Release v3.0.0: SMSD 3.1.0, CDK 2.12, full modernization

- Bump version to 3.0.0 (major: breaking dependency changes)
- Update SMSD dependency to 3.1.0 (com.bioinceptionlabs)
- Update copyright headers to 2007-2026 across all source files
- Update author email to asad.rahman@bioinceptionlabs.com
- Update CLI banner and metadata to BioInception
- Remove stale OSSRH/Sonatype publishing profile
- Update Maven plugins: compiler 3.13.0, surefire 3.5.2, assembly 3.7.1
- Update Maven prerequisite to 3.8
- Modernize GitHub Actions: checkout@v4, setup-java@v4, temurin JDK 11
- Remove redundant .travis.yml (GitHub Actions is primary CI)
- Fix nb-configuration.xml license hint (gpl30 -> lgpl30)
- Update .gitignore with modern IDE entries
- Refresh README.md for v3.0.0
- Clean remaining System.out imports in non-CLI files
- Fix System.exit(1) -> System.exit(0) for normal CLI termination

Author: asad

.github/workflows/maven-ci.yml

@@ -1,33 +1,30 @@
-# This workflow will build a package using Maven and then publish it to GitHub packages when a release is created
-# For more information see: https://github.com/actions/setup-java#apache-maven-with-a-settings-path
-
-name: Maven Package
-
-on:
-  push:
-    branches:
-      - 'master'
-  # release:
-  #   types: [created]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up JDK 11
-      uses: actions/setup-java@v1
-      with:
-        java-version: 11.0.4
-        server-id: github # Value of the distributionManagement/repository/id field of the pom.xml
-        settings-path: ${{ github.workspace }} # location for the settings.xml file
-
-    - name: Build with Maven
-      run: mvn -B package -Dmaven.test.skip=true --file pom.xml
-
-    - name: Publish to GitHub Packages Apache Maven
-      run: mvn deploy -Dmaven.test.skip=true -s $GITHUB_WORKSPACE/settings.xml
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
+# Build and publish to GitHub Packages on push to master
+
+name: Maven Package
+
+on:
+  push:
+    branches:
+      - 'master'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up JDK 11
+      uses: actions/setup-java@v4
+      with:
+        java-version: '11'
+        distribution: 'temurin'
+        server-id: github
+        settings-path: ${{ github.workspace }}
+
+    - name: Build with Maven
+      run: mvn -B clean package --file pom.xml
+
+    - name: Publish to GitHub Packages Apache Maven
+      run: mvn deploy -Dmaven.test.skip=true -s $GITHUB_WORKSPACE/settings.xml
+      env:
+        GITHUB_TOKEN: ${{ github.token }}

.gitignore

@@ -11,18 +11,30 @@
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
 
-#MAC files
+# Mac files
 .DS_Store
+
+# IDE files
 /nbproject/private/
+*.iml
+.idea/
+.vscode/
+
+# Editor swap/backup files
+*.swp
+*.swo
+*.bak
+
+# Build output
 /dist/
 /Output/
 /store/
 /temp/
 /build/
+/target/
 /rdt/core/target/
 /rdt/exec/target/
 /rdt/nbproject/
 /rdt/core/Output/
 /rdt/target/
 /rdt/Output/
-/target/

.travis.yml

@@ -1,12 +1,12 @@
 Introduction
 ============
 
-`Reaction Decoder Tool (RDT)`
------------------------------
+`Reaction Decoder Tool (RDT) v3.0.0`
+--------------------------------------
 
 `1. Atom Atom Mapping (AAM) Tool`
 
-`2. Reaction Annotator (Extract Bond Changes, Identify & Mark Reaction Centres) and `
+`2. Reaction Annotator (Extract Bond Changes, Identify & Mark Reaction Centres)`
 
 `3. Reaction Comparator (Reaction Similarity based on the Bond Changes, Reaction Centres or Substructures)`
 
@@ -18,75 +18,55 @@ e-mail: asad.rahman@bioinceptionlabs.com
 Installation
 ============
 
-`a)` You could [download the latest RDT] (https://github.com/asad/ReactionDecoder/releases) release version from the github.
+`a)` You could [download the latest RDT](https://github.com/asad/ReactionDecoder/releases) release version from the github.
 
-`b)` Compile the core code using `maven`?:
-
-`POM.xml` commands
+`b)` Compile the core code using `maven`:
 
 ```
-
-use POM.xml and mvn commands to build your project
+use pom.xml and mvn commands to build your project
 1) mvn -DskipTests=true install (skip test)
 2) mvn install (include test)
 3) mvn clean (clean)
 4) mvn package
 5) mvn -P local clean install -DskipTests=true (fast single jar compilation, skip test)
 6) mvn -P local clean install (single jar compilation with test)
-
 ```
 
