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Release 3.1.3
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@egonw
egonw committed Oct 1, 2024
1 parent 5b2a6d8 commit fc5c436
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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -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
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14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -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/):

Expand All @@ -24,27 +24,27 @@ 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>
```

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'
```


Expand Down Expand Up @@ -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
```

Expand All @@ -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
```

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2 changes: 1 addition & 1 deletion examples/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.bio/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.file.orthoxml/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.gui/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdb.construct/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdb/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.rdf/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.sql/pom.xml
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Expand Up @@ -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>
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8 changes: 4 additions & 4 deletions org.bridgedb.tools.batchmapper/pom.xml
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Expand Up @@ -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>
Expand All @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.tools.info/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.tools.qc/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.tools.voidtool/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.api/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.loader/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.sql/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.client/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.core/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.uri.ws.server/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.utils/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.webservice.biomart/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.webservice.bridgerest/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb.ws.client/pom.xml
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<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.3-SNAPSHOT</version>
<version>3.1.3</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.ws.core/pom.xml
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<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.3-SNAPSHOT</version>
<version>3.1.3</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb.ws.server/pom.xml
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<parent>
<artifactId>bridgedb-bundle</artifactId>
<groupId>org.bridgedb</groupId>
<version>3.1.3-SNAPSHOT</version>
<version>3.1.3</version>
</parent>

<build>
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2 changes: 1 addition & 1 deletion org.bridgedb/pom.xml
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Expand Up @@ -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>
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2 changes: 1 addition & 1 deletion org.bridgedb/src/main/resources/version.props
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@@ -1,2 +1,2 @@
# Current version of BridgeDb
bridgedb.version=3.1.2
bridgedb.version=3.1.3
2 changes: 1 addition & 1 deletion pom-java8.xml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -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
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