V4 release

bcarlsenca · Sep 11, 2014 · b422142 · b422142
1 parent dc17be7
commit b422142
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Showing 15 changed files with 99 additions and 30 deletions.
diff --git a/antbuild/etc/releasenotes.txt b/antbuild/etc/releasenotes.txt
@@ -1,8 +1,19 @@
-Features and bug fixes in 4.0.0
+4.0.0 10 September 2014
 
 Supported Java versions: Java 7, Java 8
 
-Features
+Features:
+    added HasAnnotationPropertiesInSignature to uniform treatment of annotation properties
+    added missing EntitySearcher methods for negative property assertions
+    Use Trove collections for ontology internals
+    improved performance of OWLAxiomImpl.equals
+    Transform functions from Collection<OWLOntoloy> and Collection<OWLOntologyID> to Collection<IRI>
+    PMD critical violations addressed
+    fix ServiceLoader use to be OSGi compatible
+    create osgidistribution: osgidistribution is a jar with embedded dependencies and including the compatibility module. It addresses the issues due to the OWLAPI dependencies not being wrapped in OSGi bundles separately.
+    enabled OWLOntologyManager to build and keep a loader configuration
+    OBO 1.2 ontologies cannot be parsed by the 1.4 parser. Added 1.2 parser from OWLAPITOOLS to compatibility package.
+    added saveOntology() methods to OWLMutableOntology
     Add a copy/move ontology method to OWLOntologyManager #12
     Search introduced to replace forSuperPosition, forSubPosition, ignoreAnnotations booleans
     Imports.INCLUDED, Imports.EXCLUDED introduced instead of boolean arguments #156
@@ -63,6 +74,18 @@ Features
     Manchester OWL syntax cleanup
 
 Bug fixes (ported to 3.5)
+    Fix #278 AutoIRIMapper is not namespace aware
+    Direct imports result not updated correctly after manual load #277
+    fix #275 DL Syntax rendering of disjoint classes missing comma
+    fix #271 OWLOntology.getXXXInSignature(boolean) and similar methods
+    fix #270 Add OWLOntology.getReferencingAxioms(OWLPrimitive)
+    fix #268 Add documentation to OWLOntologyID to clarify the relationship between isAnonymous() and getOntologyIRI()
+    fix #267 Consider adding containsXInSignature methods that do not have an imports flag to OWLOntology.
+    fix #254 OWLAsymmetricObjectPropertyAxiom not rendered in DL Syntax
+    fix OWLDocumentFormat as interface #258 #259
+    fix #260 and fix #261 data and object cardinality are quantified restricitons
+    fix #255 PrefixOWLOntologyFormat is missing from the compatibility module
+    fix #253 StructuralReasoner.getSameIndividuals does not behave as advertised
     Fixed #198 A SubClassOf B will not parse
     Fixed IRI with a space: %20 escape #146
     Old OWLEntityCollector brought forward as DeprecatedOWLEntityCollector

diff --git a/api/pom.xml b/api/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<build>

diff --git a/apibinding/pom.xml b/apibinding/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>

diff --git a/compatibility/pom.xml b/compatibility/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>

diff --git a/contract/pom.xml b/contract/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>

diff --git a/distribution/pom.xml b/distribution/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<properties>

diff --git a/fixers/pom.xml b/fixers/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>

diff --git a/impl/pom.xml b/impl/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>

diff --git a/oboformat/pom.xml b/oboformat/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<url>http://code.google.com/p/oboformat/</url>

diff --git a/osgidistribution/pom.xml b/osgidistribution/pom.xml
@@ -8,7 +8,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<properties>

