From fc5c436f22cb82bc1b1519309120dff21e8ef616 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Tue, 1 Oct 2024 07:41:49 +0200
Subject: [PATCH] Release 3.1.3

---
 CITATION.cff                                  |  4 ++--
 README.md                                     | 14 +++++++-------
 examples/pom.xml                              |  2 +-
 org.bridgedb.bio/pom.xml                      |  2 +-
 org.bridgedb.file.orthoxml/pom.xml            |  2 +-
 org.bridgedb.gui/pom.xml                      |  2 +-
 org.bridgedb.rdb.construct/pom.xml            |  2 +-
 org.bridgedb.rdb/pom.xml                      |  2 +-
 org.bridgedb.rdf/pom.xml                      |  2 +-
 org.bridgedb.sql/pom.xml                      |  2 +-
 org.bridgedb.tools.batchmapper/pom.xml        |  8 ++++----
 org.bridgedb.tools.info/pom.xml               |  2 +-
 org.bridgedb.tools.qc/pom.xml                 |  2 +-
 org.bridgedb.tools.voidtool/pom.xml           |  2 +-
 org.bridgedb.uri.api/pom.xml                  |  2 +-
 org.bridgedb.uri.loader/pom.xml               |  2 +-
 org.bridgedb.uri.sql/pom.xml                  |  2 +-
 org.bridgedb.uri.ws.client/pom.xml            |  2 +-
 org.bridgedb.uri.ws.core/pom.xml              |  2 +-
 org.bridgedb.uri.ws.server/pom.xml            |  2 +-
 org.bridgedb.utils/pom.xml                    |  2 +-
 org.bridgedb.webservice.biomart/pom.xml       |  2 +-
 org.bridgedb.webservice.bridgerest/pom.xml    |  2 +-
 org.bridgedb.ws.client/pom.xml                |  2 +-
 org.bridgedb.ws.core/pom.xml                  |  2 +-
 org.bridgedb.ws.server/pom.xml                |  2 +-
 org.bridgedb/pom.xml                          |  2 +-
 org.bridgedb/src/main/resources/version.props |  2 +-
 pom-java8.xml                                 |  2 +-
 pom.xml                                       |  2 +-
 30 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index cdd95bc91..1c035e2b9 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 title: BridgeDb
 message: 'If you use this software, please cite it as below.'
 type: software
-version: 3.1.2
-date-released: '2024-07-30'
+version: 3.1.3
+date-released: '2024-10-01'
 authors:
   - given-names: Manas
     family-names: Awasthi
diff --git a/README.md b/README.md
index 555e3e9a8..83fbdba8e 100644
--- a/README.md
+++ b/README.md
@@ -15,7 +15,7 @@ Using BridgeDb dependencies
 The [BridgeDb releases](https://github.com/bridgedb/BridgeDb/releases) are published to 
 [Maven Central](http://central.maven.org/maven2/org/bridgedb/), which means you can use the BridgeDb JARs without needing to compile BridgeDb.
 
-Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.2`:
+Usage depends on which module you require. The examples below assumes artifact `org.bridgedb.bio` and version `3.1.3`:
 
 For [Maven](https://maven.apache.org/):
 
@@ -24,7 +24,7 @@ For [Maven](https://maven.apache.org/):
     <dependency>
         <groupId>org.bridgedb</groupId>
         <artifactId>org.bridgedb.bio</artifactId>
-        <version>3.1.2</version>
+        <version>3.1.3</version>
     </dependency>
 </dependencies>
 ```
@@ -32,19 +32,19 @@ For [Maven](https://maven.apache.org/):
 For [Gradle](https://gradle.org/):
 
 ```gradle
-compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.2'
+compile group: 'org.bridgedb', name: 'org.bridgedb.bio', version: '3.1.3'
 ```
 
 For [Ivy](http://ant.apache.org/ivy/):
 
 ```xml
-<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.2"/>
+<dependency org="org.bridgedb" name="org.bridgedb.bio" rev="3.1.3"/>
 ```
 
 For [Buildr](https://buildr.apache.org/):
 
