Fix black and mypy issues

e3sm_diags/derivations/acme.py

@@ -465,7 +465,8 @@ def cosp_bin_sum(
     tau_high0: Optional[float],
 ):
     """sum of cosp bins to calculate cloud fraction in specified cloud top pressure / height and
-    cloud thickness bins, input variable has dimension (cosp_prs,cosp_tau,lat,lon)/(cosp_ht,cosp_tau,lat,lon)"""
+    cloud thickness bins, input variable has dimension (cosp_prs,cosp_tau,lat,lon)/(cosp_ht,cosp_tau,lat,lon)
+    """
     prs: FileAxis = cld.getAxis(0)
     tau: FileAxis = cld.getAxis(1)
 

e3sm_diags/driver/arm_diags_driver.py

@@ -423,7 +423,6 @@ def run_diag_aerosol_activation(parameter: ARMDiagsParameter) -> ARMDiagsParamet
         logger.info("Selected region: {}".format(region))
         # Possible variables are ccn01, ccn02, ccn05
         for variable in variables:
-
             test_data = utils.dataset.Dataset(parameter, test=True)
 
             test_a_num = test_data.get_timeseries_variable("a_num", single_point=True)[
@@ -441,7 +440,6 @@ def run_diag_aerosol_activation(parameter: ARMDiagsParameter) -> ARMDiagsParamet
             )
 
             if "armdiags" in ref_name:
-
                 ref_file = os.path.join(
                     ref_path,
                     region[:3] + "armdiagsaciactivate" + region[3:5].upper() + ".c1.nc",
@@ -568,7 +566,6 @@ def run_diag_pdf_daily(parameter: ARMDiagsParameter):
 
 
 def run_diag(parameter: ARMDiagsParameter) -> ARMDiagsParameter:
-
     if parameter.diags_set == "annual_cycle":
         return run_diag_annual_cycle(parameter)
     elif parameter.diags_set == "diurnal_cycle":

e3sm_diags/driver/enso_diags_driver.py

@@ -272,7 +272,11 @@ def run_diag_map(parameter: EnsoDiagsParameter) -> EnsoDiagsParameter:
                 )
 
                 # Reference
-                (ref_domain, ref_reg_coe, ref_confidence_levels,) = perform_regression(
+                (
+                    ref_domain,
+                    ref_reg_coe,
+                    ref_confidence_levels,
+                ) = perform_regression(
                     ref_data,
                     parameter,
                     var,

e3sm_diags/driver/lat_lon_driver.py

@@ -175,12 +175,8 @@ def run_diag(parameter: CoreParameter) -> CoreParameter:  # noqa: C901
 
                 # Select plev.
                 for ilev in range(len(plev)):
-                    mv1 = mv1_p[
-                        ilev,
-                    ]
-                    mv2 = mv2_p[
-                        ilev,
-                    ]
+                    mv1 = mv1_p[ilev,]
+                    mv2 = mv2_p[ilev,]
 
                     for region in regions:
                         parameter.var_region = region

e3sm_diags/driver/polar_driver.py

@@ -133,12 +133,8 @@ def run_diag(parameter: CoreParameter) -> CoreParameter:
 
                 # Select plev.
                 for ilev in range(len(plev)):
-                    mv1 = mv1_p[
-                        ilev,
-                    ]
-                    mv2 = mv2_p[
-                        ilev,
-                    ]
+                    mv1 = mv1_p[ilev,]
+                    mv2 = mv2_p[ilev,]
 
                     for region in regions:
                         logger.info("Selected region: {}".format(region))

e3sm_diags/driver/tc_analysis_driver.py

@@ -265,9 +265,9 @@ def _get_vars_from_te_stitch(
             vars_dict["yearmc"][k - 1, index - 1] = float(line_split[6])
             vars_dict["monthmc"][k - 1, index - 1] = float(line_split[7])
 
-    vars_dict["year_start"] = year_start
-    vars_dict["year_end"] = year_end
-    vars_dict["num_years"] = year_end - year_start + 1
+    vars_dict["year_start"] = year_start  # type: ignore
+    vars_dict["year_end"] = year_end  # type: ignore
+    vars_dict["num_years"] = year_end - year_start + 1  # type: ignore
     logger.info(
         f"TE Start Year: {vars_dict['year_start']}, TE End Year: {vars_dict['year_end']}, Total Years: {vars_dict['num_years']}"
     )
@@ -340,7 +340,6 @@ def _derive_metrics_per_basin(
             and lat[0] > basin_info[3]
             and lat[0] < basin_info[4]
         ):
-
             mod_num_ocn = mod_num_ocn + 1
             mod_mon.append(mon[0])
             mod_wnd.append(np.max(wind))
@@ -491,7 +490,7 @@ def _calc_mean_ace(vsmc: "MaskedArray", yearic: np.ndarray, num_rows: int) -> fl
                 wind_ts = wind[wind >= 35]
                 ace[i] = ace[i] + np.sum(wind_ts**2) / 1e4
 
