Updated for new Pandas warnings

skdiveMove/__init__.py

@@ -88,5 +88,5 @@
 
 __author__ = "Sebastian Luque <[email protected]>"
 __license__ = "AGPLv3"
-__version__ = "0.3.2.post2"
+__version__ = "0.3.3"
 __all__ = ["TDR", "calibrate", "dump_config_template"]

skdiveMove/helpers.py

@@ -177,10 +177,9 @@ def _one_dive_stats(x, interval, has_speed=False):
         onames = onames_nospeed
 
     res_df = pd.DataFrame(res, columns=onames)
-    for tcol in range(3):
+    for tcol in onames[:3]:
         # This is per POSIXct convention in R
-        res_df.iloc[:, tcol] = pd.to_datetime(res_df.iloc[:, tcol],
-                                              unit="s")
+        res_df[tcol] = pd.to_datetime(res_df[tcol], unit="s")
 
     return res_df
 
@@ -252,7 +251,7 @@ def rle_key(x):
     2020-01-01 00:02:30+00:00    6
     2020-01-01 00:02:40+00:00    6
     2020-01-01 00:02:50+00:00    6
-    Freq: 10S, dtype: int64
+    Freq: 10s, dtype: int64
 
     """
     xout = x.ne(x.shift()).cumsum()

skdiveMove/imutools/imu2body.py

@@ -411,14 +411,14 @@ class IMU2Body(IMUBase):
     ...                                     savgol_parms=(99, 2))
     >>> print(imu)  # doctest: +ELLIPSIS
     IMU -- Class IMU2Body object
-    Source File          ...
-    IMU: <xarray.Dataset>
+    Source File           ...
+    IMU: <xarray.Dataset> ...
     Dimensions:           ...
     Coordinates:
       * timestamp         (timestamp) datetime64[ns] ...
-      * accelerometer     (accelerometer) object 'x' 'y' 'z'
-      * magnetometer      (magnetometer) object 'x' 'y' 'z'
-      * gyroscope         (gyroscope) object 'x' 'y' 'z'
+      * accelerometer     (accelerometer) <U1 12B 'x' 'y' 'z'
+      * magnetometer      (magnetometer) <U1 12B 'x' 'y' 'z'
+      * gyroscope         (gyroscope) <U1 12B 'x' 'y' 'z'
     Data variables:
         depth             (timestamp) float64 ...
         acceleration      (timestamp, accelerometer) float64 ...

skdiveMove/imutools/imucalibrate.py

@@ -91,10 +91,10 @@ class IMUcalibrate(IMUBase):
     >>> print(imucal)  # doctest: +ELLIPSIS
     IMU -- Class IMUcalibrate object
     Source File          None
-    IMU: <xarray.Dataset>
+    IMU: <xarray.Dataset> ...
     Dimensions:           (timestamp_utc: 268081, axis: 3)
     Coordinates:
-      * axis              (axis) object 'x' 'y' 'z'
+      * axis              (axis) <U1 12B 'x' 'y' 'z'
       * timestamp_utc     (timestamp_utc) datetime64[ns] ...
     Data variables:
         acceleration      (timestamp_utc, axis) float64 ...

skdiveMove/tdr.py

@@ -253,7 +253,8 @@ def dive_stats(self, depth_deriv=True):
 
         postdive_dur = (postdive_ids.reset_index()
                         .groupby("postdive_id")
-                        .apply(lambda x: x.iloc[-1] - x.iloc[0]))
+                        .apply(lambda x: x.iloc[-1] - x.iloc[0],
+                               include_groups=False))
 
         # Enforce UTC, as otherwise rpy2 uses our locale in the output of
         # OneDiveStats
@@ -783,7 +784,7 @@ def extract_dives(self, diveNo, **kwargs):
         >>> tdrX.detect_dive_phases("unimodal", descent_crit_q=0.01,
         ...                         ascent_crit_q=0, knot_factor=20)
         >>> tdrX.extract_dives(diveNo=20)  # doctest: +ELLIPSIS
-        <xarray.Dataset>
+        <xarray.Dataset> ...
         Dimensions: ...
 
         """

skdiveMove/tdrphases.py

@@ -442,7 +442,8 @@ def detect_dive_phases(self, dive_model, smooth_par=0.1,
                 spl_list.append(spl_dict)
                 # Spline derivatives
                 spl_der = res.pop("spline_deriv")
-                spl_der_idx = pd.TimedeltaIndex(spl_der[:, 0], unit="s")
+                spl_der_idx = pd.TimedeltaIndex(
+                    pd.to_timedelta(spl_der[:, 0], unit="s"))
                 spl_der = pd.DataFrame({'y': spl_der[:, 1]},
                                        index=spl_der_idx)
                 spl_der_list.append(spl_der)
@@ -568,10 +569,12 @@ def _get_dive_spline_slot(self, diveNo, name):
                    "g", "a", "b", "variter"]
         idata = self.get_dives_details("splines")[diveNo]
         if name == "data":
-            x = pd.TimedeltaIndex(np.array(idata[name][0]), unit="s")
+            x = pd.TimedeltaIndex(
+                pd.to_timedelta(np.array(idata[name][0]), unit="s"))
             odata = pd.Series(np.array(idata[name][1]), index=x)
         elif name == "xy":
-            x = pd.TimedeltaIndex(np.array(idata["x"]), unit="s")
+            x = pd.TimedeltaIndex(
+                pd.to_timedelta(np.array(idata["x"]), unit="s"))
             odata = pd.Series(np.array(idata["y"]), index=x)
         elif name in scalars:
             odata = float(idata[name][0])

skdiveMove/tests/test_BoutsMLE.py

@@ -197,12 +197,12 @@ def test_plot_fit(self):
         _ = xbouts.plot_fit(fit2, ax=ax)
         lines = ax.get_lines()
         self.assertEqual(len(lines), 2)
-        plt.close()
+        plt.close("all")
         # Without Axes
         _ = xbouts.plot_fit(fit2)
         lines = ax.get_lines()
         self.assertEqual(len(lines), 2)
-        plt.close()
+        plt.close("all")
 
         # Three process
         # -------------
@@ -219,7 +219,7 @@ def test_plot_fit(self):
         _ = xbouts.plot_fit(fit2, ax=ax)
         lines = ax.get_lines()
         self.assertEqual(len(lines), 2)
-        plt.close()
+        plt.close("all")
 
     def test_plot_ecdf(self):
         # Two process
@@ -237,12 +237,12 @@ def test_plot_ecdf(self):
         _ = xbouts.plot_ecdf(fit2, ax=ax)
         lines = ax.get_lines()
         self.assertEqual(len(lines), 2)
-        plt.close()
+        plt.close("all")
         # Without Axes
         _ = xbouts.plot_ecdf(fit2)
         lines = ax.get_lines()
         self.assertEqual(len(lines), 2)
-        plt.close()
+        plt.close("all")
 
         # Three process
         # -------------
@@ -259,7 +259,7 @@ def test_plot_ecdf(self):
         _ = xbouts.plot_ecdf(fit2, ax=ax)
         lines = ax.get_lines()
         self.assertEqual(len(lines), 2)
-        plt.close()
+        plt.close("all")
 
     def test_compare2r(self):
         # Two process