- Big refactor to make documentation work correctly.

docs/_templates/class_custom.rst

@@ -9,6 +9,8 @@
     :undoc-members:
     :member-order: groupwise
 
+    .. automethod:: __init__
+
     {% block attributes %}
     {% if attributes %}
     .. rubric:: {{ _('Attributes') }}

docs/conf.py

@@ -12,6 +12,11 @@
 #
 import os
 import sys
+import matplotlib.pyplot as plt
+import matplotlib.axes
+import astropy.time
+import pandas
+
 
 sys.path.insert(0, os.path.abspath('../'))
 
@@ -36,10 +41,16 @@
     'sphinx.ext.inheritance_diagram',
 ]
 autosummary_generate = True  # Turn on sphinx.ext.autosummary
-autosummary_imported_members = True
-
+# autosummary_imported_members = True
+# autoclass_content = 'both'
 autodoc_typehints = "description"
 
+# autosummary_filename_map = {
+#     'kgpy.optics.Surface': 'kgpy.optics.Surface_cls',
+# }
+
+typehints_fully_qualified = True
+
 graphviz_output_format = 'svg'
 inheritance_graph_attrs = dict(rankdir='TB')
 
@@ -55,14 +66,17 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
+
 html_theme = 'bootstrap-astropy'
 html_theme_options = {
     'logotext1': 'kg',  # white,  semi-bold
     'logotext2': 'py',  # blue, light
     'logotext3': ':docs',  # white,  light
     'astropy_project_menubar': False
 }
+html_sidebars = {
+   '**': ['globaltoc.html'],
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -77,11 +91,10 @@
     'numpy': ('https://numpy.org/doc/stable/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
     'matplotlib': ('https://matplotlib.org', None),
-    'astropy': ('https://docs.astropy.org/en/stable/', None)
+    'astropy': ('https://docs.astropy.org/en/stable/', None),
+    'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
 }
 
-import matplotlib.pyplot as plt
-import matplotlib.axes
-import astropy.time
-plt.Axes.__module__ = matplotlib.axes.__name__
-astropy.time.Time.__module__ = astropy.time.__name__
+# plt.Axes.__module__ = matplotlib.axes.__name__
+# astropy.time.Time.__module__ = astropy.time.__name__
+# pandas.DataFrame.__module__ = pandas.__name__

kgpy/__init__.py

@@ -1,21 +1,109 @@
 """
 kgpy root package
 """
+import dataclasses
+import typing as typ
+import numpy as np
 
 __all__ = [
-    'AutoAxis',
     'linspace', 'midspace',
     'Name',
     'fft',
     'rebin',
-    'Obs',
 ]
 
-from ._auto_axis import AutoAxis
-from ._linspace import linspace, midspace
-from ._name import Name
-from . import fft
-from ._rebin import rebin
-from ._obs import Obs
 
-Obs.__module__ = __name__
+@dataclasses.dataclass
+class Name:
+    """
+    Representation of a hierarchical namespace.
+    Names are a composition of a parent, which is also a name, and a base which is a simple string.
+    The string representation of a name is <parent>.base, where <parent> is the parent's string expansion.
+    """
+
+    base: str = ''  #: Base of the name, this string will appear last in the string representation
+    parent: 'typ.Optional[Name]' = None     #: Parent string of the name, this itself also a name
+
+    def copy(self):
+        if self.parent is not None:
+            parent = self.parent.copy()
+        else:
+            parent = self.parent
+        return type(self)(
+            base=self.base,
+            parent=parent,
+        )
+
+    def __add__(self, other: str) -> 'Name':
+        """
+        Quickly create the name of a child's name by adding a string to the current instance.
+        Adding a string to a name instance returns
+        :param other: A string representing the basename of the new Name instance.
+        :return: A new `kgpy.Name` instance with the `self` as the `parent` and `other` as the `base`.
+        """
+        return type(self)(base=other, parent=self)
+
+    def __repr__(self):
+        if self.parent is not None:
+            return self.parent.__repr__() + '.' + self.base
+
+        else:
+            return self.base
+
+
+def rebin(arr: np.ndarray, scale_dims: typ.Tuple[int, ...]) -> np.ndarray:
+    """
+    Increases the size of an array by scale_dims in each i dimension by repeating each value scale_dims[i] times along
+    that axis.
+
+    :param arr: Array to modify
+    :param scale_dims: Tuple with length ``arr.ndim`` specifying the size increase in each axis.
+    :return: The resized array
+    """
+    new_arr = np.broadcast_to(arr, scale_dims + arr.shape)
+    start_axes = np.arange(arr.ndim)
+    new_axes = 2 * start_axes + 1
+    new_arr = np.moveaxis(new_arr, start_axes, new_axes)
+
+    new_shape = np.array(arr.shape) * np.array(scale_dims)
+    new_arr = np.reshape(new_arr, new_shape)
+    return new_arr
+
+
+def linspace(start: np.ndarray, stop: np.ndarray, num: int, axis: int = 0) -> np.ndarray:
+    """
+    A modified version of :func:`numpy.linspace()` that returns a value in the center of the range between `start`
+    and `stop` if `num == 1` unlike :func:`numpy.linspace` which would just return `start`.
+    This function is often helfpul when creating a grid.
+    Sometimes you want to test with only a single element, but you want that element to be in the center of the range
+    and not off to one side.
+
+    :param start: The starting value of the sequence.
+    :param stop: The end value of the sequence, must be broadcastable with `start`.
+    :param num: Number of samples to generate for this sequence.
+    :param axis: The axis in the result used to store the samples. The default is the first axis.
+    :return: An array the size of the broadcasted shape of `start` and `stop` with an additional dimension of length
+        `num`.
+    """
+    if num == 1:
+        return np.expand_dims((start + stop) / 2, axis=axis)
+    else:
+        return np.linspace(start=start, stop=stop, num=num, axis=axis)
+
+
+def midspace(start: np.ndarray, stop: np.ndarray, num: int, axis: int = 0) -> np.ndarray:
+    """
+    A modified version of :func:`numpy.linspace` that selects cell centers instead of cell edges.
+
+    :param start:
+    :param stop:
+    :param num:
+    :param axis:
+    :return:
+    """
+    a = np.linspace(start=start, stop=stop, num=num + 1, axis=axis)
+    i0 = [slice(None)] * a.ndim
+    i1 = i0.copy()
+    i0[axis] = slice(None, ~0)
+    i1[axis] = slice(1, None)
+    return (a[i0] + a[i1]) / 2

kgpy/__init__test.py

@@ -0,0 +1,9 @@
+import numpy as np
+from . import rebin
+
+
+def test_rebin():
+    x = np.random.rand(2, 5, 7, 3)
+    scales = (2, 2, 2, 2)
+    new_x = rebin(x, scales)
+    assert new_x.shape == tuple(x.shape * np.array(scales))