diff --git a/inputs/namelist_remote.bdy b/inputs/namelist_remote.bdy
index 72b58c848840f7985bcd296a2fc4f6b475442701..bb2a1a78e12be10461347cdd940b3bb3483b6bb1 100644
--- a/inputs/namelist_remote.bdy
+++ b/inputs/namelist_remote.bdy
@@ -56,7 +56,7 @@
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
+ ln_dyn2d = .true. ! boundary conditions for
! barotropic fields
ln_dyn3d = .false. ! boundary conditions for
! baroclinic velocities
diff --git a/pynemo/nemo_bdy_extr_tm3.py b/pynemo/nemo_bdy_extr_tm3.py
index 632e03573fc4dffafc87b7d48e0a95e0ae28dc61..584ff48b46d82e139d385976f25d8b3e3670a1b7 100644
--- a/pynemo/nemo_bdy_extr_tm3.py
+++ b/pynemo/nemo_bdy_extr_tm3.py
@@ -894,12 +894,12 @@ class Extract:
# for v in self.variables:
for v in self.var_nam:
- if self.settings['dyn2d']: # Calculate depth averaged velocity
- tile_dz = np.tile(self.bdy_dz, [len(self.time_counter), 1, 1, 1])
- tmp_var = np.reshape(self.d_bdy[v][year]['data'][:,:,:], tile_dz.shape)
- tmp_var = np.nansum(tmp_var * tile_dz, 2) /np.nansum(tile_dz, 2)
- else: # Replace NaNs with specified fill value
- tmp_var = np.where(np.isnan(self.d_bdy[v][year]['data'][:,:,:]),
+ #if self.settings['dyn2d']: # Calculate depth averaged velocity
+ # tile_dz = np.tile(self.bdy_dz, [len(self.time_counter), 1, 1, 1])
+ # tmp_var = np.reshape(self.d_bdy[v][year]['data'][:,:,:], tile_dz.shape)
+ # tmp_var = np.nansum(tmp_var * tile_dz, 2) /np.nansum(tile_dz, 2)
+ #else: # Replace NaNs with specified fill value
+ tmp_var = np.where(np.isnan(self.d_bdy[v][year]['data'][:,:,:]),
self.settings['fv'],
self.d_bdy[v][year]['data'][:,:,:])
diff --git a/pynemo/nemo_bdy_ncgen.py b/pynemo/nemo_bdy_ncgen.py
index 96e1e95c9c66c43e8bb24e34b4ded005ade37d69..c0ccccc2e3de2bacf0c75c05fe8afe2b61ebf738 100644
--- a/pynemo/nemo_bdy_ncgen.py
+++ b/pynemo/nemo_bdy_ncgen.py
@@ -240,7 +240,7 @@ def CreateBDYNetcdfFile(filename, N, I, J, K, rw, h, orig, fv, calendar, grd, va
ncid.close()
- if var_nam[0] == 'thetao' or var_nam[0] == 'so':
+ if var_nam[0] == 'thetao' or var_nam[0] == 'so' or var_nam[0] == 'uo' or var_nam[0] == 'vo':
logging.info('CMEMS variables identified, using default CMEMS variables.....')
