add docstring

change time bins for __repr__
transfer sign_type when we use index()

Author: AntSimi

requirements.txt

@@ -9,5 +9,5 @@ pyyaml
 requests
 scipy
 zarr
-# for binder
+# for binder an documentation
 pyeddytrackersample

src/py_eddy_tracker/dataset/grid.py

@@ -1317,6 +1317,15 @@ def _low_filter(self, grid_name, w_cut, **kwargs):
     def convolve_filter_with_dynamic_kernel(
         self, grid, kernel_func, lat_max=85, extend=False, **kwargs_func
     ):
+        """
+        :param str grid: grid name
+        :param func kernel_func: function of kernel to use
+        :param float lat_max: absolute latitude above no filtering apply
+        :param bool extend: if False, only non masked value will return a filtered value
+        :param dict kwargs_func: look at kernel_func
+        :return: filtered value
+        :rtype: array
+        """
         if (abs(self.y_c) > lat_max).any():
             logger.warning("No filtering above %f degrees of latitude", lat_max)
         if isinstance(grid, str):
@@ -1409,7 +1418,7 @@ def lanczos_high_filter(
             lat_max=lat_max,
             wave_length=wave_length,
             order=order,
-            **kwargs
+            **kwargs,
         )
         self.vars[grid_name] -= data_out
 
@@ -1421,7 +1430,7 @@ def lanczos_low_filter(self, grid_name, wave_length, order=1, lat_max=85, **kwar
             lat_max=lat_max,
             wave_length=wave_length,
             order=order,
-            **kwargs
+            **kwargs,
         )
         self.vars[grid_name] = data_out
 
@@ -1436,6 +1445,15 @@ def bessel_band_filter(self, grid_name, wave_length_inf, wave_length_sup, **kwar
         self.vars[grid_name] -= data_out
 
     def bessel_high_filter(self, grid_name, wave_length, order=1, lat_max=85, **kwargs):
+        """
+        :param str grid_name: grid to filter, data will replace original one
+        :param float wave_length: in km
+        :param int order: order to use, if > 1 negativ value will be present in kernel
+        :param float lat_max: absolute latitude above no filtering apply
+        :param dict kwargs: look at :py:meth:`RegularGridDataset.convolve_filter_with_dynamic_kernel`
+
+        .. minigallery:: py_eddy_tracker.RegularGridDataset.bessel_high_filter
+        """
         logger.debug(
             "Run filtering with wave of %(wave_length)s km and order of %(order)s ...",
             dict(wave_length=wave_length, order=order),
@@ -1446,7 +1464,7 @@ def bessel_high_filter(self, grid_name, wave_length, order=1, lat_max=85, **kwar
             lat_max=lat_max,
             wave_length=wave_length,
             order=order,
-            **kwargs
+            **kwargs,
         )
         logger.debug("Filtering done")
         self.vars[grid_name] -= data_out
@@ -1458,7 +1476,7 @@ def bessel_low_filter(self, grid_name, wave_length, order=1, lat_max=85, **kwarg
             lat_max=lat_max,
             wave_length=wave_length,
             order=order,
-            **kwargs
+            **kwargs,
         )
         self.vars[grid_name] = data_out
 
@@ -1688,7 +1706,14 @@ def add_uv_lagerloef(self, grid_height, uname="u", vname="v", schema=15):
 
     def add_uv(self, grid_height, uname="u", vname="v", stencil_halfwidth=4):
         """Compute a u and v grid
-               """
+
+        :param str grid_height: grid name where funtion will apply stencil method
+        :param str uname: future name of u
+        :param str vname: future name of v
+        :param int stencil_halfwidth: largest stencil could be apply
+
+        .. minigallery:: py_eddy_tracker.RegularGridDataset.add_uv
+        """
         logger.info("Add u/v variable with stencil method")
         data = self.grid(grid_height)
         h_dict = self.variables_description[grid_height]

src/py_eddy_tracker/observations/observation.py

@@ -492,6 +492,7 @@ def index(self, index, reverse=False):
             size = len(index)
         eddies = self.new_like(self, size)
         eddies.obs[:] = self.obs[index]
+        eddies.sign_type = self.sign_type
         return eddies
 
     @staticmethod
@@ -817,6 +818,14 @@ def intern(flag, public_label=False):
 
     def match(self, other, intern=False, cmin=0):
         """return index and score compute with area
+
+        :param EddiesObservations other: Observations to compare
+        :param bool intern: if True, speed contour will be used
+        :param float cmin: 0 < cmin < 1, return only couple above cmin
+        :return: return index of couple in self and other and cost value
+        :rtype: (array(int), array(int), array(float))
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.match
         """
         x_name, y_name = self.intern(intern)
         i, j = bbox_intersection(
@@ -1345,6 +1354,15 @@ def set_global_attr_netcdf(self, h_nc):
             h_nc.setncattr(key, item)
 
     def scatter(self, ax, name, ref=None, factor=1, **kwargs):
+        """
+        :param matplotlib.axes.Axes ax: matplotlib axes use to draw
+        :param str name: var which will be use to fill contour
+        :param float,None ref: if define use like west bound
+        :param dict kwargs: look at :py:meth:`matplotlib.axes.Axes.scatter`
+        :return: scatter mappable
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.scatter
+        """
         x = self.longitude
         if ref is not None:
             x = (x - ref) % 360 + ref
@@ -1478,6 +1496,16 @@ def grid_count(self, bins, intern=False, center=False):
         return regular_grid
 
     def grid_stat(self, bins, varname):
+        """
+        Compute mean of eddies in each bin
+
+        :param (numpy.array,numpy.array) bins: bins to compute count
+        :param str varname: name of variable to compute mean
+        :return: return grid of mean
+        :rtype: py_eddy_tracker.dataset.grid.RegularGridDataset
+
+        .. minigallery:: py_eddy_tracker.EddiesObservations.grid_stat
+        """
         x_bins, y_bins = arange(*bins[0]), arange(*bins[1])
         x0 = bins[0][0]
         x, y = (self.longitude - x0) % 360 + x0, self.latitude

src/py_eddy_tracker/observations/tracking.py

@@ -104,7 +104,7 @@ def __repr__(self):
         nb_obs = self.observations.shape[0]
         m = self["virtual"].astype("bool")
         nb_m = m.sum()
-        bins_t = (1, 20, 50, 100, 200, 1000, 10000)
+        bins_t = (1, 30, 90, 180, 270, 365, 1000, 10000)
         nb_tracks_by_t = histogram(nb, bins=bins_t)[0]
         nb_obs_by_t = histogram(nb, bins=bins_t, weights=nb)[0]
         pct_tracks_by_t = nb_tracks_by_t / nb_tracks_by_t.sum() * 100.0
@@ -156,6 +156,10 @@ def distance_to_next(self):
 
     def filled_by_interpolation(self, mask):
         """Filled selected values by interpolation
+
+        :param array(bool) mask: True if must be filled by interpolation
+
+        .. minigallery:: py_eddy_tracker.TrackEddiesObservations.filled_by_interpolation
         """
         nb_filled = mask.sum()
         logger.info("%d obs will be filled (unobserved)", nb_filled)