diff --git a/definitions/impatient-guide/conf.py b/definitions/impatient-guide/conf.py
index 165ad7d7a..9f3ddf6b4 100644
--- a/definitions/impatient-guide/conf.py
+++ b/definitions/impatient-guide/conf.py
@@ -16,95 +16,95 @@
 # 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 -----------------------------------------------------
 
 # 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 = []
 
 # 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'NeXus for the Impatient'
-copyright = u'2014-2016, http://nexusformat.org'
+project = u"NeXus for the Impatient"
+copyright = u"2014-2016, http://nexusformat.org"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '2016'
+version = "2016"
 # The full version, including alpha/beta/rc tags.
-release = '2016'
+release = "2016"
 
 # 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 = []
 
 
 # -- 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 = 'agogo'
-html_theme = 'sphinxdoc'
+html_theme = "agogo"
+html_theme = "sphinxdoc"
 
 # 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 = 'NeXus for the Impatient'
+html_title = "NeXus for the Impatient"
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 html_short_title = project
@@ -116,100 +116,97 @@
 # 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 = 'favicon.ico'
+html_favicon = "favicon.ico"
 
 # 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"]
 
 # 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 = False
 
 # 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 = 'NXImpatient'
+htmlhelp_basename = "NXImpatient"
 
 
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-# FIXME: roman page numbers in TOC, and no page numbers later
-#  http://osdir.com/ml/sphinx-dev/2011-03/msg00036.html
-#  BUT, latex does not recognize these two lines when in the preamble
-'preamble': '''%
+    # The paper size ('letterpaper' or 'a4paper').
+    "papersize": "letterpaper",
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    # FIXME: roman page numbers in TOC, and no page numbers later
+    #  http://osdir.com/ml/sphinx-dev/2011-03/msg00036.html
+    #  BUT, latex does not recognize these two lines when in the preamble
+    "preamble": """%
  \pagestyle{plain}
  \pagenumbering{arabic}
-''',
+""",
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'NXImpatient.tex', project,
-   u'nexusformat.org', 'howto'),
+    ("index", "NXImpatient.tex", project, u"nexusformat.org", "howto"),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-latex_logo = 'nexuslogo.png'
+latex_logo = "nexuslogo.png"
 
 # 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 = False
@@ -219,13 +216,10 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    ('index', 'nximpatient', project,
-     [u'nexusformat.org'], 1)
-]
+man_pages = [("index", "nximpatient", project, [u"nexusformat.org"], 1)]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ------------------------------------------------
@@ -234,60 +228,65 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'NXImpatient', project,
-   u'nexusformat.org', 'NXImpatient', 
-   'Brief overview of the NeXus data format.',
-   'Miscellaneous'),
+    (
+        "index",
+        "NXImpatient",
+        project,
+        u"nexusformat.org",
+        "NXImpatient",
+        "Brief overview of the NeXus data format.",
+        "Miscellaneous",
+    ),
 ]
 
 # 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'
 
 
 # -- Options for Epub output ---------------------------------------------------
 
 # Bibliographic Dublin Core info.
 epub_title = project
-epub_author = u'nexusformat.org'
-epub_publisher = u'http://nexusformat.org'
+epub_author = u"nexusformat.org"
+epub_publisher = u"http://nexusformat.org"
 epub_copyright = copyright
 
 # The language of the text. It defaults to the language option
 # or en if the language is not set.
-#epub_language = ''
+# epub_language = ''
 
 # The scheme of the identifier. Typical schemes are ISBN or URL.
-#epub_scheme = ''
+# epub_scheme = ''
 
 # The unique identifier of the text. This can be a ISBN number
 # or the project homepage.
-#epub_identifier = ''
+# epub_identifier = ''
 
 # A unique identification for the text.
-#epub_uid = ''
+# epub_uid = ''
 
 # A tuple containing the cover image and cover page html template filenames.
-#epub_cover = ()
+# epub_cover = ()
 
 # HTML files that should be inserted before the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
-#epub_pre_files = []
+# epub_pre_files = []
 
