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[WIP] Preparing for 1.0.4 #126

Merged
merged 14 commits into from
Jan 19, 2025
+201 −138
Merged

[WIP] Preparing for 1.0.4 #126

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6dea9d1
Open for development
egonw Oct 13, 2024
405b31f
Fixed the parameter name
egonw Oct 13, 2024
a18f23c
Added a method to safe RDF to file
egonw Nov 2, 2024
d9b71da
Apache Jena 5.2.0
egonw Nov 2, 2024
ca616ad
Handle transactions
egonw Nov 3, 2024
bf9e622
Updated JUnit
egonw Nov 3, 2024
4eeea9b
Guava 33.3.1
egonw Nov 3, 2024
bc70d13
Woodstox 7.1 and JSoup 1.18.1
egonw Nov 4, 2024
7e35ac1
BridgeDb 3.1.4 and CDK 2.10
egonw Jan 18, 2025
7a16eae
JUnit 5.11.4
egonw Jan 18, 2025
62e3b11
Bacting-Bioclipse 2.8.1.3
egonw Jan 18, 2025
8b73895
JSON 20250107, Log4j 2.24.3, Guava 33.4
egonw Jan 18, 2025
da26db0
Slf4j 2.0.16, Commons IO 2.18, Apache POI 5.4, JSoup 1.18.3
egonw Jan 18, 2025
7d739fa
Release 1.0.4
egonw Jan 19, 2025
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4 changes: 2 additions & 2 deletions CITATION.cff
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Original file line number Diff line number Diff line change
@@ -5,8 +5,8 @@ authors:
given-names: Egon
orcid: https://orcid.org/0000-0001-7542-0286
title: Bacting
version: 1.0.3
date-released: 2024-10-01
version: 1.0.4
date-released: 2025-01-19
doi: 10.5281/zenodo.2638709
url: "https://github.com/egonw/bacting"
preferred-citation:
4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
@@ -47,15 +47,15 @@ If these requirements are fulfilled then the following commands to the job:

```shell
export MAVEN_OPTS="--add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED --add-opens=java.base/java.text=ALL-UNNAMED --add-opens=java.desktop/java.awt.font=ALL-UNNAMED"
mvn versions:set -DnewVersion=1.0.3
mvn versions:set -DnewVersion=1.0.4
git commit -m "New release" -a
mvn deploy -P release
```

### Making snapshots

```shell
mvn versions:set -DnewVersion=1.0.4-SNAPSHOT
mvn versions:set -DnewVersion=1.0.5-SNAPSHOT
mvn deploy
```

2 changes: 1 addition & 1 deletion bacting-core/pom.xml
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Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>bacting-core</artifactId>
32 changes: 16 additions & 16 deletions bundle/pom.xml
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Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>bacting-bundle</artifactId>
@@ -15,77 +15,77 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-rdf</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-xml</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>net.bioclipse.managers.wikidata</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-bridgedb</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-biojava</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdkdebug</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-chemspider</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-inchi</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-opsin</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-oscar</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-pubchem</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-excel</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
</dependencies>

4 changes: 2 additions & 2 deletions managers-bioinfo/net.bioclipse.managers.biojava/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-bioinfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-biojava</artifactId>
@@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
6 changes: 3 additions & 3 deletions managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-bioinfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-bridgedb</artifactId>
@@ -39,7 +39,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
@@ -97,7 +97,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
<scope>test</scope>
</dependency>
</dependencies>
6 changes: 3 additions & 3 deletions managers-bioinfo/net.bioclipse.managers.libgpml/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-bioinfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-libgpml</artifactId>
@@ -34,13 +34,13 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<scope>test</scope>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
2 changes: 1 addition & 1 deletion managers-bioinfo/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -5,7 +5,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-bioinfo</artifactId>
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.cdk/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-cdk</artifactId>
@@ -34,13 +34,13 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<scope>test</scope>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>xom</groupId>
4 changes: 2 additions & 2 deletions managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-cdkdebug</artifactId>
@@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-chemspider</artifactId>
@@ -34,12 +34,12 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.inchi/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-inchi</artifactId>
@@ -49,7 +49,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
@@ -81,7 +81,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
<scope>test</scope>
</dependency>
</dependencies>
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.nm/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-nm</artifactId>
@@ -34,12 +34,12 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw</groupId>
8 changes: 4 additions & 4 deletions managers-cheminfo/net.bioclipse.managers.opsin/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-opsin</artifactId>
@@ -34,12 +34,12 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>uk.ac.cam.ch.opsin</groupId>
@@ -59,7 +59,7 @@
<dependency>
<groupId>com.fasterxml.woodstox</groupId>
<artifactId>woodstox-core</artifactId>
<version>7.0.0</version>
<version>7.1.0</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.oscar/pom.xml
View file
Original file line number Diff line number Diff line change
@@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.3</version>
<version>1.0.4</version>
</parent>

<artifactId>managers-oscar</artifactId>
@@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>uk.ac.cam.ch.wwmm.oscar</groupId>
@@ -70,7 +70,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.3</version>
<version>1.0.4</version>
</dependency>
<dependency>
<groupId>net.htmlparser.jericho</groupId>
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