removed CMEMS specifc tracer varable names, NCML remppaing now used

inputs/CMEMS.ncml

@@ -21,8 +21,10 @@
       </ns0:aggregation>
     </ns0:netcdf>
   </ns0:aggregation>
-  <ns0:variable name="thetao" orgName="thetao" />
-  <ns0:variable name="uo" orgName="uo" />
-  <ns0:variable name="vo" orgName="vo" />
-  <ns0:variable name="zos" orgName="zos" />
+  <ns0:variable name="votemper" orgName="thetao" />
+  <ns0:variable name="vozocrtx" orgName="uo" />
+  <ns0:variable name="vomecrty" orgName="vo" />
+  <ns0:variable name="sossheig" orgName="zos" />
+  <ns0:variable name="time_counter" orgName="time" />
+  <ns0:dimension name="time_counter" orgName="time" />
 </ns0:netcdf>

inputs/namelist_cmems.bdy

@@ -51,7 +51,6 @@
 !------------------------------------------------------------------------------
 !  CMEMS Data Source Configuration
 !------------------------------------------------------------------------------
-   ln_use_cmems             = .true.
    ln_download_cmems        = .false.
    sn_cmems_dir             = '/Users/thopri/Projects/PyNEMO/inputs/' ! where to download CMEMS input files (static and variable)
    ln_download_static       = .false.
@@ -96,14 +95,14 @@
                                           !  barotropic fields
     ln_dyn3d       = .false.              !  boundary conditions for
                                           !  baroclinic velocities
-    ln_tra         = .false.               !  boundary conditions for T and S
+    ln_tra         = .true.               !  boundary conditions for T and S
     ln_ice         = .false.              !  ice boundary condition   
     nn_rimwidth    = 9                    !  width of the relaxation zone
 
 !------------------------------------------------------------------------------
 !  unstructured open boundaries tidal parameters                        
 !------------------------------------------------------------------------------
-    ln_tide        = .true.              !  =T : produce bdy tidal conditions
+    ln_tide        = .false.              !  =T : produce bdy tidal conditions
     sn_tide_model  = 'fes'                !  Name of tidal model (fes|tpxo)
     clname(1)      = 'M2'                 !  constituent name
     clname(2)      = 'S2'

pynemo/nemo_bdy_dl_cmems.py

@@ -16,6 +16,7 @@ import glob
 import os
 #local imports
 from pynemo.utils import cmems_errors as errors
+from pynemo.reader import factory
 
 logger = logging.getLogger(__name__)
 # TODO: Fix double spacing issue on CMEMS download log entries.

pynemo/profile.py

@@ -521,53 +521,20 @@ def process_bdy(setup_filepath=0, mask_gui=False):
     var_in = {}
     for g in range(len(grd)):
         var_in[grd[g]] = []
-    if 'use_cmems' in settings:
-        if settings['use_cmems'] == True:
-            logger.info('using CMEMS variable names......')
-            if ln_tra:
-                var_in['t'].extend(['thetao'])
-                #var_in['t'].extend(['so'])
 
-            if ln_dyn2d or ln_dyn3d:
-                var_in['u'].extend(['uo'])
-                var_in['v'].extend(['vo'])
+    if ln_tra:
+        var_in['t'].extend(['votemper']) #, 'vosaline'])
 
-            if ln_dyn2d:
-                var_in['t'].extend(['zos'])
+    if ln_dyn2d or ln_dyn3d:
+        var_in['u'].extend(['vozocrtx'])
+        var_in['v'].extend(['vomecrty'])
 
-            if ln_ice:
-                var_in['t'].extend(['siconc', 'sithick'])
+    if ln_dyn2d:
+        var_in['t'].extend(['sossheig'])
 
-        if settings['use_cmems'] == False:
-            logger.info('using existing PyNEMO variable names.....')
-            if ln_tra:
-                var_in['t'].extend(['votemper', 'vosaline'])
+    if ln_ice:
+        var_in['t'].extend(['iicethic', 'ileadfra', 'isnowthi'])
 
