RF: Run flake8 over all files in the repo + fix outstanding formatting issues

.pep8speaks.yml

@@ -1,12 +1,14 @@
 scanner:
-    diff_only: True  # Only show errors caused by the patch
+    # Only show errors caused by the patch. False means we check everything
+    # according to the config for flake8 in setup.cfg
+    diff_only: False
     linter: flake8
 
-message:  # Customize the comment made by the bot
-    opened:  # Messages when a new PR is submitted
+message: # Customize the comment made by the bot
+    opened: # Messages when a new PR is submitted
         header: "Hello @{name}, thank you for submitting the Pull Request!"
         footer: "To test for issues locally, `pip install flake8` and then run `flake8 nibabel`."
-    updated:  # Messages when new commits are added to the PR
+    updated: # Messages when new commits are added to the PR
         header: "Hello @{name}, Thank you for updating!"
         footer: "To test for issues locally, `pip install flake8` and then run `flake8 nibabel`."
     no_errors: "Cheers! There are no style issues detected in this Pull Request. :beers: "

Makefile

@@ -8,7 +8,7 @@ PROJECT=nibabel
 # The Python executable to be used
 #
 PYTHON ?= python
-NOSETESTS = $(PYTHON) $(shell which nosetests)
+TEST_RUNNER ?= pytest
 
 #
 # Determine details on the Python/system
@@ -66,7 +66,6 @@ distclean: clean
 		 -o -iname '#*#' | xargs -L10 rm -f
 	-rm -r dist
 	-rm build-stamp
-	-rm -r .tox
 #	-rm tests/data/*.hdr.* tests/data/*.img.* tests/data/something.nii \
 #		tests/data/noise* tests/data/None.nii
 
@@ -83,22 +82,23 @@ $(WWW_DIR):
 # Tests
 #
 
-test: unittest testmanual
+test: test-style unittest testmanual
 
-
-ut-%: build
-	@PYTHONPATH=.:$(PYTHONPATH) $(NOSETESTS) nibabel/tests/test_$*.py
-
-
-unittest: build
-	@PYTHONPATH=.:$(PYTHONPATH) $(NOSETESTS) nibabel --with-doctest
+unittest: build test-clean
+	export CHECK_TYPE=test; ./tools/ci/check.sh
 
 testmanual: build
-	@cd doc/source && PYTHONPATH=../..:$(PYTHONPATH) $(NOSETESTS) --with-doctest --doctest-extension=.rst . dicom
+	export CHECK_TYPE=doc; ./tools/ci/check.sh
 
+coverage: unittest
 
-coverage: build
-	@PYTHONPATH=.:$(PYTHONPATH) $(NOSETESTS) --with-coverage --cover-package=nibabel
+.PHONY: test-style
+test-style:
+	export CHECK_TYPE=style; ./tools/ci/check.sh
+
+.PHONY: test-clean
+test-clean:
+	rm -rf for_testing
 
 
 #
@@ -252,11 +252,13 @@ sdist-venv: clean
 	rm -rf dist venv
 	unset PYTHONPATH && $(PYTHON) setup.py sdist --formats=zip
 	virtualenv --system-site-packages --python=$(PYTHON) venv
-	. venv/bin/activate && pip install --ignore-installed nose
+	. venv/bin/activate && pip install -r dev-requirements.txt
 	mkdir venv/tmp
 	cd venv/tmp && unzip ../../dist/*.zip
 	. venv/bin/activate && cd venv/tmp/nibabel* && python setup.py install
-	unset PYTHONPATH && . venv/bin/activate && cd venv && nosetests --with-doctest nibabel nisext
+	unset PYTHONPATH && . \
+		venv/bin/activate && \
+		cd venv && $(TEST_RUNNER) --doctest-modules --doctest-plus nibabel nisext
 
 source-release: distclean
 	$(PYTHON) -m compileall .
@@ -269,17 +271,7 @@ venv-tests:
 	make distclean
 	- rm -rf $(VIRTUAL_ENV)/lib/python$(PYVER)/site-packages/nibabel
 	$(PYTHON) setup.py install
-	cd .. && nosetests $(VIRTUAL_ENV)/lib/python$(PYVER)/site-packages/nibabel
-
-tox-fresh:
-	# tox tests with fresh-installed virtualenvs.  Needs network.  And
-	# pytox, obviously.
-	tox -c tox.ini
-
-tox-stale:
-	# tox tests with MB's already-installed virtualenvs (numpy and nose
-	# installed)
-	tox -e python25,python26,python27,python32,np-1.2.1
+	cd .. && $(TEST_RUNNER) $(VIRTUAL_ENV)/lib/python$(PYVER)/site-packages/nibabel
 
 refresh-readme:
 	$(PYTHON) tools/refresh_readme.py

dev-requirements.txt

@@ -1,3 +1,5 @@
 # Requirements for running tests
 -r requirements.txt
 pytest
+pytest-doctestplus
+flake8

doc-requirements.txt

@@ -1,6 +1,8 @@
 # Requirements for building docs
 -r requirements.txt
 sphinx<3
-numpydoc
+jinja2<3
+numpydoc<1.3
+MarkupSafe<2.1
 texext
 matplotlib >=1.3.1

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/source/dicom/derivations/spm_dicom_orient.py

@@ -46,7 +46,7 @@ def numbered_vector(nrows, symbol_prefix):
 R = zeros(4, 2)
 R[:3, :] = R3
 
-# The following is specific to the SPM algorithm. 
+# The following is specific to the SPM algorithm.
 x1 = ones(4, 1)
 y1 = ones(4, 1)
 y1[:3, :] = pos_pat_0

doc/source/scripts/make_coord_examples.py

@@ -68,6 +68,7 @@
 x, y = 0, 1
 # Make a rectangular box with these sides
 
+
 def make_ortho_box(bl, x_len, y_len):
     """ Make a box with sides parallel to the axes
     """
@@ -76,6 +77,7 @@ def make_ortho_box(bl, x_len, y_len):
                      [bl[x], bl[y] + y_len],
                      [bl[x] + x_len, bl[y] + y_len]))
 
+
 orth_epi_box = make_ortho_box(epi_bl, epi_x_len, epi_y_len)
 
 # Structural bounding box
@@ -126,6 +128,7 @@ def plot_localizer():
 def save_plot():
     # Plot using global variables
     plot_localizer()
+
     def vx2mm(pts):
         return pts - iso_center
     plot_box(vx2mm(rot_box), label='EPI bounding box')

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]