Release v3.1.0: bump version for Maven deploy

- Version 3.0.0 → 3.1.0 (3.0.0 already published to GitHub Packages)
- Update pom.xml, pom-local.xml, README.md
- All 135 tests pass

Author: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>

Author: asad

README.md

@@ -1,7 +1,7 @@
 Introduction
 ============
 
-`Reaction Decoder Tool (RDT) v3.0.0`
+`Reaction Decoder Tool (RDT) v3.1.0`
 --------------------------------------
 
 `1. Atom Atom Mapping (AAM) Tool`
@@ -137,7 +137,7 @@ Sub-commands
 `AAM using SMILES`
 
   ```
-  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
+  java -jar rdt-3.1.0-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
@@ -146,14 +146,14 @@ Sub-commands
 `AAM using SMILES` (accept mapping with no bond changes -b)
 
   ```
-  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
+  java -jar rdt-3.1.0-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 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
+  java -jar rdt-3.1.0-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
   ```
 
 
@@ -163,12 +163,12 @@ Sub-commands
 `Compare Reactions using SMILES with precomputed AAM mappings`
 
   ```
-  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
+  java -jar rdt-3.1.0-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 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
+  java -jar rdt-3.1.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH
   ```

pom-local.xml

@@ -4,7 +4,7 @@
     <groupId>com.bioinceptionlabs.rdt</groupId>
     <artifactId>rdt</artifactId>
     <description>Reaction Decoder Tool</description>
-    <version>3.0.0</version>
+    <version>3.1.0</version>
     <packaging>jar</packaging>
     <properties>
         <jdk.version>11</jdk.version>

pom.xml

@@ -4,7 +4,7 @@
     <groupId>com.bioinceptionlabs.rdt</groupId>
     <artifactId>rdt</artifactId>
     <description>Reaction Decoder Tool</description>
-    <version>3.0.0</version>
+    <version>3.1.0</version>
     <packaging>jar</packaging>
     <properties>
         <jdk.version>11</jdk.version>