diff --git a/README.rst b/README.rst
index 1f749a201d1c60cd3135f801accea8df82364880..e224ae5ce3b19679e1220090c5db675d80fb520b 100644
--- a/README.rst
+++ b/README.rst
@@ -98,12 +98,13 @@ The PyNEMO module can be tested using the bench marking namelist bdy file in the
Unit Tests
-------------------
-To test operation of the PyNEMO module, running the PyTest script in the unit tests folder will perform a range tests on different child grids,
-checking the interpolation of the source data on to the child grid. To do this the following command is required::
+To test operation of the PyNEMO module, running the PyTest script in the unit tests folder will perform a range of tests on different child grids,
+e.g. checking the interpolation of the source data on to the child grid. To do this the following command is required::
- $ pytest -q unit_tests/unit_test.py
+ $ pytest -q pynemo/unit_test.py
-The command should be run from the main PyNEMO directory to enable modules to be imported correctly.
+Currently **(26/03/2020)** there are 7 tests that cover checking the interpolation results of different child grids. The input data is generated as part of the
+test and is removed afterwards. The number of tests will be increased in the future to cover more PyNEMO functionality.
Who do I talk to?
-----------------
@@ -114,5 +115,6 @@ Who do I talk to?
* Other community or team contact
+ thopri
For more information regarding the use and development of PyNEMO see: [PyNEMO Wiki](https://github.com/jdha/PyNEMO/wiki)
diff --git a/pynemo/unit_test.py b/pynemo/unit_test.py
index ae95d174bd4ef5c51df992da4daf6304d88c1536..c68359e078a8da9f575dfe93c8e7d8aca577746b 100644
--- a/pynemo/unit_test.py
+++ b/pynemo/unit_test.py
@@ -8,6 +8,7 @@ from netCDF4 import Dataset
import numpy as np
import glob
import os
+from pynemo.unit_tests import UT_config as config
# generate test data by import test gen script and executing main function
# TODO: Maybe simplify this, as this import imports other scripts and is abit clunky.
@@ -19,7 +20,7 @@ if gen_data != 0:
# run PyNEMO with test data
# generate list of namelist.bdy files to run
-namelist_files = glob.glob('pynemo/unit_tests/namelist*')
+namelist_files = glob.glob(config.unit_dir+'namelist*')
for n in namelist_files:
# run each of the namelist files
stdout, stderr = Popen(['pynemo', '-s', n], stdout=PIPE, stderr=PIPE,
@@ -34,7 +35,7 @@ for n in namelist_files:
# perform tests
def test_temp():
- test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyT*')
+ test_files = glob.glob(config.output_dir+'*bdyT*')
if len(test_files) == 0:
raise Exception('DONT PANIC: no temperature test files found')
for t in test_files:
@@ -47,7 +48,7 @@ def test_temp():
assert abs(temp_[temp_ != 0.0].min() - 15) <= 0.001
def test_salinty():
- test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyT*')
+ test_files = glob.glob(config.output_dir+'*bdyT*')
if len(test_files) == 0:
raise Exception('DONT PANIC: no salinity test files found')
for t in test_files:
@@ -63,7 +64,7 @@ def test_salinty():
