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Commit 9c152e45 authored by thopri's avatar thopri
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added first stage unit testing code

parent a19e3131
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Showing with 196 additions and 13 deletions
pynemo/gui/nemo_bdy_mask.py
View file @ 9c152e45
......@@ -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
......
pynemo/nemo_bdy_ncpop.py
View file @ 9c152e45
......@@ -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:
......
pynemo/profile.py
View file @ 9c152e45
......@@ -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):
'''
......
pynemo_37.yml
View file @ 9c152e45
......@@ -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
unit_tests/namelist_unit_test.bdy 0 → 100644
View file @ 9c152e45
!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! 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
unit_tests/src_data_unit_tests.ncml 0 → 100644
View file @ 9c152e45
<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>
unit_tests/unit_test.py 0 → 100644
View file @ 9c152e45
# -*- 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
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