diff --git a/pynemo/gui/nemo_bdy_mask.py b/pynemo/gui/nemo_bdy_mask.py
index ea062abc4d3f19311d8aafe6ce516109d7ea4cff..ef5bd24e07df96af41ccce85c97e47cac23481a1 100644
--- a/pynemo/gui/nemo_bdy_mask.py
+++ b/pynemo/gui/nemo_bdy_mask.py
@@ -68,15 +68,32 @@ class Mask(object):
self.bathymetry_file = str(bathy_file)
#open the bathymetry file
self.bathy_nc = Dataset(self.bathymetry_file)
- self.lon = np.asarray(self.bathy_nc.variables['nav_lon'])
- self.lat = np.asarray(self.bathy_nc.variables['nav_lat'])
- self.bathy_data = self.bathy_nc.variables['Bathymetry'][:,:]
+ try:
+ self.lon = np.asarray(self.bathy_nc.variables['nav_lon'])
+ self.lat = np.asarray(self.bathy_nc.variables['nav_lat'])
+ except:
+ self.lon = np.asarray(self.bathy_nc.variables['lon'])
+ self.lat = np.asarray(self.bathy_nc.variables['lat'])
+ # expand lat and lon 1D arrays into 2D array matching nav_lat nav_lon
+ self.lon = np.tile(self.lon, (np.shape(self.lat)[0], 1))
+ self.lat = np.tile(self.lat, (np.shape(self.lon)[1], 1))
+ self.lat = np.rot90(self.lat)
+
+ try:
+ self.bathy_data = self.bathy_nc.variables['Bathymetry'][:,:]
+ except:
+ self.bathy_data = self.bathy_nc.variables['deptho'][:,:]
try: #check if units exists otherwise unknown. TODO
self.data_units = self.bathy_nc.variables['Bathymetry'].units
- except AttributeError:
- self.data_units = "unknown"
+ except:
+ self.data_units = self.bathy_nc.variables['deptho'].units
+# except AttributeError:
+# self.data_units = "unknown"
if self.data is None:
- self.data = self.bathy_nc.variables['Bathymetry']
+ try:
+ self.data = self.bathy_nc.variables['Bathymetry']
+ except:
+ self.data = self.bathy_nc.variables['deptho']
self.data = np.asarray(self.data[:, :])
self.data = np.around((self.data + .5).clip(0, 1))
#apply default 1px border
diff --git a/pynemo/nemo_bdy_ncpop.py b/pynemo/nemo_bdy_ncpop.py
index 45223ab93304e57e0a99f6dda0b55335b903714b..1f55c5dd98fa61ad81ce692a5327eedd06b7cd27 100644
--- a/pynemo/nemo_bdy_ncpop.py
+++ b/pynemo/nemo_bdy_ncpop.py
@@ -19,7 +19,7 @@ def write_data_to_file(filename, variable_name, data):
count = data.shape
three_dim_variables = ['votemper', 'vosaline', 'N1p', 'N3n', 'N5s','thetao','so']
- two_dim_variables = ['sossheig', 'vobtcrtx', 'vobtcrty', 'iicethic', 'ileadfra', 'isnowthi']
+ two_dim_variables = ['sossheig', 'vobtcrtx', 'vobtcrty', 'iicethic', 'ileadfra', 'isnowthi','zos']
if variable_name in three_dim_variables:
if len(count) == 3:
diff --git a/pynemo/profile.py b/pynemo/profile.py
index 1dc8b28dec46f942fc8e9ccbf9355b1a0d498468..7931c68ef7f547788315390be24bf29559ae121c 100644
--- a/pynemo/profile.py
+++ b/pynemo/profile.py
@@ -77,12 +77,6 @@ logging.basicConfig(filename='nrct.log', level=logging.INFO)
# define a Handler which writes INFO messages or higher to the sys.stderr
console = logging.StreamHandler()
console.setLevel(logging.INFO)
-# set a format which is simpler for console use
-formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')
-# tell the handler to use this format
-console.setFormatter(formatter)
-# add the handler to the root logger
-logging.getLogger('').addHandler(console)
def download_cmems(setup_filepath=0):
'''
diff --git a/pynemo_37.yml b/pynemo_37.yml
index 8c728403364e79419d2652ffcc22777b375dc8cb..8d24b7fa6bd0fd15d2968f5c1de609c1e0129d2d 100644
--- a/pynemo_37.yml
+++ b/pynemo_37.yml
@@ -9,9 +9,11 @@ dependencies:
- python=3.7.6
- pip=20.0.2
- pandas=1.0.1
+ - pytest=5.3.5
- pip:
- idna==2.9
- lxml==4.5.0
- pyjnius==1.2.1
- seawater==3.3.4
- thredds-crawler==1.5.4
+ - motuclient==1.8.4
\ No newline at end of file
diff --git a/unit_tests/namelist_unit_test.bdy b/unit_tests/namelist_unit_test.bdy
new file mode 100644
index 0000000000000000000000000000000000000000..48746cf4ec6c186c82b1b5bb34e90e11daaf64cc
--- /dev/null
+++ b/unit_tests/namelist_unit_test.bdy
@@ -0,0 +1,109 @@
+!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!! NEMO/OPA : namelist for BDY generation tool
+!!
