updated bdy_coords test script from python 2 to 3

pynemo/pynemo_exe.py

@@ -40,7 +40,7 @@ def main():
         elif opt in ("-d", "--download_cmems"):
             setup_file = arg
             t0 = time.time()
-            with yaspin(Spinners.earth, text='Download CMEMS function is running'):
+            with yaspin(Spinners.earth, text='PyNEMO: download CMEMS data is running'):
                 profile.download_cmems(setup_file)
             t1 = time.time()
             print("CMEMS download time: %s" % (t1 - t0))
@@ -53,7 +53,7 @@ def main():
     #Logger
     #logger = logging.getLogger(__name__)
     t0 = time.time()
-    with yaspin(Spinners.earth, text='PyNEMO is running'):
+    with yaspin(Spinners.earth, text='PyNEMO: boundary generation is running'):
         profile.process_bdy(setup_file, mask_gui)
     t1 = time.time()
     print("Execution Time: %s" % (t1-t0))

pynemo/tests/bdy_coords.py

@@ -8,12 +8,13 @@
 # pylint: disable=E1103
 # pylint: disable=no-name-in-module
 
-#External imports
+# External imports
 from time import clock
 import numpy as np
 import logging
+import importlib
 
-#local imports
+# local imports
 from pynemo import nemo_bdy_setup as setup
 from pynemo import nemo_bdy_gen_c as gen_grid
 from pynemo import nemo_coord_gen_pop as coord
@@ -25,18 +26,21 @@ from pynemo import pynemo_settings_editor
 from pynemo.utils import Constants
 
 from pynemo.gui.nemo_bdy_mask import Mask as Mask_File
-from PyQt4.QtGui import QMessageBox
-#import pickle
+from PyQt5.QtWidgets import QMessageBox
+
+# import pickle
 
 
 logger = logging.getLogger(__name__)
+
+
 def process_bdy(setup_filepath=0, mask_gui=False):
     """ Main entry to the processing of the bdy
     Keyword arguments:
     setup_filepath -- file path to bdy file
     mask_gui -- whether gui to select the mask file needs to be poped up
     """
-    #Logger
+    # Logger
     logger.info('START')
     start = clock()
     SourceCoord = source_coord.SourceCoord()
@@ -60,7 +64,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
     logger.info('Done Mask')
 
     DstCoord.bdy_msk = bdy_msk == 1
-    reload(gen_grid)
+    importlib.reload(gen_grid)
     start = clock()
     logger.info('start bdy_t')
     grid_t = gen_grid.Boundary(bdy_msk, settings, 't')
@@ -91,11 +95,11 @@ def process_bdy(setup_filepath=0, mask_gui=False):
 
     bdy_ind = {'t': grid_t, 'u': grid_u, 'v': grid_v, 'f': grid_f}
 
-    for k in bdy_ind.keys():
+    for k in list(bdy_ind.keys()):
         logger.info('bdy_ind %s %s %s', k, bdy_ind[k].bdy_i.shape, bdy_ind[k].bdy_r.shape)
 
     start = clock()
-    co_set = coord.Coord(settings['dst_dir']+'/coordinates.bdy.nc', bdy_ind)
+    co_set = coord.Coord(settings['dst_dir'] + '/coordinates.bdy.nc', bdy_ind)
     logger.info('done coord gen')
     logger.info(clock() - start)
     start = clock()
@@ -114,6 +118,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
     # dyn 3d over 1st rim
     # dyn 3d frs over rw
 
+
 def _get_mask(Setup, mask_gui):
     """ This method reads the mask information from the netcdf file or opens a gui
     to create a mask depending on the mask_gui input. return the mask data. The default mask
@@ -124,31 +129,31 @@ def _get_mask(Setup, mask_gui):
     """
     bdy_msk = None
     if mask_gui:
-        #Open the gui to create a mask
+        # Open the gui to create a mask
         _, mask = pynemo_settings_editor.open_settings_dialog(Setup)
         bdy_msk = mask.data
         Setup.refresh()
     else:
         try:
-            #mask filename and mask file flag is set
+            # mask filename and mask file flag is set
             if Setup.bool_settings['mask_file'] and Setup.settings['mask_file'] is not None:
                 mask = Mask_File(mask_file=Setup.settings['mask_file'])
                 bdy_msk = mask.data
             elif Setup.bool_settings['mask_file']:
                 logger.error("Mask file is not given")
                 return
-            else: #no mask file specified then use default 1px halo mask
+            else:  # no mask file specified then use default 1px halo mask
                 logger.warning("Using default mask with bathymetry!!!!")
                 mask = Mask_File(Setup.settings['bathy'])
                 mask.apply_border_mask(Constants.DEFAULT_MASK_PIXELS)
                 bdy_msk = mask.data
         except ValueError:  # why is this except here? as there is an else: statement TODO
-            print 'something wrong?'
+            print('something wrong?')
             return
     if np.amin(bdy_msk) == 0:
         # Mask is not set throw a warning message and set border to 1px.
         logger.warning("Setting the mask to 1px border")
-        QMessageBox.warning(None,"pyNEMO", "Mask is not set, setting a 1 pixel border mask")
+        QMessageBox.warning(None, "pyNEMO", "Mask is not set, setting a 1 pixel border mask")
         if bdy_msk is not None and 1 < bdy_msk.shape[0] and 1 < bdy_msk.shape[1]:
             tmp = np.ones(bdy_msk.shape, dtype=bool)
             tmp[1:-1, 1:-1] = False

pynemo_37.yml

-name: pynemo3
+name: pynemo3_tst
 channels:
   - defaults
 dependencies:
@@ -20,3 +20,4 @@ dependencies:
     - motuclient==1.8.4
     - sphinx==3.0.2
     - sphinx-rtd-theme==0.4.3
+    - yaspin==0.16.0
\ No newline at end of file

test_scripts/bdy_coords_plot.py

@@ -17,7 +17,7 @@ from pynemo.tests import bdy_coords as bdc
 
 bdc.process_bdy('/Users/thopri/Projects/PyNEMO/inputs/namelist_cmems.bdy',False)
 
-rootgrp = Dataset('/Users/thopri/Projects/PyNEMO/outputs/NNA_R12_bdyT_y2017m11.nc', "r", format="NETCDF4")
+rootgrp = Dataset('/Users/thopri/Projects/PyNEMO/outputs/NNA_R12_bdyT_y1979m11.nc', "r", format="NETCDF4")
 bdy_msk = np.squeeze(rootgrp.variables['bdy_msk'][:]) - 1
 bdy_lon = np.squeeze(rootgrp.variables['nav_lon'][:])
 bdy_lat = np.squeeze(rootgrp.variables['nav_lat'][:])