[WIP] 2.0.8 development

.github/workflows/maven.yml

@@ -6,6 +6,11 @@ on:
   pull_request:
     branches: [ main ]
 
+permissions:
+  contents: read
+  checks: write
+  pull-requests: write
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,15 +20,22 @@ jobs:
     name: Java ${{ matrix.java }}
 
     steps:
-    - uses: actions/checkout@v6
+    - uses: actions/checkout@v7
     - name: Set up Java
-      uses: actions/setup-java@v5
+      uses: actions/setup-java@v6
       with:
         distribution: temurin
         java-version: ${{ matrix.java }}
     - name: Build with Maven
       run: mvn clean install -Dgpg.skip -Dmaven.javadoc.skip=true
-    - name: push JaCoCo stats to codecov.io
-      uses: codecov/codecov-action@v3
+    - name: Publish Test Report
+      id: report
+      uses: mikepenz/action-junit-report@v6
+      if: success() || failure() # always run even if the previous step fails
+      with:
+        report_paths: '**/target/surefire-reports/TEST-*.xml'
+        comment: true
+    - name: Push JaCoCo stats to codecov.io
+      uses: codecov/codecov-action@v7
       env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

CITATION.cff

@@ -11,7 +11,7 @@ authors:
     given-names: Ammar
     orcid: https://orcid.org/0000-0002-8399-8990
 title: NanoJava
-version: 2.0.7
-date-released: 2026-05-18
+version: 2.0.8
+date-released: 2026-10-20
 doi: 10.5281/zenodo.6984324
 url: "https://github.com/enanomapper/nanojava"

README.md

@@ -53,11 +53,11 @@ If you do not have Docker or if it is an overhead for your use case, you can bun
 
 4. Now, you will have the standalone jar file in the "target" folder named: 
 
-   nanojava-2.0.7-jar-with-dependencies.jar
+   nanojava-2.0.8-jar-with-dependencies.jar
 
 5. The JAR file is used in the same way as the Docker image in the "Usage" section with replacing:
 
-   "docker run" with "java -jar nanojava-2.0.7-jar-with-dependencies.jar"
+   "docker run" with "java -jar nanojava-2.0.8-jar-with-dependencies.jar"
 
    and make sure you provide the absolute paths for your files in this case.
 

pom.xml

@@ -5,7 +5,7 @@
   <artifactId>nanojava</artifactId>
   <description>Java library extending the Chemistry Development Kit with functionality for nanomaterials.</description>
   <name>NanoJava</name>
-  <version>2.0.7</version>
+  <version>2.0.8</version>
   <url>https://github.com/enanomapper/nanojava</url>
   <licenses>
     <license>
@@ -48,7 +48,7 @@
     </repositories>
 
   <properties>
-    <cdk.version>2.12</cdk.version>
+    <cdk.version>2.13</cdk.version>
     <junit.version>5.13.3</junit.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <maven.compiler.source>11</maven.compiler.source>
@@ -71,7 +71,7 @@
     <dependency>
       <groupId>org.blueobelisk</groupId>
       <artifactId>cmlxom</artifactId>
-      <version>4.17</version>
+      <version>4.19</version>
     </dependency>
     <dependency>
       <groupId>org.openscience.cdk</groupId>
@@ -106,7 +106,7 @@
     <dependency>
       <groupId>com.github.egonw</groupId>
       <artifactId>jqudt</artifactId>
-      <version>1.5.2</version>
+      <version>1.5.4</version>
     </dependency>
     <dependency>
       <groupId>com.github.stefanbirkner</groupId>