gridNames = ['T', 'I', 'U', 'V', 'E', 'Z'] # All possible grids
@@ -286,6 +286,7 @@ def CreateBDYNetcdfFile(filename, N, I, J, K, rw, h, orig, fv, calendar, grd, va
vartmpID = ncid.createVariable('thetao', 'f4', ('time_counter', 'z', 'yb', 'xb', ),
fill_value=fv)
varsalID = ncid.createVariable('so', 'f4', ('time_counter', 'z', 'yb', 'xb', ), fill_value=fv)
+ varsshID = ncid.createVariable('zos', 'f4', ('time_counter', 'z', 'yb', 'xb',), fill_value=fv)
if grd == 'I':
varildID = ncid.createVariable('ileadfra', 'f4', ('time_counter', 'yb', 'xb',),
fill_value=fv)
@@ -297,16 +298,16 @@ def CreateBDYNetcdfFile(filename, N, I, J, K, rw, h, orig, fv, calendar, grd, va
varztID = ncid.createVariable('depthu', 'f4', ('z', 'yb', 'xb', ), fill_value=fv)
varbtuID = ncid.createVariable('vobtcrtx', 'f4', ('time_counter', 'yb', 'xb', ),
fill_value=fv)
- vartouID = ncid.createVariable('vozocrtx', 'f4', ('time_counter', 'z', 'yb', 'xb', ),
+ vartouID = ncid.createVariable('uo', 'f4', ('time_counter', 'z', 'yb', 'xb', ),
fill_value=fv)
elif grd == 'V':
varztID = ncid.createVariable('depthv', 'f4', ('z', 'yb', 'xb', ))
varbtvID = ncid.createVariable('vobtcrty', 'f4', ('time_counter', 'yb', 'xb', ),
fill_value=fv)
- vartovID = ncid.createVariable('vomecrty', 'f4', ('time_counter', 'z', 'yb', 'xb',),
+ vartovID = ncid.createVariable('vo', 'f4', ('time_counter', 'z', 'yb', 'xb',),
fill_value=fv)
elif grd == 'Z':
- varsshID = ncid.createVariable('sossheig', 'f4', ('time_counter', 'yb', 'xb', ),
+ varsshID = ncid.createVariable('zos', 'f4', ('time_counter', 'yb', 'xb', ),
fill_value=fv)
varmskID = ncid.createVariable('bdy_msk', 'f4', ('y', 'x', ), fill_value=fv)
else:
diff --git a/pynemo/nemo_bdy_ncpop.py b/pynemo/nemo_bdy_ncpop.py
index 1f55c5dd98fa61ad81ce692a5327eedd06b7cd27..7e67dc2f491e361bbf32cbe75b42e2becf544ea8 100644
--- a/pynemo/nemo_bdy_ncpop.py
+++ b/pynemo/nemo_bdy_ncpop.py
@@ -18,7 +18,7 @@ def write_data_to_file(filename, variable_name, data):
ncid = Dataset(filename, 'a', clobber=False, format='NETCDF4')
count = data.shape
- three_dim_variables = ['votemper', 'vosaline', 'N1p', 'N3n', 'N5s','thetao','so']
+ three_dim_variables = ['votemper', 'vosaline', 'N1p', 'N3n', 'N5s','thetao','so','uo','vo']
two_dim_variables = ['sossheig', 'vobtcrtx', 'vobtcrty', 'iicethic', 'ileadfra', 'isnowthi','zos']
if variable_name in three_dim_variables:
diff --git a/pynemo/profile.py b/pynemo/profile.py
index 91108281007c53e95ea68f683c2414d12aeca733..ab394b1a77632da39171b895c342b8a287e33268 100644
--- a/pynemo/profile.py
+++ b/pynemo/profile.py
@@ -490,8 +490,8 @@ def process_bdy(setup_filepath=0, mask_gui=False):
emap = {}
grd = [ 't', 'u', 'v']
- pair = [ None, 'uv', 'uv'] # TODO: devolve this to the namelist?
-
+ #pair = [ None, 'uv', 'uv'] # TODO: devolve this to the namelist?
+ pair = [None, None, None]
# TODO: The following is a temporary stop gap to assign variables for both CMEMS downloads
# and existing variable names. In future we need a slicker way of determining the variables to extract.
# Perhaps by scraping the .ncml file - this way biogeochemical tracers
diff --git a/unit_tests/namelist_unit_test_offset.bdy b/unit_tests/namelist_unit_test_offset.bdy
index b11b850c0cf00705fd82741e8704412ad45f4607..10d164b27b40d293c12864107655ab9091d3a728 100644
--- a/unit_tests/namelist_unit_test_offset.bdy
+++ b/unit_tests/namelist_unit_test_offset.bdy
@@ -30,17 +30,17 @@
!------------------------------------------------------------------------------
! grid information
!------------------------------------------------------------------------------
- sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_src_hgr_zps.nc'
- sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_src_zgr_zps.nc'
- sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_offset_dst_hgr_zps.nc'
- sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_offset_dst_zgr_zps.nc'
- sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/mask.nc'
- sn_bathy = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_offset_dst_bathy.nc'
+ sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_hgr_zps.nc'
+ sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_zgr_zps.nc'
+ sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
+ sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_offset_dst_zgr_zps.nc'
+ sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/mask.nc'
+ sn_bathy = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_offset_dst_bathy.nc'
!------------------------------------------------------------------------------
! I/O
!------------------------------------------------------------------------------
- sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/src_data_unit_tests.ncml' ! src_files/'
+ sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/unit_tests.ncml' ! src_files/'
sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
sn_fn = 'unit_test_offset' ! prefix for output files
nn_fv = -1e20 ! set fill value for output files
@@ -61,7 +61,7 @@
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
+ ln_dyn2d = .true. ! boundary conditions for
! barotropic fields
ln_dyn3d = .false. ! boundary conditions for
! baroclinic velocities
diff --git a/unit_tests/namelist_unit_test_orth.bdy b/unit_tests/namelist_unit_test_orth.bdy
index 35e9d9d55341b97355da1d81c0a6bc3db3a769d7..854265223c1d86151fc7aa2807b754e894398417 100644
--- a/unit_tests/namelist_unit_test_orth.bdy
+++ b/unit_tests/namelist_unit_test_orth.bdy
@@ -30,17 +30,17 @@
!------------------------------------------------------------------------------
! grid information
!------------------------------------------------------------------------------
- sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_src_hgr_zps.nc'
- sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_src_zgr_zps.nc'
- sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_dst_hgr_zps.nc'
- sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_dst_zgr_zps.nc'
- sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/mask.nc'
- sn_bathy = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_dst_bathy.nc'
+ sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_hgr_zps.nc'
+ sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_zgr_zps.nc'
+ sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_dst_hgr_zps.nc'
+ sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_dst_zgr_zps.nc'
+ sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/mask.nc'
+ sn_bathy = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_dst_bathy.nc'
!------------------------------------------------------------------------------
! I/O
!------------------------------------------------------------------------------
- sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/src_data_unit_tests.ncml' ! src_files/'
+ sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/unit_tests.ncml' ! src_files/'
sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
sn_fn = 'unit_test_orth' ! prefix for output files
nn_fv = -1e20 ! set fill value for output files
@@ -61,9 +61,9 @@
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
+ ln_dyn2d = .true. ! boundary conditions for
! barotropic fields
- ln_dyn3d = .false. ! boundary conditions for
+ ln_dyn3d = .false. ! boundary conditions for
! baroclinic velocities
ln_tra = .true. ! boundary conditions for T and S
ln_ice = .false. ! ice boundary condition
diff --git a/unit_tests/namelist_unit_test_rotated.bdy b/unit_tests/namelist_unit_test_rotated.bdy
index 063affb9b3cc076275e46dfe34f0959c16ff0da5..f970101f3e7466628e7b8f35c179e0e55499592c 100644
--- a/unit_tests/namelist_unit_test_rotated.bdy
+++ b/unit_tests/namelist_unit_test_rotated.bdy
@@ -30,17 +30,17 @@
!------------------------------------------------------------------------------
! grid information
!------------------------------------------------------------------------------
- sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_src_hgr_zps.nc'
- sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_src_zgr_zps.nc'
- sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_rot_dst_hgr_zps.nc'
- sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_rot_dst_zgr_zps.nc'
- sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/mask.nc'
- sn_bathy = '/Users/thopri/Projects/PyNEMO/unit_tests/test_data/test_rot_dst_bathy.nc'
