Merge pull request #3310 from cphyc/pydoctest

yt/frontends/ramses/field_handlers.py

@@ -105,7 +105,7 @@ def any_exist(cls, ds):
 
         Arguments
         ---------
-        * ds: a Ramses Dataset
+        ds : a Ramses Dataset
 
         Note
         ----

yt/frontends/ramses/hilbert.py

@@ -6,9 +6,9 @@ def hilbert3d(X, bit_length):
 
     Arguments
     ---------
-    * X: (N, ndim) float array
+    X : (N, ndim) float array
       The positions
-    * bit_length: integer
+    bit_length : integer
       The bit_length for the indexing.
     """
     X = np.atleast_2d(X)
@@ -266,9 +266,9 @@ def get_cpu_list(ds, X):
 
     Parameters
     ----------
-    * ds: Dataset
+    ds : Dataset
       The dataset containing the information
-    * X: (N, ndim) float array
+    X : (N, ndim) float array
       An array containing positions. They should be between 0 and 1.
     """
     X = np.atleast_2d(X)

yt/funcs.py

@@ -39,7 +39,10 @@
 def is_sequence(obj):
     """
     Grabbed from Python Cookbook / matplotlib.cbook.  Returns true/false for
-    *obj* iterable.
+
+    Parameters
+    ----------
+    obj : iterable
     """
     try:
         len(obj)
@@ -56,7 +59,7 @@ def iter_fields(field_or_fields):
 
     Parameters
     ----------
-    obj: str, tuple(str, str), or any iterable of the previous types.
+    field_or_fields: str, tuple(str, str), or any iterable of the previous types.
 
     Examples
     --------
@@ -1277,7 +1280,8 @@ def levenshtein_distance(seq1, seq2, max_dist=None):
 
     Parameters
     ----------
-    seq1, seq2 : str
+    seq1 : str
+    seq2 : str
         The strings to compute the distance between
     max_dist : integer
         If not None, maximum distance returned (see notes).

yt/loaders.py

@@ -1125,6 +1125,8 @@ def load_unstructured_mesh(
         Size of computational domain in units of the length unit.
     sim_time : float, optional
         The simulation time in seconds
+    length_unit : string
+        Unit to use for length.  Defaults to unitless.
     mass_unit : string
         Unit to use for masses.  Defaults to unitless.
     time_unit : string

yt/utilities/lib/octree_raytracing.py

@@ -94,7 +94,8 @@ def cast_rays(self, vp_pos, vp_dir):
 
         Parameters
         ----------
-        vp_pos, vp_dir : float arrays (Nrays, Ndim)
+        vp_pos : float arrays (Nrays, Ndim)
+        vp_dir : float arrays (Nrays, Ndim)
             The position (unitary) and direction of each ray
 
         Returns

yt/utilities/parallel_tools/parallel_analysis_interface.py

@@ -570,12 +570,6 @@ def parallel_ring(objects, generator_func, mutable=False):
     mutable : bool
         Should the arrays be considered mutable?  Currently, this will only
         work if the number of processors equals the number of objects.
-    dynamic : bool
-        This governs whether or not dynamic load balancing will be enabled.
-        This requires one dedicated processor; if this is enabled with a set of
-        128 processors available, only 127 will be available to iterate over
-        objects as one will be load balancing the rest.
-
 
     Examples
     --------

yt/visualization/color_maps.py

@@ -312,7 +312,7 @@ def make_colormap(ctuple_list, name=None, interpolate=True):
         If you wish this colormap to be added as a valid colormap to the
         current session, specify a name here.  Default: None
 
-    interpolation: boolean, optional
+    interpolate: boolean
         Designates whether or not the colormap will interpolate between
         the colors provided or just give solid colors across the intervals.
         Default: True

yt/visualization/fits_image.py

@@ -616,7 +616,7 @@ def writeto(self, fileobj, fields=None, overwrite=False, **kwargs):
         fields : list of strings, optional
             The fields to write to the file. If not specified
             all of the fields in the buffer will be written.
-        clobber : overwrite, optional
+        overwrite : boolean
             Whether or not to overwrite a previously existing file.
             Default: False
         **kwargs

