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[WIP] Preparing for 1.0.3 #125

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merged 6 commits into from
Oct 1, 2024
Merged

[WIP] Preparing for 1.0.3 #125

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3b58720
Open for development
egonw Sep 23, 2024
6e9a4f1
Handle the situation when the query returned no data
egonw Sep 23, 2024
a49632d
More empty results checking
egonw Sep 23, 2024
93575b2
Added a method for DOIs/works for a main subject
egonw Oct 1, 2024
c5d3313
Release 1.0.3
egonw Oct 1, 2024
3e969f4
Latest BridgeDb
egonw Oct 1, 2024
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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -5,8 +5,8 @@ authors:
given-names: Egon
orcid: https://orcid.org/0000-0001-7542-0286
title: Bacting
version: 1.0.2
date-released: 2024-09-23
version: 1.0.3
date-released: 2024-10-01
doi: 10.5281/zenodo.2638709
url: "https://github.com/egonw/bacting"
preferred-citation:
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8 changes: 4 additions & 4 deletions README.md
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Expand Up @@ -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=1.0.2
mvn versions:set -DnewVersion=1.0.3
git commit -m "New release" -a
mvn deploy -P release
```

### Making snapshots

```shell
mvn versions:set -DnewVersion=1.0.3-SNAPSHOT
mvn versions:set -DnewVersion=1.0.4-SNAPSHOT
mvn deploy
```

Expand Down Expand Up @@ -83,7 +83,7 @@ itself), and then converts a [SMILES](https://en.wikipedia.org/wiki/Simplified_m
string to a Bioclipse `IMolecule` data object:

```groovy
@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='1.0.2')
@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='1.0.3')

workspaceRoot = "."
def cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);
Expand Down Expand Up @@ -117,7 +117,7 @@ The code example looks like:

```python
from scyjava import config, jimport
config.add_endpoints('io.github.egonw.bacting:managers-cdk:1.0.2')
config.add_endpoints('io.github.egonw.bacting:managers-cdk:1.0.3')

workspaceRoot = "."
cdkClass = jimport("net.bioclipse.managers.CDKManager")
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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</parent>

<artifactId>bacting-core</artifactId>
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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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-rdf</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-xml</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>net.bioclipse.managers.wikidata</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-bridgedb</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-biojava</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdkdebug</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-chemspider</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-inchi</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-opsin</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-oscar</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-pubchem</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-excel</artifactId>
<version>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
<scope>test</scope>
</dependency>
</dependencies>
Expand Down
6 changes: 3 additions & 3 deletions managers-bioinfo/net.bioclipse.managers.libgpml/pom.xml
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Expand Up @@ -4,7 +4,7 @@
<parent>
<artifactId>managers-bioinfo</artifactId>
<groupId>io.github.egonw.bacting</groupId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</parent>

<artifactId>managers-libgpml</artifactId>
Expand Down Expand Up @@ -34,13 +34,13 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>bacting-core</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<scope>test</scope>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<scope>test</scope>
<version>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.openscience.cdk</groupId>
Expand Down
6 changes: 3 additions & 3 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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</parent>

<artifactId>managers-chemspider</artifactId>
Expand Down Expand Up @@ -34,12 +34,12 @@
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-ui</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-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>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>io.github.egonw.bacting</groupId>
<artifactId>managers-cdk</artifactId>
<version>1.0.2</version>
<version>1.0.3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>uk.ac.cam.ch.opsin</groupId>
Expand Down
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