-    return np.mean(ace)
+    return np.mean(ace)  # type: ignore
 
 
 def _calc_ts_intensity_dist(wind_speeds: List[int]) -> np.ndarray:

e3sm_diags/driver/utils/general.py

@@ -293,7 +293,7 @@ def save_transient_variables_to_netcdf(set_num, variables_dict, label, parameter
     Save the transient variables to nc file.
     """
     if parameter.save_netcdf:
-        for (variable_name, variable) in variables_dict.items():
+        for variable_name, variable in variables_dict.items():
             # Set cdms preferences - no compression, no shuffling, no complaining
             cdms2.setNetcdfDeflateFlag(1)
             # 1-9, min to max - Comes at heavy IO (read/write time cost)

e3sm_diags/driver/zonal_mean_xy_driver.py

@@ -171,12 +171,8 @@ def run_diag(parameter: CoreParameter) -> CoreParameter:
 
                 # Select plev.
                 for ilev in range(len(plev)):
-                    mv1 = mv1_p[
-                        ilev,
-                    ]
-                    mv2 = mv2_p[
-                        ilev,
-                    ]
+                    mv1 = mv1_p[ilev,]
+                    mv2 = mv2_p[ilev,]
 
                     for region in regions:
                         logger.info(f"Selected region: {region}")

e3sm_diags/plot/cartopy/annual_cycle_zonal_mean_plot.py

@@ -40,7 +40,6 @@ def get_ax_size(fig, ax):
 
 
 def plot_panel(n, fig, var, clevels, cmap, title, parameters, stats=None):
-
     mon = var.getTime()
     lat = var.getLatitude()
     var = np.transpose(var)
@@ -172,7 +171,7 @@ def plot(reference, test, diff, metrics_dict, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/plot/cartopy/cosp_histogram_plot.py

@@ -39,7 +39,6 @@ def get_ax_size(fig, ax):
 
 
 def plot_panel(n, fig, _, var, clevels, cmap, title, parameters, stats=None):
-
     # Contour levels
     levels = None
     norm = None
@@ -170,7 +169,6 @@ def plot_panel(n, fig, _, var, clevels, cmap, title, parameters, stats=None):
 
 
 def plot(reference, test, diff, _, parameter):
-
     # Create figure, projection
     fig = plt.figure(figsize=parameter.figsize, dpi=parameter.dpi)
 
@@ -251,7 +249,7 @@ def plot(reference, test, diff, _, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/plot/cartopy/diurnal_cycle_plot.py

@@ -65,7 +65,6 @@ def determine_tick_step(degrees_covered):
 
 
 def plot_panel(n, fig, proj, var, amp, amp_ref, title, parameter):
-
     normalize_test_amp = parameter.normalize_test_amp
     specified_max_amp = parameter.normalize_amp_int
 
@@ -129,7 +128,7 @@ def plot_panel(n, fig, proj, var, amp, amp_ref, title, parameter):
     # If less than 0.50 is subtracted, then 0 W will overlap 0 E on the left side of the plot.
     # If a number is added, then the value won't show up at all.
     if global_domain or full_lon:
-        xticks = [0, 60, 120, 180, 240, 300, 359.99]
+        xticks = [0, 60, 120, 180, 240, 300, 359.99]  # type: ignore
     else:
         xticks = np.append(xticks, lon_east)
         proj = ccrs.PlateCarree()
@@ -309,7 +308,7 @@ def plot(test_tmax, test_amp, ref_tmax, ref_amp, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             subplot_suffix = ".%i." % (i) + f

e3sm_diags/plot/cartopy/enso_diags_plot.py

@@ -63,7 +63,6 @@ def determine_tick_step(degrees_covered):
 def plot_panel_map(
     n, fig, proj, var, clevels, cmap, title, parameter, conf=None, stats={}
 ):
-
     var = add_cyclic(var)
     lon = var.getLongitude()
     lat = var.getLatitude()
@@ -330,7 +329,7 @@ def plot_map(
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             subplot_suffix = ".%i." % (i) + f

e3sm_diags/plot/cartopy/lat_lon_land_plot.py

@@ -4,5 +4,4 @@
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     return base_plot(reference, test, diff, metrics_dict, parameter)

e3sm_diags/plot/cartopy/lat_lon_plot.py

@@ -65,7 +65,6 @@ def determine_tick_step(degrees_covered):
 def plot_panel(  # noqa: C901
     n, fig, proj, var, clevels, cmap, title, parameters, stats=None
 ):
-
     var = add_cyclic(var)
     lon = var.getLongitude()
     lat = var.getLatitude()
@@ -249,7 +248,6 @@ def plot_panel(  # noqa: C901
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     # Create figure, projection
     fig = plt.figure(figsize=parameter.figsize, dpi=parameter.dpi)
     proj = ccrs.PlateCarree()
@@ -337,7 +335,7 @@ def plot(reference, test, diff, metrics_dict, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/plot/cartopy/lat_lon_river_plot.py