 # HTML files shat should be inserted after the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
-#epub_post_files = []
+# epub_post_files = []
 
 # A list of files that should not be packed into the epub file.
-#epub_exclude_files = []
+# epub_exclude_files = []
 
 # The depth of the table of contents in toc.ncx.
-#epub_tocdepth = 3
+# epub_tocdepth = 3
 
 # Allow duplicate toc entries.
-#epub_tocdup = True
+# epub_tocdup = True
diff --git a/definitions/manual/source/conf.py b/definitions/manual/source/conf.py
index 0160d58f2..1188a3615 100644
--- a/definitions/manual/source/conf.py
+++ b/definitions/manual/source/conf.py
@@ -19,37 +19,37 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'nexus'
-author = 'NIAC, https://www.nexusformat.org'
-copyright = u'1996-{}, {}'.format(datetime.datetime.now().year, author)
-description = u'NeXus: A Common Data Format for Neutron, X-ray, and Muon Science'
+project = "nexus"
+author = "NIAC, https://www.nexusformat.org"
+copyright = u"1996-{}, {}".format(datetime.datetime.now().year, author)
+description = u"NeXus: A Common Data Format for Neutron, X-ray, and Muon Science"
 
 # The full version, including alpha/beta/rc tags
-version = u'unknown NXDL version'
-release = u'unknown NXDL release'
-nxdl_version = open('../../NXDL_VERSION').read().strip()
+version = u"unknown NXDL version"
+release = u"unknown NXDL release"
+nxdl_version = open("../../NXDL_VERSION").read().strip()
 if nxdl_version is not None:
-    version = nxdl_version.split('.')[0]
+    version = nxdl_version.split(".")[0]
     release = nxdl_version
 
 
 # -- General configuration ---------------------------------------------------
 
 # https://github.com/nexusformat/definitions/issues/659#issuecomment-577438319
-needs_sphinx = '2.3'
+needs_sphinx = "2.3"
 
 # 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.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.githubpages',
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -63,27 +63,27 @@
 # a list of builtin themes.
 #
 # html_theme = 'alabaster'
-html_theme = 'sphinxdoc'
+html_theme = "sphinxdoc"
 
 # 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"]
 
 html_sidebars = {
-    '**': [
-        'localtoc.html', 
-        'relations.html', 
-        'sourcelink.html', 
-        'searchbox.html', 
-        'google_search.html'
+    "**": [
+        "localtoc.html",
+        "relations.html",
+        "sourcelink.html",
+        "searchbox.html",
+        "google_search.html",
     ],
 }
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'NeXusManualdoc'
+htmlhelp_basename = "NeXusManualdoc"
 
 # -- Options for Latex output -------------------------------------------------
 latex_elements = {
-    'maxlistdepth':7, # some application definitions are deeply nested
+    "maxlistdepth": 7,  # some application definitions are deeply nested
 }
diff --git a/definitions/manual/source/examples/epics/write_nexus_file.py b/definitions/manual/source/examples/epics/write_nexus_file.py
index 1dd61bafb..a6ef7e108 100755
--- a/definitions/manual/source/examples/epics/write_nexus_file.py
+++ b/definitions/manual/source/examples/epics/write_nexus_file.py
@@ -2,81 +2,83 @@
 import h5py
 import datetime
 
+
 def write_nexus_file(fname, image, md={}):
-	"""
-	write the image to a NeXus HDF5 data file
+    """
+    write the image to a NeXus HDF5 data file
+
+    Parameters
+    ----------
+    fname : str
+            name of the file (relative or absolute) to be written
+    image : numpy array
+            the image data
+    md : dictionary
+            key: value where value is something that can be written by h5py
+                     (such as str, int, float, numpy array, ...)
+    """
+    nexus = h5py.File(fname, "w")
+    nexus.attrs["filename"] = fname
+    nexus.attrs["file_time"] = str(datetime.datetime.now())
+    nexus.attrs["creator"] = "write_nexus_file()"
+    nexus.attrs["H5PY_VERSION"] = h5py.__version__
 
