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[WIP] release 0.5.0 #115

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merged 18 commits into from
Dec 31, 2023
Merged

[WIP] release 0.5.0 #115

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06b7a10
Open for development
egonw Dec 18, 2023
2b0ad7f
Require Java 17
egonw Dec 18, 2023
1ba07f2
Depend on the J17 Bacting-Bioclipse
egonw Dec 18, 2023
8d387e5
Match what we have for snapshots in the bacting-bioclipse repo
egonw Dec 18, 2023
b4ba436
Coverage testing with Java 17
egonw Dec 18, 2023
c5fa1ab
Added more Wikidata helper methods
egonw Dec 29, 2023
a9d6dd6
Null is not a valid Wikidata Q identifier
egonw Dec 29, 2023
04acc30
Removed debug output
egonw Dec 29, 2023
fda8ed3
More testing
egonw Dec 29, 2023
61472fe
More test coverage
egonw Dec 29, 2023
ecf5513
Tests for getEntityIDsForType()
egonw Dec 29, 2023
f96d430
Added a negative test, to creep up the coverage a bit more
egonw Dec 29, 2023
931d31b
Guava 33.0.0 and BridgeDb 3.1.1
egonw Dec 30, 2023
1785084
Java 17 also on compiler level
egonw Dec 30, 2023
c4e780f
Maven plugin updates: Compiler 3.12.1, Shade 3.5.1, Enforcer 3.4.1, G…
egonw Dec 30, 2023
e6af2a2
Ported the last method, jsoup.parse(file)
egonw Dec 31, 2023
fbbb6a5
Added missing JavaDoc
egonw Dec 31, 2023
0a3229a
The new Bioclipse version is released
egonw Dec 31, 2023
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7 changes: 6 additions & 1 deletion .github/workflows/maven.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
java: [ 11, 17, 19 ]
java: [ 17, 19 ]
name: Java ${{ matrix.java }}

steps:
Expand All @@ -29,6 +29,11 @@ jobs:
needs: build
steps:
- uses: actions/checkout@v3
- name: Set up Java
uses: actions/setup-java@v3
with:
distribution: temurin
java-version: 17
- name: Build with Maven
run: mvn clean install -Dgpg.skip -Dmaven.javadoc.skip=true -Dmaven.test.failure.ignore=true -Djunit5.excludeGroups=
- name: push JaCoCo stats to codecov.io
Expand Down
2 changes: 1 addition & 1 deletion bacting-core/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>bacting-core</artifactId>
Expand Down
32 changes: 16 additions & 16 deletions bundle/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>bacting-bundle</artifactId>
Expand All @@ -15,77 +15,77 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-rdf</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-xml</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>net.bioclipse.managers.wikidata</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-bridgedb</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-biojava</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdkdebug</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-chemspider</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-inchi</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-opsin</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-oscar</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-pubchem</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-excel</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
</dependencies>

Expand Down
4 changes: 2 additions & 2 deletions managers-bioinfo/net.bioclipse.managers.biojava/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-bioinfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-biojava</artifactId>
Expand Down Expand Up @@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
Expand Down
6 changes: 3 additions & 3 deletions managers-bioinfo/net.bioclipse.managers.bridgedb/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-bioinfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-bridgedb</artifactId>
Expand Down Expand Up @@ -39,7 +39,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.bridgedb</groupId>
Expand Down Expand Up @@ -97,7 +97,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand Down
2 changes: 1 addition & 1 deletion managers-bioinfo/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-bioinfo</artifactId>
Expand Down
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.cdk/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-cdk</artifactId>
Expand Down Expand Up @@ -34,13 +34,13 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<scope>test</scope>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>xom</groupId>
Expand Down
4 changes: 2 additions & 2 deletions managers-cheminfo/net.bioclipse.managers.cdkdebug/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-cdkdebug</artifactId>
Expand Down Expand Up @@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
Expand Down
4 changes: 2 additions & 2 deletions managers-cheminfo/net.bioclipse.managers.chemspider/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-chemspider</artifactId>
Expand Down Expand Up @@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
Expand Down
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.inchi/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-inchi</artifactId>
Expand Down Expand Up @@ -49,7 +49,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
Expand Down Expand Up @@ -81,7 +81,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand Down
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.nm/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-nm</artifactId>
Expand Down Expand Up @@ -34,12 +34,12 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw</groupId>
Expand Down
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.opsin/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-opsin</artifactId>
Expand Down Expand Up @@ -34,12 +34,12 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>uk.ac.cam.ch.opsin</groupId>
Expand Down
6 changes: 3 additions & 3 deletions managers-cheminfo/net.bioclipse.managers.oscar/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-oscar</artifactId>
Expand Down Expand Up @@ -34,7 +34,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>uk.ac.cam.ch.wwmm.oscar</groupId>
Expand Down Expand Up @@ -70,7 +70,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>net.htmlparser.jericho</groupId>
Expand Down
10 changes: 5 additions & 5 deletions managers-cheminfo/net.bioclipse.managers.pubchem/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-cheminfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-pubchem</artifactId>
Expand Down Expand Up @@ -49,7 +49,7 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
Expand All @@ -64,17 +64,17 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-rdf</artifactId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
Expand Down
2 changes: 1 addition & 1 deletion managers-cheminfo/pom.xml
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Expand Up @@ -5,7 +5,7 @@
<parent>
<artifactId>bacting</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>0.4.1</version>
<version>0.5.0-SNAPSHOT</version>
</parent>

<artifactId>managers-cheminfo</artifactId>
Expand Down
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