RF: Fix all remaining flake8 complaints

Author: Jacob Roberts

doc/source/conf.py

@@ -19,18 +19,17 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
 import os
 from runpy import run_path
 from configparser import ConfigParser
 
 # Check for external Sphinx extensions we depend on
 try:
-    import numpydoc
+    import numpydoc  # noqa: F401
 except ImportError:
     raise RuntimeError('Need to install "numpydoc" package for doc build')
 try:
-    import texext
+    import texext  # noqa: F401
 except ImportError:
     raise RuntimeError('Need to install "texext" package for doc build')
 
@@ -64,7 +63,6 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.doctest',
-              #'sphinx.ext.intersphinx',
               'sphinx.ext.todo',
               'sphinx.ext.mathjax',
               'sphinx.ext.inheritance_diagram',
@@ -76,7 +74,7 @@
 
 # the following doesn't work with sphinx < 1.0, but will make a separate
 # sphinx-autogen run obsolete in the future
-#autosummary_generate = True
+# autosummary_generate = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -85,7 +83,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8'
+# source_encoding = 'utf-8'
 
 # The master toctree document.
 master_doc = 'index'
@@ -105,11 +103,11 @@
 
 # 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, %H:%M PDT'
 
@@ -124,24 +122,24 @@
 exclude_trees = ['_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'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # -- Sphinxext configuration --------------------------------------------------
 
@@ -168,26 +166,26 @@
 # 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 = ''
+# html_title = ''
 
 # 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,
@@ -196,42 +194,42 @@
 
 # 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'
 
 # Content template for the index page.
 html_index = 'index.html'
 
 # 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 = {'index': ['localtoc.html', 'relations.html', 'sourcelink.html',
                            'indexsidebar.html', 'searchbox.html', 'reggie.html']}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {'index': 'index.html'}
+# html_additional_pages = {'index': 'index.html'}
 
 # If false, no module index is generated.
-#html_use_modindex = True
+# html_use_modindex = 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
 
 # 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 = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
+# html_file_suffix = ''
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'nibabeldoc'
@@ -241,34 +239,34 @@
 # -- Options for LaTeX output -------------------------------------------------
 
 # The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+# latex_font_size = '10pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author,
-#  documentclass [howto/manual]).
+# documentclass [howto/manual]).
 latex_documents = [
     ('index', 'nibabel.tex', u'NiBabel Documentation', u'NiBabel Authors',
      '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
 
 # Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
+# latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_use_modindex = True
+# latex_use_modindex = True
 
 
 # Example configuration for intersphinx: refer to the Python standard library.

doc/tools/apigen.py

@@ -407,7 +407,6 @@ def discover_modules(self):
 
     def write_modules_api(self, modules, outdir):
         # upper-level modules
-        main_module = modules[0].split('.')[0]
         ulms = ['.'.join(m.split('.')[:2]) if m.count('.') >= 1
                 else m.split('.')[0] for m in modules]
 

nisext/py3builder.py

@@ -6,20 +6,22 @@
 except ImportError:
     # 2.x - no parsing of code
     from distutils.command.build_py import build_py
-else: # Python 3
+else:  # Python 3
     # Command to also apply 2to3 to doctests
     from distutils import log
+
     class build_py(build_py_2to3):
         def run_2to3(self, files):
             # Add doctest parsing; this stuff copied from distutils.utils in
             # python 3.2 source
             if not files:
                 return
-            fixer_names, options, explicit = (self.fixer_names,
-                                              self.options,
-                                              self.explicit)
+            fixer_names, options, _ = (self.fixer_names,
+                                       self.options,
+                                       self.explicit)
             # Make this class local, to delay import of 2to3
             from lib2to3.refactor import RefactoringTool, get_fixers_from_package
+
             class DistutilsRefactoringTool(RefactoringTool):
                 def log_error(self, msg, *args, **kw):
                     log.error(msg, *args)

nisext/sexts.py

@@ -131,7 +131,7 @@ def package_check(pkg_name, version=None,
        dependencies.  If dict fill key values ``install_requires`` and
        ``extras_require`` for non-optional and optional dependencies.
     """
-    setuptools_mode = not setuptools_args is None
+    setuptools_mode = setuptools_args is not None
     optional_tf = bool(optional)
     if version_getter is None:
         def version_getter(pkg_name):
@@ -169,7 +169,7 @@ def version_getter(pkg_name):
         log.warn(msgs['version too old'] % (have_version,
                                             pkg_name,
                                             version)
-                    + msgs['opt suffix'])
+                 + msgs['opt suffix'])
         return
     # setuptools mode
     if optional_tf and not isinstance(optional, str):
@@ -178,7 +178,7 @@ def version_getter(pkg_name):
     if version:
         dependency += '>=' + version
     if optional_tf:
-        if not 'extras_require' in setuptools_args:
+        if 'extras_require' not in setuptools_args:
             setuptools_args['extras_require'] = {}
         _add_append_key(setuptools_args['extras_require'],
                         optional,
@@ -205,7 +205,7 @@ def _package_status(pkg_name, version, version_getter, checker):
 
 
 BAT_TEMPLATE = \
-r"""@echo off
+r"""@echo off # noqa: E122
 REM wrapper to use shebang first line of {FNAME}
 set mypath=%~dp0
 set pyscript="%mypath%{FNAME}"
@@ -218,6 +218,7 @@ def _package_status(pkg_name, version, version_getter, checker):
 call "%py_exe%" %pyscript% %*
 """
 
+
 class install_scripts_bat(install_scripts):
     """ Make scripts executable on Windows
 
@@ -247,7 +248,7 @@ def run(self):
             if not (first_line.startswith('#!') and
                     'python' in first_line.lower()):
                 log.info("No #!python executable found, skipping .bat "
-                            "wrapper")
+                         "wrapper")
                 continue
             pth, fname = psplit(filepath)
             froot, ext = splitext(fname)

setup.cfg

@@ -102,11 +102,6 @@ exclude =
     *sphinx*
     nibabel/externals/*
     */__init__.py
-    # temporary -- should be removed in another PR
-    ./doc/source/conf.py
-    ./doc/tools/apigen.py
-    ./nisext
-    ./tools
 
 [versioneer]
 VCS = git