+ sn_src_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_hgr_zps.nc'
+ sn_src_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_src_zgr_zps.nc'
+ sn_dst_hgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
+ sn_dst_zgr = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_rot_dst_zgr_zps.nc'
+ sn_src_msk = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/mask.nc'
+ sn_bathy = '/Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/test_rot_dst_bathy.nc'
!------------------------------------------------------------------------------
! I/O
!------------------------------------------------------------------------------
- sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/src_data_unit_tests.ncml' ! src_files/'
+ sn_src_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/unit_tests.ncml' ! src_files/'
sn_dst_dir = '/Users/thopri/Projects/PyNEMO/unit_tests/test_outputs'
sn_fn = 'unit_test_rotated' ! prefix for output files
nn_fv = -1e20 ! set fill value for output files
@@ -61,7 +61,7 @@
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
+ ln_dyn2d = .true. ! boundary conditions for
! barotropic fields
ln_dyn3d = .false. ! boundary conditions for
! baroclinic velocities
diff --git a/unit_tests/src_data_unit_tests.ncml b/unit_tests/src_data_unit_tests.ncml
deleted file mode 100644
index 3016c52e5a5d5da17889f49ac04430d7d57c5503..0000000000000000000000000000000000000000
--- a/unit_tests/src_data_unit_tests.ncml
+++ /dev/null
@@ -1,10 +0,0 @@
-<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:aggregation>
- <ns0:variable name="thetao" orgName="thetao" />
-</ns0:netcdf>
diff --git a/unit_tests/test_gen.py b/unit_tests/test_gen.py
index 0d6f98213109ab4f19f0650980e1fba1780b3046..9c27327be8ae3d3232b013f80c565d2c69fd35d9 100644
--- a/unit_tests/test_gen.py
+++ b/unit_tests/test_gen.py
@@ -21,8 +21,8 @@ def _main():
max_dep = 100
min_dep = 10
z_end_dim = 1
- h_fname = 'unit_tests/test_data/test_src_hgr_zps.nc'
- z_fname = 'unit_tests/test_data/test_src_zgr_zps.nc'
+ h_fname = 'unit_tests/test_inputs/test_src_hgr_zps.nc'
+ z_fname = 'unit_tests/test_inputs/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 +42,14 @@ def _main():
min_dep = 10
z_end_dim = 1
sf = 10
- h_fname = 'unit_tests/test_data/test_dst_hgr_zps.nc'
- z_fname = 'unit_tests/test_data/test_dst_zgr_zps.nc'
+ h_fname = 'unit_tests/test_inputs/test_dst_hgr_zps.nc'
+ z_fname = 'unit_tests/test_inputs/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 = 'unit_tests/test_data/test_dst_bathy.nc'
+ bathy_fname = 'unit_tests/test_inputs/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 +60,8 @@ def _main():
origin = (8,8)
# rotate grid
- rot_h_fname = 'unit_tests/test_data/test_rot_dst_hgr_zps.nc'
- rot_z_fname = 'unit_tests/test_data/test_rot_dst_zgr_zps.nc'
+ rot_h_fname = 'unit_tests/test_inputs/test_rot_dst_hgr_zps.nc'
+ rot_z_fname = 'unit_tests/test_inputs/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 +70,7 @@ 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 = 'unit_tests/test_data/test_rot_dst_bathy.nc'
+ bathy_fname = 'unit_tests/test_inputs/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 +87,14 @@ def _main():
min_dep = 10
z_end_dim = 1
sf = 10
- h_fname = 'unit_tests/test_data/test_offset_dst_hgr_zps.nc'
- z_fname = 'unit_tests/test_data/test_offset_dst_zgr_zps.nc'
+ h_fname = 'unit_tests/test_inputs/test_offset_dst_hgr_zps.nc'
+ z_fname = 'unit_tests/test_inputs/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 = 'unit_tests/test_data/test_offset_dst_bathy.nc'
+ bathy_fname = 'unit_tests/test_inputs/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 +104,7 @@ def _main():
# grid_h3['lont'],grid_h1['latt'],grid_h1['lont'])
# write boundary files (constant parameters)
- out_fname = 'unit_tests/test_data/output_boundary' #drop file extension
+ out_fname = 'unit_tests/test_inputs/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 +121,7 @@ def _main():
print('Boundary file generation successful!')
#write_mask
- mask_fname = 'unit_tests/test_data/mask.nc'
+ mask_fname = 'unit_tests/test_inputs/mask.nc'
mask = gt.write_mask(mask_fname,grid_h1,grid_z1)
if mask == 0:
print('Mask file generation successful!')
