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Add fmt comments for black #229

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Aug 17, 2018
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Add fmt comments for black #229

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166 changes: 88 additions & 78 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,50 +20,50 @@
# directory, 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.
#sys.path.insert(0, os.path.abspath('.'))
# sys.path.insert(0, os.path.abspath('.'))

# Get the project root dir, which is the parent dir of this
#cwd = os.getcwd()
#project_root = os.path.dirname(cwd)
# cwd = os.getcwd()
# project_root = os.path.dirname(cwd)

# Insert the project root dir as the first element in the PYTHONPATH.
# This lets us ensure that the source package is imported, and that its
# version is used.
#sys.path.insert(0, project_root)
sys.path.insert(0, os.path.abspath('../'))
# sys.path.insert(0, project_root)
sys.path.insert(0, os.path.abspath("../"))

import pyswarms

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

# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# needs_sphinx = '1.0'

# 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.ext.autodoc',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'sphinx.ext.mathjax'
]
"sphinx.ext.autodoc",
"sphinx.ext.viewcode",
"sphinx.ext.napoleon",
"sphinx.ext.mathjax",
]

exclude_patterns = ['_build', '**.ipynb_checkpoints']
exclude_patterns = ["_build", "**.ipynb_checkpoints"]

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

# The suffix of source filenames.
source_suffix = '.rst'
source_suffix = ".rst"

# The encoding of source files.
#source_encoding = 'utf-8-sig'
# source_encoding = 'utf-8-sig'

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

# General information about the project.
project = u'PySwarms'
project = u"PySwarms"
copyright = u"2017, Lester James V. Miranda"

# The version info for the project you're documenting, acts as replacement
Expand All @@ -77,188 +77,195 @@

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# language = None

# There are two options for replacing |today|: either, you set today to
# some non-false value, then it is used:
#today = ''
# today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# today_fmt = '%B %d, %Y'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
exclude_patterns = ["_build"]

# The reST default role (used for this markup: `text`) to use for all
# documents.
#default_role = None
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# add_function_parentheses = True

# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# add_module_names = True

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# show_authors = False

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

# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# modindex_common_prefix = []

# If true, keep warnings as "system message" paragraphs in the built
# documents.
#keep_warnings = False
# keep_warnings = False


# -- Options for HTML output -------------------------------------------

# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'sphinx_rtd_theme'
html_theme = "sphinx_rtd_theme"

# 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 = {}
# html_theme_options = {}

# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# html_theme_path = []

# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# html_title = None

# A shorter title for the navigation bar. Default is the same as
# html_title.
#html_short_title = None
# html_short_title = None

# The name of an image file (relative to this directory) to place at the
# top of the sidebar.
#html_logo = None
# html_logo = None

# The name of an image file (within the static path) to use as favicon
# of the docs. This file should be a Windows icon file (.ico) being
# 16x16 or 32x32 pixels large.
#html_favicon = None
# html_favicon = None

# 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"]


def setup(app):
# overrides for wide tables in RTD theme
app.add_stylesheet('theme_overrides.css') # path relative to static
app.add_stylesheet("theme_overrides.css") # path relative to static


# If not '', a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
html_last_updated_fmt = '%b %d, %Y'
html_last_updated_fmt = "%b %d, %Y"

# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# html_use_smartypants = True

# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# html_sidebars = {}

# Additional templates that should be rendered to pages, maps page names
# to template names.
#html_additional_pages = {}
# html_additional_pages = {}

# If false, no module index is generated.
#html_domain_indices = True
# html_domain_indices = True

# If false, no index is generated.
#html_use_index = True
# html_use_index = True

# If true, the index is split into individual pages for each letter.
#html_split_index = False
# html_split_index = False

# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# html_show_sourcelink = True

# If true, "Created using Sphinx" is shown in the HTML footer.
# Default is True.
#html_show_sphinx = True
# html_show_sphinx = True

# If true, "(C) Copyright ..." is shown in the HTML footer.
# Default is True.
#html_show_copyright = True
# html_show_copyright = True

# If true, an OpenSearch description file will be output, and all pages
# will contain a <link> tag referring to it. The value of this option
# must be the base URL from which the finished HTML is served.
#html_use_opensearch = ''
# html_use_opensearch = ''

# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# html_file_suffix = None

# Output file base name for HTML help builder.
htmlhelp_basename = 'pyswarmsdoc'
htmlhelp_basename = "pyswarmsdoc"


# -- Options for LaTeX output ------------------------------------------

latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
'papersize': 'a4paper',

"papersize": "a4paper",
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',

# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
# 'preamble': '',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass
# [howto/manual]).
latex_documents = [
('index', 'pyswarms.tex',
u'PySwarms Documentation',
u'Lester James V. Miranda', 'manual'),
(
"index",
"pyswarms.tex",
u"PySwarms Documentation",
u"Lester James V. Miranda",
"manual",
)
]

# The name of an image file (relative to this directory) to place at
# the top of the title page.
#latex_logo = None
# latex_logo = None

# For "manual" documents, if this is true, then toplevel headings
# are parts, not chapters.
#latex_use_parts = False
# latex_use_parts = False

# If true, show page references after internal links.
#latex_show_pagerefs = False
# latex_show_pagerefs = False

# If true, show URL addresses after external links.
#latex_show_urls = False
# latex_show_urls = False

# Documents to append as an appendix to all manuals.
#latex_appendices = []
# latex_appendices = []

# If false, no module index is generated.
#latex_domain_indices = True
# latex_domain_indices = True


# -- Options for manual page output ------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'pyswarms',
u'PySwarms Documentation',
[u'Lester James V. Miranda'], 1)
(
"index",
"pyswarms",
u"PySwarms Documentation",
[u"Lester James V. Miranda"],
1,
)
]

# If true, show URL addresses after external links.
#man_show_urls = False
# man_show_urls = False


# -- Options for Texinfo output ----------------------------------------
Expand All @@ -267,22 +274,25 @@ def setup(app):
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'pyswarms',
u'PySwarms Documentation',
u'Lester James V. Miranda',
'pyswarms',
'PySwarms is a simple, Python-based, Particle Swarm Optimization (PSO) library.',
'Research'),
(
"index",
"pyswarms",
u"PySwarms Documentation",
u"Lester James V. Miranda",
"pyswarms",
"PySwarms is a simple, Python-based, Particle Swarm Optimization (PSO) library.",
"Research",
)
]

# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# texinfo_appendices = []

# If false, no module index is generated.
#texinfo_domain_indices = True
# texinfo_domain_indices = True

# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'
# texinfo_show_urls = 'footnote'

# If true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
# texinfo_no_detailmenu = False
27 changes: 21 additions & 6 deletions pyswarms/backend/topology/pyramid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,24 +61,39 @@ def compute_gbest(self, swarm):
try:
# If there are less than (swarm.dimensions + 1) particles they are all connected
if swarm.n_particles < swarm.dimensions + 1:
self.neighbor_idx = np.tile(np.arange(swarm.n_particles), (swarm.n_particles, 1))
self.neighbor_idx = np.tile(
np.arange(swarm.n_particles), (swarm.n_particles, 1)
)
best_pos = swarm.pbest_pos[np.argmin(swarm.pbest_cost)]
best_cost = np.min(swarm.pbest_cost)
else:
# Check if the topology is static or dynamic and assign neighbors
if (self.static and self.neighbor_idx is None) or not self.static:
pyramid = Delaunay(swarm.position, qhull_options="QJ0.001 Qbb Qc Qx")
if (
self.static and self.neighbor_idx is None
) or not self.static:
pyramid = Delaunay(
swarm.position, qhull_options="QJ0.001 Qbb Qc Qx"
)
indices, index_pointer = pyramid.vertex_neighbor_vertices
# Insert all the neighbors for each particle in the idx array
self.neighbor_idx = np.array(
[index_pointer[indices[i]:indices[i + 1]] for i in range(swarm.n_particles)]
[
index_pointer[indices[i] : indices[i + 1]]
for i in range(swarm.n_particles)
]
)

idx_min = np.array(
[swarm.pbest_cost[self.neighbor_idx[i]].argmin() for i in range(len(self.neighbor_idx))]
[
swarm.pbest_cost[self.neighbor_idx[i]].argmin()
for i in range(len(self.neighbor_idx))
]
)
best_neighbor = np.array(
[self.neighbor_idx[i][idx_min[i]] for i in range(len(self.neighbor_idx))]
[
self.neighbor_idx[i][idx_min[i]]
for i in range(len(self.neighbor_idx))
]
).astype(int)

# Obtain best cost and position
Expand Down
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