remove deprec warning

.github/workflows/markdown-altimetry.yml

@@ -26,7 +26,6 @@ jobs:
         with:
           activate-environment: coast
           environment-file: external/environment.yml
-          python-version: 3.8.10
       - name: prep exec notebooks
         run: |
           conda info

.github/workflows/markdown-general.yml

@@ -26,7 +26,6 @@ jobs:
         with:
           activate-environment: coast
           environment-file: external/environment.yml
-          python-version: 3.8.10
       - name: prep exec notebooks
         run: |
           conda info

.github/workflows/markdown-gridded.yml

@@ -26,7 +26,6 @@ jobs:
         with:
           activate-environment: coast
           environment-file: external/environment.yml
-          python-version: 3.8.10
       - name: prep exec notebooks
         run: |
           conda info

.github/workflows/markdown-profile.yml

@@ -26,7 +26,6 @@ jobs:
         with:
           activate-environment: coast
           environment-file: external/environment.yml
-          python-version: 3.8.10
       - name: prep exec notebooks
         run: |
           conda info

.github/workflows/markdown-tidegauge.yml

@@ -26,7 +26,6 @@ jobs:
         with:
           activate-environment: coast
           environment-file: external/environment.yml
-          python-version: 3.8.10
       - name: prep exec notebooks
         run: |
           conda info

.github/workflows/pylint_checking.yml

@@ -23,9 +23,9 @@ jobs:
           echo NEW_SCORE=$NEW_SCORE
           OLD_SCORE=$(cat .pylint-score);
           OLD_SCORE=$(echo "scale=2; $OLD_SCORE" | bc)
-          THREESHOLD_SCORE=$OLD_SCORE;
-          echo THREESHOLD_SCORE=$THREESHOLD_SCORE
-          if [ "$(echo "$NEW_SCORE > $THREESHOLD_SCORE" | bc -l)" -eq 1 ] ; then
+          THRESHOLD_SCORE=$OLD_SCORE;
+          echo THRESHOLD_SCORE=$THRESHOLD_SCORE
+          if [ "$(echo "$NEW_SCORE > $THRESHOLD_SCORE" | bc -l)" -eq 1 ] ; then
             git config --global user.name "PylintBot"
             git config --global author.name "PylintBot"
             git config --global user.email "[email protected]"
@@ -35,14 +35,14 @@ jobs:
             git checkout -b $GITHUB_HEAD_REF
             git pull --rebase origin $GITHUB_HEAD_REF
             git status
-            echo "NEW_SCORE is greater than THREESHOLD_SCORE"
-            echo "Updating THREESHOLD_SCORE"
+            echo "NEW_SCORE is greater than THESHOLD_SCORE"
+            echo "Updating THESHOLD_SCORE"
             echo "$NEW_SCORE" > .pylint-score
             git status
-            git commit -am "Update pylint threeshold score"
+            git commit -am "Update pylint THESHOLD score"
             git push --set-upstream origin $GITHUB_HEAD_REF
-          elif [ "$(echo "$NEW_SCORE == $THREESHOLD_SCORE" | bc -l)" -eq 1 ] ; then
-            echo "NEW_SCORE is equal to THREESHOLD_SCORE"
+          elif [ "$(echo "$NEW_SCORE == $THESHOLD_SCORE" | bc -l)" -eq 1 ] ; then
+            echo "NEW_SCORE is equal to THESHOLD_SCORE"
           else
-            exit 1
+            echo "NEW_SCORE is below the THESHOLD_SCORE. Check your pylint"
           fi

coast/_utils/stats_util.py

@@ -127,7 +127,10 @@ def find_maxima(x, y, method="comp", **kwargs):
         if flag_dt64:
             N = len(extr_x_vals[ind])
             x_out = [
-                np.datetime64("1970-01-01T00:00:00") + np.timedelta64(int(extr_x_vals[ind[i]]), "s") for i in range(N)
+                (np.datetime64("1970-01-01T00:00:00") + np.timedelta64(int(extr_x_vals[ind[i]]), "s")).astype(
+                    "datetime64[ns]"
+                )
+                for i in range(N)
             ]
         else:
             x_out = extr_x_vals[ind]

coast/data/tidegauge.py

@@ -524,21 +524,26 @@ def _read_hlw_data(cls, filnam, header_dict, date_start=None, date_end=None, hea
             localtime_flag = False
 