# U and V and SSH tests are required. e.g. ln_dyn2d is set to true.
def test_ssh():
- test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyT*')
+ test_files = glob.glob(config.output_dir+'*bdyT*')
if len(test_files) == 0:
raise Exception('DONT PANIC: no SSH test files found')
for t in test_files:
@@ -76,7 +77,7 @@ def test_ssh():
assert abs(ssh_[ssh_ != 0.0].min() - 1.0) <= 0.001
def test_U():
- test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyU*')
+ test_files = glob.glob(config.output_dir+'*bdyU*')
if len(test_files) == 0:
raise Exception('DONT PANIC: no U current test files found')
for t in test_files:
@@ -89,7 +90,7 @@ def test_U():
assert abs(U_[U_ != 0.0].min() - 0.5) <= 0.001
def test_V():
- test_files = glob.glob('pynemo/unit_tests/test_outputs/*bdyV*')
+ test_files = glob.glob(config.output_dir+'*bdyV*')
if len(test_files) == 0:
raise Exception('DONT PANIC: no V current test files found')
for t in test_files:
@@ -103,16 +104,16 @@ def test_V():
# clean up test I/O
def test_rm_out():
- files = glob.glob('pynemo/unit_tests/test_outputs/*')
+ files = glob.glob(config.output_dir+'*')
for f in files:
os.remove(f)
- files = glob.glob('pynemo/unit_tests/test_outputs/*')
+ files = glob.glob(config.output_dir+'*')
assert len(files) == 0
def test_rm_in():
- files = glob.glob('pynemo/unit_tests/test_inputs/*')
+ files = glob.glob(config.output_dir+'*')
for f in files:
os.remove(f)
- files = glob.glob('pynemo/unit_tests/test_inputs/*')
+ files = glob.glob(config.output_dir+'*')
assert len(files) == 0
diff --git a/pynemo/unit_tests/UT_config.py b/pynemo/unit_tests/UT_config.py
new file mode 100644
index 0000000000000000000000000000000000000000..37184849fd161d97ae67cefb20a61ea0df29cf80
--- /dev/null
+++ b/pynemo/unit_tests/UT_config.py
@@ -0,0 +1,12 @@
+# -*- coding: utf-8 -*-
+"""
+Config file for Unit test functions, file paths for I/O etc are defined here.
+
+"""
+
+# test input directory
+input_dir = 'pynemo/unit_tests/test_inputs/'
+# test output directory
+output_dir = 'pynemo/unit_tests/test_outputs/'
+# unit test directory
+unit_dir = 'pynemo/unit_tests/'
diff --git a/pynemo/unit_tests/gen_tools.py b/pynemo/unit_tests/gen_tools.py
index cd5556497957653772848d2b194767eb4174315d..f09f7978611946c4663d09b4837ae1997bff62a0 100644
--- a/pynemo/unit_tests/gen_tools.py
+++ b/pynemo/unit_tests/gen_tools.py
@@ -260,152 +260,152 @@ def write_coord_Z(fileout, grid_h,grid_z):
return 0
-def write_domcfg(fileout, ln_zco, ln_zps, ln_sco, ln_isfcav, jperio, bat,
- lont, latt, lonu, latu, lonv, latv, lonf, latf,
- e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f, ff_f, ff_t,
- dept_1d, e3t_1d, e3w_1d, e3t, e3u, e3v, e3f, e3w, e3uw, e3vw,
- ktop, kbot):
- '''
- Writes out a NEMO formatted domcfg file.
-
- Args:
- fileout (string): filename
- ln_zco (logical): vertical coordinate flag [z-level]
- ln_zps (logical): vertical coordinate flag [z-partial-step]
- ln_sco (logical): vertical coordinate flag [sigma]
- ln_isfcav (logical): ice cavity flag
- jperio (int): domain type
- bat (np.ndarray): bathymetry array at t-points (2D)
- lon[t/u/v/f](np.ndarray): longitude array at [t/u/v/f]-points (2D)
- lat[t/u/v/f](np.ndarray): latitude array at [t/u/v/f]-points (2D)
- e1[t/u/v/f] (np.ndarray): zonal scale factors at [t/u/v/f]-points
- e2[t/u/v/f] (np.ndarray): meridional scale factors at [t/u/v/f]-points
- ff_[f/t] (np.ndarray): coriolis parameter at [t/f]-points
- dept_1d (np.ndarray): 1D depth levels at t-points
- e3[t/w]_1d (np.ndarray): 1D vertical scale factors at [t/w]-points
