correct v3.4 names to current naming convention

CHANGELOG.md

 All notable changes to Pantools will be documented in this file.
 
-## [3.5] - TODO: add date for release
+## [4.0.0] - TODO: add date for release
 
 ### Added
 - CI/CD pipeline that for now only runs `mvn test` (merge request !41).
@@ -55,7 +55,7 @@ All notable changes to Pantools will be documented in this file.
 - Distinguish between homology groups as file or as list for `msa`, `core_snp_tree` and `consensus_tree` (merge request !86).
 - `build_panproteome` no longer creates inconsistent 'header' and 'protein_ID' properties (merge request !89).
 
-## [3.4] - 2022-05-04
+## [3.4.0] - 2022-05-04
 
 ### Added
 - Version and commit ID are reported when PanTools is initialized.

docs/source/conf.py

@@ -6,8 +6,8 @@ project = 'PanTools'
 copyright = '2016, the PanTools team'
 author = 'Sandra Smit'
 
-release = '3.5'
-version = '3.5'
+release = '4,0.0'
+version = '4,0.0'
 
 # -- General configuration
 

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>nl.wur.bif</groupId>
     <artifactId>pantools</artifactId>
-    <version>3.5</version>
+    <version>4.0.0</version>
 
     <properties>
         <maven.compiler.source>8</maven.compiler.source>

src/main/java/nl/wur/bif/pantools/pangenome/Classification.java

@@ -3848,7 +3848,7 @@ public class Classification {
     }
     /**
-     * With the new gff parser introduced in v3.4 the "name" property now holds a String[] value instead of a String
+     * With the new gff parser introduced in v4.0.0 the "name" property now holds a String[] value instead of a String
      * By using this function the code still works on older versions
      *
      * String[] value is converted to string. Example [genA,genB] becomes genA/genB
@@ -3867,7 +3867,7 @@ public class Classification {
     }
     /**
-     * With the new gff parser introduced in v3.4 the "name" property now holds a String[] value instead of a String
+     * With the new gff parser introduced in v4.0.0 the "name" property now holds a String[] value instead of a String
      * By using this function the code still works on older versions
      *
      * String value is placed in String[]. Example genA becomes [genA]