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Format repo: black/isort/flake8 repo #230

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Nov 21, 2022
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Format repo: black/isort/flake8 repo #230

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black/isort/flake8 repo
jGaboardi Nov 20, 2022
d10e9ea
minor typos
jGaboardi Nov 21, 2022
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184 changes: 91 additions & 93 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,15 +16,15 @@
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import sys, os
import sphinx_bootstrap_theme

import os
import sys

sys.path.insert(0, os.path.abspath('../'))
import sphinx_bootstrap_theme

#import your package to obtain the version info to display on the docs website
import esda
sys.path.insert(0, os.path.abspath("../"))

# import your package to obtain the version info to display on the docs website
import esda # noqa E402

# -- General configuration ------------------------------------------------

Expand All @@ -34,43 +34,44 @@
# 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',
'nbsphinx']
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",
"nbsphinx",
]


# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
templates_path = ["_templates"]

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
source_suffix = ".rst"

# The master toctree document.
master_doc = 'index'
master_doc = "index"

# General information about the project.
project = "esda" # string of your project name, for example, 'giddy'
copyright = '2018, pysal developers'
author = 'pysal developers'
copyright = "2018, pysal developers"
author = "pysal developers"

# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The full version.
version = esda.__version__ #should replace it with your PACKAGE_NAME
release = esda.__version__ #should replace it with your PACKAGE_NAME
version = esda.__version__ # should replace it with your PACKAGE_NAME
release = esda.__version__ # should replace it with your PACKAGE_NAME

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
Expand All @@ -82,10 +83,10 @@
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'tests/*']
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "tests/*"]

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
pygments_style = "sphinx"

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
Expand All @@ -96,13 +97,14 @@
# a list of builtin themes.
#
# html_theme = 'alabaster'
html_theme = 'bootstrap'
html_theme = "bootstrap"
html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
html_title = "%s v%s Manual" % (project, version)

# (Optional) Logo of your package. Should be small enough to fit the navbar (ideally 24x24).
# (Optional) Logo of your package.
# Should be small enough to fit the navbar (ideally 24x24).
# Path should be relative to the ``_static`` files directory.
#html_logo = "_static/images/package_logo.jpg"
# html_logo = "_static/images/package_logo.jpg"

# (Optional) PySAL favicon
html_favicon = "_static/images/pysal_favicon.ico"
Expand All @@ -113,82 +115,67 @@
# documentation.
#
html_theme_options = {

# Navigation bar title. (Default: ``project`` value)
'navbar_title': "esda", # string of your project name, for example, 'giddy'

"navbar_title": "esda", # 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,

# '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",

# '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?
#
# Note: If this is "false", you cannot have mixed ``:hidden:`` and
# non-hidden ``toctree`` directives in the same page, or else the build
# 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",

# '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"),
("Tutorial", "tutorial"),
("API", "api"),
("References", "references"),
],

"navbar_links": [
("Installation", "installation"),
("Tutorial", "tutorial"),
("API", "api"),
("References", "references"),
],
}

# 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,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_static_path = ["_static"]

# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# html_sidebars = {}
# html_sidebars = {'sidebar': ['localtoc.html', 'sourcelink.html', 'searchbox.html']}

# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'esda'+'doc'
htmlhelp_basename = "esda" + "doc"


# -- Options for LaTeX output ---------------------------------------------
Expand All @@ -197,15 +184,12 @@
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',

# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',

# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',

# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
Expand All @@ -215,19 +199,15 @@
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'esda.tex', u'esda Documentation',
u'pysal developers', 'manual'),
(master_doc, "esda.tex", "esda Documentation", "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, 'esda', u'esda Documentation',
[author], 1)
]
man_pages = [(master_doc, "esda", "esda Documentation", [author], 1)]


# -- Options for Texinfo output -------------------------------------------
Expand All @@ -236,9 +216,15 @@
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'esda', u'esda Documentation',
author, 'esda developers', 'One line description of project.',
'Miscellaneous'),
(
master_doc,
"esda",
"esda Documentation",
author,
"esda developers",
"One line description of project.",
"Miscellaneous",
),
]


Expand All @@ -264,22 +250,34 @@ def setup(app):

