From a7a185037d84ea3f1754777e87bda955d3635185 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 7 Mar 2026 20:08:12 +0100
Subject: [PATCH 1/7] Open for development

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 1c1f36e..0734c41 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
   <artifactId>nanojava</artifactId>
   <description>Java library extending the Chemistry Development Kit with functionality for nanomaterials.</description>  
   <name>NanoJava</name>
-  <version>2.0.5</version>
+  <version>2.0.6-SNAPSHOT</version>
   <url>https://github.com/enanomapper/nanojava</url>
 
   <licenses>

From 761a21b196c4b59a90ab3e88b81089f1cd28ffad Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 7 Mar 2026 20:11:12 +0100
Subject: [PATCH 2/7] Updated GH actions

---
 .github/workflows/maven.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
index 74d6e06..1eb1017 100644
--- a/.github/workflows/maven.yml
+++ b/.github/workflows/maven.yml
@@ -15,9 +15,9 @@ jobs:
     name: Java ${{ matrix.java }}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v6
     - name: Set up Java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v5
       with:
         distribution: temurin
         java-version: ${{ matrix.java }}

From 180d63b99a4662478d3f354940872957260413a0 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 7 Mar 2026 20:25:09 +0100
Subject: [PATCH 3/7] Updated build plugins and dependencies

---
 pom.xml | 335 +++++++++++++++++++++++++++-----------------------------
 1 file changed, 164 insertions(+), 171 deletions(-)