 ```buildr
-'org.bridgedb:org.bridgedb.bio:jar:3.1.2'
+'org.bridgedb:org.bridgedb.bio:jar:3.1.3'
 ```
 
 
@@ -135,7 +135,7 @@ To make the release, run the following commands. Mind you, this requires you
 to have an approved Sonatype (http://oss.sonatype.org/) account with push rights:
 
 ```shell
-mvn versions:set -DnewVersion=3.1.2
+mvn versions:set -DnewVersion=3.1.3
 mvn clean deploy
 ```
 
@@ -145,7 +145,7 @@ and everything.
 To make a development (SNAPSHOT) release, use:
 
 ```shell
-mvn versions:set -DnewVersion=3.1.3-SNAPSHOT
+mvn versions:set -DnewVersion=3.1.4-SNAPSHOT
 mvn clean deploy
 ```
 
diff --git a/examples/pom.xml b/examples/pom.xml
index 3fe355949..046535746 100644
--- a/examples/pom.xml
+++ b/examples/pom.xml
@@ -3,7 +3,7 @@
   <parent>
     <artifactId>bridgedb-bundle</artifactId>
     <groupId>org.bridgedb</groupId>
-    <version>3.1.3-SNAPSHOT</version>
+    <version>3.1.3</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.bridgedb.examples</groupId>
diff --git a/org.bridgedb.bio/pom.xml b/org.bridgedb.bio/pom.xml
index cbcc44086..32af86677 100644
--- a/org.bridgedb.bio/pom.xml
+++ b/org.bridgedb.bio/pom.xml
@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.file.orthoxml/pom.xml b/org.bridgedb.file.orthoxml/pom.xml
index 88b5d884f..609362c96 100644
--- a/org.bridgedb.file.orthoxml/pom.xml
+++ b/org.bridgedb.file.orthoxml/pom.xml
@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.gui/pom.xml b/org.bridgedb.gui/pom.xml
index 22a091701..e4e9c498a 100644
--- a/org.bridgedb.gui/pom.xml
+++ b/org.bridgedb.gui/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.rdb.construct/pom.xml b/org.bridgedb.rdb.construct/pom.xml
index 2fdee3665..1ee0d0da8 100644
--- a/org.bridgedb.rdb.construct/pom.xml
+++ b/org.bridgedb.rdb.construct/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.rdb/pom.xml b/org.bridgedb.rdb/pom.xml
index 75ea6d092..169b5be78 100644
--- a/org.bridgedb.rdb/pom.xml
+++ b/org.bridgedb.rdb/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.rdf/pom.xml b/org.bridgedb.rdf/pom.xml
index 14e4863d9..d7a497f28 100644
--- a/org.bridgedb.rdf/pom.xml
+++ b/org.bridgedb.rdf/pom.xml
@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
     <build>
diff --git a/org.bridgedb.sql/pom.xml b/org.bridgedb.sql/pom.xml
index e33449052..22fec0bd2 100644
--- a/org.bridgedb.sql/pom.xml
+++ b/org.bridgedb.sql/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
         <build>
diff --git a/org.bridgedb.tools.batchmapper/pom.xml b/org.bridgedb.tools.batchmapper/pom.xml
index 4a489cede..be079f4b8 100644
--- a/org.bridgedb.tools.batchmapper/pom.xml
+++ b/org.bridgedb.tools.batchmapper/pom.xml
@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
@@ -33,19 +33,19 @@
                 <dependency>
                         <groupId>org.bridgedb</groupId>
                         <artifactId>org.bridgedb</artifactId>
-                        <version>3.1.3-SNAPSHOT</version>
+                        <version>3.1.3</version>
                         <scope>compile</scope>
                 </dependency>
 		<dependency>
 			<groupId>org.bridgedb</groupId>
 			<artifactId>org.bridgedb.bio</artifactId>
-			<version>3.1.3-SNAPSHOT</version>
+			<version>3.1.3</version>
 			<scope>compile</scope>