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
'python': ('https://docs.python.org/3/', None),
'numpy': ('https://docs.scipy.org/doc/numpy', None),
'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
'geopandas': ('https://geopandas.readthedocs.io/en/latest/', None),
'sklearn': ('https://scikit-learn.org/stable/', None),
'giddy': ('https://giddy.readthedocs.io/en/latest/', None),
'libpysal': ('https://pysal.org/libpysal/', None),
'esda': ('https://esda.readthedocs.io/en/latest/', None),
'region': ('https://region.readthedocs.io/en/latest/', None),
'hdbscan': ('https://hdbscan.readthedocs.io/en/latest/', None)

"python": ("https://docs.python.org/3/", None),
"numpy": ("https://docs.scipy.org/doc/numpy", None),
"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
"geopandas": ("https://geopandas.readthedocs.io/en/latest/", None),
"sklearn": ("https://scikit-learn.org/stable/", None),
"giddy": ("https://giddy.readthedocs.io/en/latest/", None),
"libpysal": ("https://pysal.org/libpysal/", None),
"esda": ("https://esda.readthedocs.io/en/latest/", None),
"region": ("https://region.readthedocs.io/en/latest/", None),
"hdbscan": ("https://hdbscan.readthedocs.io/en/latest/", None),
}

numpydoc_xref_ignore = {'type', 'optional', 'default', 'shape', 'fitted', 'instance',
'cluster', 'of', 'or', 'if', 'using', 'otherwise', 'required',
'from'}
numpydoc_xref_ignore = {
"type",
"optional",
"default",
"shape",
"fitted",
"instance",
"cluster",
"of",
"or",
"if",
"using",
"otherwise",
"required",
"from",
}


# This is processed by Jinja2 and inserted before each notebook
Expand All @@ -306,7 +304,7 @@ def setup(app):
\nbsphinxstartnotebook{\scriptsize\noindent\strut
\textcolor{gray}{The following section was generated from
\sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
"""
""" # noqa E501

# This is processed by Jinja2 and inserted after each notebook
nbsphinx_epilog = r"""
Expand Down
45 changes: 21 additions & 24 deletions esda/__init__.py
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Expand Up @@ -3,40 +3,37 @@
=================================================

"""
from . import adbscan
from .gamma import Gamma
from .geary import Geary
from .geary_local import Geary_Local
from .geary_local_mv import Geary_Local_MV
from .getisord import G, G_Local
from .join_counts import Join_Counts
from .join_counts_local import Join_Counts_Local
from .join_counts_local_bv import Join_Counts_Local_BV
from .join_counts_local_mv import Join_Counts_Local_MV
from .lee import Spatial_Pearson, Spatial_Pearson_Local
from .losh import LOSH
from .map_comparison import (
external_entropy,
from . import _version, adbscan, shape # noqa F401
from .gamma import Gamma # noqa F401
from .geary import Geary # noqa F401
from .geary_local import Geary_Local # noqa F401
from .geary_local_mv import Geary_Local_MV # noqa F401
from .getisord import G, G_Local # noqa F401
from .join_counts import Join_Counts # noqa F401
from .join_counts_local import Join_Counts_Local # noqa F401
from .join_counts_local_bv import Join_Counts_Local_BV # noqa F401
from .join_counts_local_mv import Join_Counts_Local_MV # noqa F401
from .lee import Spatial_Pearson, Spatial_Pearson_Local # noqa F401
from .losh import LOSH # noqa F401
from .map_comparison import ( # noqa F401
areal_entropy,
completeness,
external_entropy,
homogeneity,
overlay_entropy,
areal_entropy,
)
from .moran import (
from .moran import ( # noqa F401
Moran,
Moran_BV,
Moran_BV_matrix,
Moran_Local,
Moran_Local_BV,
Moran_Rate,
Moran_Local_Rate,
Moran_Rate,
)
from .silhouettes import path_silhouette, boundary_silhouette
from . import shape
from .smaup import Smaup
from .topo import prominence, isolation
from .util import fdr

from . import _version
from .silhouettes import boundary_silhouette, path_silhouette # noqa F401
from .smaup import Smaup # noqa F401
from .topo import isolation, prominence # noqa F401
from .util import fdr # noqa F401

__version__ = _version.get_versions()["version"]
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