fixes in documentation string, also changed the randomseed file location and...

fixes in documentation string, also changed the randomseed file location and RestartFileList writing

da/tools/initexit.py

@@ -40,7 +40,8 @@ like this:::
 The most important method of the CycleControl object are listed below:
 
 .. autoclass:: da.tools.initexit.CycleControl 
-   :members: Initialize, Finalize, SubmitNextCycle, CleanUpCycle, SetupFileStructure, RecoverRun, RandomSeed
+   :members: Initialize, Finalize,  CollectRestartData, MoveRestartData, 
+             SubmitNextCycle, CleanUpCycle, SetupFileStructure, RecoverRun, RandomSeed
 
 Two important attributes of the CycleControl object are:
     (1) DaSystem, an instance of a :ref:`dasystem`
@@ -209,13 +210,13 @@ class CycleControl(dict):
     def RandomSeed(self,action='read'):
         """ 
         Get the randomseed and save it, or read the random seed and set it. The seed is currently stored
-        in a python :mod:`pickle` file, residing in the save directory
+        in a python :mod:`pickle` file, residing in the ``exec`` directory
 
         """
         import cPickle
         import numpy as np
 
-        filename = os.path.join(self['dir.restart.current'],'randomseed.pickle')
+        filename = os.path.join(self['dir.exec'],'randomseed.pickle')
 
         if action == 'write':
             f        = open(filename,'wb')
@@ -235,6 +236,11 @@ class CycleControl(dict):
 
         logging.info(msg)
 
+        dummy    = self.RestartFileList.append(filename)
+
+        msg      = "Added the randomseed.pickle file to the RestartFileList" ; logging.debug(msg)
+
+
         return None
 
     def Initialize(self):
@@ -329,11 +335,11 @@ class CycleControl(dict):
             * ``${da_rundir}/restart/current``
             * ``${da_rundir}/restart/one-ago``
 
-        .. note: The exec dir will actually be a simlink to the directory where
+        .. note:: The exec dir will actually be a simlink to the directory where
                  the observation operator executable lives. This directory is passed through
                  the ``da.rc`` file. 
 
-        .. note: The observation input files will be placed in the exec dir,
+        .. note:: The observation input files will be placed in the exec dir,
                  and the resulting simulated values will be retrieved from there as well.
 
         """
@@ -421,7 +427,7 @@ class CycleControl(dict):
             attribute "RestartFileList" which is a simple list of files that can be appended by other objects/methods that
             require restart data to be saved.
 
-            .. note: Before collecting the files in the ``RestartFileList``, the restart/current directory will be emptied and
+            .. note:: Before collecting the files in the ``RestartFileList``, the restart/current directory will be emptied and
                      recreated. This prevents files from accumulating in the restart/current and restart/one-ago folders. It 
                      also means that if a file is missing from the ``RestartFileList``, it will not be available for check-pointing
                      if your run crashes or dies!
@@ -429,17 +435,17 @@ class CycleControl(dict):
             Currently, the following files are included:
 
                 * The ``da_runtime.rc`` file
+                * The ``randomseed.pickle`` file
                 * The savestate.nc file
                 * The files in the ``ObservationOperator.RestartFileList``, i.e., restart data for the transport model
 
-            .. note: We assume that the restart files for the :class:`~da.baseclasses.observationoprator.ObservationOperator` 
-            reside in a separate folder, i.e, the ObservationOperator does *not* write directly to the restart dir!
+
+            .. note:: We assume that the restart files for the :class:`~da.baseclasses.observationoperator.ObservationOperator` 
+                      reside in a separate folder, i.e, the ObservationOperator does *not* write directly to the CTDAS restart dir!
 
         """
 
-        self.RestartFileList.append( os.path.join(self['dir.exec'],'da_runtime.rc') )
         self.RestartFileList.append( os.path.join(self['dir.output'],'savestate.nc') )
-        #self.RestartFileList.append( os.path.join(self['dir.exec'],'randomseed.pickle') )
 
         targetdir   = os.path.join(self['dir.restart.current'])
 
@@ -461,8 +467,6 @@ class CycleControl(dict):
 
     def MoveRestartData(self, io_option='restore'):
         """ 
-        :
-
         Store or restore model state to/from a restart directory. 
 
             Two IO options are available:
@@ -513,10 +517,12 @@ class CycleControl(dict):
 
 #
     def WriteNewRCfile(self):
-        """ Write the rc-file for the next DA cycle. Note that the start time for the next cycle is the end time of this one, while 
-            the end time for the next cycle is the current end time + one cycle length. The resulting rc-file is written to:
-            
-            (1) to the dir.exec so that it can be used when resubmitting the next cycle
+        """ Write the rc-file for the next DA cycle. 
+
+            .. note:: The start time for the next cycle is the end time of this one, while 
+                      the end time for the next cycle is the current end time + one cycle length. 
+                      
+            The resulting rc-file is written to the ``dir.exec`` so that it can be used when resubmitting the next cycle
             
         """
         from da.tools.general import AdvanceTime
@@ -533,10 +539,13 @@ class CycleControl(dict):
         #self['time.finish']      = self['time.finish'].strftime('%Y-%m-%d %H:%M:%S')
 
         fname                                = os.path.join(self['dir.exec'],'da_runtime.rc')
-        self['da.restart.fname'] = fname
+        self['da.restart.fname']             = fname
         dummy                                = rc.write(fname,self)
 
-        msg = 'Wrote new da_runtime.rc (%s)'%fname ; logging.debug(msg)
+        dummy                                = self.RestartFileList.append(fname)
+
+        msg = 'Added da_runtime.rc to the RestartFileList for later collection' ; logging.debug(msg)
+        msg = 'Wrote new da_runtime.rc (%s) to exec dir'%fname ; logging.debug(msg)
 
 
     def WriteRC(self,fname):