- e3[t/u/v/f] (np.ndarray): vertcal scale factors at [t/u/v/f]-points
- e3[w/uw/vw] (np.ndarray): vertcal scale factors at [w/uw/vw]-points
- ktop (np.ndarray): upper most wet point
- kbot (np.ndarray): lower most wet point
-
- Returns:
- '''
-
- # Open pointer to netcdf file
- dataset = Dataset(fileout, 'w', format='NETCDF4_CLASSIC')
-
- # Get input size and create appropriate dimensions
- # TODO: add some sort of error handling
- nx, ny, nz = np.shape(e3t)
- dataset.createDimension('x', nx)
- dataset.createDimension('y', ny)
- dataset.createDimension('z', nz)
-
- # create Variables
- nav_lon = dataset.createVariable('nav_lon', np.float32, ('y', 'x'))
- nav_lat = dataset.createVariable('nav_lat', np.float32, ('y', 'x'))
- nav_lev = dataset.createVariable('nav_lev', np.float32, 'z')
-
- giglo = dataset.createVariable('jpiglo', "i4")
- gjglo = dataset.createVariable('jpjglo', "i4")
- gkglo = dataset.createVariable('jpkglo', "i4")
-
- gperio = dataset.createVariable('jperio', "i4")
-
- gzco = dataset.createVariable('ln_zco', "i4")
- gzps = dataset.createVariable('ln_zps', "i4")
- gsco = dataset.createVariable('ln_sco', "i4")
- gcav = dataset.createVariable('ln_isfcav', "i4")
-
- ge3t1d = dataset.createVariable('e3t_1d', np.float64, 'z')
- ge3w1d = dataset.createVariable('e3w_1d', np.float64, 'z')
- gitop = dataset.createVariable('top_level', "i4", ('y', 'x'))
- gibot = dataset.createVariable('bottom_level', "i4", ('y', 'x'))
- gbat = dataset.createVariable('Bathymetry', np.float64, ('y', 'x'))
- glamt = dataset.createVariable('glamt', np.float64, ('y', 'x'))
- glamu = dataset.createVariable('glamu', np.float64, ('y', 'x'))
- glamv = dataset.createVariable('glamv', np.float64, ('y', 'x'))
- glamf = dataset.createVariable('glamf', np.float64, ('y', 'x'))
- gphit = dataset.createVariable('gphit', np.float64, ('y', 'x'))
- gphiu = dataset.createVariable('gphiu', np.float64, ('y', 'x'))
- gphiv = dataset.createVariable('gphiv', np.float64, ('y', 'x'))
- gphif = dataset.createVariable('gphif', np.float64, ('y', 'x'))
- ge1t = dataset.createVariable('e1t', np.float64, ('y', 'x'))
- ge1u = dataset.createVariable('e1u', np.float64, ('y', 'x'))
- ge1v = dataset.createVariable('e1v', np.float64, ('y', 'x'))
- ge1f = dataset.createVariable('e1f', np.float64, ('y', 'x'))
- ge2t = dataset.createVariable('e2t', np.float64, ('y', 'x'))
- ge2u = dataset.createVariable('e2u', np.float64, ('y', 'x'))
- ge2v = dataset.createVariable('e2v', np.float64, ('y', 'x'))
- ge2f = dataset.createVariable('e2f', np.float64, ('y', 'x'))
- gfff = dataset.createVariable('ff_f', np.float64, ('y', 'x'))
- gfft = dataset.createVariable('ff_t', np.float64, ('y', 'x'))
- ge3t = dataset.createVariable('e3t_0', np.float64, ('z', 'y', 'x'))
- ge3w = dataset.createVariable('e3w_0', np.float64, ('z', 'y', 'x'))
- ge3u = dataset.createVariable('e3u_0', np.float64, ('z', 'y', 'x'))
- ge3v = dataset.createVariable('e3v_0', np.float64, ('z', 'y', 'x'))
- ge3f = dataset.createVariable('e3f_0', np.float64, ('z', 'y', 'x'))
- ge3uw = dataset.createVariable('e3uw_0', np.float64, ('z', 'y', 'x'))
- ge3vw = dataset.createVariable('e3vw_0', np.float64, ('z', 'y', 'x'))
-
- nav_lon.units, nav_lon.long_name = 'km', 'X'
- nav_lat.units, nav_lat.long_name = 'km', 'Y'
-
- # Populate file with input data
- giglo[:] = nx
- gjglo[:] = ny
- gkglo[:] = nz
-
- gzco[:] = ln_zco
- gzps[:] = ln_zps
- gsco[:] = ln_sco
- gcav[:] = ln_isfcav
-
- gperio[:] = jperio
-
- # TODO: do we need to transpose?
