-invoker-plugin</artifactId>
+ <version>1.5</version>
<executions>
<execution>
<id>integration-test</id>
@@ -68,6 +70,7 @@
</configuration>
</plugin>
<plugin>
+ <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-clean-plugin</artifactId>
<version>2.4.1</version>
<executions>
Modified:
cytoscape/trunk/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml
===================================================================
---
cytoscape/trunk/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml
2011-03-10 20:10:31 UTC (rev 24381)
+++
cytoscape/trunk/archetypes/sample-plugin/src/main/resources/archetype-resources/pom.xml
2011-03-10 20:39:22 UTC (rev 24382)
@@ -4,7 +4,7 @@
<groupId>${groupId}</groupId>
<artifactId>${artifactId}</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<packaging>jar</packaging>
<name>sample-plugin</name>
Modified: cytoscape/trunk/corelibs/ding/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/ding/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/corelibs/ding/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -41,62 +41,62 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-dynamic</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-fixed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>giny</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-immed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-stateful</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-export</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>fing</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>phoebe-dnd</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-spacial</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-rtree</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>undo-support</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/corelibs/docs/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/docs/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/corelibs/docs/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -40,7 +40,9 @@
<build>
<plugins>
<plugin>
+ <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
+ <version>2.2.1</version>
<configuration>
<descriptors>
<descriptor>src/main/assembly/html.xml</descriptor>
@@ -113,6 +115,7 @@
<plugin>
<groupId>com.agilejava.docbkx</groupId>
<artifactId>docbkx-maven-plugin</artifactId>
+ <version>2.0.9</version>
<executions>
<execution>
<goals>
Modified: cytoscape/trunk/corelibs/fing/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/fing/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/corelibs/fing/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -41,22 +41,22 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-dynamic</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-fixed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>giny</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/corelibs/geom.rtree/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/geom.rtree/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/corelibs/geom.rtree/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -41,12 +41,12 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-spacial</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/corelibs/geom.spacial/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/geom.spacial/pom.xml 2011-03-10 20:10:31 UTC
(rev 24381)
+++ cytoscape/trunk/corelibs/geom.spacial/pom.xml 2011-03-10 20:39:22 UTC
(rev 24382)
@@ -41,7 +41,7 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/corelibs/graph.dynamic/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/graph.dynamic/pom.xml 2011-03-10 20:10:31 UTC
(rev 24381)
+++ cytoscape/trunk/corelibs/graph.dynamic/pom.xml 2011-03-10 20:39:22 UTC
(rev 24382)
@@ -41,12 +41,12 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-fixed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/corelibs/graph.fixed/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/graph.fixed/pom.xml 2011-03-10 20:10:31 UTC
(rev 24381)
+++ cytoscape/trunk/corelibs/graph.fixed/pom.xml 2011-03-10 20:39:22 UTC
(rev 24382)
@@ -41,7 +41,7 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/corelibs/render.stateful/pom.xml
===================================================================
--- cytoscape/trunk/corelibs/render.stateful/pom.xml 2011-03-10 20:10:31 UTC
(rev 24381)
+++ cytoscape/trunk/corelibs/render.stateful/pom.xml 2011-03-10 20:39:22 UTC
(rev 24382)
@@ -41,22 +41,22 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-spacial</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-fixed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-immed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/coreplugins/EquationFunctions/pom.xml
===================================================================
--- cytoscape/trunk/coreplugins/EquationFunctions/pom.xml 2011-03-10
20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/coreplugins/EquationFunctions/pom.xml 2011-03-10
20:39:22 UTC (rev 24382)
@@ -49,7 +49,7 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>equations</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<scope>provided</scope>
</dependency>
</dependencies>
Modified: cytoscape/trunk/coreplugins/ManualLayout/pom.xml
===================================================================
--- cytoscape/trunk/coreplugins/ManualLayout/pom.xml 2011-03-10 20:10:31 UTC
(rev 24381)
+++ cytoscape/trunk/coreplugins/ManualLayout/pom.xml 2011-03-10 20:39:22 UTC
(rev 24382)