 Atom Atom Mapping using Java API
 =================================
 
-View mapped reaction using [CDKDEPICT Tool](http://www.simolecule.com/cdkdepict/depict.html).
-
-```
-
-public static void main(String[] args) throws CloneNotSupportedException, CDKException, AssertionError, Exception {
-        final SmilesGenerator sg = new SmilesGenerator(SmiFlavor.AtomAtomMap);
-        final SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
-
-        String reactionSM = "CC(=O)C=C.CC=CC=C>>CC1CC(CC=C1)C(C)=O";
-        String reactionName = "Test";
-
-        IReaction cdkReaction = smilesParser.parseReactionSmiles(reactionSM);
-
-        IReaction performAtomAtomMapping = performAtomAtomMapping(cdkReaction, reactionName);
-        System.out.println("AAM sm: " + sg.create(performAtomAtomMapping));
-    }
-
-    /**
-     *
-     * @param cdkReaction
-     * @param reactionName
-     * @return
-     * @throws InvalidSmilesException
-     * @throws AssertionError
-     * @throws Exception
-     */
-    public static IReaction performAtomAtomMapping(IReaction cdkReaction, String reactionName) throws InvalidSmilesException, AssertionError, Exception {
-        cdkReaction.setID(reactionName);
-        /*
-         RMT for the reaction mapping
-         */
-        boolean forceMapping = true;//Overrides any mapping present int the reaction
-        boolean generate2D = true;//2D perception of the stereo centers
-        boolean generate3D = false;//2D perception of the stereo centers
-        StandardizeReaction standardizeReaction = new StandardizeReaction(); //Standardize the reaction
-        ReactionMechanismTool rmt = new ReactionMechanismTool(cdkReaction, forceMapping, generate2D, generate3D, standardizeReaction);
-        MappingSolution s = rmt.getSelectedSolution();//Fetch the AAM Solution
-        IReaction reaction = s.getReaction();//Fetch Mapped Reaction
-        return reaction;
-    }
-
+```java
+public static void main(String[] args) throws Exception {
+    final SmilesGenerator sg = new SmilesGenerator(SmiFlavor.AtomAtomMap);
+    final SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+
+    String reactionSM = "CC(=O)C=C.CC=CC=C>>CC1CC(CC=C1)C(C)=O";
+    String reactionName = "DielsAlder";
+
+    IReaction cdkReaction = smilesParser.parseReactionSmiles(reactionSM);
+
+    IReaction performAtomAtomMapping = performAtomAtomMapping(cdkReaction, reactionName);
+    System.out.println("AAM sm: " + sg.create(performAtomAtomMapping));
+}
+
+public static IReaction performAtomAtomMapping(IReaction cdkReaction, String reactionName) throws Exception {
+    cdkReaction.setID(reactionName);
+    boolean forceMapping = true;
+    boolean generate2D = true;
+    boolean generate3D = false;
+    StandardizeReaction standardizeReaction = new StandardizeReaction();
+    ReactionMechanismTool rmt = new ReactionMechanismTool(cdkReaction, forceMapping, generate2D, generate3D, standardizeReaction);
+    MappingSolution s = rmt.getSelectedSolution();
+    IReaction reaction = s.getReaction();
+    return reaction;
+}
 ```
 
 
 License
 =======
 
-`RDT` is released under the [GNU General Public License version 3](http://www.gnu.org/licenses/gpl.html).
+`RDT` is released under the [GNU Lesser General Public License (LGPL) version 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.html).
 
 ```
 Author: Syed Asad Rahman
@@ -113,40 +93,40 @@ Sub-commands
 -------------
 
 `AAM using SMILES`
-  
+
   ```
-  java -jar ReactionDecoder.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT
+  java -jar rdt-3.0.0-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT
   ```
 
 `Perform AAM` for Transporters
 -------------
 
 `AAM using SMILES` (accept mapping with no bond changes -b)
-  
+
   ```
-  java -jar ReactionDecoder.jar -Q SMI -q "O=C(O)C(N)CC(=O)N.O=C(O)C(N)CS>>C(N)(CC(=O)N)C(=O)O.O=C(O)C(N)CS" -b -g -c -j AAM -f TEXT
+  java -jar rdt-3.0.0-jar-with-dependencies.jar -Q SMI -q "O=C(O)C(N)CC(=O)N.O=C(O)C(N)CS>>C(N)(CC(=O)N)C(=O)O.O=C(O)C(N)CS" -b -g -c -j AAM -f TEXT
   ```
-  
+
 `Annotate Reaction using SMILES`
 ---------------------------------
 
   ```
-  java -jar ReactionDecoder.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j ANNOTATE -f XML
+  java -jar rdt-3.0.0-jar-with-dependencies.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j ANNOTATE -f XML
   ```
 
 
 `Compare Reactions`
 --------------------
 
 `Compare Reactions using SMILES with precomputed AAM mappings`
-  
+
   ```
-  java -jar ReactionDecoder.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u
+  java -jar rdt-3.0.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u
   ```
 
 
 `Compare Reactions using RXN files`
-  
+
   ```
-  java -jar ReactionDecoder.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH
+  java -jar rdt-3.0.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH
   ```

README.md

@@ -16,6 +16,6 @@
         <org-netbeans-modules-whitelist.whitelist-oracle>false</org-netbeans-modules-whitelist.whitelist-oracle>
         <org-netbeans-modules-javascript2-requirejs.enabled>true</org-netbeans-modules-javascript2-requirejs.enabled>
         <netbeans.checkstyle.format>true</netbeans.checkstyle.format>
-        <netbeans.hint.license>gpl30</netbeans.hint.license>
+        <netbeans.hint.license>lgpl30</netbeans.hint.license>
     </properties>
 </project-shared-configuration>