added commandline spinner

docs/source/intro.rst

@@ -18,4 +18,7 @@ algorithm. The idea behind this targetted method is that it provides a generic
 method of interpolation for any flavour of ocean model in order to set up a
 regional NEMO model configuration.  At present (alpha release) the tools do not
 contain many options, but those that exist are accessed either through a NEMO style
-namelist or a convient GUI. 
+namelist or a convient GUI.
+
+PyNEMO has been updated to include integration with CMEMS data repository and the ability to produce tidal boundaries
+using TPXO or FES2014 as boundary input.

docs/source/troubleshooting.rst

 Troubleshooting
 ===============
 
+**Always** check the PyNEMO log file. This is usually saved in the working directory of PyNEMO as nrct.log. It gives helpful information
+which may help to diagnose issues. E.g. ValueErrors that are result of a THREDDS server being down and unable to provide data files.
+
 1. pyNEMO crashing in MacOSX (Yosemite)?
 
 *  Downgrade the scipy package to 0.15

inputs/namelist_cmems.bdy

@@ -52,10 +52,10 @@
 !  CMEMS Data Source Configuration
 !------------------------------------------------------------------------------
    ln_use_cmems             = .true.
-   ln_download_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.
-   ln_subset_static         = .false.
+   ln_download_static       = .true.
+   ln_subset_static         = .true.
    nn_num_retry             = 4 ! how many times to retry CMEMS download after non critical errors?
 !------------------------------------------------------------------------------
 !  CMEMS MOTU Configuration (for Boundary Data)

inputs/namelist_remote.bdy

@@ -68,7 +68,7 @@
 !  unstructured open boundaries tidal parameters                        
 !------------------------------------------------------------------------------
     ln_tide        = .true.              !  =T : produce bdy tidal conditions
-    sn_tide_model  = 'fes'                !  Name of tidal model (fes|tpxo)
+    sn_tide_model  = 'tpxo'                !  Name of tidal model (fes|tpxo)
     clname(1)      = 'M2'                 !  constituent name
     clname(2)      = 'S2'
     clname(3)      = 'O1'
@@ -86,9 +86,9 @@
     sn_dst_calendar = 'gregorian' !  output calendar format
     nn_base_year    = 1960        !  base year for time counter
     ! TPXO file locations
-	sn_tide_grid   = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/grid_tpxo7.2.nc'
-	sn_tide_h      = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/h_tpxo7.2.nc'
-	sn_tide_u      = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/u_tpxo7.2.nc'
+	sn_tide_grid   = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/grid_tpxo9.nc'
+	sn_tide_h      = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/h_tpxo9.v2a.nc'
+	sn_tide_u      = '/Users/thopri/Projects/PyNEMO/DATA/TPXO/u_tpxo9.v2a.nc'
 	! location of FES data
 	sn_tide_fes      = '/Users/thopri/Projects/PyNEMO/DATA/FES/'
 	

pynemo/pynemo_exe.py

@@ -11,6 +11,9 @@ import logging
 # Logging set to info
 logging.basicConfig(level=logging.INFO)
 import time
+from yaspin import yaspin
+from yaspin.spinners import Spinners
+
 def main():
     """ Main function which checks the command line parameters and
         passes them to the profile module for processing """
@@ -37,7 +40,8 @@ def main():
         elif opt in ("-d", "--download_cmems"):
             setup_file = arg
             t0 = time.time()
-            profile.download_cmems(setup_file)
+            with yaspin(Spinners.earth, text='PyNEMO is running'):
+                profile.download_cmems(setup_file)
             t1 = time.time()
             print("CMEMS download time: %s" % (t1 - t0))
             sys.exit(0)
@@ -49,7 +53,8 @@ def main():
     #Logger
     #logger = logging.getLogger(__name__)
     t0 = time.time()
-    profile.process_bdy(setup_file, mask_gui)
+    with yaspin(Spinners.earth, text='PyNEMO is running'):
+        profile.process_bdy(setup_file, mask_gui)
     t1 = time.time()
     print("Execution Time: %s" % (t1-t0))
     

pynemo/reader/ncml.py

@@ -14,6 +14,7 @@ from cftime import utime
 ncmlpath, file_name = os.path.split(__file__)
 ncmlpath = os.path.join(ncmlpath, "jars", "netcdfAll-4.6.jar") 
 jnius_config.set_classpath('.',ncmlpath)
+logger = logging.getLogger(__name__)
 try:
     if os.environ['http_proxy'] is not None:
         #split the proxy name and port
@@ -22,7 +23,7 @@ try:
         proxy_port = proxylist[1]        
         jnius_config.add_options('-Dhttp.proxyHost='+proxy_host,'-Dhttp.proxyPort='+proxy_port)
 except:
-    print("Didn't find a proxy environment variable")
+    logger.info("Didn't find a proxy environment variable")
 NetcdfDataset = None
 NcMLReader = None
 Section = None