- nav_lon[:, :] = lont.T
- nav_lat[:, :] = latt.T
- nav_lev[:] = dept_1d
-
- ge3t1d[:] = e3t_1d
- ge3w1d[:] = e3w_1d
-
- gitop[:, :] = ktop.T
- gibot[:, :] = kbot.T
-
- gbat[:, :] = bat.T
-
- glamt[:, :] = lont.T
- glamu[:, :] = lonu.T
- glamv[:, :] = lonv.T
- glamf[:, :] = lonf.T
- gphit[:, :] = latt.T
- gphiu[:, :] = latu.T
- gphiv[:, :] = latv.T
- gphif[:, :] = latf.T
-
- ge1t[:, :] = e1t.T
- ge1u[:, :] = e1u.T
- ge1v[:, :] = e1v.T
- ge1f[:, :] = e1f.T
- ge2t[:, :] = e2t.T
- ge2u[:, :] = e2u.T
- ge2v[:, :] = e2v.T
- ge2f[:, :] = e2f.T
- gfff[:, :] = ff_f.T
- gfft[:, :] = ff_t.T
-
- ge3t[:, :, :] = e3t.T
- ge3w[:, :, :] = e3w.T
- ge3u[:, :, :] = e3u.T
- ge3v[:, :, :] = e3v.T
- ge3f[:, :, :] = e3f.T
- ge3uw[:, :, :] = e3uw.T
- ge3vw[:, :, :] = e3vw.T
-
- # Close off pointer
- dataset.close()
+# def write_domcfg(fileout, ln_zco, ln_zps, ln_sco, ln_isfcav, jperio, bat,
+# lont, latt, lonu, latu, lonv, latv, lonf, latf,
+# e1t, e2t, e1u, e2u, e1v, e2v, e1f, e2f, ff_f, ff_t,
+# dept_1d, e3t_1d, e3w_1d, e3t, e3u, e3v, e3f, e3w, e3uw, e3vw,
+# ktop, kbot):
+# '''
+# Writes out a NEMO formatted domcfg file.
+#
+# Args:
+# fileout (string): filename
+# ln_zco (logical): vertical coordinate flag [z-level]
+# ln_zps (logical): vertical coordinate flag [z-partial-step]
+# ln_sco (logical): vertical coordinate flag [sigma]
+# ln_isfcav (logical): ice cavity flag
+# jperio (int): domain type
+# bat (np.ndarray): bathymetry array at t-points (2D)
+# lon[t/u/v/f](np.ndarray): longitude array at [t/u/v/f]-points (2D)
+# lat[t/u/v/f](np.ndarray): latitude array at [t/u/v/f]-points (2D)
+# e1[t/u/v/f] (np.ndarray): zonal scale factors at [t/u/v/f]-points
+# e2[t/u/v/f] (np.ndarray): meridional scale factors at [t/u/v/f]-points
+# ff_[f/t] (np.ndarray): coriolis parameter at [t/f]-points
+# dept_1d (np.ndarray): 1D depth levels at t-points
+# e3[t/w]_1d (np.ndarray): 1D vertical scale factors at [t/w]-points
+# e3[t/u/v/f] (np.ndarray): vertcal scale factors at [t/u/v/f]-points
+# e3[w/uw/vw] (np.ndarray): vertcal scale factors at [w/uw/vw]-points
+# ktop (np.ndarray): upper most wet point
+# kbot (np.ndarray): lower most wet point
+#
+# Returns:
+# '''
+#
+# # Open pointer to netcdf file
+# dataset = Dataset(fileout, 'w', format='NETCDF4_CLASSIC')
+#
+# # Get input size and create appropriate dimensions
+# # TODO: add some sort of error handling
+# nx, ny, nz = np.shape(e3t)
+# dataset.createDimension('x', nx)
+# dataset.createDimension('y', ny)
+# dataset.createDimension('z', nz)
+#
+# # create Variables
+# nav_lon = dataset.createVariable('nav_lon', np.float32, ('y', 'x'))
+# nav_lat = dataset.createVariable('nav_lat', np.float32, ('y', 'x'))
+# nav_lev = dataset.createVariable('nav_lev', np.float32, 'z')
+#