+!! User inputs for generating open boundary conditions
+!! employed by the BDY module in NEMO. Boundary data
+!! can be set up for v3.2 NEMO and above.
+!!
+!! More info here.....
+!!
+!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+
+!------------------------------------------------------------------------------
+! vertical coordinate
+!------------------------------------------------------------------------------
+ ln_zco = .false. ! z-coordinate - full steps (T/F)
+ ln_zps = .true. ! z-coordinate - partial steps (T/F)
+ ln_sco = .false. ! s- or hybrid z-s-coordinate (T/F)
+ rn_hmin = -10 ! min depth of the ocean (>0) or
+ ! min number of ocean level (<0)
+
+!------------------------------------------------------------------------------
+! s-coordinate or hybrid z-s-coordinate
+!------------------------------------------------------------------------------
+ rn_sbot_min = 10. ! minimum depth of s-bottom surface (>0) (m)
+ rn_sbot_max = 7000. ! maximum depth of s-bottom surface
+ ! (= ocean depth) (>0) (m)
+ ln_s_sigma = .false. ! hybrid s-sigma coordinates
+ rn_hc = 150.0 ! critical depth with s-sigma
+
+!------------------------------------------------------------------------------
+! grid information
+!------------------------------------------------------------------------------
+ sn_src_hgr = '/Users/thopri/Projects/PyNEMO/inputs/subset_coordinates.nc'
+ sn_src_zgr = '/Users/thopri/Projects/PyNEMO/inputs/subset_coordinates.nc'
+ sn_dst_hgr = 'http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_grid_C/mesh_hgr_zps.nc'
+ sn_dst_zgr = 'http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_grid_C/mesh_zgr_zps.nc'
+ sn_src_msk = '/Users/thopri/Projects/PyNEMO/inputs/subset_bathy.nc'
+ sn_bathy = 'http://opendap4gws.jasmin.ac.uk/thredds/noc_msm/dodsC/pynemo_grid_C/NNA_R12_bathy_meter_bench.nc'
+
+!------------------------------------------------------------------------------
+! I/O
+!------------------------------------------------------------------------------
+ sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/src_data_unit_tests.ncml' ! src_files/'
+ sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
+ sn_fn = 'unit_test' ! prefix for output files
+ nn_fv = -1e20 ! set fill value for output files
+ nn_src_time_adj = 0 ! src time adjustment
+ sn_dst_metainfo = 'Benchmarking Data'
+
+!------------------------------------------------------------------------------
+! CMEMS Data Source Configuration
+!------------------------------------------------------------------------------
+ ln_use_cmems = .true.
+
+!------------------------------------------------------------------------------
+! unstructured open boundaries
+!------------------------------------------------------------------------------
+ ln_coords_file = .true. ! =T : produce bdy coordinates files
+ cn_coords_file = 'coordinates.bdy.nc' ! name of bdy coordinates files
+ ! (if ln_coords_file=.TRUE.)
+ ln_mask_file = .false. ! =T : read mask from file
+ cn_mask_file = 'mask.nc' ! name of mask file
+ ! (if ln_mask_file=.TRUE.)
