Add fmt comments for black (#229)

Resolves: #201

Added fmt: off and fmt: on commments to n-dimensional arrays in the test suite to prevent the ugly wrapping of arrays. Ran the black package to format the whole project.

docs/conf.py

@@ -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
@@ -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 ----------------------------------------
@@ -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

pyswarms/backend/topology/pyramid.py

@@ -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