-	Parameters
-	----------
-	fname : str
-		name of the file (relative or absolute) to be written
-	image : numpy array
-		the image data
-	md : dictionary
-		key: value where value is something that can be written by h5py
-			 (such as str, int, float, numpy array, ...)
-	"""
-	nexus = h5py.File(fname, "w")
-	nexus.attrs["filename"] = fname
-	nexus.attrs["file_time"] = str(datetime.datetime.now())
-	nexus.attrs["creator"] = "write_nexus_file()"
-	nexus.attrs["H5PY_VERSION"] = h5py.__version__
+    # /entry
+    nxentry = nexus.create_group("entry")
+    nxentry.attrs["NX_class"] = "NXentry"
+    nexus.attrs["default"] = nxentry.name
 
-	# /entry
-	nxentry = nexus.create_group("entry")
-	nxentry.attrs["NX_class"] = "NXentry"
-	nexus.attrs["default"] = nxentry.name
+    # /entry/instrument
+    nxinstrument = nxentry.create_group("instrument")
+    nxinstrument.attrs["NX_class"] = "NXinstrument"
 
-	# /entry/instrument
-	nxinstrument = nxentry.create_group("instrument")
-	nxinstrument.attrs["NX_class"] = "NXinstrument"
+    # /entry/instrument/detector
+    nxdetector = nxinstrument.create_group("detector")
+    nxdetector.attrs["NX_class"] = "NXdetector"
 
-	# /entry/instrument/detector
-	nxdetector = nxinstrument.create_group("detector")
-	nxdetector.attrs["NX_class"] = "NXdetector"
+    # /entry/instrument/detector/image
+    ds = nxdetector.create_dataset("image", data=image, compression="gzip")
+    ds.attrs["units"] = "counts"
+    ds.attrs["target"] = "/entry/instrument/detector/image"
 
-	# /entry/instrument/detector/image
-	ds = nxdetector.create_dataset("image", data=image, compression="gzip")
-	ds.attrs["units"] = "counts"
-	ds.attrs["target"] = "/entry/instrument/detector/image"
+    # /entry/data
+    nxdata = nxentry.create_group("data")
+    nxdata.attrs["NX_class"] = "NXdata"
+    nxentry.attrs["default"] = nxdata.name
 
-	# /entry/data
-	nxdata = nxentry.create_group("data")
-	nxdata.attrs["NX_class"] = "NXdata"
-	nxentry.attrs["default"] = nxdata.name
+    # /entry/data/data --> /entry/instrument/detector/image
+    nxdata["data"] = nexus["/entry/instrument/detector/image"]
+    nxdata.attrs["signal"] = "data"
 
-	# /entry/data/data --> /entry/instrument/detector/image
-	nxdata["data"] = nexus["/entry/instrument/detector/image"]
-	nxdata.attrs["signal"] = "data"
+    if len(md) > 0:
+        # /entry/instrument/metadata (optional, for metadata)
+        metadata = nxinstrument.create_group("metadata")
+        metadata.attrs["NX_class"] = "NXcollection"
+        for k, v in md.items():
+            try:
+                metadata.create_dataset(k, data=v)
+            except Exception:
+                metadata.create_dataset(k, data=str(v))
 
-	if len(md) > 0:
-		# /entry/instrument/metadata (optional, for metadata)
-		metadata = nxinstrument.create_group("metadata")
-		metadata.attrs["NX_class"] = "NXcollection"
-		for k, v in md.items():
-			try:
-				metadata.create_dataset(k, data=v)
-			except Exception:
-				metadata.create_dataset(k, data=str(v))
+    nexus.close()
 
-	nexus.close()
 
-	
 if __name__ == "__main__":
-	"""demonstrate how to use this code"""
-	import epics
-	prefix = "13SIM1:"
-	img = epics.caget(prefix+"image1:ArrayData")
-	size_x = epics.caget(prefix+"cam1:ArraySizeX_RBV")
-	size_y = epics.caget(prefix+"cam1:ArraySizeY_RBV")
-	# edit the full image for just the binned data
-	img = img[:size_x*size_y].reshape((size_x, size_y))
+    """demonstrate how to use this code"""
+    import epics
+
+    prefix = "13SIM1:"
+    img = epics.caget(prefix + "image1:ArrayData")
+    size_x = epics.caget(prefix + "cam1:ArraySizeX_RBV")
+    size_y = epics.caget(prefix + "cam1:ArraySizeY_RBV")
+    # edit the full image for just the binned data
+    img = img[: size_x * size_y].reshape((size_x, size_y))
 