diff --git a/unit_tests/unit_test.py b/unit_tests/unit_test.py
index 2f5a5c8d7ee91498fe3f1524576366646f6a4fa6..2f041ade946dbf909bfc3d28e6089d08534e599d 100644
--- a/unit_tests/unit_test.py
+++ b/unit_tests/unit_test.py
@@ -34,7 +34,9 @@ for n in namelist_files:
# perform tests
def test_temp():
- test_files = glob.glob('unit_tests/test_outputs/unit_test*')
+ test_files = glob.glob('unit_tests/test_outputs/*bdyT*')
+ if len(test_files) == 0:
+ raise Exception('DONT PANIC: no temperature test files found')
for t in test_files:
results = Dataset(t) # open results
temp = results['thetao'][:]
@@ -45,7 +47,9 @@ def test_temp():
assert abs(temp_[temp_ != 0.0].min() - 15) <= 0.001
def test_salinty():
- test_files = glob.glob('unit_tests/test_outputs/unit_test*')
+ test_files = glob.glob('unit_tests/test_outputs/*bdyT*')
+ if len(test_files) == 0:
+ raise Exception('DONT PANIC: no salinity test files found')
for t in test_files:
results = Dataset(t) # open results
sal = results['so'][:]
@@ -55,18 +59,57 @@ def test_salinty():
assert abs(sal_[sal_ != 0.0].max() - 35) <= 0.001
assert abs(sal_[sal_ != 0.0].min() - 35) <= 0.001
+def test_ssh():
+ test_files = glob.glob('unit_tests/test_outputs/*bdyT*')
+ if len(test_files) == 0:
+ raise Exception('DONT PANIC: no SSH test files found')
+ for t in test_files:
+ results = Dataset(t) # open results
+ ssh = results['zos'][:]
+ results.close()
+ ssh_ = np.ma.masked_array(ssh,ssh == -32767.0)
+ assert abs(ssh_[ssh_!=0.0].mean() - 1.0) <= 0.001
+ assert abs(ssh_[ssh_ != 0.0].max() - 1.0) <= 0.001
+ assert abs(ssh_[ssh_ != 0.0].min() - 1.0) <= 0.001
+
+def test_U():
+ test_files = glob.glob('unit_tests/test_outputs/*bdyU*')
+ if len(test_files) == 0:
+ raise Exception('DONT PANIC: no U current test files found')
+ for t in test_files:
+ results = Dataset(t) # open results
+ U = results['uo'][:]
+ results.close()
+ U_ = np.ma.masked_array(U,U == -32767.0)
+ assert abs(U_[U_!=0.0].mean() - 0.5) <= 0.001
+ assert abs(U_[U_ != 0.0].max() - 0.5) <= 0.001
+ assert abs(U_[U_ != 0.0].min() - 0.5) <= 0.001
+
+def test_V():
+ test_files = glob.glob('unit_tests/test_outputs/*bdyV*')
+ if len(test_files) == 0:
+ raise Exception('DONT PANIC: no V current test files found')
+ for t in test_files:
+ results = Dataset(t) # open results
+ V = results['vo'][:]
+ results.close()
+ V_ = np.ma.masked_array(V,V == -32767.0)
+ assert abs(V_[V_!=0.0].mean() - 0.5) <= 0.001
+ assert abs(V_[V_ != 0.0].max() - 0.5) <= 0.001
+ assert abs(V_[V_ != 0.0].min() - 0.5) <= 0.001
+
# clean up test I/O
-files = glob.glob('unit_tests/test_outputs/*')
-for f in files:
- os.remove(f)
-files = glob.glob('unit_tests/test_outputs/*')
-if len(files) != 0:
- raise Exception('DONT PANIC: output folder not cleaned')
+def test_rm_out():
+ 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
-files = glob.glob('unit_tests/test_data/*')
-for f in files:
- os.remove(f)
-files = glob.glob('unit_tests/test_data/*')
-if len(files) != 0:
- raise Exception('DONT PANIC: input folder not cleaned')
+def test_rm_in():
+ files = glob.glob('unit_tests/test_inputs/*')
+ for f in files:
+ os.remove(f)
+ files = glob.glob('unit_tests/test_inputs/*')
+ assert len(files) == 0
diff --git a/unit_tests/unit_tests.ncml b/unit_tests/unit_tests.ncml
new file mode 100644
index 0000000000000000000000000000000000000000..d376a10e7d9f6a9a1ae4511f74b400c994515b50
--- /dev/null
+++ b/unit_tests/unit_tests.ncml
@@ -0,0 +1,28 @@
+<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_inputs/" regExp=".*T\.nc$" />
+ </ns0:aggregation>
+ </ns0:netcdf>
+ <ns0:netcdf>
+ <ns0:aggregation dimName="time" name="zonal_velocity" type="joinExisting">
+ <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/" regExp=".*U\.nc$" />
+ </ns0:aggregation>
+ </ns0:netcdf>
+ <ns0:netcdf>
+ <ns0:aggregation dimName="time" name="meridian_velocity" type="joinExisting">
+ <ns0:scan location="file://Users/thopri/Projects/PyNEMO/unit_tests/test_inputs/" regExp=".*V\.nc$" />
+ </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_inputs/" regExp=".*T\.nc$" />
+ </ns0:aggregation>
+ </ns0:netcdf>
+ </ns0:aggregation>
+ <ns0:variable name="thetao" orgName="thetao" />
+ <ns0:variable name="uo" orgName="uo" />
+ <ns0:variable name="vo" orgName="vo" />
+ <ns0:variable name="zos" orgName="zos" />
+</ns0:netcdf>