JAL-1854 checkstyle relocated to /utils, newlines to Unix (?)

diff --git a/.checkstyle b/.checkstyle
index c2a7260..0329bb7 100644 (file)
--- a/.checkstyle
+++ b/.checkstyle
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
 <fileset-config file-format-version="1.2.0" simple-config="false" sync-formatter="false">
-  <local-check-config name="JalviewCheckstyle" location="resources/checkstyle/checkstyle.xml" type="project" description="">
+  <local-check-config name="JalviewCheckstyle" location="utils/checkstyle/checkstyle.xml" type="project" description="">
     <additional-data name="protect-config-file" value="false"/>
   </local-check-config>
   <fileset name="source" enabled="true" check-config-name="JalviewCheckstyle" local="true">

diff --git a/resources/checkstyle/README.txt b/utils/checkstyle/README.txt
similarity index 90%
rename from resources/checkstyle/README.txt
rename to utils/checkstyle/README.txt
index 1c2aced..119c68e 100644 (file)
--- a/resources/checkstyle/README.txt
+++ b/utils/checkstyle/README.txt
@@ -18,7 +18,7 @@ Config
        This includes confining its scope to src/*.java and resources/*.properties.
        This can be modified interactively through the checkstyle properties editor.
        
-       Checkstyle config files in resources/checkstyle:
+       Checkstyle config files in utils/checkstyle:
                checkstyle.xml          : main configuration file with selected checkstyle modules
                checkstyle-suppress.xml : rules to exclude certain checks / files
                import-control.xml      : package import rules
@@ -36,6 +36,7 @@ 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)
 
 Checkstyle rules
 ----------------
@@ -49,13 +50,13 @@ Checkstyle rules
        
 Suppressing findings
 --------------------
-       If there are warnings you judge it ok to suppress, your options are
-       (from most global to most local scope):
+       If there are warnings you judge it ok to suppress (false positives), 
+       your options are (from most global to most local impact):
        - remove the rule entirely
        - adjust its properties
        - add an entry in checkstyle-suppress.xml to skip the file for the rule
        - add comments around the reported source lines
-               // CHECKSTYLE.OFF: RuleName
+               // CHECKSTYLE.OFF: RuleName 'a comment to justify suppression'
                source code here
                // CHECKSTYLE.ON: RuleName
        The suppression should be as localised as possible, to avoid false negatives.

diff --git a/resources/checkstyle/checkstyle-suppress.xml b/utils/checkstyle/checkstyle-suppress.xml
similarity index 96%
rename from resources/checkstyle/checkstyle-suppress.xml
rename to utils/checkstyle/checkstyle-suppress.xml
index 0c1d2ee..ac9e260 100644 (file)
--- a/resources/checkstyle/checkstyle-suppress.xml
+++ b/utils/checkstyle/checkstyle-suppress.xml
@@ -1,46 +1,46 @@
-<?xml version="1.0" encoding="UTF-8"?>\r
-\r
-<!DOCTYPE suppressions PUBLIC\r
-    "-//Puppy Crawl//DTD Suppressions 1.1//EN"\r
-    "http://www.puppycrawl.com/dtds/suppressions_1_1.dtd">\r
-\r
-<suppressions>\r
-       <!-- \r
-               Do not put individual file-level suppressions here.\r
-               Instead use embedded comments to switch checks on and off.\r
-    -->\r
-        \r
-    <!-- \r
-        Suppress check of XML binding generated code packages \r
-    --> \r
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]schemabinding[\\/]*"/>\r
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]binding[\\/]*"/>\r
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]json[\\/]binding[\\/]*"/>\r
-    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]xml[\\/]binding[\\/]*"/>\r
-        \r
-    <!-- \r
-       Suppress check of externally sourced code \r
-    --> \r
-    <suppress checks="[a-zA-Z0-9]*" files="com[\\/]*"/>\r
-    <suppress checks="[a-zA-Z0-9]*" files="ext[\\/]*"/>\r
-    <suppress checks="[a-zA-Z0-9]*" files="org[\\/]*"/>\r
-    <suppress checks="[a-zA-Z0-9]*" files="uk[\\/]*"/>\r
-    \r
-    <!-- \r
-       ImportControl can only handle one top level package\r
-    -->\r
-    <suppress checks="ImportControl" files="MCview[\\/]*" />\r
-    <suppress checks="ImportControl" files="vamsas[\\/]*" />\r
-    \r
-    <!--  \r
-       Suppress checks by name \r
-    -->\r
-       <suppress checks="FinalLocalVariable" files=".*\.java"/>\r
-    \r
-    <!--  \r
-       Suppress checks by id \r
-    -->\r
-       <suppress id="InterfaceNaming" files=".*\.java"/>\r
-       <suppress id="NoStaticInitialization" files=".*\.java"/>\r
-         \r
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!DOCTYPE suppressions PUBLIC
+    "-//Puppy Crawl//DTD Suppressions 1.1//EN"
+    "http://www.puppycrawl.com/dtds/suppressions_1_1.dtd">
+
+<suppressions>
+       <!-- 
+               Do not put individual file-level suppressions here.
+               Instead use embedded comments to switch checks on and off.
+    -->
+        
+    <!-- 
+        Suppress check of XML binding generated code packages 
+    --> 
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]schemabinding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]binding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]json[\\/]binding[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="jalview[\\/]xml[\\/]binding[\\/]*"/>
+        
+    <!-- 
+       Suppress check of externally sourced code 
+    --> 
+    <suppress checks="[a-zA-Z0-9]*" files="com[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="ext[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="org[\\/]*"/>
+    <suppress checks="[a-zA-Z0-9]*" files="uk[\\/]*"/>
+    
+    <!-- 
+       ImportControl can only handle one top level package
+    -->
+    <suppress checks="ImportControl" files="MCview[\\/]*" />
+    <suppress checks="ImportControl" files="vamsas[\\/]*" />
+    
+    <!--  
+       Suppress checks by name 
+    -->
+       <suppress checks="FinalLocalVariable" files=".*\.java"/>
+    
+    <!--  
+       Suppress checks by id 
+    -->
+       <suppress id="InterfaceNaming" files=".*\.java"/>
+       <suppress id="NoStaticInitialization" files=".*\.java"/>
+         
 </suppressions>
\ No newline at end of file

diff --git a/resources/checkstyle/checkstyle.xml b/utils/checkstyle/checkstyle.xml
similarity index 98%
rename from resources/checkstyle/checkstyle.xml
rename to utils/checkstyle/checkstyle.xml
index 423f698..7ca2d26 100644 (file)
--- a/resources/checkstyle/checkstyle.xml
+++ b/utils/checkstyle/checkstyle.xml
@@ -12,7 +12,7 @@
                Add any metrics that you wish to suppress to the following file.
        -->
        <module name="SuppressionFilter">
-               <property name="file" value="${basedir}/resources/checkstyle/checkstyle-suppress.xml"/>
+               <property name="file" value="${basedir}/utils/checkstyle/checkstyle-suppress.xml"/>
        </module>
 
        <!-- 
@@ -327,7 +327,7 @@
                        see http://checkstyle.sourceforge.net/config_imports.html#ImportControl 
                -->
                <module name="ImportControl">
-                   <property name="file" value="${basedir}/resources/checkstyle/import-control.xml"/>
+                   <property name="file" value="${basedir}/utils/checkstyle/import-control.xml"/>
                        <property name="severity" value="error"/>
                </module>
                

diff --git a/resources/checkstyle/import-control.xml b/utils/checkstyle/import-control.xml
similarity index 100%
rename from resources/checkstyle/import-control.xml
rename to utils/checkstyle/import-control.xml