DOC: Update documentation

Author: effigies

doc/users/config_file.rst

@@ -237,16 +237,23 @@ Debug configuration
 
 To enable debug mode, one can insert the following lines::
 
-  from nipype import config, logging
+  from nipype import config
   config.enable_debug_mode()
-  logging.update_logging(config)
 
 In this mode the following variables are set::
 
   config.set('execution', 'stop_on_first_crash', 'true')
   config.set('execution', 'remove_unnecessary_outputs', 'false')
+  config.set('execution', 'keep_inputs', 'true')
   config.set('logging', 'workflow_level', 'DEBUG')
   config.set('logging', 'interface_level', 'DEBUG')
+  config.set('logging', 'utils_level', 'DEBUG')
+
+The primary loggers (``workflow``, ``interface`` and ``utils``) are also reset
+to level ``DEBUG``.
+You may wish to adjust these manually using::
 
+  from nipype import logging
+  logging.getLogger(<logger>).setLevel(<level>)
 
 .. include:: ../links_names.txt

doc/users/debug.rst

@@ -20,15 +20,17 @@ performance issues.
       from nipype import config
       config.enable_debug_mode()
 
-   as the first import of your nipype script. To enable debug logging use::
-
-       from nipype import logging
-       logging.update_logging(config)
+   as the first import of your nipype script.
 
    .. note::
 
-     Turning on debug will rerun your workflows and will rerun them after debugging
-     is turned off.
+     Turning on debug will rerun your workflows and will rerun them after
+     debugging is turned off.
+
+     Turning on debug mode will also override log levels specified elsewhere,
+     such as in the nipype configuration.
+     ``workflow``, ``interface`` and ``utils`` loggers will all be set to
+     level ```DEBUG``.
 
 #. There are several configuration options that can help with debugging. See
    :ref:`config_file` for more details::