-	extra_information = dict(
-		unique_id = epics.caget(prefix+"image1:UniqueId_RBV"),
-		size_x = size_x,
-		size_y = size_y,
-		detector_state = epics.caget(prefix+"cam1:DetectorState_RBV"),
-		bitcoin_value="15000",
-	)
-	write_nexus_file("example.h5", img, md=extra_information)
+    extra_information = dict(
+        unique_id=epics.caget(prefix + "image1:UniqueId_RBV"),
+        size_x=size_x,
+        size_y=size_y,
+        detector_state=epics.caget(prefix + "cam1:DetectorState_RBV"),
+        bitcoin_value="15000",
+    )
+    write_nexus_file("example.h5", img, md=extra_information)
diff --git a/definitions/manual/source/examples/epics/write_nexus_file2.py b/definitions/manual/source/examples/epics/write_nexus_file2.py
index 8c63a068d..ac883c809 100755
--- a/definitions/manual/source/examples/epics/write_nexus_file2.py
+++ b/definitions/manual/source/examples/epics/write_nexus_file2.py
@@ -17,37 +17,39 @@ def write_nexus_file(fname, image, md={}):
              (such as str, int, float, numpy array, ...)
     """
     nx = NXroot()
-    nx['/entry'] = NXentry(NXinstrument(NXdetector()))
-    nx['entry/instrument/detector/image'] = NXfield(image, units='counts',
-                                                    compression='gzip')
-    nx['entry/data'] = NXdata()
-    nx['entry/data'].makelink(nx['entry/instrument/detector/image'])
-    nx['entry/data'].nxsignal = nx['entry/data/image']
+    nx["/entry"] = NXentry(NXinstrument(NXdetector()))
+    nx["entry/instrument/detector/image"] = NXfield(
+        image, units="counts", compression="gzip"
+    )
+    nx["entry/data"] = NXdata()
+    nx["entry/data"].makelink(nx["entry/instrument/detector/image"])
+    nx["entry/data"].nxsignal = nx["entry/data/image"]
 
     if len(md) > 0:
         # /entry/instrument/metadata (optional, for metadata)
-        metadata = nx['/entry/instrument/metadata'] = NXcollection()
+        metadata = nx["/entry/instrument/metadata"] = NXcollection()
         for k, v in md.items():
             metadata[k] = v
 
-    nx.save(fname, 'w')
+    nx.save(fname, "w")
+
 
-	
 if __name__ == "__main__":
-	"""demonstrate how to use this code"""
-	import epics
-	prefix = "13SIM1:"
-	img = epics.caget(prefix+"image1:ArrayData")
-	size_x = epics.caget(prefix+"cam1:ArraySizeX_RBV")
-	size_y = epics.caget(prefix+"cam1:ArraySizeY_RBV")
-	# edit the full image for just the binned data
-	img = img[:size_x*size_y].reshape((size_x, size_y))
-
-	extra_information = dict(
-		unique_id = epics.caget(prefix+"image1:UniqueId_RBV"),
-		size_x = size_x,
-		size_y = size_y,
-		detector_state = epics.caget(prefix+"cam1:DetectorState_RBV"),
-		bitcoin_value="15000",
-	)
-	write_nexus_file("example.h5", img, md=extra_information)
+    """demonstrate how to use this code"""
+    import epics
+
+    prefix = "13SIM1:"
+    img = epics.caget(prefix + "image1:ArrayData")
+    size_x = epics.caget(prefix + "cam1:ArraySizeX_RBV")
+    size_y = epics.caget(prefix + "cam1:ArraySizeY_RBV")
+    # edit the full image for just the binned data
+    img = img[: size_x * size_y].reshape((size_x, size_y))
+
+    extra_information = dict(
+        unique_id=epics.caget(prefix + "image1:UniqueId_RBV"),
+        size_x=size_x,
+        size_y=size_y,
+        detector_state=epics.caget(prefix + "cam1:DetectorState_RBV"),
+        bitcoin_value="15000",
+    )
+    write_nexus_file("example.h5", img, md=extra_information)
diff --git a/definitions/manual/source/examples/h5py/BasicReader.py b/definitions/manual/source/examples/h5py/BasicReader.py
index 3a499c5c7..a3e2875ba 100755
--- a/definitions/manual/source/examples/h5py/BasicReader.py
+++ b/definitions/manual/source/examples/h5py/BasicReader.py
@@ -1,14 +1,14 @@
 #!/usr/bin/env python
-'''Reads NeXus HDF5 files using h5py and prints the contents'''
+"""Reads NeXus HDF5 files using h5py and prints the contents"""
 