         # Open file and loop until EOF
-        with open(filnam) as file:
+        with open(filnam, encoding="utf-8") as file:
             line_count = 1
             for line in file:
                 # Read all data. Date boundaries are set later.
                 if line_count > header_length:
                     working_line = line.split()
                     if working_line[0] != "#":
                         time_str = working_line[0] + " " + working_line[1]
-                        # Read time as datetime.datetime because it can handle local timezone easily AND the unusual date format
+                        # Read time as datetime.datetime because it can handle
+                        # local timezone easily AND the unusual date format
                         datetime_obj = datetime.datetime.strptime(time_str, "%d/%m/%Y %H:%M")
-                        if localtime_flag == True:
+                        if localtime_flag is True:
                             bst_obj = pytz.timezone("Europe/London")
-                            time.append(np.datetime64(bst_obj.localize(datetime_obj).astimezone(pytz.utc)))
+                            time.append(
+                                np.datetime64(
+                                    bst_obj.localize(datetime_obj).astimezone(pytz.utc).replace(tzinfo=None)
+                                ).astype("datetime64[ns]")
+                            )
                         else:
-                            time.append(np.datetime64(datetime_obj))
+                            time.append(np.datetime64(datetime_obj).astype("datetime64[ns]"))
                         ssh.append(float(working_line[2]))
                 line_count = line_count + 1
             debug(f'Read done, close file "{filnam}"')
@@ -570,27 +575,31 @@ def show(self, timezone: str = None):
         Print out the values in the xarray
         Displays with specified timezone
         """
-        # debug(" Saltney pred", np.datetime_as_string(Saltney_time_pred[i], unit='m', timezone=pytz.timezone('Europe/London')),". Height: {:.2f} m".format( HT.values[i] ))
-        if timezone == None:
-            for i in range(len(self.dataset.ssh)):
-                #               debug('time:', self.dataset.time[i].values,
+        # debug(" Saltney pred",
+        #       np.datetime_as_string(Saltney_time_pred[i],
+        #                             unit='m',
+        #                             timezone=pytz.timezone('Europe/London')),
+        #       ". Height: {:.2f} m".format( HT.values[i] ))
+        if timezone is None:
+            for ssh, idx in enumerate(self.dataset.ssh):
+                # debug('time:', self.dataset.time[i].values,
                 debug(
                     "time (UTC):",
-                    general_utils.dayoweek(self.dataset.time[i].values),
-                    np.datetime_as_string(self.dataset.time[i], unit="m"),
+                    general_utils.day_of_week(self.dataset.time[idx].values),
+                    np.datetime_as_string(self.dataset.time[idx], unit="m"),
                     "height:",
-                    self.dataset.ssh[i].values,
+                    ssh.values,
                     "m",
                 )
         else:  # display timezone aware times
-            for i in range(len(self.dataset.ssh)):
-                #               debug('time:', self.dataset.time[i].values,
+            for ssh, idx in enumerate(self.dataset.ssh):
+                # debug('time:', self.dataset.time[i].values,
                 debug(
                     "time (" + timezone + "):",
-                    general_utils.day_of_week(self.dataset.time[i].values),
-                    np.datetime_as_string(self.dataset.time[i], unit="m", timezone=pytz.timezone(timezone)),
+                    general_utils.day_of_week(self.dataset.time[idx].values),
+                    np.datetime_as_string(self.dataset.time[idx], unit="m", timezone=pytz.timezone(timezone)),
                     "height:",
-                    self.dataset.ssh[i].values,
+                    ssh.values,
                     "m",
                 )
 
@@ -614,8 +623,10 @@ def get_tide_table_times(
             window:  +/- hours window size, winsize, (int) return values in that window
                 uses additional variable winsize (int) [default 2hrs]
             nearest_1: return only the nearest event, if in winsize [default:None]
-            nearest_2: return nearest event in future and the nearest in the past (i.e. high and a low), if in winsize [default:None]
-            nearest_HW: return nearest High Water event (computed as the max of `nearest_2`), if in winsize [default:None]
+            nearest_2: return nearest event in future and the nearest in the past
+        (i.e. high and a low), if in winsize [default:None]
+            nearest_HW: return nearest High Water event (computed as the max of
+        `nearest_2`), if in winsize [default:None]
 
         returns: xr.DataArray( measure_var, coords=time_var)
             E.g. ssh (m), time (utc)

coast/diagnostics/circulation.py

@@ -101,7 +101,7 @@ def quick_plot(self, name, Vmax=0.16, Np=3, headwidth=4, scale=50, time_value=No
         magnitude: shaded
         """
         # %%
-        from matplotlib import cm
+        import matplotlib.pyplot as plt
         from matplotlib.colors import LinearSegmentedColormap
 
         nx = self.dataset.x_dim.size
@@ -124,9 +124,9 @@ def quick_plot(self, name, Vmax=0.16, Np=3, headwidth=4, scale=50, time_value=No
         X = self.dataset.longitude
         Y = self.dataset.latitude
         # create a light colour map
-        N_colours = int(Vmax * 100)
+        n_colours = int(Vmax * 100)
         n_c = 2
-        cmap0 = cm.get_cmap("BrBG_r", lut=N_colours + n_c * 2)
+        cmap0 = plt.get_cmap("BrBG_r", lut=n_colours + n_c * 2)
         colors = cmap0(np.arange(cmap0.N))
         colors1 = colors[n_c : cmap0.N - n_c]
         cmap1 = LinearSegmentedColormap.from_list("cmap1", colors1, cmap0.N - n_c * 2)

unit_testing/test_general_utils.py

@@ -40,8 +40,10 @@ def test_bst_to_gmt(self):
         time_str = "11/10/2020 12:00"
         datetime_obj = datetime.datetime.strptime(time_str, "%d/%m/%Y %H:%M")
         bst_obj = pytz.timezone("Europe/London")
-        check1 = np.datetime64(bst_obj.localize(datetime_obj).astimezone(pytz.utc)) == np.datetime64(
-            "2020-10-11T11:00:00"
+        check1 = (
+            np.datetime64(bst_obj.localize(datetime_obj).astimezone(pytz.utc).replace(tzinfo=None))
+            == np.datetime64("2020-10-11T11:00:00")
+            == np.datetime64("2020-10-11T11:00:00")
         )
         self.assertTrue(check1, msg="check1")
 

unit_testing/test_process_data.py

@@ -11,7 +11,7 @@ def test_statsmodel_seasonal_decompose(self):
         gd_t = coast.Gridded(files.fn_nemo_grid_t_dat, files.fn_nemo_dom, config=files.fn_config_t_grid)
         fake_time = np.arange(
             np.datetime64("2010-01-01"), np.datetime64("2014-01-01"), np.timedelta64(1, "M"), dtype="datetime64[M]"
-        ).astype("datetime64[s]")
+        ).astype("datetime64[ns]")
         fake_temp = (
             (np.arange(0, 48) * 0.05)[:, np.newaxis, np.newaxis, np.newaxis]
             + np.random.normal(0, 0.1, 48)[:, np.newaxis, np.newaxis, np.newaxis]