Update Spring dependencies and add in new functionality

.github/workflows/maven.yml

@@ -7,19 +7,23 @@ on: [push, pull_request]
 
 jobs:
   build:
-    runs-on: ubuntu-24.04
-    strategy:
-      matrix:
-        # test against latest update of each major Java version:
-        java: [ 17, 21, 25 ]
-    name: Java ${{ matrix.java }}
+    runs-on: ubuntu-22.04
+    env:
+      # Pinned for reproducible builds (ReactionDecoder is not on Maven Central).
+      RDT_REF: 0d6632251108e7a8f625d15c60607a136093c4d8
+    name: Java 25
     steps:
       - uses: actions/checkout@v4
-      - name: Setup java
+      - name: Setup Java 25
         uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: ${{ matrix.java }}
+          distribution: 'temurin'
+          java-version: '25'
           cache: 'maven'
+      - name: Build and install ReactionDecoder (RDT) into local Maven repo
+        run: |
+          git clone https://github.com/asad/ReactionDecoder.git "${RUNNER_TEMP}/ReactionDecoder"
+          git -C "${RUNNER_TEMP}/ReactionDecoder" checkout --detach "${RDT_REF}"
+          mvn -B -f "${RUNNER_TEMP}/ReactionDecoder/pom.xml" clean install -DskipTests=true
       - name: Build with Maven
         run: mvn -B clean test javadoc:javadoc package

.gitignore

@@ -3,8 +3,9 @@
 .settings
 .classpath
 target
-
-
+.idea
+.DS_Store
+.vscode
 # Mobile Tools for Java (J2ME)
 .mtj.tmp/
 

README.md

@@ -4,6 +4,25 @@ A web application for generating chemical structure depictions from SMILES.
 
 ## [https://www.simolecule.com/cdkdepict](http://www.simolecule.com/cdkdepict)
 
+## Atom and bond tagging
+
+The `/depict/{style}/{fmt}` endpoint now understands an optional `atomlists`
+query parameter that can be used to colour specific atoms and their connecting
+bonds. Provide the parameter as a semicolon (or pipe) separated list of atom
+index collections, for example:
+
+```
+atomlists=0,1,2;#ff8800:5,6
+```
+
+Each sublist receives its own highlight colour; when a colour is not provided,
+the server cycles through the default palette that is already used for atom-map
+visualisation. Any bond between atoms in the same sublist is highlighted using
+the same colour. The indices refer to the zero-based ordering of atoms in the
+depicted molecule. Colours can be supplied in hexadecimal form (for example
+`#ff8800` or `0xff8800`) or as comma-separated RGB(A) components such as
+`255,136,0`.
+
 ## Docker
 
 An image is available on DockerHub, [https://hub.docker.com/r/simolecule/cdkdepict/](https://hub.docker.com/r/simolecule/cdkdepict/). To launch a CDK Depict web serivce running on 8081:
@@ -17,7 +36,7 @@ $ docker run -p 8081:8080 simolecule/cdkdepict:latest
 You can download prebuilt release from GitHub, this is a runnable WAR and will
 launch a standalone server using Spring Boot:
 
- * [`cdkdepict.war`](https://github.com/cdk/depict/releases/download/1.14/cdkdepict.war)
+ * [`cdkdepict.war`](https://github.com/cdk/depict/releases/download/1.13/cdkdepict.war)
 
 #### Build
 
@@ -30,7 +49,7 @@ target directory. The WAR file can be deployed to an application server (e.g.
 TomCat, Jetty, GlassFish, JBOSS) whilst the JAR launches it's own embedded server.
 
 ```
-$ target/cdkdepict-webapp-1.14.war
+$ target/cdkdepict-1.10.war
 ```
 
 #### Standalone Bootable App

cdkdepict-lib/pom.xml

@@ -5,10 +5,9 @@
   <parent>
     <artifactId>cdkdepict</artifactId>
     <groupId>org.openscience.cdk</groupId>
-    <version>1.15</version>
+    <version>1.14</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
-  <name>cdkdepict-lib</name>
   <artifactId>cdkdepict-lib</artifactId>
   <dependencies>
     <dependency>
@@ -44,12 +43,22 @@
     <dependency>
       <groupId>com.simolecule.centres</groupId>
       <artifactId>centres-cdk</artifactId>
-      <version>1.4</version>
+      <version>1.2.1</version>
+    </dependency>
+    <dependency>
+      <groupId>com.bioinceptionlabs</groupId>
+      <artifactId>rdt</artifactId>
+      <version>${rdt.version}</version>
     </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-api</artifactId>
       <version>1.7.36</version>
     </dependency>
+    <dependency>
+     <groupId>com.google.guava</groupId>
+     <artifactId>guava</artifactId>
+     <version>33.1.0-jre</version>
+    </dependency>
   </dependencies>
 </project>