@@ -49,7 +49,7 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>nerius-math-xform</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
Modified: cytoscape/trunk/coreplugins/PSI-MI/pom.xml
===================================================================
--- cytoscape/trunk/coreplugins/PSI-MI/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/coreplugins/PSI-MI/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -46,6 +46,7 @@
<plugin>
<groupId>org.jvnet.jaxb2.maven2</groupId>
<artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.7.4</version>
<executions>
<execution>
<id>mi1</id>
@@ -88,16 +89,8 @@
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Maven 2 Repository</name>
- <url>http://download.java.net/maven/2
- </url>
+ <url>http://download.java.net/maven/2</url>
</pluginRepository>
- <pluginRepository>
- <id>maven-repository.dev.java.net</id>
- <name>Java.net Maven 1 Repository (legacy)</name>
- <url>http://download.java.net/maven/1
- </url>
- <layout>legacy</layout>
- </pluginRepository>
</pluginRepositories>
Modified: cytoscape/trunk/coreplugins/cPath2/pom.xml
===================================================================
--- cytoscape/trunk/coreplugins/cPath2/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/coreplugins/cPath2/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -71,6 +71,7 @@
<plugin>
<groupId>org.jvnet.jaxb2.maven2</groupId>
<artifactId>maven-jaxb2-plugin</artifactId>
+ <version>0.7.4</version>
<executions>
<execution>
<id>SearchResponse</id>
@@ -113,16 +114,8 @@
<pluginRepository>
<id>maven2-repository.dev.java.net</id>
<name>Java.net Maven 2 Repository</name>
- <url>http://download.java.net/maven/2
- </url>
+ <url>http://download.java.net/maven/2</url>
</pluginRepository>
- <pluginRepository>
- <id>maven-repository.dev.java.net</id>
- <name>Java.net Maven 1 Repository (legacy)</name>
- <url>http://download.java.net/maven/1
- </url>
- <layout>legacy</layout>
- </pluginRepository>
</pluginRepositories>
</project>
Modified: cytoscape/trunk/coreplugins/pom.xml
===================================================================
--- cytoscape/trunk/coreplugins/pom.xml 2011-03-10 20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/coreplugins/pom.xml 2011-03-10 20:39:22 UTC (rev 24382)
@@ -126,7 +126,7 @@
<dependency>
<groupId>cytoscape</groupId>
<artifactId>application</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<scope>provided</scope>
</dependency>
</dependencies>
Modified: cytoscape/trunk/distribution/pom.xml
===================================================================
--- cytoscape/trunk/distribution/pom.xml 2011-03-10 20:10:31 UTC (rev
24381)
+++ cytoscape/trunk/distribution/pom.xml 2011-03-10 20:39:22 UTC (rev
24382)
@@ -73,7 +73,7 @@
<dependency>
<groupId>cytoscape</groupId>
<artifactId>application</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
@@ -81,14 +81,14 @@
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>docs</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>html</classifier>
<type>zip</type>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>docs</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>pdf</classifier>
<type>zip</type>
</dependency>
@@ -97,121 +97,121 @@
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>advanced-network-merge</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>automatic-layout</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>biomart-client</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>biopax</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>editor</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>equation-functions</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>manual-layout</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>ncbi-client</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>psi-mi</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>rfilters</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>sbml-reader</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>table-import</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>attribute-browser</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>cpath</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>cpath2</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>linkout</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>quickfind</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>filters</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>core-commands</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>network-analyzer</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
Modified: cytoscape/trunk/javadoc/pom.xml
===================================================================
--- cytoscape/trunk/javadoc/pom.xml 2011-03-10 20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/javadoc/pom.xml 2011-03-10 20:39:22 UTC (rev 24382)
@@ -24,8 +24,8 @@
<links>
<link>http://download.oracle.com/javase/1.5.0/docs/api/</link>
</links>
- <footer>Cytoscape ${version} API</footer>
- <header>Cytoscape ${version} API</header>
+ <footer>Cytoscape ${project.version} API</footer>
+ <header>Cytoscape ${project.version} API</header>
<bottom>Copyright 2010 Cytoscape Consortium. All rights
reserved.</bottom>
<maxmemory>2g</maxmemory>
<additionalJOption>-J-Xmx2g</additionalJOption>
@@ -83,94 +83,94 @@
<dependency>
<groupId>cytoscape</groupId>
<artifactId>application</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<!-- corelibs -->