@@ -4,5 +4,4 @@
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     return base_plot(reference, test, diff, metrics_dict, parameter)

e3sm_diags/plot/cartopy/meridional_mean_2d_plot.py

@@ -45,7 +45,6 @@ def get_ax_size(fig, ax):
 
 
 def plot_panel(n, fig, proj, var, clevels, cmap, title, parameters, stats=None):
-
     #    var_min = float(var.min())
     #    var_max = float(var.max())
     #    var_mean = cdutil.averager(var, axis='xy', weights='generate')
@@ -167,7 +166,6 @@ def plot_panel(n, fig, proj, var, clevels, cmap, title, parameters, stats=None):
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     # Create figure, projection
     fig = plt.figure(figsize=parameter.figsize, dpi=parameter.dpi)
     # proj = ccrs.PlateCarree(central_longitude=180)
@@ -255,7 +253,7 @@ def plot(reference, test, diff, metrics_dict, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/plot/cartopy/polar_plot.py

@@ -47,7 +47,6 @@ def get_ax_size(fig, ax):
 
 
 def plot_panel(n, fig, proj, pole, var, clevels, cmap, title, parameters, stats=None):
-
     var = add_cyclic(var)
     lon = var.getLongitude()
     lat = var.getLatitude()
@@ -158,7 +157,6 @@ def plot_panel(n, fig, proj, pole, var, clevels, cmap, title, parameters, stats=
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     # Create figure, projection
     fig = plt.figure(figsize=parameter.figsize, dpi=parameter.dpi)
 
@@ -262,7 +260,7 @@ def plot(reference, test, diff, metrics_dict, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/plot/cartopy/tc_analysis_plot.py

@@ -63,7 +63,6 @@ def get_ax_size(fig, ax):
 
 
 def plot_panel(n, fig, proj, var, var_num_years, region, title):
-
     ax = fig.add_axes(panel[n], projection=proj)
     ax.set_extent(plot_info[region][0], ccrs.PlateCarree())
 

e3sm_diags/plot/cartopy/zonal_mean_2d_plot.py

@@ -46,7 +46,6 @@ def get_ax_size(fig, ax):
 
 
 def plot_panel(n, fig, proj, var, clevels, cmap, title, parameters, stats=None):
-
     #    var_min = float(var.min())
     #    var_max = float(var.max())
     #    var_mean = cdutil.averager(var, axis='xy', weights='generate')
@@ -187,7 +186,6 @@ def plot_panel(n, fig, proj, var, clevels, cmap, title, parameters, stats=None):
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     # Create figure, projection
     fig = plt.figure(figsize=parameter.figsize, dpi=parameter.dpi)
     # proj = ccrs.PlateCarree(central_longitude=180)
@@ -277,7 +275,7 @@ def plot(reference, test, diff, metrics_dict, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/plot/cartopy/zonal_mean_2d_stratosphere_plot.py

@@ -4,5 +4,4 @@
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     return base_plot(reference, test, diff, metrics_dict, parameter)

e3sm_diags/plot/cartopy/zonal_mean_xy_plot.py

@@ -37,7 +37,6 @@ def get_ax_size(fig, ax):
 
 
 def plot(reference, test, diff, metrics_dict, parameter):
-
     # Create figure
     fig = plt.figure(figsize=parameter.figsize, dpi=parameter.dpi)
 
@@ -121,7 +120,7 @@ def plot(reference, test, diff, metrics_dict, parameter):
             subpage = np.array(p).reshape(2, 2)
             subpage[1, :] = subpage[0, :] + subpage[1, :]
             subpage = subpage + np.array(border).reshape(2, 2)
-            subpage = list(((subpage) * page).flatten())
+            subpage = list(((subpage) * page).flatten())  # type: ignore
             extent = matplotlib.transforms.Bbox.from_extents(*subpage)
             # Save subplot
             fname = fnm + ".%i." % (i) + f

e3sm_diags/viewer/lat_lon_viewer.py

@@ -253,7 +253,6 @@ def _create_lat_lon_table_index(
 
 # --- Function to read CMIP6 model metrics  ---
 def read_cmip6_metrics_from_csv(path, variables, seasons):
-
     models = []
 
     with open(path, "r") as fin:
@@ -292,7 +291,6 @@ def read_cmip6_metrics_from_csv(path, variables, seasons):
 
 # --- Function to read E3SM Diags metrics  ---
 def read_e3sm_diags_metrics(path, variables, seasons, names=None):
-
     # List of available models
     models = []
     paths = []
@@ -674,7 +672,6 @@ def _create_csv_from_dict_taylor_diag(
         # Add samples for baseline simulation.
 
         if run_type == "model_vs_obs":
-
             # Read the control run data.
             # Example base line csv file name: JJA_metrics_table_taylor_diag_historical_1985-2014_E3SMv1.csv
             for ibase, base_line_csv_path in enumerate(base_line_csv_paths):

e3sm_diags/viewer/mean_2d_viewer.py

@@ -39,7 +39,6 @@ def create_viewer(root_dir, parameters):
         for var in param.variables:
             for season in param.seasons:
                 for region in param.regions:
-
                     try:
                         viewer.set_group(param.case_id)
                     except RuntimeError: