Prevent duplicate warnings

Output CommentedMap starting at queues:

fsl_sub_plugin_sge/__init__.py

@@ -1105,6 +1105,11 @@ def _minutes_to_seconds(minutes):
     return minutes * 60
 
 
+def _add_warning(warnings, warning):
+    if warning not in warnings:
+        warnings.append(warning)
+
+
 def build_queue_defs():
     '''Return YAML suitable for configuring queues'''
     logger = _get_logger()
@@ -1116,7 +1121,9 @@ def build_queue_defs():
     except BadSubmission as e:
         logger.error('Unable to query Grid Engine: ' + str(e))
         return ('', [])
-    queues = CommentedMap()
+    q_base = CommentedMap()
+    q_base['queues'] = CommentedMap()
+    queues = q_base['queues']
     for q in queue_list:
         qinfo = _get_queue_info(q)
         if 'BATCH' not in qinfo['qtype']:
@@ -1128,7 +1135,8 @@ def build_queue_defs():
         warnings = []
         for coproc_m in ('gpu', 'cuda', 'phi', ):
             if coproc_m in q:
-                warnings.append(
+                _add_warning(
+                    warnings,
                     "Quene name looks like it might be a queue supporting co-processors."
                     " Cannot auto-configure."
                 )
@@ -1155,7 +1163,8 @@ def build_queue_defs():
             qd['max_size'] = int(queue_ram_map[q][0])
             add_comment("Maximum RAM size of a job", 'max_size', column=0)
             if queue_ram_map[q][1]:
-                warnings.append(
+                _add_warning(
+                    warnings,
                     "Queue has hosts of different total memory size, consider creating multiple queues"
                     " for the different host hardware in Grid Engine and then set the same 'group' integer"
                     " to allow fsl_sub to maximise hardware your job can run on. Alternatively consider turning"
@@ -1176,7 +1185,8 @@ def build_queue_defs():
 
         unique_vmem = list(set(q_vmem))
         if len(unique_vmem) > 0:
-            warnings.append(
+            _add_warning(
+                warnings,
                 "Queue has hosts of different per-slot memory size, consider creating multiple"
                 " queues for the different host hardware in Grid Engine and then add these queues "
                 " to the configuration setting the same 'group' integer in the configuration to "
@@ -1189,7 +1199,8 @@ def build_queue_defs():
             unique_rss = list(set(q_rss))
             if len(unique_rss) > 0:
                 if not warnings:
-                    warnings.append(
+                    _add_warning(
+                        warnings,
                         "Queue has hosts of different per-slot memory size, consider creating multiple"
                         " queues for the different host hardware in Grid Engine and then add these queues "
                         " to the configuration setting the same 'group' integer in the configuration to "
@@ -1200,11 +1211,13 @@ def build_queue_defs():
                 qd['slot_size'] = human_to_ram(unique_rss[0], output=ram_units)
             else:
                 qd['slot_size'] = int(qd['max_size']) // queue_ram_map[q][2]
-                warnings.append(
+                _add_warning(
+                    warnings,
                     "Queue has no h_vmem or h_rss specified, "
                     "slot_size calculated with max_size divided by slots.")
                 if queue_ram_map[q][3]:
-                    warnings.append(
+                    _add_warning(
+                        warnings,
                         "Queue has multiple slot sizes "
                         "- this calculation will not be correct for all hosts."
                     )
@@ -1218,4 +1231,4 @@ def build_queue_defs():
         for w in warnings:
             queues.yaml_set_comment_before_after_key(qinfo['qname'], after=w)
 
-    return queues
+    return q_base