+# giglo = dataset.createVariable('jpiglo', "i4")
+# gjglo = dataset.createVariable('jpjglo', "i4")
+# gkglo = dataset.createVariable('jpkglo', "i4")
+#
+# gperio = dataset.createVariable('jperio', "i4")
+#
+# gzco = dataset.createVariable('ln_zco', "i4")
+# gzps = dataset.createVariable('ln_zps', "i4")
+# gsco = dataset.createVariable('ln_sco', "i4")
+# gcav = dataset.createVariable('ln_isfcav', "i4")
+#
+# ge3t1d = dataset.createVariable('e3t_1d', np.float64, 'z')
+# ge3w1d = dataset.createVariable('e3w_1d', np.float64, 'z')
+# gitop = dataset.createVariable('top_level', "i4", ('y', 'x'))
+# gibot = dataset.createVariable('bottom_level', "i4", ('y', 'x'))
+# gbat = dataset.createVariable('Bathymetry', np.float64, ('y', 'x'))
+# glamt = dataset.createVariable('glamt', np.float64, ('y', 'x'))
+# glamu = dataset.createVariable('glamu', np.float64, ('y', 'x'))
+# glamv = dataset.createVariable('glamv', np.float64, ('y', 'x'))
+# glamf = dataset.createVariable('glamf', np.float64, ('y', 'x'))
+# gphit = dataset.createVariable('gphit', np.float64, ('y', 'x'))
+# gphiu = dataset.createVariable('gphiu', np.float64, ('y', 'x'))
+# gphiv = dataset.createVariable('gphiv', np.float64, ('y', 'x'))
+# gphif = dataset.createVariable('gphif', np.float64, ('y', 'x'))
+# ge1t = dataset.createVariable('e1t', np.float64, ('y', 'x'))
+# ge1u = dataset.createVariable('e1u', np.float64, ('y', 'x'))
+# ge1v = dataset.createVariable('e1v', np.float64, ('y', 'x'))
+# ge1f = dataset.createVariable('e1f', np.float64, ('y', 'x'))
+# ge2t = dataset.createVariable('e2t', np.float64, ('y', 'x'))
+# ge2u = dataset.createVariable('e2u', np.float64, ('y', 'x'))
+# ge2v = dataset.createVariable('e2v', np.float64, ('y', 'x'))
+# ge2f = dataset.createVariable('e2f', np.float64, ('y', 'x'))
+# gfff = dataset.createVariable('ff_f', np.float64, ('y', 'x'))
+# gfft = dataset.createVariable('ff_t', np.float64, ('y', 'x'))
+# ge3t = dataset.createVariable('e3t_0', np.float64, ('z', 'y', 'x'))
+# ge3w = dataset.createVariable('e3w_0', np.float64, ('z', 'y', 'x'))
+# ge3u = dataset.createVariable('e3u_0', np.float64, ('z', 'y', 'x'))
+# ge3v = dataset.createVariable('e3v_0', np.float64, ('z', 'y', 'x'))
+# ge3f = dataset.createVariable('e3f_0', np.float64, ('z', 'y', 'x'))
+# ge3uw = dataset.createVariable('e3uw_0', np.float64, ('z', 'y', 'x'))
+# ge3vw = dataset.createVariable('e3vw_0', np.float64, ('z', 'y', 'x'))
+#
+# nav_lon.units, nav_lon.long_name = 'km', 'X'
+# nav_lat.units, nav_lat.long_name = 'km', 'Y'
+#
+# # Populate file with input data
+# giglo[:] = nx
+# gjglo[:] = ny
+# gkglo[:] = nz
+#
+# gzco[:] = ln_zco
+# gzps[:] = ln_zps
+# gsco[:] = ln_sco
+# gcav[:] = ln_isfcav
+#
+# gperio[:] = jperio
+#
+# # TODO: do we need to transpose?