diff --git a/pom.xml b/pom.xml
index 0734c41..2bfaf74 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,12 +1,12 @@
+<?xml version="1.0"?>
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <groupId>io.github.egonw</groupId>
   <artifactId>nanojava</artifactId>
-  <description>Java library extending the Chemistry Development Kit with functionality for nanomaterials.</description>  
+  <description>Java library extending the Chemistry Development Kit with functionality for nanomaterials.</description>
   <name>NanoJava</name>
   <version>2.0.6-SNAPSHOT</version>
   <url>https://github.com/enanomapper/nanojava</url>
-
   <licenses>
     <license>
       <name>GNU LGPL 2.1 or later</name>
@@ -14,14 +14,12 @@
       <distribution>repo</distribution>
     </license>
   </licenses>
-
   <scm>
     <connection>scm:git:git://github.com/egonw/nanojava.git</connection>
     <developerConnection>scm:git:ssh://git@github.com/egonw/nanojava.git</developerConnection>
     <url>http://github.com/egonw/nanojava/tree/master</url>
     <tag>HEAD</tag>
   </scm>
-
   <distributionManagement>
     <snapshotRepository>
       <id>central</id>
@@ -32,7 +30,13 @@
       <url>https://central.sonatype.com</url>
     </repository>
   </distributionManagement>
-
+  <properties>
+    <cdk.version>2.12</cdk.version>
+    <junit.version>5.13.3</junit.version>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <maven.compiler.source>11</maven.compiler.source>
+    <maven.compiler.target>11</maven.compiler.target>
+  </properties>
   <dependencies>
     <dependency>
       <groupId>org.junit.jupiter</groupId>
@@ -52,59 +56,50 @@
     <dependency>
       <groupId>org.blueobelisk</groupId>
       <artifactId>cmlxom</artifactId>
-      <version>4.13</version>
+      <version>4.15</version>
+    </dependency>
+    <dependency>
+      <groupId>org.openscience.cdk</groupId>
+      <artifactId>cdk-formula</artifactId>
+      <version>${cdk.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.openscience.cdk</groupId>
+      <artifactId>cdk-inchi</artifactId>
+      <version>${cdk.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.openscience.cdk</groupId>
+      <artifactId>cdk-libiocml</artifactId>
+      <version>${cdk.version}</version>
     </dependency>
-	<dependency>
-	    <groupId>org.openscience.cdk</groupId>
-	    <artifactId>cdk-formula</artifactId>
-	    <version>${cdk.version}</version>
-	</dependency>
-	<dependency>
-	    <groupId>org.openscience.cdk</groupId>
-	    <artifactId>cdk-inchi</artifactId>
-	    <version>${cdk.version}</version>
-	</dependency>
-	<dependency>
-	    <groupId>org.openscience.cdk</groupId>
-	    <artifactId>cdk-libiocml</artifactId>
-	    <version>${cdk.version}</version>
-	</dependency>
-	<dependency>
-	    <groupId>org.openscience.cdk</groupId>
-	    <artifactId>cdk-silent</artifactId>
-	    <version>${cdk.version}</version>
-	</dependency>
-	<dependency>
-	    <groupId>org.openscience.cdk</groupId>
-	    <artifactId>cdk-smiles</artifactId>
-	    <version>${cdk.version}</version>
-	</dependency>
-	<dependency>
-		<groupId>info.picocli</groupId>
-		<artifactId>picocli</artifactId>
-		<version>4.7.7</version>
-	</dependency>
-	<dependency>
-	    <groupId>com.github.egonw</groupId>
-	    <artifactId>jqudt</artifactId>
-	    <version>1.5.1</version>
-	</dependency>
     <dependency>
-        <groupId>com.github.stefanbirkner</groupId>
-        <artifactId>system-rules</artifactId>
-        <version>1.19.0</version>
-        <scope>test</scope>
+      <groupId>org.openscience.cdk</groupId>
+      <artifactId>cdk-silent</artifactId>
+      <version>${cdk.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.openscience.cdk</groupId>
+      <artifactId>cdk-smiles</artifactId>
+      <version>${cdk.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>info.picocli</groupId>
+      <artifactId>picocli</artifactId>
+      <version>4.7.7</version>
+    </dependency>
+    <dependency>
+      <groupId>com.github.egonw</groupId>
+      <artifactId>jqudt</artifactId>
+      <version>1.5.1</version>
+    </dependency>
+    <dependency>
+      <groupId>com.github.stefanbirkner</groupId>
+      <artifactId>system-rules</artifactId>
+      <version>1.19.0</version>
+      <scope>test</scope>
     </dependency>
   </dependencies>
-
-  <properties>
-    <cdk.version>2.11</cdk.version>
-    <junit.version>5.13.3</junit.version>
-    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <maven.compiler.source>1.8</maven.compiler.source>
-    <maven.compiler.target>1.8</maven.compiler.target>
-  </properties>
-
   <!-- developer = commit access -->
   <developers>
     <developer>
@@ -113,7 +108,6 @@
       <url>https://chem-bla-ics.linkedchemistry.info/</url>
     </developer>
   </developers>
-
   <contributors>
     <contributor>
       <name>Ammar Ammar</name>
@@ -122,7 +116,6 @@
       <name>Nina Jeliazkova</name>
     </contributor>
   </contributors>
-
   <build>
     <resources>
       <resource>
@@ -134,7 +127,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.6.1</version>
+        <version>3.6.2</version>
         <executions>
           <execution>
             <id>enforce-maven</id>
@@ -154,119 +147,119 @@
           </execution>
         </executions>
       </plugin>
-		<plugin>
-			<artifactId>maven-assembly-plugin</artifactId>
-			<version>3.7.1</version>
-			<configuration>
-				<descriptorRefs>
-					<descriptorRef>jar-with-dependencies</descriptorRef>
-				</descriptorRefs>
-				<archive>
-					<manifest>
-						<mainClass>io.github.egonw.nanojava.NanoJava</mainClass>
-					</manifest>
-				</archive>
-			</configuration>
-			<executions>
