Merge pull request #158 from pysal/docsupdate

update docs
pysal · Dec 29, 2020 · aa3b4cc · aa3b4cc
2 parents 0236651 + 1a53534
commit aa3b4cc
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Showing 3 changed files with 82 additions and 32 deletions.
diff --git a/docs/api.rst b/docs/api.rst
@@ -7,6 +7,9 @@ API reference
 
 Aspatial Indices
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
@@ -26,6 +29,9 @@ Aspatial Indices
 
 Spatial Indices
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
@@ -44,9 +50,22 @@ Spatial Indices
       spatial.AbsoluteCentralization
       spatial.RelativeCentralization
       spatial.SpatialMinMax
-
+
+Multi-Scalar Spatial Measures
+----------------------------------
+
+.. currentmodule:: segregation
+
+.. autosummary::
+ :toctree: generated/
+
+ 	   spatial.compute_segregation_profile
+
 Multigroup Indices
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
@@ -63,6 +82,9 @@ Multigroup Indices
 
 Local Indices
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
@@ -75,6 +97,9 @@ Local Indices
 
 Batch Compute Wrappers
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
@@ -84,6 +109,9 @@ Batch Compute Wrappers
 
 Inference Wrappers
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
@@ -92,15 +120,31 @@ Inference Wrappers
 
 Decomposition
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
    :toctree: generated/
 
       decomposition.DecomposeSegregation
 
 Network
 ---------------------
+
+.. currentmodule:: segregation
+
 .. autosummary::
  :toctree: generated/
 
       network.get_osm_network
       network.calc_access
+
+Util
+----------------
+
+.. currentmodule:: segregation
+
+.. autosummary::
+ :toctree: generated/
+
+      util.project_gdf
diff --git a/docs/conf.py b/docs/conf.py
@@ -53,7 +53,6 @@
               'matplotlib.sphinxext.plot_directive']
 
 
-
 # sphinx_gallery_conf = {
 #      # path to your examples scripts
 #      'examples_dirs': '../examples',
@@ -146,7 +145,7 @@
 
     # Global TOC depth for "site" navbar tab. (Default: 1)
     # Switching to -1 shows all levels.
-    'globaltoc_depth': 2,
+    'globaltoc_depth': 1,
 
     # Include hidden TOCs in Site navbar?
     #
@@ -268,10 +267,11 @@
 
 # Generate the API documentation when building
 autosummary_generate = True
-numpydoc_show_class_members = True
+numpydoc_show_class_members = False
 class_members_toctree = True
-numpydoc_show_inherited_class_members = True
+numpydoc_show_inherited_class_members = False
 numpydoc_use_plots = True
+numpydoc_xref_param_type = True
 
 # display the source code for Plot directive
 plot_include_source = True
@@ -280,4 +280,15 @@ def setup(app):
     app.add_stylesheet("pysal-styles.css")
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/3.6/': None}
+intersphinx_mapping = {
+    "esda": ("https://pysal.org/esda/", None),
+    "geopandas": ("https://geopandas.readthedocs.io/en/latest/", None),
+    "libpysal": ("https://pysal.org/libpysal/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "python": ("https://docs.python.org/3.9/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
+}
+
+autodoc_default_options = {"members": True, "undoc-members": True}
diff --git a/segregation/decomposition/decompose_segregation.py b/segregation/decomposition/decompose_segregation.py
@@ -107,35 +107,30 @@ class DecomposeSegregation:
     to measure whether the differences between index measures arise from
     differences in spatial structure or population structure
 
-    Examples
-    --------
-    Several examples can be found at https://github.com/pysal/segregation/blob/master/notebooks/decomposition_wrapper_example.ipynb.
-    """
+    Parameters
+    ----------
+    index1 : segregation.SegIndex class
+        First SegIndex class to compare.
+    index2 : segregation.SegIndex class
+        Second SegIndex class to compare.
+    counterfactual_approach : str, one of {"composition", "share", "dual_composition"}
+        The technique used to generate the counterfactual population
+        distributions.
 
-    def __init__(self, index1, index2, counterfactual_approach="composition"):
-        """Decompose segregation differences into spatial and attribute components.
+    Attributes
+    ----------
+    c_s : float
+        Shapley's Spatial Component of the decomposition
+    c_a : float
+        Shapley's Attribute Component of the decomposition
+    indices : dict
+        Dictionary of index values for all four combinations of spatial/attribute data
 
-        Given two segregation indices of the same type, use Shapley decomposition
-        to measure whether the differences between index measures arise from
-        differences in spatial structure or population structure
 
-        Parameters
-        ----------
-        index1 : segregation.SegIndex class
-            First SegIndex class to compare.
-        index2 : segregation.SegIndex class
-            Second SegIndex class to compare.
-        counterfactual_approach : str, one of {"composition", "share", "dual_composition"}
-            The technique used to generate the counterfactual population
-            distributions.
-
-        Attributes
-        ----------
-        c_s : float
-            Shapley's Spatial Component of the decomposition
-        c_a : float
-            Shapley's Attribute Component of the decomposition
-        """
+    """
+
+    def __init__(self, index1, index2, counterfactual_approach="composition"):
+        """Initialize class."""
         aux = _decompose_segregation(index1, index2, counterfactual_approach)
 
         self.c_s = aux[0]