Dropped support for Python 3.7 and incorporated latest rpy2 changes

.github/workflows/builds.yml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
     env:
-      PY_LATEST: 3.9
+      PY_LATEST: "3.10"
 
     steps:
       - name: Checkout
@@ -100,7 +100,7 @@ jobs:
           name: dist-pkg
 
       - name: Publish GitHub Pages
-        uses: JamesIves/github-pages-deploy-action@v4.3.0
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages
           folder: docs/build/html

.github/workflows/testpypi.yml

@@ -14,7 +14,7 @@ jobs:
     name: Build and publish to TestPyPI
     runs-on: ubuntu-latest
     env:
-      PY_LATEST: 3.9
+      PY_LATEST: "3.10"
 
     steps:
       - uses: actions/checkout@v3

setup.py

@@ -27,7 +27,7 @@ def get_requirements():
 setup(
     name="scikit-diveMove",
     version=__version__,
-    python_requires=">=3.7",
+    python_requires=">=3.8",
     packages=PACKAGES,
     include_package_data=True,
     # Below is redundant but safe

skdiveMove/helpers.py

@@ -161,8 +161,6 @@ def _one_dive_stats(x, interval, has_speed=False):
 
     """
     xx = x.iloc[:, 1:]
-    rstr = "one_dive_stats_fun <- diveMove::oneDiveStats"
-    one_dive_stats_fun = robjs.r(rstr)
     onames_speed = ["begdesc", "enddesc", "begasc", "desctim", "botttim",
                     "asctim", "divetim", "descdist", "bottdist", "ascdist",
                     "bottdep_mean", "bottdep_median", "bottdep_sd",
@@ -173,7 +171,7 @@ def _one_dive_stats(x, interval, has_speed=False):
 
     with cv.localconverter(robjs.default_converter +
                            pandas2ri.converter):
-        res = one_dive_stats_fun(xx, interval, has_speed)
+        res = diveMove.oneDiveStats(xx, interval, has_speed)
 
     if has_speed:
         onames = onames_speed

skdiveMove/imutools/imu.py

@@ -13,7 +13,7 @@
 from .vector import rotate_vector
 
 _TIME_NAME = "timestamp"
-_DEPTH_NAMES = ["depth", ]
+_DEPTH_NAME = "depth"
 _ACCEL_NAME = "acceleration"
 _OMEGA_NAME = "angular_velocity"
 _MAGNT_NAME = "magnetic_density"
@@ -83,7 +83,8 @@ def __init__(self, dataset,
                  angular_velocity_name=_OMEGA_NAME,
                  magnetic_density_name=_MAGNT_NAME,
                  time_name=_TIME_NAME,
-                 has_depth=False, imu_filename=None):
+                 has_depth=False, depth_name=_DEPTH_NAME,
+                 imu_filename=None):
         """Set up attributes for IMU objects
 
         Parameters
@@ -100,8 +101,9 @@ def __init__(self, dataset,
         time_name : str, optional
             Name of the time dimension in the dataset.
         has_depth : bool, optional
-            Whether input data include depth measurements.  Variable must
-            be named "depth".
+            Whether input data include depth measurements.
+        depth_name : str, optional
+            Name of the depth ``DataArray`` in the ``Dataset``.
         imu_filename : str, optional
             Name of the file from which ``dataset`` originated.
 
@@ -111,11 +113,9 @@ def __init__(self, dataset,
         self.imu_var_names = [acceleration_name,
                               angular_velocity_name,
                               magnetic_density_name]
-        depth_var = [x for x in list(self.imu.data_vars.keys())
-                     if has_depth and x in _DEPTH_NAMES]
-        if (len(depth_var) > 0) and has_depth:
+        if has_depth:
             self.has_depth = True
-            self.depth_name = depth_var[0]
+            self.depth_name = depth_name
         else:
             self.has_depth = False
             self.depth_name = None
@@ -129,7 +129,8 @@ def read_netcdf(cls, imu_file,
                     angular_velocity_name=_OMEGA_NAME,
                     magnetic_density_name=_MAGNT_NAME,
                     time_name=_TIME_NAME,
-                    has_depth=False, **kwargs):
+                    has_depth=False, depth_name=_DEPTH_NAME,
+                    **kwargs):
         """Instantiate object by loading Dataset from NetCDF file
 
         Provided all ``DataArray`` in the NetCDF file have the same
@@ -148,8 +149,9 @@ def read_netcdf(cls, imu_file,
         dimension_names : list, optional
             Names of the dimensions of the data in each of the sensors.
         has_depth : bool, optional
-            Whether input data include depth measurements.  Variable must
-            be named "depth".
+            Whether input data include depth measurements.
+        depth_name : str, optional
+            Name of the depth ``DataArray`` in the ``Dataset``.
         **kwargs : optional keyword arguments
             Arguments passed to :func:`xarray.load_dataset`.
 

skdiveMove/imutools/imucalibrate.py

@@ -13,10 +13,10 @@
 import xarray as xr
 from skdiveMove.tdrsource import _load_dataset
 from .imu import (IMUBase,
-                  _ACCEL_NAME, _OMEGA_NAME, _MAGNT_NAME, _DEPTH_NAMES)
+                  _ACCEL_NAME, _OMEGA_NAME, _MAGNT_NAME, _DEPTH_NAME)
 
 _TRIAXIAL_VARS = [_ACCEL_NAME, _OMEGA_NAME, _MAGNT_NAME]
-_MONOAXIAL_VARS = _DEPTH_NAMES + ["light_levels"]
+_MONOAXIAL_VARS = [_DEPTH_NAME, "light_levels"]
 _AXIS_NAMES = list("xyz")
 
 logger = logging.getLogger(__name__)

skdiveMove/tdr.py

@@ -174,8 +174,14 @@ def dive_stats(self, depth_deriv=True):
         idx_name = phases_df.index.name
 
         # calib_speed=False if no fit object
-        tdr = self.get_tdr(calib_depth=True,
-                           calib_speed=bool(self.speed_calib_fit))
+        if self.has_speed:
+            tdr = (self.get_tdr(calib_depth=True,
+                                calib_speed=bool(self.speed_calib_fit))
+                   [[self.depth_name, self.speed_name]])
+        else:
+            tdr = (self.get_tdr(calib_depth=True,
+                                calib_speed=bool(self.speed_calib_fit))
+                   [[self.depth_name]])
 
         intvl = (get_var_sampling_interval(tdr[self.depth_name])
                  .total_seconds())
@@ -191,8 +197,11 @@ def dive_stats(self, depth_deriv=True):
                         .groupby("postdive_id")
                         .apply(lambda x: x.iloc[-1] - x.iloc[0]))
 
+        # Enforce UTC, as otherwise rpy2 uses our locale in the output of
+        # OneDiveStats
         tdrf = (pd.concat((phases_df[["dive_id", "dive_phase"]][ok],
-                           tdr[ok]), axis=1).reset_index())
+                           tdr.loc[ok.index[ok]]), axis=1)
+                .tz_localize("UTC").reset_index())
 
         # Ugly hack to re-order columns for `diveMove` convention
         names0 = ["dive_id", "dive_phase", idx_name, self.depth_name]
@@ -205,7 +214,7 @@ def dive_stats(self, depth_deriv=True):
 
         ones_list = []
         for name, grp in tdrf_grp:
-            res = _one_dive_stats(grp, interval=intvl,
+            res = _one_dive_stats(grp.loc[:, names0], interval=intvl,
                                   has_speed=self.has_speed)
             # Rename to match dive number
             res = res.rename({0: name})