yt/visualization/fixed_resolution.py

@@ -1,5 +1,5 @@
-import types
 import weakref
+from functools import wraps
 
 import numpy as np
 
@@ -505,10 +505,31 @@ def setup_filters(self):
             if key in ignored:
                 continue
             filtername = filter_registry[key]._filter_name
-            FilterMaker = filter_registry[key]
-            filt = apply_filter(FilterMaker)
-            filt.__doc__ = FilterMaker.__doc__
-            self.__dict__["apply_" + filtername] = types.MethodType(filt, self)
+
+            # We need to wrap to create a closure so that
+            # FilterMaker is bound to the wrapped method.
+            def closure():
+                FilterMaker = filter_registry[key]
+
+                @wraps(FilterMaker)
+                def method(*args, **kwargs):
+                    # We need to also do it here as "invalidate_plot"
+                    # and "apply_callback" require the functions'
+                    # __name__ in order to work properly
+                    @wraps(FilterMaker)
+                    def cb(self, *a, **kwa):
+                        # We construct the callback method
+                        # skipping self
+                        return FilterMaker(*a, **kwa)
+
+                    # Create callback
+                    cb = apply_filter(cb)
+
+                    return cb(self, *args, **kwargs)
+
+                return method
+
+            self.__dict__["apply_" + filtername] = closure()
 
 
 class CylindricalFixedResolutionBuffer(FixedResolutionBuffer):

yt/visualization/line_plot.py

@@ -161,8 +161,8 @@ def __init__(
         start_point,
         end_point,
         npoints,
-        figure_size=5.0,
-        fontsize=14.0,
+        figure_size=5,
+        fontsize=14,
         field_labels=None,
     ):
         """
@@ -175,7 +175,7 @@ def __init__(
 
     @classmethod
     def _initialize_instance(
-        cls, obj, ds, fields, figure_size=5.0, fontsize=14.0, field_labels=None
+        cls, obj, ds, fields, figure_size=5, fontsize=14, field_labels=None
     ):
         obj._x_unit = None
         obj._y_units = {}
@@ -204,7 +204,7 @@ def _initialize_instance(
 
     @classmethod
     def from_lines(
-        cls, ds, fields, lines, figure_size=5.0, font_size=14.0, field_labels=None
+        cls, ds, fields, lines, figure_size=5, font_size=14, field_labels=None
     ):
         """
         A class method for constructing a line plot from multiple sampling lines
@@ -222,7 +222,7 @@ def from_lines(
         figure_size : int or two-element iterable of ints
             Size in inches of the image.
             Default: 5 (5x5)
-        fontsize : int
+        font_size : int
             Font size for all text in the plot.
             Default: 14
         field_labels : dictionary

yt/visualization/plot_window.py

@@ -1,6 +1,6 @@
-import types
 from collections import defaultdict
 from distutils.version import LooseVersion
+from functools import wraps
 from numbers import Number
 
 import matplotlib
@@ -1262,10 +1262,31 @@ def setup_callbacks(self):
             if key in ignored:
                 continue
             cbname = callback_registry[key]._type_name
-            CallbackMaker = callback_registry[key]
-            callback = invalidate_plot(apply_callback(CallbackMaker))
-            callback.__doc__ = CallbackMaker.__doc__
-            self.__dict__["annotate_" + cbname] = types.MethodType(callback, self)
+
+            # We need to wrap to create a closure so that
+            # CallbackMaker is bound to the wrapped method.
+            def closure():
+                CallbackMaker = callback_registry[key]
+
+                @wraps(CallbackMaker)
+                def method(*args, **kwargs):
+                    # We need to also do it here as "invalidate_plot"
+                    # and "apply_callback" require the functions'
+                    # __name__ in order to work properly
+                    @wraps(CallbackMaker)
+                    def cb(self, *a, **kwa):
+                        # We construct the callback method
+                        # skipping self
+                        return CallbackMaker(*a, **kwa)
+
+                    # Create callback
+                    cb = invalidate_plot(apply_callback(cb))
+
+                    return cb(self, *args, **kwargs)
+
+                return method
+
+            self.__dict__["annotate_" + cbname] = closure()
 
     def annotate_clear(self, index=None):
         """

yt/visualization/profile_plotter.py

@@ -594,7 +594,7 @@ def set_unit(self, field, unit):
         field : string
            The name of the field that is to be changed.
 
-        new_unit : string or Unit object
+        unit : string or Unit object
            The name of the new unit.
         """
         fd = self.profiles[0].data_source._determine_fields(field)[0]
@@ -809,8 +809,8 @@ def annotate_text(self, xpos=0.0, ypos=0.0, text=None, field="all", **text_kwarg
           The text to insert onto the plot.
         field : str or tuple
           The name of the field to add text to.
-        text_kwargs : dict
-          Dictionary of text keyword arguments to be passed to matplotlib
+        **text_kwargs : dict
+          Extra keyword arguments will be passed to matplotlib text instance
 
         >>> import yt
         >>> from yt.units import kpc
@@ -1250,16 +1250,14 @@ def annotate_text(self, xpos=0.0, ypos=0.0, text=None, **text_kwargs):
 
         Parameters
         ----------
-        field : str or tuple
-          The name of the field to add text to.
         xpos : float
           Position on plot in x-coordinates.
         ypos : float
           Position on plot in y-coordinates.
         text : str
           The text to insert onto the plot.
-        text_kwargs : dict
-          Dictionary of text keyword arguments to be passed to matplotlib
+        **text_kwargs : dict
+          Extra keyword arguments will be passed to matplotlib text instance
 
         >>> plot.annotate_text(1e-15, 5e4, "Hello YT")
 
@@ -1495,7 +1493,7 @@ def set_unit(self, field, unit):
         field : string
            The name of the field that is to be changed.
 
