JAL-1854 Checkstyle updated to 8.12

diff --git a/utils/checkstyle/README.txt b/utils/checkstyle/README.txt
index e38064e..54f4e48 100644 (file)
--- a/utils/checkstyle/README.txt
+++ b/utils/checkstyle/README.txt
@@ -1,6 +1,8 @@
 Checkstyle for Jalview
 ----------------------
 
+See
+https://issues.jalview.org/browse/JAL-1854
 http://checkstyle.sourceforge.net/
 GNU LGPL
 
@@ -9,8 +11,16 @@ To get the Eclipse Checkstyle plugin
        - Help | Eclipse Marketplace
        - search for checkstyle
        - install eclipse-cs checkstyle plugin
-The current version is 6.19.1 (August 2016).
 
+Change Log
+----------
+See http://checkstyle.sourceforge.net/releasenotes.html
+Aug 2016       Initial version used is 6.19.1
+Dec 2018       Updated to 8.12.0 (latest on Eclipse Marketplace, 8.15 is latest release)
+                       SuppressionCommentFilter relocated (changed in 8.1)
+                       FileContentsHolder removed (changed in 8.2)
+                       Updates to import-control.xml for code changes (htsjdk, stackoverflowusers)
+                       
 Config
 ------
 
@@ -37,6 +47,7 @@ How to use checkstyle
        Option 2: on demand on selected code
                - right-click on a class or package and Checkstyle | Check code with checkstyle
                - (or Clear Checkstyle violations to remove checkstyle warnings)
+               - recommended to use this as a QA step when changing or reviewing code
 
 Checkstyle rules
 ----------------
@@ -64,11 +75,11 @@ Suppressing findings
 Tips
 ----
        Sometimes checkstyle needs a kick before it will refresh its findings.
-       A whitespace edit in checkstyle.xml usually does this. There may be better ways.
+       Click the 'refresh' icon at top right in Eclipse | Preferences | Checkstyle.
        
        Invalid configuration files may result in checkstyle failing with an error reported
        in the Eclipse log file. 
-       Help | Installation Details | Configuration takes you to a screen with a 
+       Eclipse | About | Installation Details | Configuration takes you to a screen with a 
        'View Error Log' button.
        
        Sometimes checkstyle can fail silently. Try 'touching' (editing) config files, failing

diff --git a/utils/checkstyle/checkstyle-suppress.xml b/utils/checkstyle/checkstyle-suppress.xml
index 122b8d0..29a3047 100644 (file)
--- a/utils/checkstyle/checkstyle-suppress.xml
+++ b/utils/checkstyle/checkstyle-suppress.xml
@@ -26,6 +26,7 @@
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]ext[\\/]edu*"/>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]ext[\\/]vamsas*"/>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]org[\\/]jibble*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="[\\/]org[\\/]stackoverflowusers*"/>
     <suppress checks="[a-zA-Z0-9]*" files="[\\/]uk[\\/]ac*"/>
     
     <!-- 

diff --git a/utils/checkstyle/checkstyle.xml b/utils/checkstyle/checkstyle.xml
index 85ac8e6..17946f7 100644 (file)
--- a/utils/checkstyle/checkstyle.xml
+++ b/utils/checkstyle/checkstyle.xml
@@ -16,18 +16,6 @@
        </module>
 
        <!-- 
-               Allow suppression of rules by comments, e.g.:
-               // CHECKSTYLE.OFF: ParameterNumber
-               ..method declaration
-               // CHECKSTYLE.ON: ParameterNumber
-       -->
-       <module name="SuppressionCommentFilter">
-               <property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
-               <property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
-               <property name="checkFormat" value="$1"/>
-       </module>
-
-       <!-- 
                Check language bundles have the same keys and no duplicates
                (ensure Checkstyle is configured to scan non-source files)
         -->
@@ -54,10 +42,16 @@
                <property name="tabWidth" value="4"/>
 
                <!-- 
-                       Enables parsing of suppressions comments
-                       see http://checkstyle.sourceforge.net/config_filters.html#SuppressionCommentFilter 
+                       Allow suppression of rules by comments, e.g.:
+                       // CHECKSTYLE.OFF: ParameterNumber
+                       ..method declaration
+                       // CHECKSTYLE.ON: ParameterNumber
                -->
-               <module name="FileContentsHolder"/>
+               <module name="SuppressionCommentFilter">
+                       <property name="offCommentFormat" value="CHECKSTYLE.OFF\: ([\w\|]+)"/>
+                       <property name="onCommentFormat" value="CHECKSTYLE.ON\: ([\w\|]+)"/>
+                       <property name="checkFormat" value="$1"/>
+               </module>
 
        <!-- ****************************** -->
        <!--         NAMING STANDARDS       -->

diff --git a/utils/checkstyle/import-control.xml b/utils/checkstyle/import-control.xml
index c47aaec..478966f 100644 (file)
--- a/utils/checkstyle/import-control.xml
+++ b/utils/checkstyle/import-control.xml
@@ -94,6 +94,7 @@
                <allow pkg="compbio.metadata" class="jalview.gui.WsJobParameters"/>
                <allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarna"/>
                <allow pkg="fr.orsay.lri.varna" class="jalview.gui.AppVarnaBinding"/>
+               <allow pkg="org.stackoverflowusers.file" class="jalview.gui.Desktop"/>
                <allow pkg="uk.ac.vamsas" class="jalview.gui.VamsasApplication"/>
            </subpackage>
                
@@ -116,6 +117,9 @@
                <allow pkg="uk.ac.vamsas"/>
                <allow pkg="fr.orsay.lri.varna"/>
                <allow pkg="MCview"/>
+                       <subpackage name="vcf">
+                       <allow pkg="htsjdk\.*" regex="true"/>
+                       </subpackage>       
                </subpackage>       
                                
                <subpackage name="javascript">