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>util-intr</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-dynamic</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>graph-fixed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>giny</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-immed</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-stateful</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>render-export</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>fing</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>phoebe-dnd</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-spacial</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>geom-rtree</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>undo-support</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>equations</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>task</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>ding</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>obo</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
<dependency>
<groupId>cytoscape.corelibs</groupId>
<artifactId>commons-cli-1-x-cytocape-custom</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
</dependency>
</dependencies>
</project>
Modified: cytoscape/trunk/packaging/pom.xml
===================================================================
--- cytoscape/trunk/packaging/pom.xml 2011-03-10 20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/packaging/pom.xml 2011-03-10 20:39:22 UTC (rev 24382)
@@ -120,19 +120,19 @@
<dependency>
<groupId>cytoscape</groupId>
<artifactId>cytoscape</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<type>zip</type>
</dependency>
<dependency>
<groupId>cytoscape</groupId>
<artifactId>cytoscape</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<type>tar.gz</type>
</dependency>
<dependency>
<groupId>cytoscape</groupId>
<artifactId>javadoc</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>javadoc</classifier>
</dependency>
</dependencies>
Modified: cytoscape/trunk/pom.xml
===================================================================
--- cytoscape/trunk/pom.xml 2011-03-10 20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/pom.xml 2011-03-10 20:39:22 UTC (rev 24382)
@@ -27,7 +27,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
- <version>2.0</version>
+ <version>2.3.1</version>
<configuration>
<tagBase>svn+ssh://grenache.ucsd.edu/cellar/common/svn/cytoscape/tags</tagBase>
<autoVersionSubmodules>true</autoVersionSubmodules>
@@ -40,6 +40,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
+ <version>2.3.2</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
@@ -51,6 +52,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
+ <version>2.7.1</version>
<configuration>
<argLine>-Xmx256m</argLine>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
@@ -59,6 +61,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.7</version>
<configuration>
<encoding>UTF-8</encoding>
<locale>en</locale>
@@ -66,8 +69,8 @@
<links>
<link>http://download.oracle.com/javase/1.5.0/docs/api/</link>
</links>
- <footer>Cytoscape ${version} API</footer>
- <header>Cytoscape ${version} API</header>
+ <footer>Cytoscape ${project.version} API</footer>
+ <header>Cytoscape ${project.version} API</header>
<bottom>Copyright 2010 Cytoscape Consortium. All rights
reserved.</bottom>
<maxmemory>2g</maxmemory>
<additionalJOption>-J-Xmx2g</additionalJOption>
@@ -84,6 +87,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
+ <version>2.1.2</version>
<executions>
<execution>
<id>attach-sources</id>
Modified: cytoscape/trunk/webstart/pom.xml
===================================================================
--- cytoscape/trunk/webstart/pom.xml 2011-03-10 20:10:31 UTC (rev 24381)
+++ cytoscape/trunk/webstart/pom.xml 2011-03-10 20:39:22 UTC (rev 24382)
@@ -88,128 +88,128 @@
<dependency>
<groupId>cytoscape</groupId>
<artifactId>application</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<!-- coreplugins -->
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>advanced-network-merge</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>automatic-layout</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>biomart-client</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>biopax</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>editor</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>equation-functions</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>manual-layout</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>ncbi-client</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>psi-mi</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>rfilters</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>sbml-reader</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>table-import</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>attribute-browser</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>cpath</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>cpath2</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>linkout</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>quickfind</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>filters</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>core-commands</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
<groupId>cytoscape.coreplugins</groupId>
<artifactId>network-analyzer</artifactId>
- <version>${version}</version>
+ <version>${project.version}</version>
<classifier>jar-with-dependencies</classifier>
</dependency>
<dependency>
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