 		</dependency>
                 <dependency>
                         <groupId>org.bridgedb</groupId>
                         <artifactId>org.bridgedb.rdb</artifactId>
-                        <version>3.1.3-SNAPSHOT</version>
+                        <version>3.1.3</version>
                         <scope>compile</scope>
                 </dependency>
 	</dependencies>
diff --git a/org.bridgedb.tools.info/pom.xml b/org.bridgedb.tools.info/pom.xml
index b5ecac8a0..26c9f2308 100644
--- a/org.bridgedb.tools.info/pom.xml
+++ b/org.bridgedb.tools.info/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.tools.qc/pom.xml b/org.bridgedb.tools.qc/pom.xml
index 04e125150..3fafb090e 100644
--- a/org.bridgedb.tools.qc/pom.xml
+++ b/org.bridgedb.tools.qc/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.tools.voidtool/pom.xml b/org.bridgedb.tools.voidtool/pom.xml
index e592e3388..a7e5b5a3b 100644
--- a/org.bridgedb.tools.voidtool/pom.xml
+++ b/org.bridgedb.tools.voidtool/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.uri.api/pom.xml b/org.bridgedb.uri.api/pom.xml
index 8b74b4eea..f8d17ca80 100644
--- a/org.bridgedb.uri.api/pom.xml
+++ b/org.bridgedb.uri.api/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
         <build>
diff --git a/org.bridgedb.uri.loader/pom.xml b/org.bridgedb.uri.loader/pom.xml
index 4fc3d983e..3fe0993f3 100644
--- a/org.bridgedb.uri.loader/pom.xml
+++ b/org.bridgedb.uri.loader/pom.xml
@@ -6,7 +6,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 	
    <dependencies>
diff --git a/org.bridgedb.uri.sql/pom.xml b/org.bridgedb.uri.sql/pom.xml
index 00a76920c..523efff03 100644
--- a/org.bridgedb.uri.sql/pom.xml
+++ b/org.bridgedb.uri.sql/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
         <build>
diff --git a/org.bridgedb.uri.ws.client/pom.xml b/org.bridgedb.uri.ws.client/pom.xml
index 2beeba819..5f0f5b744 100644
--- a/org.bridgedb.uri.ws.client/pom.xml
+++ b/org.bridgedb.uri.ws.client/pom.xml
@@ -8,7 +8,7 @@
     <parent>
         <artifactId>bridgedb-bundle</artifactId>
         <groupId>org.bridgedb</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.1.3</version>
     </parent>
 
     <build>
diff --git a/org.bridgedb.uri.ws.core/pom.xml b/org.bridgedb.uri.ws.core/pom.xml
index a1349048c..2027b7914 100644
--- a/org.bridgedb.uri.ws.core/pom.xml
+++ b/org.bridgedb.uri.ws.core/pom.xml
@@ -8,7 +8,7 @@
     <parent>
         <artifactId>bridgedb-bundle</artifactId>
         <groupId>org.bridgedb</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.1.3</version>
     </parent>
 
         <build>
diff --git a/org.bridgedb.uri.ws.server/pom.xml b/org.bridgedb.uri.ws.server/pom.xml
index f3672d4e3..f6ae18627 100644
--- a/org.bridgedb.uri.ws.server/pom.xml
+++ b/org.bridgedb.uri.ws.server/pom.xml
@@ -8,7 +8,7 @@
     <parent>
         <artifactId>bridgedb-bundle</artifactId>
         <groupId>org.bridgedb</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.1.3</version>
     </parent>
 	
     <build>
diff --git a/org.bridgedb.utils/pom.xml b/org.bridgedb.utils/pom.xml
index f8ac233e2..468fcf5cb 100644
--- a/org.bridgedb.utils/pom.xml
+++ b/org.bridgedb.utils/pom.xml
@@ -7,7 +7,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
         <build>
