[WIP] Upgrade CDK 2.13 (currently -SNAPSHOT)

.github/workflows/maven.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        java: [ 8, 11, 17]
+        java: [ 8, 11, 17, 21, 25 ]
     name: Java ${{ matrix.java }}
 
     steps:

README.md

@@ -13,9 +13,10 @@
 # CDK-Scaffold Module
 ## Scaffold Functionalities for the Chemistry Development Kit (CDK)
 
-Copyright © 2023 The CDK Development Team, especially
+Copyright © 2023-2026 The CDK Development Team, especially
 [Julian Zander](mailto:zanderjulian@gmx.de),
 [Jonas Schaub](mailto:jonas.schaub@uni-jena.de),
+[Egon Willighagen](https://github.com/egonw),
 [Achim Zielesny](mailto:achim.zielesny@w-hs.de),
 [Christoph Steinbeck](mailto:christoph.steinbeck@uni-jena.de)
 
@@ -51,13 +52,13 @@ If you are using Maven, you can install the cdk-scaffold package using:
 <dependency>
   <artifactId>cdk-scaffold</artifactId>
   <groupId>org.openscience.cdk</groupId>
-  <version>2.8</version>
+  <version>2.12</version>
 </dependency>
 ```
 
 ### Snapshot releases
 
-For snapshot releases (currently `2.9-SNAPSHOT`) include the following fragment to define the
+For snapshot releases (currently `2.13-SNAPSHOT`) include the following fragment to define the
 snapshot repository:
 
 ```xml

pom.xml

@@ -6,7 +6,7 @@
     <groupId>org.openscience.cdk</groupId>
     <artifactId>cdk-scaffold</artifactId>
     <name>cdk-scaffold</name>
-    <version>2.9-SNAPSHOT</version>
+    <version>2.12-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <url>https://github.com/cdk/cdk-scaffold</url>
@@ -26,7 +26,7 @@
         <!--suppress UnresolvedMavenProperty -->
         <sonar.coverage.jacoco.xmlReportPaths>${maven.multiModuleProjectDirectory}/bundle/target/site/jacoco-aggregate/jacoco.xml</sonar.coverage.jacoco.xmlReportPaths>
         <sonar.host.url>https://sonarcloud.io</sonar.host.url>
-        <cdk.version>2.9</cdk.version>
+        <cdk.version>2.13-SNAPSHOT</cdk.version>
         <junit.version>5.9.3</junit.version>
         <hamcrest.version>2.2</hamcrest.version>
         <jacoco.version>0.8.15</jacoco.version>

src/main/java/org/openscience/cdk/tools/scaffold/NetworkNode.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -35,7 +35,8 @@
  * @param <MoleculeType> As MoleculeType, any data type can be defined.
  *                     In our scenario, the node contains a CDK IAtomContainer.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.0.0
  */
 public class NetworkNode <MoleculeType> extends ScaffoldNodeBase<MoleculeType> {

src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldGenerator.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -69,7 +69,8 @@
  * Mining for Bioactive Scaffolds with Scaffold Networks</a> paper.
  * Different trees or networks can also be merged together.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.4.0
  */
 public class ScaffoldGenerator {

src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNetwork.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -38,7 +38,8 @@
  * Top-level class to organise the NetworkNodes
  * A network can have several roots and leaves.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.2.1
  */
 public class ScaffoldNetwork extends ScaffoldNodeCollectionBase {

src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeBase.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -37,7 +37,8 @@
  * @param <MoleculeType> As MoleculeType, any data type can be defined.
  *                      In our scenario, the node contains a CDK IAtomContainer.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.1.0
  */
 public abstract class ScaffoldNodeBase<MoleculeType> {

src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldNodeCollectionBase.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -39,7 +39,8 @@
  * Base class of node collection objects.
  * Top-level class to organise the ScaffoldNodeBase objects.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.2.0
  */
 public abstract class ScaffoldNodeCollectionBase {

src/main/java/org/openscience/cdk/tools/scaffold/ScaffoldTree.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -35,7 +35,8 @@
  * Top-level class to organise the TreeNodes as a tree.
  * A tree can have one root and several leaves.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.2.0
  */
 public class ScaffoldTree extends ScaffoldNodeCollectionBase {

src/main/java/org/openscience/cdk/tools/scaffold/TreeNode.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -34,7 +34,8 @@
  * @param <MoleculeType> As MoleculeType, any data type can be defined.
  *                      In our scenario, the node contains a CDK IAtomContainer.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.0.0
  */
 public class TreeNode<MoleculeType> extends ScaffoldNodeBase<MoleculeType> {

src/test/java/org/openscience/cdk/tools/scaffold/GitHubWikiCodeExamplesTest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>

src/test/java/org/openscience/cdk/tools/scaffold/ScaffoldGeneratorTest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2022 Julian Zander <zanderjulian@gmx.de>
+ * Copyright (c) 2026 Julian Zander <zanderjulian@gmx.de>
  *                    Jonas Schaub <jonas.schaub@uni-jena.de>
  *                    Achim Zielesny <achim.zielesny@w-hs.de>
  *                    Christoph Steinbeck <christoph.steinbeck@uni-jena.de>
@@ -57,7 +57,8 @@
 /**
  * JUnit test class for the Scaffold Generator.
  *
- * @author Julian Zander, Jonas Schaub (zanderjulian@gmx.de, jonas.schaub@uni-jena.de)
+ * @author Julian Zander (zanderjulian@gmx.de)
+ * @author Jonas Schaub (jonas.schaub@uni-jena.de)
  * @version 1.0.7.0
  */
 public class ScaffoldGeneratorTest extends ScaffoldGenerator {
@@ -944,7 +945,7 @@ public void stereoFragmentationTest() throws Exception {
                 "C1CCCC(/C(=C(/C2CCCNCCC2)\\C3CCCCC(C4CCCC(CC(CC5CCNCC5)=C)C4)CC3)/C6CCCCCNC6)CCC1",
                 "C1CCCC(/C(=C(/C2CCCNCCC2)\\C3CCCCC(C4CCCCC4)CC3)/C5CCCCCNC5)CCC1",
                 "C1CCCC(/C(=C(/C2CCCNCCC2)\\C3CCCCCCC3)/C4CCCCCNC4)CCC1",
-                "C(=C(C1CCCNCCC1)C2CCCCCCC2)C3CCCCCNC3",
+                "C(=C(\\C1CCCNCCC1)/C2CCCCCCC2)\\C3CCCCCNC3",
                 "C(C1CCCNCCC1)(C2CCCCCCC2)=C",
                 "C1CCCNCCC1"
         };