-import h5py    # HDF5 support
+import h5py  # HDF5 support
 
 fileName = "prj_test.nexus.hdf5"
-f = h5py.File(fileName,  "r")
+f = h5py.File(fileName, "r")
 for item in f.attrs.keys():
     print(item + ":", f.attrs[item])
-mr = f['/entry/mr_scan/mr']
-i00 = f['/entry/mr_scan/I00']
+mr = f["/entry/mr_scan/mr"]
+i00 = f["/entry/mr_scan/I00"]
 print("%s\t%s\t%s" % ("#", "mr", "I00"))
 for i in range(len(mr)):
     print("%d\t%g\t%d" % (i, mr[i], i00[i]))
diff --git a/definitions/manual/source/examples/h5py/BasicWriter.py b/definitions/manual/source/examples/h5py/BasicWriter.py
index 63ccffde1..f71925d96 100755
--- a/definitions/manual/source/examples/h5py/BasicWriter.py
+++ b/definitions/manual/source/examples/h5py/BasicWriter.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
-'''Writes a NeXus HDF5 file using h5py and numpy'''
+"""Writes a NeXus HDF5 file using h5py and numpy"""
 
-import h5py    # HDF5 support
+import h5py  # HDF5 support
 import numpy
 
 print("Write a NeXus HDF5 file")
@@ -11,44 +11,46 @@
 # load data from two column format
 data = numpy.loadtxt("input.dat").T
 mr_arr = data[0]
-i00_arr = numpy.asarray(data[1],'int32')
+i00_arr = numpy.asarray(data[1], "int32")
 
 # create the HDF5 NeXus file
 f = h5py.File(fileName, "w")
 # point to the default data to be plotted
-f.attrs['default']          = 'entry'
+f.attrs["default"] = "entry"
 # give the HDF5 root some more attributes
-f.attrs['file_name']        = fileName
-f.attrs['file_time']        = timestamp
-f.attrs['instrument']       = 'APS USAXS at 32ID-B'
-f.attrs['creator']          = 'BasicWriter.py'
-f.attrs['NeXus_version']    = '4.3.0'
-f.attrs['HDF5_Version']     = h5py.version.hdf5_version
-f.attrs['h5py_version']     = h5py.version.version
+f.attrs["file_name"] = fileName
+f.attrs["file_time"] = timestamp
+f.attrs["instrument"] = "APS USAXS at 32ID-B"
+f.attrs["creator"] = "BasicWriter.py"
+f.attrs["NeXus_version"] = "4.3.0"
+f.attrs["HDF5_Version"] = h5py.version.hdf5_version
+f.attrs["h5py_version"] = h5py.version.version
 
 # create the NXentry group
-nxentry = f.create_group('entry')
-nxentry.attrs['NX_class'] = 'NXentry'
-nxentry.attrs['default'] = 'mr_scan'
-nxentry.create_dataset('title', data='1-D scan of I00 v. mr')
+nxentry = f.create_group("entry")
+nxentry.attrs["NX_class"] = "NXentry"
+nxentry.attrs["default"] = "mr_scan"
+nxentry.create_dataset("title", data="1-D scan of I00 v. mr")
 
 # create the NXentry group
-nxdata = nxentry.create_group('mr_scan')
-nxdata.attrs['NX_class'] = 'NXdata'
-nxdata.attrs['signal'] = 'I00'      # Y axis of default plot
-nxdata.attrs['axes'] = 'mr'         # X axis of default plot
-nxdata.attrs['mr_indices'] = [0,]   # use "mr" as the first dimension of I00
+nxdata = nxentry.create_group("mr_scan")
+nxdata.attrs["NX_class"] = "NXdata"
+nxdata.attrs["signal"] = "I00"  # Y axis of default plot
+nxdata.attrs["axes"] = "mr"  # X axis of default plot
+nxdata.attrs["mr_indices"] = [
+    0,
+]  # use "mr" as the first dimension of I00
 
 # X axis data
-ds = nxdata.create_dataset('mr', data=mr_arr)
-ds.attrs['units'] = 'degrees'
-ds.attrs['long_name'] = 'USAXS mr (degrees)'    # suggested X axis plot label
+ds = nxdata.create_dataset("mr", data=mr_arr)
+ds.attrs["units"] = "degrees"
+ds.attrs["long_name"] = "USAXS mr (degrees)"  # suggested X axis plot label
 
 # Y axis data
-ds = nxdata.create_dataset('I00', data=i00_arr)
-ds.attrs['units'] = 'counts'
-ds.attrs['long_name'] = 'USAXS I00 (counts)'    # suggested Y axis plot label
+ds = nxdata.create_dataset("I00", data=i00_arr)
+ds.attrs["units"] = "counts"
+ds.attrs["long_name"] = "USAXS I00 (counts)"  # suggested Y axis plot label
 
-f.close()	# be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
 
 print("wrote file:", fileName)
diff --git a/definitions/manual/source/examples/h5py/TestReader.py b/definitions/manual/source/examples/h5py/TestReader.py
index e654ec54c..538622066 100755
--- a/definitions/manual/source/examples/h5py/TestReader.py
+++ b/definitions/manual/source/examples/h5py/TestReader.py
@@ -1,7 +1,6 @@
+"""Reads NeXus HDF5 files using h5py and prints the contents"""
 
-'''Reads NeXus HDF5 files using h5py and prints the contents'''
-
-import h5py    # HDF5 support
+import h5py  # HDF5 support
 
 
 testFiles = ("prj_test.nexus.hdf5",)
@@ -16,18 +15,18 @@ def print_attr(parent, label):
 
 
 def print_child(item, label):
-    print("#" + "-"*40)
+    print("#" + "-" * 40)
     print("%s  %s" % (label, type(item)))
     print_attr(item, label)
-    if (repr(type(item)) == GROUP_TYPE_MATCH):
+    if repr(type(item)) == GROUP_TYPE_MATCH:
         base = label
         if "NX_class" in item.attrs:
             base += ":" + item.attrs["NX_class"]
         for k in item.keys():
             key = "%s/%s" % (base, k)
             print_child(item[k], key)
-    if (repr(type(item)) == DATASET_TYPE_MATCH):
-        #print label, item.value
+    if repr(type(item)) == DATASET_TYPE_MATCH:
+        # print label, item.value
         print(label)
         print("shape:", item.shape)
         print("size:", len(item.shape))
@@ -48,8 +47,8 @@ def process(fileName):
     return True
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     for fileName in testFiles:
-        print("#" + "="*60)
-        if not process( fileName ):
+        print("#" + "=" * 60)
+        if not process(fileName):
             print("Could not open:", fileName)
diff --git a/definitions/manual/source/examples/h5py/TestWriter.py b/definitions/manual/source/examples/h5py/TestWriter.py
index 64a358411..cab40f985 100755
--- a/definitions/manual/source/examples/h5py/TestWriter.py
+++ b/definitions/manual/source/examples/h5py/TestWriter.py
@@ -1,6 +1,6 @@
-'''Writes a NeXus HDF5 file using h5py'''
+"""Writes a NeXus HDF5 file using h5py"""
 
-import h5py    # HDF5 support
+import h5py  # HDF5 support
 import time
 
 
@@ -39,17 +39,17 @@
 """
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     print("Write a NeXus HDF5 file")
     fileName = "prj_test.nexus.hdf5"
     tzsecs = abs(time.timezone)
     if time.timezone < 0:
-        tzhhmm = "+"    # reverse logic, it seems
+        tzhhmm = "+"  # reverse logic, it seems
     else:
         tzhhmm = "-"
     if time.daylight:
         tzsecs -= 3600
-    tzhhmm += "%02d%02d" % (tzsecs / 3600, (tzsecs % 3600)/60)
+    tzhhmm += "%02d%02d" % (tzsecs / 3600, (tzsecs % 3600) / 60)
     timestamp = time.strftime("%Y-%m-%dT%H:%M:%S") + tzhhmm
 
     # prepare the data
@@ -69,17 +69,17 @@
     f.attrs["h5py_version"] = h5py.version.version
     f.attrs["file_time"] = timestamp
     f.attrs["file_update_time"] = timestamp
-    f.attrs["default"] = "entry"    # identify default NXentry group
+    f.attrs["default"] = "entry"  # identify default NXentry group
 
     nxentry = f.create_group("entry")
-    nxentry.attrs["NX_class"] = "NXentry"   # identify NeXus base class
-    nxentry.attrs["default"] = "mr_scan"    # identify default NXdata group
+    nxentry.attrs["NX_class"] = "NXentry"  # identify NeXus base class
+    nxentry.attrs["default"] = "mr_scan"  # identify default NXdata group
 
     # store the scan data
     nxdata = nxentry.create_group("mr_scan")
-    nxdata.attrs["NX_class"] = "NXdata"   # identify NeXus base class
-    nxdata.attrs["signal"] = "I00"        # identify default data to plot
-    nxdata.attrs["axes"] = "mr"           # identify default dimension scale to plot
+    nxdata.attrs["NX_class"] = "NXdata"  # identify NeXus base class
+    nxdata.attrs["signal"] = "I00"  # identify default data to plot
+    nxdata.attrs["axes"] = "mr"  # identify default dimension scale to plot
 
     mr = nxdata.create_dataset("mr", data=data["mr"])
     mr.attrs["units"] = "degrees"
@@ -88,14 +88,13 @@
     i00.attrs["units"] = "counts"
 
     # fill in some optional metadata
-    nxentry.create_dataset("title", 
-    	data="APS USAXS instrument MR (alignment) scan")
+    nxentry.create_dataset("title", data="APS USAXS instrument MR (alignment) scan")
     nxentry.create_dataset("start_time", data="2010-04-25T10:20:56-0500")
     nxentry.create_dataset("end_time", data="2010-04-25T10:21:16-0500")
-    nxentry.create_dataset("experiment_identifier", 
-       data="spec file 04_25.dat, scan #8")
-    nxentry.create_dataset("experiment_description", 
-       data="alignment scan of the USAXS collimating optics")
+    nxentry.create_dataset("experiment_identifier", data="spec file 04_25.dat, scan #8")
+    nxentry.create_dataset(
+        "experiment_description", data="alignment scan of the USAXS collimating optics"
+    )
 
     # be CERTAIN to close the file
     f.close()
diff --git a/definitions/manual/source/examples/h5py/externalExample.py b/definitions/manual/source/examples/h5py/externalExample.py
index 809cb1e1f..fad5078c6 100755
--- a/definitions/manual/source/examples/h5py/externalExample.py
+++ b/definitions/manual/source/examples/h5py/externalExample.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python
-'''
+"""
 Writes a NeXus HDF5 file using h5py with links to data in other HDF5 files.
 
