Pre-commit clean up

compass/ocean/tests/mitgcm_baroclinic_gyre/__init__.py

@@ -1,5 +1,7 @@
+from compass.ocean.tests.mitgcm_baroclinic_gyre.gyre_test_case import (
+    GyreTestCase,
+)
 from compass.testgroup import TestGroup
-from compass.ocean.tests.mitgcm_baroclinic_gyre.gyre_test_case import GyreTestCase
 
 
 class MitgcmBaroclinicGyre(TestGroup):
@@ -15,8 +17,8 @@ def __init__(self, mpas_core):
 
         for resolution in ['80km']:
             self.add_test_case(
-                GyreTestCase(test_group=self, resolution=resolution, long=False))
+                GyreTestCase(test_group=self, resolution=resolution,
+                             long=False))
             self.add_test_case(
-                GyreTestCase(test_group=self, resolution=resolution, long=True))
-
-
+                GyreTestCase(test_group=self, resolution=resolution,
+                             long=True))

compass/ocean/tests/mitgcm_baroclinic_gyre/cull_mesh.py

@@ -1,6 +1,5 @@
+import numpy as np
 import xarray as xr
-import numpy as np 
-
 from mpas_tools.io import write_netcdf
 from mpas_tools.mesh.conversion import convert, cull
 

compass/ocean/tests/mitgcm_baroclinic_gyre/forward.py

@@ -1,10 +1,10 @@
+from compass.model import run_model
 from compass.step import Step
-from compass.model import partition, run_model
 
 
 class Forward(Step):
     """
-    A step for performing forward MPAS-Ocean runs as part of 
+    A step for performing forward MPAS-Ocean runs as part of
     the MITgcm baoclinic gyre test cases.
 
     Attributes
@@ -14,7 +14,7 @@ class Forward(Step):
 
     """
     def __init__(self, test_case, resolution, name='forward', subdir=None,
-                  long=False):
+                 long=False):
         """
         Create a new test case
 
@@ -59,18 +59,20 @@ def __init__(self, test_case, resolution, name='forward', subdir=None,
         # make sure output is double precision
         self.add_streams_file('compass.ocean.streams', 'streams.output')
 
-        self.add_namelist_file('compass.ocean.tests.mitgcm_baroclinic_gyre', 'namelist.forward')
+        self.add_namelist_file('compass.ocean.tests.mitgcm_baroclinic_gyre',
+                               'namelist.forward')
         if long:
             output_interval = "0010_00:00:00"
             restart_interval = "0010_00:00:00"
         else:
             output_interval = res_params['run_duration'].replace("'", "")
             restart_interval = "0030_00:00:00"
-        replacements = dict(
-            output_interval=output_interval, restart_interval=restart_interval)
-        self.add_streams_file(package='compass.ocean.tests.mitgcm_baroclinic_gyre',
-                              streams='streams.forward',
-                              template_replacements=replacements)
+        replacements = dict(output_interval=output_interval,
+                            restart_interval=restart_interval)
+        self.add_streams_file(
+            package='compass.ocean.tests.mitgcm_baroclinic_gyre',
+            streams='streams.forward',
+            template_replacements=replacements)
         options = dict()
         for option in ['dt', 'btr_dt', 'mom_del4', 'run_duration']:
             options[f'config_{option}'] = res_params[option]

compass/ocean/tests/mitgcm_baroclinic_gyre/initial_state.py

@@ -1,6 +1,5 @@
-import xarray as xr
 import numpy as np
-
+import xarray as xr
 from mpas_tools.io import write_netcdf
 
 from compass.ocean.vertical import init_vertical_coord
@@ -52,9 +51,8 @@ def run(self):
 
         _write_forcing(config, ds.latCell)
 
-def _write_initial_state(config, dsMesh):
-    section = config['mitgcm_baroclinic_gyre']
 
+def _write_initial_state(config, dsMesh):
     ds = dsMesh.copy()
 
     bottom_depth = config.getfloat('vertical_grid', 'bottom_depth')
@@ -63,11 +61,13 @@ def _write_initial_state(config, dsMesh):
 
     init_vertical_coord(config, ds)
 
-    # setting the initial conditions 
-    temperature = (-11. * np.log(0.0414*
-                 (-1.*ds.zMid + 100.3)) + 48.8)
+    # setting the initial conditions
+    temperature = (-11. * np.log(0.0414 *
+                   (-1. * ds.zMid + 100.3)) + 48.8)
     temperature = temperature.transpose('Time', 'nCells', 'nVertLevels')
-    print(f'bottom T: {temperature[0, 200, -1]} and surface : {temperature[0, 200, 0]}')
+    bottT = temperature[0, 200, -1].values
+    surfT = temperature[0, 200, 0].values
+    print(f'bottom T: {bottT} and surface : {surfT}')
     salinity = 34.0 * xr.ones_like(temperature)
 
     normalVelocity = xr.zeros_like(ds.xEdge)
@@ -76,17 +76,18 @@ def _write_initial_state(config, dsMesh):
     normalVelocity = normalVelocity.expand_dims(dim='Time', axis=0)
 
     ds['temperature'] = temperature
-    ds['salinity'] = salinity 
+    ds['salinity'] = salinity
     ds['normalVelocity'] = normalVelocity
 