diff --git a/owlapi-parent/pom.xml b/owlapi-parent/pom.xml
@@ -66,11 +66,11 @@
 			<version>3.0.3</version>
 		</dependency>
 		<dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
-            <version>1.3</version>
-            <scope>test</scope>
-        </dependency>
+			<groupId>org.hamcrest</groupId>
+			<artifactId>hamcrest-core</artifactId>
+			<version>1.3</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
@@ -287,12 +287,35 @@
 					<argLine>-Xmx1024M -Djava.awt.headless=true</argLine>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.sonatype.plugins</groupId>
+				<artifactId>nexus-staging-maven-plugin</artifactId>
+				<version>1.6.2</version>
+				<extensions>true</extensions>
+				<configuration>
+					<serverId>ossrh</serverId>
+					<nexusUrl>https://oss.sonatype.org/</nexusUrl>
+					<autoReleaseAfterClose>true</autoReleaseAfterClose>
+				</configuration>
+			</plugin>
 			<!-- the FindBugs plugin for extra checks -->
-			<!--plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>findbugs-maven-plugin</artifactId> 
-				<version>2.5.3</version> <executions> <execution> <id>findbugs-check</id> 
-				<phase>verify</phase> <goals> <goal>check</goal> </goals> <configuration> 
-				<failOnError>false</failOnError> </configuration> </execution> </executions> 
-			</plugin-->
+			<!--plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>findbugs-maven-plugin</artifactId>
+				<version>2.5.3</version>
+				<executions>
+					<execution>
+						<id>findbugs-check</id>
+						<phase>verify</phase>
+						<goals>
+							<goal>check</goal>
+						</goals>
+						<configuration>
+							<failOnError>false</failOnError>
+						</configuration>
+					</execution>
+				</executions>
+				</plugin -->
 		</plugins>
 	</build>
 
@@ -307,4 +330,4 @@
 		<developerConnection>scm:git:git@github.com:owlcs/owlapi.git</developerConnection>
 		<url>https://github.com/owlcs/owlapi</url>
 	</scm>
-</project>
+</project>
diff --git a/parsers/pom.xml b/parsers/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>

diff --git a/pom.xml b/pom.xml
@@ -17,7 +17,7 @@
 	<groupId>net.sourceforge.owlapi</groupId>
 	<artifactId>owlapi-parent</artifactId>
 	<packaging>pom</packaging>
-	<version>4.0.0-RC3</version>
+	<version>4.0.0</version>
 	<name>OWLAPI</name>
 	<description>The OWL API is a Java API and reference implementation for creating, manipulating and serialising OWL Ontologies. The latest version of the API is focused towards OWL 2</description>
 	<url>http://owlapi.sourceforge.net/</url>
@@ -287,11 +287,34 @@
 					<argLine>-Xmx1024M -Djava.awt.headless=true</argLine>
 				</configuration>
 			</plugin>
+			<plugin>
+				<groupId>org.sonatype.plugins</groupId>
+				<artifactId>nexus-staging-maven-plugin</artifactId>
+				<version>1.6.2</version>
+				<extensions>true</extensions>
+				<configuration>
+					<serverId>ossrh</serverId>
+					<nexusUrl>https://oss.sonatype.org/</nexusUrl>
+					<autoReleaseAfterClose>true</autoReleaseAfterClose>
+				</configuration>
+			</plugin>
 			<!-- the FindBugs plugin for extra checks -->
-			<!--plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>findbugs-maven-plugin</artifactId> 
-				<version>2.5.3</version> <executions> <execution> <id>findbugs-check</id> 
-				<phase>verify</phase> <goals> <goal>check</goal> </goals> <configuration> 
-				<failOnError>false</failOnError> </configuration> </execution> </executions> 
+			<!--plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>findbugs-maven-plugin</artifactId>
+				<version>2.5.3</version>
+				<executions>
+					<execution>
+						<id>findbugs-check</id>
+						<phase>verify</phase>
+						<goals>
+							<goal>check</goal>
+						</goals>
+						<configuration>
+							<failOnError>false</failOnError>
+						</configuration>
+					</execution>
+				</executions>
 				</plugin -->
 		</plugins>
 	</build>

diff --git a/rio/pom.xml b/rio/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<artifactId>owlapi-parent</artifactId>
 		<groupId>net.sourceforge.owlapi</groupId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 	</parent>
 	<artifactId>owlapi-rio</artifactId>
 	<name>OWLAPI :: Sesame Rio module</name>

diff --git a/tools/pom.xml b/tools/pom.xml
@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>net.sourceforge.owlapi</groupId>
 		<artifactId>owlapi-parent</artifactId>
-		<version>4.0.0-RC3</version>
+		<version>4.0.0</version>
 		<relativePath>../</relativePath>
 	</parent>
 	<dependencies>