-				<execution>
-					<id>make-assembly</id>
-					<phase>package</phase>
-					<goals>
-						<goal>single</goal>
-					</goals>
-				</execution>
-			</executions>
-		</plugin>
-            <plugin>
-                <groupId>org.jacoco</groupId>
-                <artifactId>jacoco-maven-plugin</artifactId>
-                <version>0.8.13</version>
-                <executions>
-                    <execution>
-                        <id>start-agent</id>
-                        <goals>
-                            <goal>prepare-agent</goal>
-                        </goals>
-                    </execution>
-                    <execution>
-                        <id>generate-report</id>
-                        <goals>
-                            <goal>report</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.sonatype.central</groupId>
-                <artifactId>central-publishing-maven-plugin</artifactId>
-                <version>0.8.0</version>
-                <extensions>true</extensions>
-                <configuration>
-                    <publishingServerId>central</publishingServerId>
-                    <autoPublish>true</autoPublish>
-                    <waitUntil>published</waitUntil>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-gpg-plugin</artifactId>
-                <version>3.2.8</version>
-                <executions>
-                    <execution>
-                        <id>sign-artifacts</id>
-                        <phase>verify</phase>
-                        <goals>
-                            <goal>sign</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <version>3.5.3</version>
-                <configuration>
-                    <groups>${junit5.groups}</groups>
-                    <excludedGroups>${junit5.excludeGroups}</excludedGroups>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-source-plugin</artifactId>
-                <version>3.3.1</version>
-                <executions>
-                    <execution>
-                        <id>attach-sources</id>
-                        <goals>
-                            <goal>jar-no-fork</goal>
-                       </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.11.2</version>
-                <executions>
-                    <execution>
-                        <id>attach-javadocs</id>
-                        <goals>
-                            <goal>jar</goal>
-                        </goals>
-                    </execution>
-                    <execution>
-                        <id>aggregate</id>
-                        <goals>
-                            <goal>aggregate</goal>
-                        </goals>
-                        <phase>site</phase>
-                        <configuration>
-                        </configuration>
-                    </execution>
-                </executions>
-                <configuration>
-                    <source>8</source>
-                </configuration>
-            </plugin>
-	</plugins> 
+      <plugin>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <version>3.8.0</version>
+        <configuration>
+          <descriptorRefs>
+            <descriptorRef>jar-with-dependencies</descriptorRef>
+          </descriptorRefs>
+          <archive>
+            <manifest>
+              <mainClass>io.github.egonw.nanojava.NanoJava</mainClass>
+            </manifest>
+          </archive>
+        </configuration>
+        <executions>
+          <execution>
+            <id>make-assembly</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <version>0.8.14</version>
+        <executions>
+          <execution>
+            <id>start-agent</id>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>generate-report</id>
+            <goals>
+              <goal>report</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.sonatype.central</groupId>
+        <artifactId>central-publishing-maven-plugin</artifactId>
+        <version>0.10.0</version>
+        <extensions>true</extensions>
+        <configuration>
+          <publishingServerId>central</publishingServerId>
+          <autoPublish>true</autoPublish>
+          <waitUntil>published</waitUntil>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-gpg-plugin</artifactId>
+        <version>3.2.8</version>
+        <executions>
+          <execution>
+            <id>sign-artifacts</id>
+            <phase>verify</phase>
+            <goals>
+              <goal>sign</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>3.5.5</version>
+        <configuration>
+          <groups>${junit5.groups}</groups>
+          <excludedGroups>${junit5.excludeGroups}</excludedGroups>
+        </configuration>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-source-plugin</artifactId>
+        <version>3.4.0</version>
+        <executions>
+          <execution>
+            <id>attach-sources</id>
+            <goals>
+              <goal>jar-no-fork</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-javadoc-plugin</artifactId>
+        <version>3.12.0</version>
+        <executions>
+          <execution>
+            <id>attach-javadocs</id>
+            <goals>
+              <goal>jar</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>aggregate</id>
+            <goals>
+              <goal>aggregate</goal>
+            </goals>
+            <phase>site</phase>
+            <configuration>
+            </configuration>
+          </execution>
+        </executions>
+        <configuration>
+          <source>8</source>
+        </configuration>
+      </plugin>
+    </plugins>
   </build>
 </project>

