Index: wflow-py/Scripts/mapstack.py
===================================================================
diff -u
--- wflow-py/Scripts/mapstack.py	(revision 0)
+++ wflow-py/Scripts/mapstack.py	(revision 2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8)
@@ -0,0 +1,230 @@
+#!/usr/bin/python
+
+"""
+mapstack.py - process mapstacks
+--------------------------------
+
+Usage:
+mapstack  -c inifile -C casename --clone clonemap
+
+    
+    -c name of the config file (in the case directory)
+    
+$Author: schelle $
+$Id: wflow_sceleton.py 898 2014-01-09 14:47:06Z schelle $
+$Rev: 898 $
+"""
+
+import numpy
+import os
+import os.path
+import shutil, glob
+import getopt
+
+from wflow.wf_DynamicFramework import *
+from wflow.wflow_adapt import *
+#import scipy
+
+
+
+def usage(*args):
+    sys.stdout = sys.stderr
+    for msg in args: print msg
+    print __doc__
+    sys.exit(0)
+
+class WflowModel(DynamicModel):  
+  """
+  The user defined model class. This is your work!
+  """
+  
+  def __init__(self, cloneMap,Dir,RunDir,configfile):
+      """
+      *Required*
+      
+      The init function **must** contain what is shown below. Other functionality
+      may be added by you if needed.
+      
+      """
+      DynamicModel.__init__(self)   
+      setclone(os.path.join(Dir,cloneMap))
+      self.runId=RunDir      
+      self.caseName=Dir
+      self.Dir = Dir
+      self.configfile = configfile
+     
+
+  def parameters(self):
+      """
+      List all the parameters (both static and forcing here). Use the wf_updateparameters()
+      function to update them in the initial section (static) and the dynamic section for
+      dynamic parameters and forcing date.
+
+      Possible parameter types are:
+
+      + staticmap: Read at startup from map
+      + statictbl: Read at startup from tbl, fallback to map (need Landuse, Soil and TopoId (subcatch) maps!
+      + timeseries: read map for each timestep
+      + monthlyclim: read a map corresponding to the current month (12 maps in total)
+      + dailyclim: read a map corresponding to the current day of the year
+      + hourlyclim: read a map corresponding to the current hour of the day (24 in total)
+
+
+      :return: List of modelparameters
+      """
+      modelparameters = []
+
+      return modelparameters
+
+  def stateVariables(self):
+      """ 
+      *Required*
+      
+      Returns a list of state variables that are essential to the model. 
+      This list is essential for the resume and suspend functions to work.
+      
+      This function is specific for each model and **must** be present. This is
+      where you specify the state variables of you model. If your model is stateless
+      this function must return and empty array (states = [])
+      
+      In the simple example here the TSoil variable is a state 
+      for the model.
+
+      """
+      states = []
+      
+      return states
+      
+      
+  def supplyCurrentTime(self):
+      """
+      *Optional*
+      
+      Supplies the current time in seconds after the start of the run
+      This function is optional. If it is not set the framework assumes
+      the model runs with daily timesteps.
+      
+      Output:
+      
+          - time in seconds since the start of the model run
+          
+      """
+      
+      return self.currentTimeStep() * int(configget(self.config,'model','timestepsecs','86400'))
+
+      
+  def initial(self):
+      
+    """
+    *Required*
+    
+    Initial part of the model, executed only once. It reads all static model
+    information (parameters) and sets-up the variables used in modelling.
+    
+    This function is required. The contents is free. However, in order to
