fix that generates list of FES harmonics automatically

docs/source/tides.rst

+Tidal Boundary Conditions Generation
+====================================
+
+By providing a global tidal model dataset (TPXO and FES are currently supported) PyNEMO can generate boundary conditions for the
+NEMO configuration supplied using the namelist file.
+
+To use the namelist needs to be configured with the required options. These are listed below::
+
+    ln_tide        = .true.              !  =T : produce bdy tidal conditions
+    sn_tide_model  = 'fes'                !  Name of tidal model (fes|tpxo)
+    clname(1)      = 'M2'                 !  constituent name
+    clname(2)      = 'S2'
+    clname(3)      = 'O1'
+    clname(4)      = 'K1'
+    clname(5)      = 'N2'
+    ln_trans       = .false.               !  interpolate transport rather than velocities
+    ! TPXO file locations
+    sn_tide_grid   = './grid_tpxo7.2.nc'
+    sn_tide_h      = './h_tpxo7.2.nc'
+    sn_tide_u      = './u_tpxo7.2.nc'
+    ! location of FES data
+    sn_tide_fes      = './FES/'
+
+these options define the location of the tidal model datasets, note this differs depending on model as TPXO has all harmonic
+constants in one netcdf file whereas FES has three separate netcdf files for each constant. Extra harmonics can be appended
+to the clname(n) list FES supports 34 constants and TPXO7.2 has 13 to choose from. Other versions of TPXO should work with PyNEMO
+but have not been yet been tested.
+
+So far the tidal model datasets have been downloaded and used locally but could also be stored on a TREDDS server although this has
+not been tested to generate tidal boundaries
+
+Future work
+-----------
+
+Create options of harmonic constants to request rather than manually specifying a list. These could be based on common requirements
+and/or based on the optimal harmonics to use for a specified time frame.
+
+

inputs/namelist_remote.bdy

@@ -75,7 +75,7 @@
     clname(4)      = 'K1'
     clname(5)      = 'N2'
     ln_trans       = .false.               !  interpolate transport rather than
-                                          !  velocities
+                                           !  velocities
 !------------------------------------------------------------------------------
 !  Time information
 !------------------------------------------------------------------------------

pynemo/tide/fes_extract_HC.py

@@ -37,10 +37,12 @@ class HcExtract(object):
             mu_name = 'mask_u'
             mv_name = 'mask_v'
 
-            #constituents = ['2N2', 'EPS2', 'J1', 'K1', 'K2', 'L2', 'LA2', 'M2', 'M3', 'M4', 'M6', 'M8', 'MF', 'MKS2',
-                            #'MM', 'MN4', 'MS4', 'MSF', 'MSQM', 'MTM', 'MU2', 'N2', 'N4', 'NU2', 'O1', 'P1', 'Q1', 'R2',
-                            #'S1', 'S2', 'S4', 'SA', 'SSA', 'T2']
-            constituents = ['M2','S2','O1','K1','N2']
+            # create list of HC using namelist file as reference
+            constituents = list(settings['clname'].values())
+            # clean strings in list and change to upper case if not already
+            for i in range(len(constituents)):
+                constituents[i] = constituents[i].strip("',/\n")
+                constituents[i] = constituents[i].upper()
 
             self.cons = constituents
             self.mask_dataset = {}

pynemo/tide/nemo_bdy_tide3.py

@@ -2,6 +2,7 @@
 Module to extract constituents for the input grid mapped onto output grid
 
 @author: Mr. Srikanth Nagella
+@author: thopri
 '''
 
 # pylint: disable=E1103