diff -u b/module_filter.install b/module_filter.install
--- b/module_filter.install
+++ b/module_filter.install
@@ -48,3 +48,3 @@
   // longer want to lose the variable setting, so we just comment it out.
-  // variable_del('module_filter_dynamic_save_position');
+  // variable_del('module_filter_dynamic_save_position');.
 }
diff -u b/module_filter.theme.inc b/module_filter.theme.inc
--- b/module_filter.theme.inc
+++ b/module_filter.theme.inc
@@ -2,10 +2,14 @@
 
 /**
  * @file
+ * File for theme functions.
  *
  * @author greenSkin
  */
 
+/**
+ * Function theme_module_filter().
+ */
 function theme_module_filter($variables) {
   $element = $variables['element'];
   return '<div class="module-filter-inputs-wrapper">' . drupal_render_children($element) . '</div>';
@@ -64,7 +68,16 @@
     $package_ids[] = $package_id;
 
     // Package title and header.
-    $rows[] = array('data' => array(array('data' => '<h3>' . $form['modules'][$package]['#title'] . '</h3>', 'colspan' => 4)), 'id' => $package_id . '-package', 'class' => array('admin-package-title'));
+    $rows[] = array(
+      'data' => array(
+        array(
+          'data' => '<h3>' . $form['modules'][$package]['#title'] . '</h3>',
+          'colspan' => 4,
+        ),
+      ),
+      'id' => $package_id . '-package',
+      'class' => array('admin-package-title'),
+    );
     $rows[] = array('data' => $header, 'class' => array('admin-package-header'));
 
     $stripe = 'odd';
@@ -152,7 +165,7 @@
     $form['modules'][$package]['#printed'] = TRUE;
   }
 
-  //Get packages and count number of modules
+  // Get packages and count number of modules.
   $enabled_counts = array();
   foreach ($enabled as $package_id => $value) {
     $enabled_counts[$package_id] = array(
@@ -164,7 +177,7 @@
     'moduleFilter' => array(
       'packageIDs' => $package_ids,
       'enabledCounts' => $enabled_counts,
-    )
+    ),
   ), 'setting');
 
   // Add first and last class to rows.
@@ -182,8 +195,10 @@
 
 /**
  * Theme function for module filter operations.
+ *
  * @param $variables
- * @return
+ *
+ * @return string
  *   HTML for admin status operations.
  */
 function theme_module_filter_operations(&$vars) {
@@ -214,7 +229,18 @@
   if (!empty($operations)) {
     if ($dropbutton) {
-      return '<div class="admin-operations">' . theme('links__ctools_dropbutton', array('title' => t('Operations'), 'links' => $operations, 'attributes' => array('class' => array('links')))) . '</div>';
+      return '<div class="admin-operations">' . theme('links__ctools_dropbutton', array(
+        'title' => t('Operations'),
+        'links' => $operations,
+        'attributes' => array(
+          'class' => array('links'),
+        ),
+      )) . '</div>';
     }
-    return '<div class="admin-operations">' . theme('item_list', array('items' => $operations, 'attributes' => array('class' => array('links', 'inline')))) . '</div>';
+    return '<div class="admin-operations">' . theme('item_list', array(
+      'items' => $operations,
+      'attributes' => array(
+        'class' => array('links', 'inline'),
+      ),
+    )) . '</div>';
   }
 }