+    easily connect to other models it is advised to adhere to the directory
+    structure used in the other models.
+    
+    """
+    #: pcraster option to calculate with units or cells. Not really an issue
+    #: in this model but always good to keep in mind.
+    setglobaloption("unittrue")
+
+
+    self.timestepsecs = int(configget(self.config,'model','timestepsecs','86400'))
+    self.basetimestep=86400
+    # Reads all parameter from disk
+    self.wf_updateparameters()
+
+
+
+  def resume(self):
+    """ 
+    *Required*
+
+    This function is required. Read initial state maps (they are output of a 
+    previous call to suspend()). The implementation shown here is the most basic
+    setup needed.
+    
+    """
+    pass
+
+  def suspend(self):
+    """
+      *Required*
+
+      Suspends the model to disk. All variables needed to restart the model
+      are saved to disk as pcraster maps. Use resume() to re-read them
+
+      This function is required.
+
+    """
+
+    self.wf_suspend(self.Dir)
+
+  def dynamic(self):
+      """
+      *Required*
+      
+      This is where all the time dependent functions are executed. Time dependent
+      output should also be saved here.
+      """
+      self.logger.debug("Processing step: " + str(self.currentTimeStep()))
+      self.wf_updateparameters() # read the temperature map for each step (see parameters())
+
+
+# The main function is used to run the program from the command line
+
+def main(argv=None):  
+    """
+    *Optional but needed it you want to run the model from the command line*
+    
+    Perform command line execution of the model. This example uses the getopt
+    module to parse the command line options.
+    
+    The user can set the caseName, the runDir, the timestep and the configfile.
+    """      
+    global multpars
+    caseName = "default"
+    runId = "run_default"
+    configfile="mapstack.ini"
+    _lastTimeStep = 10
+    _firstTimeStep = 1
+    timestepsecs=86400
+    wflow_cloneMap = 'wflow_subcatch.map'
+    
+    # This allows us to use the model both on the command line and to call 
+    # the model usinge main function from another python script.
+    
+    if argv is None:
+        argv = sys.argv[1:]
+        if len(argv) == 0:
+            usage()
+            return     
+
+    opts, args = getopt.getopt(argv, 'C:S:T:c:s:R:',['clone='])
+
+    for o, a in opts:
+        if o == '-C': caseName = a
+        if o == '-R': runId = a
+        if o == '-c': configfile = a
+        if o == '-s': timestepsecs = int(a)
+        if o == '-T': _lastTimeStep=int(a)
+        if o == '-S': _firstTimeStep=int(a)
+        if o == '--clone': wflow_cloneMap= a
+
+    if (len(opts) <=1):
+        usage()
+        
+    myModel = WflowModel(wflow_cloneMap, caseName,runId,configfile)
+    dynModelFw = wf_DynamicFramework(myModel, _lastTimeStep,firstTimestep=_firstTimeStep)
+    dynModelFw.createRunId(NoOverWrite=False,level=logging.DEBUG)    
+    dynModelFw._runInitial()
+    dynModelFw._runResume()
+    dynModelFw._runDynamic(_firstTimeStep,_lastTimeStep)
+    dynModelFw._runSuspend()
+    dynModelFw._wf_shutdown()
+    
+
+if __name__ == "__main__":
+    main()
Index: wflow-py/Scripts/wflow_prepare_step2.py
===================================================================
diff -u -r19ba123a81340a60d1901a26ad6b0af20496b933 -r2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8
--- wflow-py/Scripts/wflow_prepare_step2.py	(.../wflow_prepare_step2.py)	(revision 19ba123a81340a60d1901a26ad6b0af20496b933)
+++ wflow-py/Scripts/wflow_prepare_step2.py	(.../wflow_prepare_step2.py)	(revision 2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8)
@@ -31,6 +31,7 @@
 import getopt
 import ConfigParser
 import sys
+import numpy as np
 
