General improvements and upgrades

README.rst

@@ -3,6 +3,8 @@ Community Analysis Pipeline (CAP)
 
 Welcome to the Mars Climate Modeling Center (MCMC) **Community Analysis Pipeline (CAP)**.
 
+For instructions and documentation please see our `online documentation <https://amescap.readthedocs.io>`_.
+
 About
 -----
 **CAP** is a set of Python3 libraries and command-line executables that streamline downloading, processing, and plotting output from the NASA Ames Mars Global Climate Models:

amescap/FV3_utils.py

@@ -1275,7 +1275,13 @@ def mass_stream(v_avg, lat, level, type="pstd", psfc=700, H=8000.,
             .g. ⌡ f(z)dz = (Zn-Zn-1){f(Zn) + f(Zn-1)}/2
               n-1
     """
-
+    reverting = False
+    if level[0] < level[-1]:
+        reverting = True
+        print("Reversing pstd array for mass stream function calculation...")
+        level = level[::-1]
+        v_avg = v_avg[::-1, ...]
+
     g = 3.72 # m/s2
     a = 3400*1000 # m
     nlev = len(level)
@@ -1335,6 +1341,11 @@ def mass_stream(v_avg, lat, level, type="pstd", psfc=700, H=8000.,
         MSF[mask] = np.nan
     if isMasked:
         MSF = np.ma.array(MSF, mask = mask)
+
+    if reverting:
+        print("Reversing pstd dimension of MSF array for compatibility...")
+        MSF = MSF[::-1, ...]
+
     return MSF.reshape(shape_out)
 
 
@@ -1916,6 +1927,12 @@ def daily_to_diurn(varIN, time_in):
 
     iperday = int(np.round(1/dt_in))
     vshape_in = varIN.shape
+
+    # Add safety check for integer sols
+    if not(np.mod(vshape_in[0],iperday) == 0):
+        print("Error: File cannot be split evenly into sols")
+        return None
+
     vreshape = np.append([-1, iperday], vshape_in[1:]).astype(int)
     varOUT = varIN.reshape(vreshape)
 

amescap/Ncdf_wrapper.py

@@ -119,19 +119,19 @@ def add_constant(self, variable_name, value, longname_txt="",
 
     # Private Definitions
     def _def_variable(self, variable_name, dim_array, longname_txt="",
-                      units_txt=""):
+                      units_txt="",datatype="f4"):
         self.var_dict[variable_name] = self.f_Ncdf.createVariable(variable_name,
-                                                                  "f4",
+                                                                  datatype,
                                                                   dim_array)
         self.var_dict[variable_name].units = units_txt
         self.var_dict[variable_name].long_name = longname_txt
         self.var_dict[variable_name].dim_name = str(dim_array)
 
 
     def _def_axis1D(self, variable_name, dim_array, longname_txt="",
-                    units_txt="", cart_txt=""):
+                    units_txt="", cart_txt="",datatype="f8"):
         self.var_dict[variable_name] = self.f_Ncdf.createVariable(variable_name,
-                                                                 "f4",
+                                                                 datatype,
                                                                  dim_array)
         self.var_dict[variable_name].units = units_txt
         self.var_dict[variable_name].long_name = longname_txt
@@ -167,17 +167,16 @@ def _is_cart_axis(self, Ncvar):
 
 
     def log_variable(self, variable_name, DATAin, dim_array, longname_txt="",
-                     units_txt=""):
+                     units_txt="",datatype="f4"):
         """
         EX::
 
             Log.log_variable("sfcT", sfcT, ("time", "Nx"),
                              "soil temperature", "K")
         """
-
         if variable_name not in self.var_dict.keys():
             self._def_variable(variable_name, dim_array, longname_txt,
-                               units_txt)
+                               units_txt,datatype)
         self.var_dict[variable_name].long_name = longname_txt
         self.var_dict[variable_name].dim_name = str(dim_array)
         self.var_dict[variable_name].units = units_txt
@@ -263,7 +262,7 @@ def copy_Ncvar(self, Ncvar, swap_array=None):
             longname_txt = getattr(Ncvar, "long_name", Ncvar._name)
             units_txt = getattr(Ncvar, "units", "")
             self._def_variable(Ncvar._name, Ncvar.dimensions, longname_txt,
-                               units_txt)
+                               units_txt,Ncvar.dtype)
             if np.any(swap_array):
                 self.log_variable(Ncvar._name, swap_array[:], Ncvar.dimensions,
                                   longname_txt, units_txt)

amescap/Script_utils.py

@@ -928,7 +928,6 @@ def filter_vars(fNcdf, include_list=None, giveExclude=False):
         else:
             print(f"{Yellow}***Warning*** from filter_vars(): "
                   f"{ivar} not found in file.\n")
-            exit()
 
     baseline_var = []
     for ivar in  var_list: