pysal · Ziqi-Li · Mar 19, 2019 · Feb 21, 2019 · Feb 21, 2019 · Feb 21, 2019
diff --git a/doc/conf.py b/doc/conf.py
@@ -17,13 +17,11 @@
 import sys, os
 import sphinx_bootstrap_theme
 
-
 sys.path.insert(0, os.path.abspath('../../'))
 
 #import your package to obtain the version info to display on the docs website
 import mgwr
 
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -32,17 +30,11 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [#'sphinx_gallery.gen_gallery',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.viewcode',
-              'sphinxcontrib.bibtex',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.doctest',
-              'sphinx.ext.intersphinx',
-              'numpydoc',
-              'matplotlib.sphinxext.plot_directive']
-
+extensions = [  #'sphinx_gallery.gen_gallery',
+    'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.viewcode',
+    'sphinxcontrib.bibtex', 'sphinx.ext.mathjax', 'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx', 'numpydoc', 'matplotlib.sphinxext.plot_directive'
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -66,8 +58,8 @@
 # built documents.
 #
 # The full version.
-version = mgwr.__version__ #should replace it with your PACKAGE_NAME
-release = mgwr.__version__ #should replace it with your PACKAGE_NAME
+version = mgwr.__version__  #should replace it with your PACKAGE_NAME
+release = mgwr.__version__  #should replace it with your PACKAGE_NAME
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -104,32 +96,35 @@
 # (Optional) PySAL favicon
 html_favicon = "_static/images/pysal_favicon.ico"
 
-
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
 html_theme_options = {
 
     # Navigation bar title. (Default: ``project`` value)
-    'navbar_title': "mgwr", # string of your project name, for example, 'giddy'
+    'navbar_title':
+    "mgwr",  # string of your project name, for example, 'giddy'
 
     # Render the next and previous page links in navbar. (Default: true)
-    'navbar_sidebarrel': False,
+    'navbar_sidebarrel':
+    False,
 
     # Render the current pages TOC in the navbar. (Default: true)
     #'navbar_pagenav': True,
     #'navbar_pagenav': False,
 
     # No sidebar
-    'nosidebar': True,
+    'nosidebar':
+    True,
 
     # Tab name for the current pages TOC. (Default: "Page")
     #'navbar_pagenav_name': "Page",
 
     # Global TOC depth for "site" navbar tab. (Default: 1)
     # Switching to -1 shows all levels.
-    'globaltoc_depth': 2,
+    'globaltoc_depth':
+    2,
 
     # Include hidden TOCs in Site navbar?
     #
@@ -138,38 +133,41 @@
     # will break.
     #
     # Values: "true" (default) or "false"
-    'globaltoc_includehidden': "true",
+    'globaltoc_includehidden':
+    "true",
 
     # HTML navbar class (Default: "navbar") to attach to <div> element.
     # For black navbar, do "navbar navbar-inverse"
     #'navbar_class': "navbar navbar-inverse",
 
     # Fix navigation bar to top of page?
     # Values: "true" (default) or "false"
-    'navbar_fixed_top': "true",
-
+    'navbar_fixed_top':
+    "true",
 
     # Location of link to source.
     # Options are "nav" (default), "footer" or anything else to exclude.
-    'source_link_position': 'footer',
+    'source_link_position':
+    'footer',
 
     # Bootswatch (http://bootswatch.com/) theme.
     #
     # Options are nothing (default) or the name of a valid theme
     # such as "amelia" or "cosmo", "yeti", "flatly".
-    'bootswatch_theme': "yeti",
+    'bootswatch_theme':
+    "yeti",
 
     # Choose Bootstrap version.
     # Values: "3" (default) or "2" (in quotes)
-    'bootstrap_version': "3",
+    'bootstrap_version':
+    "3",
 
     # Navigation bar menu
     'navbar_links': [
-                     ("Installation", "installation"),
-                     ("API", "api"),
-                     ("References", "references"),
-                     ],
-
+        ("Installation", "installation"),
+        ("API", "api"),
+        ("References", "references"),
+    ],
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,
@@ -184,8 +182,7 @@
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mgwr'+'doc'
-
+htmlhelp_basename = 'mgwr' + 'doc'
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -211,33 +208,26 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'mgwr.tex', u'mgwr Documentation',
-     u'pysal developers', 'manual'),
+    (master_doc, 'mgwr.tex', u'mgwr Documentation', u'pysal developers',
+     'manual'),
 ]
 