+# nav_lon[:, :] = lont.T
+# nav_lat[:, :] = latt.T
+# nav_lev[:] = dept_1d
+#
+# ge3t1d[:] = e3t_1d
+# ge3w1d[:] = e3w_1d
+#
+# gitop[:, :] = ktop.T
+# gibot[:, :] = kbot.T
+#
+# gbat[:, :] = bat.T
+#
+# glamt[:, :] = lont.T
+# glamu[:, :] = lonu.T
+# glamv[:, :] = lonv.T
+# glamf[:, :] = lonf.T
+# gphit[:, :] = latt.T
+# gphiu[:, :] = latu.T
+# gphiv[:, :] = latv.T
+# gphif[:, :] = latf.T
+#
+# ge1t[:, :] = e1t.T
+# ge1u[:, :] = e1u.T
+# ge1v[:, :] = e1v.T
+# ge1f[:, :] = e1f.T
+# ge2t[:, :] = e2t.T
+# ge2u[:, :] = e2u.T
+# ge2v[:, :] = e2v.T
+# ge2f[:, :] = e2f.T
+# gfff[:, :] = ff_f.T
+# gfft[:, :] = ff_t.T
+#
+# ge3t[:, :, :] = e3t.T
+# ge3w[:, :, :] = e3w.T
+# ge3u[:, :, :] = e3u.T
+# ge3v[:, :, :] = e3v.T
+# ge3f[:, :, :] = e3f.T
+# ge3uw[:, :, :] = e3uw.T
+# ge3vw[:, :, :] = e3vw.T
+#
+# # Close off pointer
+# dataset.close()
def rotate_around_point(lat_in,lon_in, radians , origin=(0, 0)):
"""Rotate a point around a given point.
diff --git a/pynemo/unit_tests/test_gen.py b/pynemo/unit_tests/test_gen.py
index 51505767abcf2bdb69d20b82b01d85c2546125d7..90725d8d81d3081338cdd31411f947a17ba931b7 100644
--- a/pynemo/unit_tests/test_gen.py
+++ b/pynemo/unit_tests/test_gen.py
@@ -7,11 +7,14 @@ The source coordinate grid is also plotted (green).
"""
from pynemo.unit_tests import gen_tools as gt
+from pynemo.unit_tests import UT_config as config
# TODO: remove hard coded file names and directories.
# TODO: organise the variables better, (maybe in a single dict?)
def _main():
+ #define directory for test input data for PyNEMO
+
#Source Coords
dx = 1000 # units in km
dy = 1000 # units in Km
@@ -21,8 +24,8 @@ def _main():
max_dep = 100
min_dep = 10
z_end_dim = 1
- h_fname = 'pynemo/unit_tests/test_inputs/test_src_hgr_zps.nc'
- z_fname = 'pynemo/unit_tests/test_inputs/test_src_zgr_zps.nc'
+ h_fname = config.input_dir+'test_src_hgr_zps.nc'
+ z_fname = config.input_dir+'test_src_zgr_zps.nc'
grid_h1 = gt.set_hgrid(dx,dy,jpi,jpj)
grid_z1 = gt.set_zgrid(grid_h1,jpk,max_dep,min_dep,z_end_dim)
write_coord_H = gt.write_coord_H(h_fname,grid_h1)
@@ -42,14 +45,14 @@ def _main():
min_dep = 10
z_end_dim = 1
sf = 10
- h_fname = 'pynemo/unit_tests/test_inputs/test_dst_hgr_zps.nc'
- z_fname = 'pynemo/unit_tests/test_inputs/test_dst_zgr_zps.nc'
+ h_fname = config.input_dir+'test_dst_hgr_zps.nc'
+ z_fname = config.input_dir+'test_dst_zgr_zps.nc'
grid_h2 = gt.set_hgrid(dx,dy,jpi,jpj,zoffx,zoffy,sf)
grid_z2 = gt.set_zgrid(grid_h2,jpk,max_dep,min_dep,z_end_dim)
write_coord_H = gt.write_coord_H(h_fname,grid_h2)
write_coord_Z = gt.write_coord_Z(z_fname,grid_h2,grid_z2)
# write bathy files (constant bathy)
- bathy_fname = 'pynemo/unit_tests/test_inputs/test_dst_bathy.nc'
+ bathy_fname = config.input_dir+'test_dst_bathy.nc'
bathy = gt.write_bathy(bathy_fname,grid_h2,grid_z2)
if write_coord_H + write_coord_Z + bathy == 0:
print("Org child grid generation successful!")