-            if ln_dyn2d or ln_dyn3d:
-                var_in['u'].extend(['vozocrtx'])
-                var_in['v'].extend(['vomecrty'])
-
-            if ln_dyn2d:
-                var_in['t'].extend(['sossheig'])
-
-            if ln_ice:
-                var_in['t'].extend(['iicethic', 'ileadfra', 'isnowthi'])
-
-    if 'use_cmems' not in settings:
-        logger.info('using existing PyNEMO variable names.....')
-        if ln_tra:
-            var_in['t'].extend(['votemper', 'vosaline'])
-
-        if ln_dyn2d or ln_dyn3d:
-            var_in['u'].extend(['vozocrtx'])
-            var_in['v'].extend(['vomecrty'])
-
-        if ln_dyn2d:
-            var_in['t'].extend(['sossheig'])
-
-        if ln_ice:
-            var_in['t'].extend(['iicethic', 'ileadfra', 'isnowthi'])
-    
     # As variables are associated with grd there must be a filename attached
     # to each variable
     

pynemo/reader/ncml.py

@@ -40,21 +40,7 @@ try:
 except ImportError:
     print('Warning: Please make sure pyjnius is installed and jvm.dll/libjvm.so/libjvm.dylib is in the path')
 
-import sys
-from pynemo import nemo_bdy_setup as setup
-try:
-    Setup = setup.Setup(sys.argv[2]) # default settings file
-    settings = Setup.settings
-    if 'use_cmems' in settings:
-        if settings['use_cmems'] == True:
-            time_counter_const = "time"
-        if settings['use_cmems'] == False:
-            time_counter_const = "time_counter"
-    if 'use_cmems' not in settings:
-        time_counter_const = "time_counter"
-    del settings, Setup
-except IndexError:
-    time_counter_const = "time_counter"
+time_counter_const = "time_counter"
 
 class Reader(object):
     """ This class is the high level of object for the NCML reader, from here using grid type

test_scripts/meta_data.py

@@ -7,7 +7,10 @@ Set of functions to download CMEMS files using FTP (for static mask data) and MO
 from netCDF4 import Dataset
 import re
 # list of datasets to check
-datasets = [ "http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_data/ORCA025-N206_19791101d05T.nc",
+datasets = [ "/Users/thopri/Projects/PyNEMO/inputs/subset_2017-01-01_2017-01-31_T.nc",
+             "/Users/thopri/Projects/PyNEMO/inputs/subset_2017-01-01_2017-01-31_U.nc",
+             "/Users/thopri/Projects/PyNEMO/inputs/subset_2017-01-01_2017-01-31_V.nc",
+             "http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_data/ORCA025-N206_19791101d05T.nc",
              "http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_data/ORCA025-N206_19791101d05U.nc",
              "http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_data/ORCA025-N206_19791101d05V.nc",
              "http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_data/ORCA025-N206_19791101d05I.nc"
@@ -27,13 +30,12 @@ chk_list = {'temperature': ['temp'],
             'SSH': ['surface', 'sea'],
             'depth': ['depth'],
             'time': ['time', 'counter'],
+            'Ucomponent': ['zonal', 'current', 'eastward', 'uo'],
+            'Vcomponent': ['meridional', 'current', 'northward', 'vo'],
+            'windstress-i': ['i-axis'],
+            'windstress-j': ['j-axis'],
             'latitude': ['latitude', 'nav_lat','lat','y'],
             'longitude': ['longitude','nav_lon','lon','x'],
-            'depth': ['depth'],
-            'Ucomponent': ['zonal', 'current'],
-            'Vcomponent': ['meridional', 'current'],
-            'windstress-i':['i-axis'],
-            'windstress-j':['j-axis'],
             }
 
 # function to use regex to find if string is in variable name or if not check long name. Case of string is ignored
@@ -42,12 +44,16 @@ def data_chk(data, str, key):
     for i in range(len(str)):
         try:
             chk = re.search(str[i], data[key].name, re.IGNORECASE)
+            if chk is not None:
+                return chk
             if chk is None:
                 chk = re.search(str[i], data[key].long_name, re.IGNORECASE)
-            return chk
+                if chk is not None:
+                    return chk
         except AttributeError:
             pass
 
+
 i = 0
 meta_dataset = {}