DEP: remove/fix deprecated objects/command (columncolab#124)

* DEP: remove/fix deprecated objects/command

emc2/core/model.py

@@ -252,7 +252,7 @@ def num_subcolumns(self):
         Gets the number of subcolumns in the model. Will
         return 0 if the number of subcolumns has not yet been set.
         """
-        if 'subcolumn' in self.ds.dims.keys():
+        if 'subcolumn' in self.ds.dims:
             return self.ds.dims['subcolumn']
         else:
             return 0
@@ -378,15 +378,15 @@ def check_and_stack_time_lat_lon(self, out_coord_name="time_lat_lon", file_path=
         do_process = 0  # 0 - do nothing, 1 - stack lat+lon, 2 - stack lat dim only
 
         # Add time dimension for processing (remove later if length = 1)
-        if not self.time_dim in [x for x in self.ds.dims.keys()]:
+        if not self.time_dim in [x for x in self.ds.dims]:
             self.ds = self.ds.expand_dims(self.time_dim)
 
         # Check to make sure we are loading a single column
-        if self.lat_dim in [x for x in self.ds.dims.keys()]:
-            if self.ds.dims[self.lat_dim] != 1:
+        if self.lat_dim in [x for x in self.ds.dims]:
+            if self.ds.sizes[self.lat_dim] != 1:
                 do_process = 1
-            if self.lon_dim in [x for x in self.ds.dims.keys()]:
-                if self.ds.dims[self.lon_dim] != 1:
+            if self.lon_dim in [x for x in self.ds.dims]:
+                if self.ds.sizes[self.lon_dim] != 1:
                     do_process = 1
             elif do_process == 1:
                 do_process = 2
@@ -411,7 +411,7 @@ def check_and_stack_time_lat_lon(self, out_coord_name="time_lat_lon", file_path=
                     self.ds = self.ds.stack({out_coord_name: (self.lat_dim, self.time_dim)})
                 self.stacked_time_dim, self.time_dim = self.time_dim, out_coord_name
             else:
-                if self.lon_dim in [x for x in self.ds.dims.keys()]:
+                if self.lon_dim in [x for x in self.ds.dims]:
                     # No need for lat and lon dimensions
                     self.ds = self.ds.squeeze(dim=(self.lat_dim, self.lon_dim))
                 else:

emc2/io/load_mie_file.py

@@ -18,7 +18,7 @@ def load_mie_file(filename):
         descriptive metadata.
     """
 
-    my_df = pd.read_csv(filename, delim_whitespace=True,
+    my_df = pd.read_csv(filename, sep='\s+',
                         names=["wavelength", "p_diam", "size_parameter", "compre_real",
                                "compre_im", "scat_p", "alpha_p", "beta_p", "scat_eff",
                                "ext_eff", "backscat_eff"])

tests/test_plotting.py

@@ -12,7 +12,7 @@ def test_plot_timeseries():
     model_display.plot_subcolumn_timeseries('sub_col_Ze_cl_strat', 2, subplot_index=(1, 0))
     model_display.plot_subcolumn_timeseries('sub_col_Ze_cl_strat', 3, subplot_index=(0, 1))
     model_display.plot_subcolumn_timeseries('sub_col_Ze_cl_strat', 4, subplot_index=(1, 1))
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -21,7 +21,7 @@ def test_plot_single_time():
 
     model_display = emc2.plotting.SubcolumnDisplay(model, ds_name="ModelE", figsize=(10, 10))
     model_display.plot_single_profile('sub_col_Ze_cl_strat', time='2016-08-16T09:30:00')
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -30,7 +30,7 @@ def test_plot_profile():
 
     model_display = emc2.plotting.SubcolumnDisplay(model, ds_name="ModelE", figsize=(10, 10))
     model_display.plot_subcolumn_mean_profile('sub_col_Ze_cl_strat', time='2016-08-16T09:30:00')
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -44,7 +44,7 @@ def test_plot_instrument():
                                              subplot_index=(0, 0), vmin=0.0, vmax=0.5)
     model_display.plot_instrument_timeseries(HSRL, "beta_a_backscat", log_plot=True, cmap='magma',
                                              subplot_index=(0, 1), vmin=1e-8, vmax=1e-3)
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -55,7 +55,7 @@ def test_plot_instrument_profile():
 
     model_display = emc2.plotting.SubcolumnDisplay(model, ds_name="ModelE", figsize=(10, 10))
     model_display.plot_instrument_mean_profile(HSRL, 'linear_depol', pressure_coords=False)
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -66,7 +66,7 @@ def test_plot_classification():
     _, cb = model_display.plot_subcolumn_timeseries('phase_mask_KAZR_sounding_all_hyd', 1)
     model_display.change_plot_to_class_mask(cb, variable="phase_mask_KAZR_sounding_all_hyd",
                                             class_legend=["Cloud", "precip", "mixed"])
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -104,7 +104,7 @@ def test_plot_SR_subcol_timeseries():
         Ncolumns, Npoints, Nlevels, Nglevels, col_num, newgrid_bot, newgrid_top)
     emc2.statistics_LLNL.statistical_plots.plot_every_subcolumn_timeseries_SR(
         my_e3sm, atb_total_4D, atb_mol_4D, col_index, '', '', 'addpl_rad')
-    return plt.gcf()
+    assert plt.gcf()
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -164,7 +164,7 @@ def test_plot_get_CFAD_SR():
     cfadSR_cal_alltime = np.nanmean(cfadSR_cal_alltime_col, axis=2)
     emc2.statistics_LLNL.statistical_plots.plot_lidar_SR_CFAD(
         SR_EDGES, newgrid_mid, cfadSR_cal_alltime, '', '', 'addpl_rad')
-    return plt.gcf()
+    assert plt.gcf()
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -224,7 +224,7 @@ def test_plot_regridded_CF_timeseries():
             CF_3D, newgrid_mid, col_index, y_range=y_range,
             cmap=cmap, title='',
             vmin=vmin_max[ii][0], vmax=vmin_max[ii][1], cbar_label=cbar_label[ii])
-    return model_display3.fig
+    assert model_display3.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -262,7 +262,7 @@ def test_plot_subcolumn_timeseries():
             field_to_plot[ii], subcol_ind, log_plot=log_plot[ii], y_range=y_range,
             subplot_index=(0, ii),  cmap=cmap, title='',
             vmin=vmin_max[ii][0], vmax=vmin_max[ii][1], pressure_coords=False)
-    return model_display.fig
+    assert model_display.fig
 
 
 @pytest.mark.mpl_image_compare(tolerance=30)
@@ -280,4 +280,4 @@ def test_plotting_every_subcolumn_timeseries_radarlidarsignal():
         unstack_dims=True, finalize_fields=True, use_rad_logic=True)
     emc2.statistics_LLNL.statistical_plots.plot_every_subcolumn_timeseries_radarlidarsignal(
         my_e3sm, col_index, '', '', 'addpl_radiation')
-    return plt.gcf()
+    assert plt.gcf()