Reformat without quote normalization

doc/source/conf.py

@@ -49,7 +49,7 @@
 # If extensions (or modules to document with autodoc) are in another 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('.'))
 
 # -- General configuration ------------------------------------------------
 
@@ -66,7 +66,7 @@
 templates_path = ['_templates']
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # General information about the project.
 project = u'NeuroM'
@@ -86,38 +86,38 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-#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 = []
 
 # 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
 
 # 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
 
 suppress_warnings = ["ref.python"]
 autosummary_generate = True
@@ -127,7 +127,7 @@
 }
 autosummary_mock_imports = ['plotly']
 
-#autoclass_content = 'both'
+# autoclass_content = 'both'
 
 # -- Options for HTML output ----------------------------------------------
 
@@ -140,7 +140,7 @@
 # documentation.
 html_theme_options = {
     "repo_url": "https://github.com/BlueBrain/NeuroM/",
-    "repo_name": "BlueBrain/NeuroM"
+    "repo_name": "BlueBrain/NeuroM",
 }
 
 
@@ -149,7 +149,7 @@
 html_title = 'NeuroM'
 
 # 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.
@@ -158,7 +158,7 @@
 # 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,
@@ -168,98 +168,97 @@
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # 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'
 
 # 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 = False
 
 # 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
 
 # Language to be used for generating the HTML full-text search index.
 # Sphinx supports the following languages:
 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
 #   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
+# html_search_language = 'en'
 
 # A dictionary with options for the search language support, empty by default.
 # Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
+# html_search_options = {'type': 'default'}
 
 # The name of a javascript file (relative to the configuration directory) that
 # implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# html_search_scorer = 'scorer.js'
 
 # -- Options for LaTeX output ---------------------------------------------
 
 # 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 ---------------------------------------
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
-
+# man_show_urls = False
 
 
 # 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'

neurom/__init__.py

@@ -56,13 +56,18 @@
     >>> n_points = [n for n in nm.iter_neurites(pop, mapping, filter)]
 """
 from neurom.core.dataformat import COLS
-from neurom.core.morphology import (graft_morphology, iter_neurites,
-                                    iter_sections, iter_segments)
+from neurom.core.morphology import graft_morphology
+from neurom.core.morphology import iter_neurites
+from neurom.core.morphology import iter_sections
+from neurom.core.morphology import iter_segments
 from neurom.core.types import NEURITES as NEURITE_TYPES
-from neurom.core.types import NeuriteIter, NeuriteType
+from neurom.core.types import NeuriteIter
+from neurom.core.types import NeuriteType
 from neurom.exceptions import NeuroMDeprecationWarning
 from neurom.features import get
-from neurom.io.utils import MorphLoader, load_morphologies, load_morphology
+from neurom.io.utils import MorphLoader
+from neurom.io.utils import load_morphologies
+from neurom.io.utils import load_morphology
 
 APICAL_DENDRITE = NeuriteType.apical_dendrite
 BASAL_DENDRITE = NeuriteType.basal_dendrite

neurom/apps/annotate.py

@@ -46,21 +46,29 @@ def generate_annotation(result, settings):
     if result.status:
         return ''
 
-    header = ('\n\n'
-              f'({settings["label"]}   ; MUK_ANNOTATION\n'
-              f'    (Color {settings["color"]})   ; MUK_ANNOTATION\n'
-              f'    (Name "{settings["name"]}")   ; MUK_ANNOTATION')
+    header = (
+        '\n\n'
+        f'({settings["label"]}   ; MUK_ANNOTATION\n'
+        f'    (Color {settings["color"]})   ; MUK_ANNOTATION\n'
+        f'    (Name "{settings["name"]}")   ; MUK_ANNOTATION'
+    )
     points = [p for _, _points in result.info for p in _points]
-    annotations = '\n'.join((f'    '
-                             f'({p[COLS.X]:10.2f} {p[COLS.Y]:10.2f} {p[COLS.Z]:10.2f} 0.50)'
-                             f'   ; MUK_ANNOTATION' for p in points))
+    annotations = '\n'.join(
+        (
+            f'    '
+            f'({p[COLS.X]:10.2f} {p[COLS.Y]:10.2f} {p[COLS.Z]:10.2f} 0.50)'
+            f'   ; MUK_ANNOTATION'
+            for p in points
+        )
+    )
     footer = ')   ; MUK_ANNOTATION\n'
 
     return f'{header}\n{annotations}\n{footer}'
 
 
 def annotate(results, settings):
     """Concatenate the annotations of all checkers."""
-    annotations = (generate_annotation(result, setting)
-                   for result, setting in zip(results, settings))
+    annotations = (
+        generate_annotation(result, setting) for result, setting in zip(results, settings)
+    )
     return '\n'.join(annot for annot in annotations if annot)