From 50969a700d981f8b33d0b2db43773ebaa49a4cb1 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 7 Mar 2026 20:29:50 +0100
Subject: [PATCH 4/7] jQUDT snapshot

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 2bfaf74..2e53e3a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -91,7 +91,7 @@
     <dependency>
       <groupId>com.github.egonw</groupId>
       <artifactId>jqudt</artifactId>
-      <version>1.5.1</version>
+      <version>1.5.2-SNAPSHOT</version>
     </dependency>
     <dependency>
       <groupId>com.github.stefanbirkner</groupId>

From b17b3e23494fba3fd216f0e77798b69e61ac5c37 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sat, 7 Mar 2026 23:24:57 +0100
Subject: [PATCH 5/7] Added the snapshot repo

---
 pom.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/pom.xml b/pom.xml
index 2e53e3a..50ba541 100644
--- a/pom.xml
+++ b/pom.xml
@@ -14,12 +14,14 @@
       <distribution>repo</distribution>
     </license>
   </licenses>
+
   <scm>
     <connection>scm:git:git://github.com/egonw/nanojava.git</connection>
     <developerConnection>scm:git:ssh://git@github.com/egonw/nanojava.git</developerConnection>
     <url>http://github.com/egonw/nanojava/tree/master</url>
     <tag>HEAD</tag>
   </scm>
+
   <distributionManagement>
     <snapshotRepository>
       <id>central</id>
@@ -30,6 +32,21 @@
       <url>https://central.sonatype.com</url>
     </repository>
   </distributionManagement>
+
+    <repositories>
+        <repository>
+            <id>sonatypeSnapshots</id>
+            <name>Sonatype Snapshots</name>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+            <url>https://central.sonatype.com/repository/maven-snapshots/</url>
+        </repository>
+    </repositories>
+
   <properties>
     <cdk.version>2.12</cdk.version>
     <junit.version>5.13.3</junit.version>
@@ -37,6 +54,7 @@
     <maven.compiler.source>11</maven.compiler.source>
     <maven.compiler.target>11</maven.compiler.target>
   </properties>
+
   <dependencies>
     <dependency>
       <groupId>org.junit.jupiter</groupId>

From 3e456075b7779140f958bbc484cdf79e3136737e Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sun, 8 Mar 2026 11:04:03 +0100
Subject: [PATCH 6/7] jQUDT 1.5.2 is out

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 50ba541..59a2252 100644
--- a/pom.xml
+++ b/pom.xml
@@ -109,7 +109,7 @@
     <dependency>
       <groupId>com.github.egonw</groupId>
       <artifactId>jqudt</artifactId>
-      <version>1.5.2-SNAPSHOT</version>
+      <version>1.5.2</version>
     </dependency>
     <dependency>
       <groupId>com.github.stefanbirkner</groupId>

From 528bd9b310653db4609296cc7ef5d73a91a97b1c Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egon.willighagen@gmail.com>
Date: Sun, 8 Mar 2026 11:06:38 +0100
Subject: [PATCH 7/7] Release 2.0.6

---
 CITATION.cff | 4 ++--
 README.md    | 4 ++--
 pom.xml      | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 99d67f1..19748bd 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -11,7 +11,7 @@ authors:
     given-names: Ammar
     orcid: https://orcid.org/0000-0002-8399-8990
 title: NanoJava
-version: 2.0.5
-date-released: 2025-08-16
+version: 2.0.6
+date-released: 2026-03-08
 doi: 10.5281/zenodo.6984324
 url: "https://github.com/enanomapper/nanojava"
diff --git a/README.md b/README.md
index 93c23c3..2cc7fdb 100644
--- a/README.md
+++ b/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-2.0.4-SNAPSHOT-jar-with-dependencies.jar
+   nanojava-2.0.6-SNAPSHOT-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-2.0.4-SNAPSHOT-jar-with-dependencies.jar"
+   "docker run" with "java -jar nanojava-2.0.6-SNAPSHOT-jar-with-dependencies.jar"
 
    and make sure you provide the absolute paths for your files in this case.
 
diff --git a/pom.xml b/pom.xml
index 59a2252..a8baf30 100644
--- a/pom.xml
+++ b/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>2.0.6-SNAPSHOT</version>
+  <version>2.0.6</version>
   <url>https://github.com/enanomapper/nanojava</url>
   <licenses>
     <license>