-        new_unit : string or Unit object
+        unit : string or Unit object
            The name of the new unit.
         """
         fd = self.data_source._determine_fields(field)[0]

yt/visualization/streamlines.py

@@ -29,7 +29,7 @@ class Streamlines(ParallelAnalysisInterface):
     ----------
     ds : ~yt.data_objects.static_output.Dataset
         This is the dataset to streamline
-    pos : array_like
+    positions : array_like
         An array of initial starting positions of the streamlines.
     xfield : str or tuple of str, optional
         The x component of the vector field to be streamlined.

yt/visualization/volume_rendering/camera.py

@@ -384,13 +384,13 @@ def set_position(self, position, north_vector=None):
         Parameters
         ----------
 
-        width : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
+        position : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
             If a scalar, assumes that the position is the same in all three
             coordinates. If an iterable, must contain only scalars or
             (length, unit) tuples.
 
         north_vector : array_like, optional
-            The 'up' direction for the plane of rays.  If not specific,
+            The 'up' direction for the plane of rays. If not specific,
             calculated automatically.
 
         """
@@ -408,7 +408,7 @@ def set_focus(self, new_focus):
         Parameters
         ----------
 
-        focus : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
+        new_focus : number, YTQuantity, :obj:`!iterable`, or 3 element YTArray
             If a scalar, assumes that the focus is the same is all three
             coordinates. If an iterable, must contain only scalars or
             (length, unit) tuples.

yt/visualization/volume_rendering/camera_path.py

@@ -218,11 +218,8 @@ def prob(self, prev, next, temperature):
             return np.exp(-abs(next - prev) / temperature)
 
     def get_shortest_path(self):
-        r"""Determine shortest path between all keyframes.
-
-        Parameters
-        ----------
-        None.
+        """
+        Determine shortest path between all keyframes.
         """
         # this obviously doesn't work. When someone fixes it, remove the NOQA
         self.setup_tsp(niter, init_temp, alpha, fixed_start)  # NOQA

yt/visualization/volume_rendering/old_camera.py

@@ -96,9 +96,6 @@ class Camera(ParallelAnalysisInterface):
     ds : ~yt.data_objects.static_output.Dataset
         For now, this is a require parameter!  But in the future it will become
         optional.  This is the dataset to volume render.
-    use_kd: bool, optional
-        Specifies whether or not to use a kd-Tree framework for
-        the Homogenized Volume and ray-casting.  Default to True.
     max_level: int, optional
         Specifies the maximum level to be rendered.  Also
         specifies the maximum level used in the kd-Tree
@@ -1441,7 +1438,7 @@ def yaw(self, theta, rot_center):
         theta : float, in radians
              Angle (in radians) by which to yaw the view.
 
-        center : a tuple (x, y, z)
+        rot_center : a tuple (x, y, z)
              The point to rotate about
 
         Examples

yt/visualization/volume_rendering/render_source.py

@@ -915,14 +915,6 @@ def apply_colormap(self):
 
         Applies a colormap to the current image without re-rendering.
 
-        Parameters
-        ----------
-        cmap_name : string, optional
-            An acceptable colormap.  See either yt.visualization.color_maps or
-            https://scipy-cookbook.readthedocs.io/items/Matplotlib_Show_colormaps.html .
-        color_bounds : tuple of floats, optional
-            The min and max to scale between.  Outlying values will be clipped.
-
         Returns
         -------
         current_image : A new image with the specified color scale applied to

yt/visualization/volume_rendering/scene.py

@@ -40,10 +40,6 @@ class Scene:
     This does very little setup, and requires additional input
     to do anything useful.
 
-    Parameters
-    ----------
-    None
-
     Examples
     --------
 

yt/visualization/volume_rendering/transfer_function_helper.py

@@ -90,9 +90,6 @@ def build_transfer_function(self):
         Builds the transfer function according to the current state of the
         TransferFunctionHelper.
 
-        Parameters
-        ----------
-        None
 
         Returns
         -------