diff --git a/org.bridgedb.webservice.biomart/pom.xml b/org.bridgedb.webservice.biomart/pom.xml
index c5ac195d8..0ad3609ea 100644
--- a/org.bridgedb.webservice.biomart/pom.xml
+++ b/org.bridgedb.webservice.biomart/pom.xml
@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.webservice.bridgerest/pom.xml b/org.bridgedb.webservice.bridgerest/pom.xml
index 6726e0633..820d4039a 100644
--- a/org.bridgedb.webservice.bridgerest/pom.xml
+++ b/org.bridgedb.webservice.bridgerest/pom.xml
@@ -8,7 +8,7 @@
   <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb.ws.client/pom.xml b/org.bridgedb.ws.client/pom.xml
index ea57e2096..05d56cc59 100644
--- a/org.bridgedb.ws.client/pom.xml
+++ b/org.bridgedb.ws.client/pom.xml
@@ -8,7 +8,7 @@
     <parent>
         <artifactId>bridgedb-bundle</artifactId>
         <groupId>org.bridgedb</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.1.3</version>
     </parent>
 
     <build>
diff --git a/org.bridgedb.ws.core/pom.xml b/org.bridgedb.ws.core/pom.xml
index d39248962..6494251c5 100644
--- a/org.bridgedb.ws.core/pom.xml
+++ b/org.bridgedb.ws.core/pom.xml
@@ -8,7 +8,7 @@
     <parent>
         <artifactId>bridgedb-bundle</artifactId>
         <groupId>org.bridgedb</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.1.3</version>
     </parent>
 
         <build>
diff --git a/org.bridgedb.ws.server/pom.xml b/org.bridgedb.ws.server/pom.xml
index ebbe3b200..378d6371a 100644
--- a/org.bridgedb.ws.server/pom.xml
+++ b/org.bridgedb.ws.server/pom.xml
@@ -8,7 +8,7 @@
     <parent>
         <artifactId>bridgedb-bundle</artifactId>
         <groupId>org.bridgedb</groupId>
-        <version>3.1.3-SNAPSHOT</version>
+        <version>3.1.3</version>
     </parent>
 
      <build>
diff --git a/org.bridgedb/pom.xml b/org.bridgedb/pom.xml
index 7b96e71fb..29cd03789 100644
--- a/org.bridgedb/pom.xml
+++ b/org.bridgedb/pom.xml
@@ -33,7 +33,7 @@
     <parent>
   	<artifactId>bridgedb-bundle</artifactId>
   	<groupId>org.bridgedb</groupId>
-  	<version>3.1.3-SNAPSHOT</version>
+  	<version>3.1.3</version>
   </parent>
 
 	<build>
diff --git a/org.bridgedb/src/main/resources/version.props b/org.bridgedb/src/main/resources/version.props
index 6cc9da92d..0da9c3ac6 100644
--- a/org.bridgedb/src/main/resources/version.props
+++ b/org.bridgedb/src/main/resources/version.props
@@ -1,2 +1,2 @@
 # Current version of BridgeDb
-bridgedb.version=3.1.2
+bridgedb.version=3.1.3
diff --git a/pom-java8.xml b/pom-java8.xml
index 4b568673d..e994adb9a 100644
--- a/pom-java8.xml
+++ b/pom-java8.xml
@@ -4,7 +4,7 @@
   <groupId>org.bridgedb</groupId>
   <artifactId>bridgedb-bundle-pv</artifactId>
   <packaging>pom</packaging>
-  <version>3.1.2</version>
+  <version>3.1.3-java8</version>
   <name>BridgeDb 4 PathVisio bundle</name>
 	<description>
 		BridgeDb is a framework for finding and mapping equivalent database
diff --git a/pom.xml b/pom.xml
index 502cb7f58..d95abc4a0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
   <groupId>org.bridgedb</groupId>
   <artifactId>bridgedb-bundle</artifactId>
   <packaging>pom</packaging>
-  <version>3.1.3-SNAPSHOT</version>	
+  <version>3.1.3</version>	
   <name>BridgeDb bundle</name>
 	<description>
 		BridgeDb is a framework for finding and mapping equivalent database