@@ -60,8 +63,8 @@ def _main():
origin = (8,8)
# rotate grid
- rot_h_fname = 'pynemo/unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
- rot_z_fname = 'pynemo/unit_tests/test_inputs/test_rot_dst_zgr_zps.nc'
+ rot_h_fname = config.input_dir+'test_rot_dst_hgr_zps.nc'
+ rot_z_fname = config.input_dir+'test_rot_dst_zgr_zps.nc'
grid_rot = grid_h2.copy()
grid_rot['latt'], grid_rot['lont'] = gt.rotate_around_point(grid_h2['latt'],grid_h2['lont'],theta,origin)
grid_rot['latu'], grid_rot['lonu'] = gt.rotate_around_point(grid_h2['latu'], grid_h2['lonu'], theta, origin)
@@ -70,7 +73,7 @@ def _main():
write_coord_H = gt.write_coord_H(rot_h_fname,grid_rot)
write_coord_Z = gt.write_coord_Z(rot_z_fname,grid_rot,grid_z2)
# write bathy files (constant bathy)
- bathy_fname = 'pynemo/unit_tests/test_inputs/test_rot_dst_bathy.nc'
+ bathy_fname = config.input_dir+'test_rot_dst_bathy.nc'
bathy = gt.write_bathy(bathy_fname,grid_rot,grid_z2)
if write_coord_H + write_coord_Z + bathy == 0:
print("Rotated child grid generation Successful!")
@@ -87,14 +90,14 @@ def _main():
min_dep = 10
z_end_dim = 1
sf = 10
- h_fname = 'pynemo/unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
- z_fname = 'pynemo/unit_tests/test_inputs/test_offset_dst_zgr_zps.nc'
+ h_fname = config.input_dir+'test_offset_dst_hgr_zps.nc'
+ z_fname = config.input_dir+'test_offset_dst_zgr_zps.nc'
grid_h3 = gt.set_hgrid(dx,dy,jpi,jpj,zoffx,zoffy,sf)
grid_z3 = gt.set_zgrid(grid_h2,jpk,max_dep,min_dep,z_end_dim)
write_coord_H = gt.write_coord_H(h_fname,grid_h3)
write_coord_Z = gt.write_coord_Z(z_fname,grid_h3,grid_z3)
# write bathy files (constant bathy)
- bathy_fname = 'pynemo/unit_tests/test_inputs/test_offset_dst_bathy.nc'
+ bathy_fname = config.input_dir+'test_offset_dst_bathy.nc'
bathy = gt.write_bathy(bathy_fname,grid_h3,grid_z3)
if write_coord_H + write_coord_Z + bathy == 0:
print("Offset child grid gneration successful!")
@@ -104,7 +107,7 @@ def _main():
# grid_h3['lont'],grid_h1['latt'],grid_h1['lont'])
# write boundary files (constant parameters)
- out_fname = 'pynemo/unit_tests/test_inputs/output_boundary' #drop file extension
+ out_fname = config.input_dir+'output_boundary' #drop file extension
params_t = {'param1': {'name':'thetao','const_value':15.0,'longname':'temperature','units':'degreesC'},
'param2': {'name':'so','const_value':35.0,'longname':'salinity','units':'PSU'},
'param3': {'name': 'zos', 'const_value': 1.0, 'longname': 'sea surface height', 'units': 'metres'}
@@ -121,7 +124,7 @@ def _main():
print('Boundary file generation successful!')
#write_mask
- mask_fname = 'pynemo/unit_tests/test_inputs/mask.nc'
+ mask_fname = config.input_dir+'mask.nc'
mask = gt.write_mask(mask_fname,grid_h1,grid_z1)
if mask == 0:
print('Mask file generation successful!')