-    omega = 2. * np.pi / 86164.   
+    omega = 2. * np.pi / 86164.
     ds['fCell'] = 2. * omega * np.sin(ds.latCell)
-    ds['fEdge'] = 2. * omega * np.sin(ds.latEdge) 
-    ds['fVertex'] =  2. * omega * np.sin(ds.latVertex)
+    ds['fEdge'] = 2. * omega * np.sin(ds.latEdge)
+    ds['fVertex'] = 2. * omega * np.sin(ds.latVertex)
 
     write_netcdf(ds, 'initial_state.nc')
     return ds
 
+
 def _write_forcing(config, lat):
     section = config['mitgcm_baroclinic_gyre']
     latMin = section.getfloat('lat_min')
@@ -97,8 +98,8 @@ def _write_forcing(config, lat):
     restoring_temp_piston_vel = section.getfloat('restoring_temp_piston_vel')
     lat = np.rad2deg(lat)
     # set wind stress
-    windStressZonal = -tauMax * np.cos(2 * np.pi * (lat - latMin) \
-                      / (latMax - latMin))
+    windStressZonal = -tauMax * np.cos(2 * np.pi * (lat - latMin) /
+                                       (latMax - latMin))
 
     windStressZonal = windStressZonal.expand_dims(dim='Time', axis=0)
 
@@ -118,7 +119,6 @@ def _write_forcing(config, lat):
         34.0 * xr.ones_like(temperatureSurfaceRestoringValue)
     salinityPistonVelocity = xr.zeros_like(temperaturePistonVelocity)
 
-
     dsForcing = xr.Dataset()
     dsForcing['windStressZonal'] = windStressZonal
     dsForcing['windStressMeridional'] = windStressMeridional
@@ -129,4 +129,3 @@ def _write_forcing(config, lat):
     dsForcing['salinitySurfaceRestoringValue'] = salinitySurfaceRestoringValue
 
     write_netcdf(dsForcing, 'forcing.nc')
-

compass/ocean/vertical/grid_1d.py

@@ -1,8 +1,9 @@
-import numpy
-from importlib import resources
 import json
-from netCDF4 import Dataset
+from importlib import resources
+
+import numpy
 import numpy as np
+from netCDF4 import Dataset
 from scipy.optimize import root_scalar
 
 
@@ -52,7 +53,7 @@ def generate_1d_grid(config):
             grid_type != 'tanh_dz':
         bottom_depth = section.getfloat('bottom_depth')
         # renormalize to the requested range
-        interfaces = (bottom_depth/interfaces[-1]) * interfaces
+        interfaces = (bottom_depth / interfaces[-1]) * interfaces
 
     return interfaces
 
@@ -128,7 +129,7 @@ def add_1d_grid(config, ds):
 
 def _generate_uniform(vert_levels):
     """ Generate uniform layer interfaces between 0 and 1 """
-    interfaces = numpy.linspace(0., 1., vert_levels+1)
+    interfaces = numpy.linspace(0., 1., vert_levels + 1)
     return interfaces
 
 
@@ -146,7 +147,8 @@ def _read_json(grid_type):
 def _create_linear_dz_grid(num_vert_levels, bottom_depth,
                            linear_dz_rate):
     """
-    Creates the linear vertical grid for MPAS-Ocean and writes it to a NetCDF file
+    Creates the linear vertical grid for MPAS-Ocean and
+    writes it to a NetCDF file
 
     Parameters
     ----------
@@ -166,11 +168,13 @@ def _create_linear_dz_grid(num_vert_levels, bottom_depth,
     """
 
     nz = num_vert_levels
-    layerThickness = [(bottom_depth / nz) - (np.floor(nz/2) - k) * linear_dz_rate for k in np.arange(0, nz)]
-    min_layer_thickness  = layerThickness[0]
+    layerThickness = [(bottom_depth / nz) - (np.floor(nz / 2) - k) *
+                      linear_dz_rate for k in np.arange(0, nz)]
+    min_layer_thickness = layerThickness[0]
     max_layer_thickness = layerThickness[-1]
     print('Linear dz vertical grid')
-    print(f'min layer thickness: {min_layer_thickness}; max layer thickness {max_layer_thickness} in m;')
+    print(f'min layer thickness: {min_layer_thickness}; '
+          f'max layer thickness {max_layer_thickness} in m;')
     interfaces = - np.append([0], np.cumsum(layerThickness))
 
     return interfaces
@@ -179,7 +183,8 @@ def _create_linear_dz_grid(num_vert_levels, bottom_depth,
 def _create_tanh_dz_grid(num_vert_levels, bottom_depth, min_layer_thickness,
                          max_layer_thickness):
     """
-    Creates the tanh vertical grid for MPAS-Ocean and writes it to a NetCDF file
+    Creates the tanh vertical grid for MPAS-Ocean and
+    writes it to a NetCDF file
 
     Parameters
     ----------
@@ -224,7 +229,7 @@ def _create_tanh_dz_grid(num_vert_levels, bottom_depth, min_layer_thickness,
 
 def _tanh_match_bottom(delta, nz, dz1, dz2, bottom_depth):
     """
-    For tanh layer thickness, compute the difference between the 
+    For tanh layer thickness, compute the difference between the
     bottom depth computed with the given
     parameters and the target ``bottom_depth``, used in the root finding
     algorithm to determine which value of ``delta`` to use.
@@ -262,7 +267,8 @@ def _tanh_match_bottom(delta, nz, dz1, dz2, bottom_depth):
 
 def _tanh_cumsum_z(delta, nz, dz1, dz2):
     """
-    Compute tanh layer interface depths and layer thicknesses over ``nz`` layers
+    Compute tanh layer interface depths and layer thicknesses
+    over ``nz`` layers
 
     Parameters
     ----------