+ ln_dyn2d = .false. ! boundary conditions for
+ ! barotropic fields
+ ln_dyn3d = .false. ! boundary conditions for
+ ! baroclinic velocities
+ 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 = .false. ! =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) = 'K2'
+ ln_trans = .true. ! interpolate transport rather than
+ ! velocities
+!------------------------------------------------------------------------------
+! Time information
+!------------------------------------------------------------------------------
+ nn_year_000 = 2017 ! year start
+ nn_year_end = 2017 ! year end
+ nn_month_000 = 01 ! month start (default = 1 is years>1)
+ nn_month_end = 01 ! month end (default = 12 is years>1)
+ sn_dst_calendar = 'gregorian' ! output calendar format
+ nn_base_year = 1960 ! base year for time counter
+ sn_tide_grid = './src_data/tide/grid_tpxo7.2.nc'
+ sn_tide_h = './src_data/tide/h_tpxo7.2.nc'
+ sn_tide_u = './src_data/tide/u_tpxo7.2.nc'
+
+!------------------------------------------------------------------------------
+! Additional parameters
+!------------------------------------------------------------------------------
+ nn_wei = 1 ! smoothing filter weights
+ rn_r0 = 0.041666666 ! decorrelation distance use in gauss
+ ! smoothing onto dst points. Need to
+ ! make this a funct. of dlon
+ sn_history = 'Benchmarking test case'
+ ! history for netcdf file
+ ln_nemo3p4 = .true. ! else presume v3.2 or v3.3
+ nn_alpha = 0 ! Euler rotation angle
+ nn_beta = 0 ! Euler rotation angle
+ nn_gamma = 0 ! Euler rotation angle
+ rn_mask_max_depth = 100.0 ! Maximum depth to be ignored for the mask
+ rn_mask_shelfbreak_dist = 20000.0 ! Distance from the shelf break
diff --git a/unit_tests/src_data_unit_tests.ncml b/unit_tests/src_data_unit_tests.ncml
new file mode 100644
index 0000000000000000000000000000000000000000..2b91153cd46adf38c560f7f129d523d434108cf6
--- /dev/null
+++ b/unit_tests/src_data_unit_tests.ncml
@@ -0,0 +1,16 @@
+<ns0:netcdf xmlns:ns0="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2" title="NEMO aggregation">
+ <ns0:aggregation type="union">
+ <ns0:netcdf>
+ <ns0:aggregation dimName="time" name="temperature" type="joinExisting">
+ <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_data/" regExp=".*T\.nc$" />
+ </ns0:aggregation>
+ </ns0:netcdf>
+ <ns0:netcdf>
+ <ns0:aggregation dimName="time" name="sea_surface_height" type="joinExisting">
+ <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_data/" regExp=".*T\.nc$" />
+ </ns0:aggregation>
+ </ns0:netcdf>
+ </ns0:aggregation>
+ <ns0:variable name="thetao" orgName="thetao" />
+ <ns0:variable name="zos" orgName="zos" />
+</ns0:netcdf>
diff --git a/unit_tests/unit_test.py b/unit_tests/unit_test.py
new file mode 100644
index 0000000000000000000000000000000000000000..bbfe4a0f882d26d14fbb6e76b9461345fbbdb0e8
--- /dev/null
+++ b/unit_tests/unit_test.py
@@ -0,0 +1,45 @@
+# -*- coding: utf-8 -*-
+"""
+Set of test functions to test PyNEMO functionality.
+
+"""
+from subprocess import Popen, PIPE
+from netCDF4 import Dataset
+import numpy as np
+import glob
+import os
+
+def test_run():
+ stdout, stderr = Popen(['pynemo','-s','unit_tests/namelist_unit_test.bdy'], stdout=PIPE, stderr=PIPE,
+ universal_newlines=True).communicate()
+ assert 'Execution Time' in stdout
+
+def test_temp():
+ test_files = glob.glob('unit_tests/test_outputs/unit_test*')
+ for t in test_files:
+ results = Dataset(t) # open results
+ temp = results['thetao'][:]
+ results.close()
+ temp_ = np.ma.masked_array(temp,temp == -32767.0)
+ assert abs(temp_[temp_!=0.0].mean() - 15) <= 0.001
+ assert abs(temp_[temp_ != 0.0].max() - 15) <= 0.001
+ assert abs(temp_[temp_ != 0.0].min() - 15) <= 0.001
+
+#def test_salinty():
+# test_files = glob.glob('unit_tests/test_outputs/unit_test*')
+# for t in test_files:
+# results = Dataset(t) # open results
+# sal = results['so'][:]
+# results.close()
+# sal_ = np.ma.masked_array(sal,sal == -32767.0)
+# assert abs(sal_[sal_!=0.0].mean() - 35) <= 0.001
+# assert abs(sal_[sal_ != 0.0].max() - 35) <= 0.001
+# assert abs(sal_[sal_ != 0.0].min() - 35) <= 0.001
+
+def test_rm_output():
+ files = glob.glob('unit_tests/test_outputs/*')
+ for f in files:
+ os.remove(f)
+ files = glob.glob('unit_tests/test_outputs/*')
+ assert len(files) == 0
+