 tr.Verbose=1
 
@@ -249,8 +250,8 @@
 
     # make subcatchments
     #os.system("col2map --clone " + step2dir + "/cutout.map gauges.col " + step2dir + "/wflow_gauges.map")
-    exec "X=tr.array(" + gauges_x + ")" 
-    exec "Y=tr.array(" + gauges_y + ")" 
+    exec "X=np.array(" + gauges_x + ")"
+    exec "Y=np.array(" + gauges_y + ")"
 
 
     tr.setglobaloption("unittrue")
Index: wflow-py/UnitTests/TestBMI.py
===================================================================
diff -u -reb5531aa1d2fd1da6de0ad4d35e1a4b63bc70951 -r2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8
--- wflow-py/UnitTests/TestBMI.py	(.../TestBMI.py)	(revision eb5531aa1d2fd1da6de0ad4d35e1a4b63bc70951)
+++ wflow-py/UnitTests/TestBMI.py	(.../TestBMI.py)	(revision 2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8)
@@ -54,6 +54,9 @@
         print("-------------- Current time: ")
         print(bmiobj.get_current_time())
 
+        print("-------------- Grid shape: ")
+        print(bmiobj.get_grid_shape('Altitude'))
+
         print("-------------- End time: ")
         print(bmiobj.get_end_time())
 
Index: wflow-py/wflow/wf_DynamicFramework.py
===================================================================
diff -u -rf0f9c075d66820b08dfbce3e1ab773b04a84df83 -r2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8
--- wflow-py/wflow/wf_DynamicFramework.py	(.../wf_DynamicFramework.py)	(revision f0f9c075d66820b08dfbce3e1ab773b04a84df83)
+++ wflow-py/wflow/wf_DynamicFramework.py	(.../wf_DynamicFramework.py)	(revision 2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8)
@@ -325,6 +325,7 @@
                 if par.type == 'timeseries':
                     if not hasattr(self._userModel(),par.name):
                         self._userModel().logger.info("Adding " + par.name + " to model.")
+
                     theparmap = self.wf_readmap(os.path.join(self._userModel().caseName,par.stack), par.default,verbose=par.verbose)
                     theparmap = cover(theparmap,par.default)
                     setattr(self._userModel(),par.name,theparmap)
@@ -558,7 +559,7 @@
     self.ncoutfile = configget(self._userModel().config,'framework','netcdfoutput',"None")
 
 
-    # Set teh re-init hint fro the local model
+    # Set the re-init hint for the local model
     self.reinit = int(configget(self._userModel().config,'run','reinit',str(self.reinit)))
     self._userModel().reinit = self.reinit
     # Now finally set the start end time. First check if set in ini otherwise check if the ini defines
@@ -620,7 +621,7 @@
     for sttype in _type.availtypes:
         _maps = configsection(self._userModel().config,"summary_" + sttype)
         for thismap in _maps:
-            thismapname = caseName + "/" + runId + "/outsum/" + self._userModel().config.get("summary_" + sttype,thismap)
+            thismapname = os.path.join(caseName,runId,'outsum',self._userModel().config.get("summary_" + sttype,thismap))
             thismap = thismap.split('self.')[1]
             self.statslst.append(wf_sumavg(thismap,mode=sttype,filename=thismapname))
 
Index: wflow-py/wflow/wf_netcdfio.py
===================================================================
diff -u -rbf65fb743568cb9c44c6e4d96791dcc1c332a015 -r2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8
--- wflow-py/wflow/wf_netcdfio.py	(.../wf_netcdfio.py)	(revision bf65fb743568cb9c44c6e4d96791dcc1c332a015)
+++ wflow-py/wflow/wf_netcdfio.py	(.../wf_netcdfio.py)	(revision 2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8)
@@ -124,7 +124,6 @@
 
         globmetadata.update(metadata)
 
-
         prepare_nc(self.ncfile,timeList,x,y,globmetadata,logger,Format=netcdfformat)
 
 
Index: wflow-py/wflow/wflow_bmi.py
===================================================================
diff -u -r043cc93152a2b84e31b26a39f523e4930957b981 -r2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8
--- wflow-py/wflow/wflow_bmi.py	(.../wflow_bmi.py)	(revision 043cc93152a2b84e31b26a39f523e4930957b981)
+++ wflow-py/wflow/wflow_bmi.py	(.../wflow_bmi.py)	(revision 2aef8b1c3a3d5c674d3112cc60a67f20594c2cb8)
@@ -555,7 +555,7 @@
         dim =  self.dynModel.wf_supplyGridDim()
         #[ Xul, Yul, xsize, ysize, rows, cols]
 
-        return dim[4,5]
+        return [dim[4], dim[5]]
 
     def get_grid_spacing(self, long_var_name):
         """
@@ -565,8 +565,9 @@
 
         :return: The size of a grid cell for each of the dimensions of the given variable, e.g. [width, height]: for a 2D grid cell.
         """
-        raise NotImplementedError
 
+        return self.dynModel.wf_supplyGridDim()[2:4]
+
     def get_grid_origin(self, long_var_name):
         """
         gets the origin of the model grid.