Merge branch 'feature-xml_dependency_fix' into 'develop'

Feature xml dependency fix

See commits :) ~ we've been packaging 2 dependencies that are required only for testing in our JAR files. This should fix that.

See merge request !32

biopet-framework/BiopetFramework.iml

@@ -5,7 +5,8 @@
       <configuration>
         <option name="compilerLibraryLevel" value="Project" />
         <option name="compilerLibraryName" value="Maven: org.scala-lang:scala-compiler-bundle:2.11.2" />
-        <option name="compilerOptions" value="-dependencyfile $MODULE_DIR$/target/.scala_dependencies" />
+        <option name="compilerOptions" value="-dependencyfile $MODULE_DIR$/target/.scala_dependencies -feature" />
+        <option name="deprecationWarnings" value="true" />
         <option name="languageLevel" value="Scala 2.11" />
         <option name="vmOptions" value="" />
       </configuration>
@@ -29,15 +30,15 @@
     <orderEntry type="sourceFolder" forTests="false" />
     <orderEntry type="library" name="com.twitter:algebird-core_2.10:0.8.1" level="project" />
     <orderEntry type="library" name="gatk-protected" level="project" />
-    <orderEntry type="library" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
     <orderEntry type="library" scope="TEST" name="Maven: org.testng:testng:6.8" level="project" />
     <orderEntry type="library" scope="TEST" name="Maven: junit:junit:4.10" level="project" />
     <orderEntry type="library" scope="TEST" name="Maven: org.hamcrest:hamcrest-core:1.1" level="project" />
     <orderEntry type="library" scope="TEST" name="Maven: org.beanshell:bsh:2.0b4" level="project" />
     <orderEntry type="library" scope="TEST" name="Maven: com.beust:jcommander:1.27" level="project" />
     <orderEntry type="library" scope="TEST" name="Maven: org.yaml:snakeyaml:1.6" level="project" />
-    <orderEntry type="library" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
-    <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scalatest:scalatest_2.11:2.2.1" level="project" />
+    <orderEntry type="library" scope="TEST" name="Maven: org.scala-lang:scala-reflect:2.11.2" level="project" />
     <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
     <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
     <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3" level="project" />
@@ -49,6 +50,5 @@
     <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
     <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
     <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
-    <orderEntry type="library" name="Maven: org.mockito:mockito-all:1.9.5" level="project" />
   </component>
-</module>
+</module>
\ No newline at end of file

biopet-framework/pom.xml

@@ -31,10 +31,17 @@
             <version>6.8</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-all</artifactId>
+            <version>1.9.5</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.scalatest</groupId>
             <artifactId>scalatest_2.11</artifactId>
             <version>2.2.1</version>
+            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.scala-lang</groupId>
@@ -71,11 +78,6 @@
             <artifactId>scopt_2.10</artifactId>
             <version>3.2.0</version>
         </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-all</artifactId>
-            <version>1.9.5</version>
-        </dependency>
     </dependencies>
     <build>
         <resources>