-
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'mgwr', u'mgwr Documentation',
-     [author], 1)
-]
-
+man_pages = [(master_doc, 'mgwr', u'mgwr Documentation', [author], 1)]
 
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'mgwr', u'mgwr Documentation',
-     author, 'mgwr', 'multiscale gwr',
-     'Miscellaneous'),
+    (master_doc, 'mgwr', u'mgwr Documentation', author, 'mgwr',
+     'multiscale gwr', 'Miscellaneous'),
 ]
 
-
 # -----------------------------------------------------------------------------
 # Autosummary
 # -----------------------------------------------------------------------------
@@ -252,9 +242,10 @@
 # display the source code for Plot directive
 plot_include_source = True
 
+
 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}
-
diff --git a/mgwr/__init__.py b/mgwr/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "2.0.2"
+__version__ = "2.1.0"
 
 from . import gwr
 from . import sel_bw

diff --git a/mgwr/diagnostics.py b/mgwr/diagnostics.py
@@ -7,6 +7,7 @@
 from scipy import linalg
 from spglm.family import Gaussian, Poisson, Binomial
 
+
 def get_AICc(gwr):
     """
     Get AICc value
@@ -20,13 +21,15 @@ def get_AICc(gwr):
     k = gwr.tr_S
     #sigma2 = gwr.sigma2
     if isinstance(gwr.family, Gaussian):
-        aicc = -2.0*gwr.llf + 2.0*n*(k + 1.0)/(n-k-2.0) #equivalent to below but
+        aicc = -2.0 * gwr.llf + 2.0 * n * (k + 1.0) / (
+            n - k - 2.0)  #equivalent to below but
         #can't control denominator of sigma without altering GLM familt code
         #aicc = n*np.log(sigma2) + n*np.log(2.0*np.pi) + n*(n+k)/(n-k-2.0)
     elif isinstance(gwr.family, (Poisson, Binomial)):
-        aicc = get_AIC(gwr) + 2.0 * k * (k+1.0) / (n - k - 1.0) 
+        aicc = get_AIC(gwr) + 2.0 * k * (k + 1.0) / (n - k - 1.0)
     return aicc
 
+
 def get_AIC(gwr):
     """
     Get AIC calue
@@ -36,16 +39,17 @@ def get_AIC(gwr):
     GWGLM:  AIC(G)=D(G) + 2K(G), where D and K denote the deviance and the effective
     number of parameters in the model with bandwidth G, respectively.
 
-    """   
+    """
     k = gwr.tr_S
     #deviance = -2*log-likelihood
     y = gwr.y
     mu = gwr.mu
     if isinstance(gwr.family, Gaussian):
-        aic = -2.0 * gwr.llf + 2.0 * (k+1)
+        aic = -2.0 * gwr.llf + 2.0 * (k + 1)
     elif isinstance(gwr.family, (Poisson, Binomial)):
         aic = np.sum(gwr.family.resid_dev(y, mu)**2) + 2.0 * k
-    return aic 
+    return aic
+
 
 def get_BIC(gwr):
     """
@@ -57,16 +61,17 @@ def get_BIC(gwr):
     GWGLM: BIC = dev + tr_S * log(n)
 
     """
-    n = gwr.n      # (scalar) number of observations
-    k = gwr.tr_S  
+    n = gwr.n  # (scalar) number of observations
+    k = gwr.tr_S
     y = gwr.y
     mu = gwr.mu
     if isinstance(gwr.family, Gaussian):
-        bic = -2.0 * gwr.llf + (k+1) * np.log(n) 
+        bic = -2.0 * gwr.llf + (k + 1) * np.log(n)
     elif isinstance(gwr.family, (Poisson, Binomial)):
         bic = np.sum(gwr.family.resid_dev(y, mu)**2) + k * np.log(n)
     return bic
 
+
 def get_CV(gwr):
     """
     Get CV value
@@ -79,11 +84,12 @@ def get_CV(gwr):
     Modification: sum of residual squared is divided by n according to GWR4 results
 
     """
-    aa = gwr.resid_response.reshape((-1,1))/(1.0-gwr.influ)
-    cv = np.sum(aa**2)/gwr.n
+    aa = gwr.resid_response.reshape((-1, 1)) / (1.0 - gwr.influ)
+    cv = np.sum(aa**2) / gwr.n
     return cv
 
+
 def corr(cov):
-    invsd = np.diag(1/np.sqrt(np.diag(cov)))
+    invsd = np.diag(1 / np.sqrt(np.diag(cov)))
     cors = np.dot(np.dot(invsd, cov), invsd)
     return cors