 This example is based on ``writer_2_1``.
-'''
+"""
 
 import h5py
 import numpy
@@ -12,21 +12,21 @@
 FILE_HDF5_ANGLES = u"external_angles.hdf5"
 FILE_HDF5_COUNTS = u"external_counts.hdf5"
 
-#---------------------------
+# ---------------------------
 
 # get some data
 buffer = numpy.loadtxt("input.dat").T
-tthData = buffer[0]                             # float[]
-countsData = numpy.asarray(buffer[1],'int32')   # int[]
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 # put the angle data in an external (non-NeXus) HDF5 data file
 f = h5py.File(FILE_HDF5_ANGLES, "w")
 ds = f.create_dataset(u"angles", data=tthData)
 ds.attrs[u"units"] = u"degrees"
-f.close()    # be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
 
 
-# put the detector counts in an external HDF5 data file 
+# put the detector counts in an external HDF5 data file
 # with *incomplete* NeXus structure (no NXdata group)
 f = h5py.File(FILE_HDF5_COUNTS, "w")
 nxentry = f.create_group(u"entry")
@@ -46,13 +46,13 @@
 f = h5py.File(FILE_HDF5_MASTER, "w")
 f.attrs[u"default"] = u"entry"
 nxentry = f.create_group(u"entry")
-nxentry.attrs[u"NX_class"] =u"NXentry"
+nxentry.attrs[u"NX_class"] = u"NXentry"
 nxentry.attrs[u"default"] = u"data"
 nxdata = nxentry.create_group(u"data")
 nxdata.attrs[u"NX_class"] = u"NXdata"
 
 # link in the signal data
-local_addr = '/entry/data/counts'
+local_addr = "/entry/data/counts"
 external_addr = u"/entry/instrument/detector/counts"
 f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, external_addr)
 nxdata.attrs[u"signal"] = u"counts"
@@ -61,7 +61,9 @@
 local_addr = u"/entry/data/two_theta"
 f[local_addr] = h5py.ExternalLink(FILE_HDF5_ANGLES, u"/angles")
 nxdata.attrs[u"axes"] = u"two_theta"
-nxdata.attrs[u"two_theta_indices"] = [0,]
+nxdata.attrs[u"two_theta_indices"] = [
+    0,
+]
 
 local_addr = u"/entry/instrument"
 f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, u"/entry/instrument")
diff --git a/definitions/manual/source/examples/h5py/reader_attributes_trail.py b/definitions/manual/source/examples/h5py/reader_attributes_trail.py
index acb0127ea..908ca7bed 100644
--- a/definitions/manual/source/examples/h5py/reader_attributes_trail.py
+++ b/definitions/manual/source/examples/h5py/reader_attributes_trail.py
@@ -1,4 +1,3 @@
-
 import h5py
 
 with h5py.File("prj_test.nexus.hdf5", "r") as nx:
diff --git a/definitions/manual/source/examples/h5py/writer_1_3.py b/definitions/manual/source/examples/h5py/writer_1_3.py
index dd4e15d67..3126f932f 100755
--- a/definitions/manual/source/examples/h5py/writer_1_3.py
+++ b/definitions/manual/source/examples/h5py/writer_1_3.py
@@ -1,18 +1,18 @@
 #!/usr/bin/env python
-'''
+"""
 Writes the simplest NeXus HDF5 file using h5py 
 
 Uses method accepted at 2014NIAC
 according to the example from Figure 1.3 
 in the Introduction chapter
-'''
+"""
 
 import h5py
 import numpy
 
 buffer = numpy.loadtxt("input.dat").T
-tthData = buffer[0]                             # float[]
-countsData = numpy.asarray(buffer[1],'int32')   # int[]
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 f = h5py.File("writer_1_3.hdf5", "w")  # create the HDF5 NeXus file
 # since this is a simple example, no attributes are used at this point
@@ -24,7 +24,9 @@
 nxdata.attrs["NX_class"] = u"NXdata"
 nxdata.attrs[u"signal"] = u"counts"
 nxdata.attrs[u"axes"] = u"two_theta"
-nxdata.attrs[u"two_theta_indices"] = [0,]
+nxdata.attrs[u"two_theta_indices"] = [
+    0,
+]
 
 tth = nxdata.create_dataset(u"two_theta", data=tthData)
 tth.attrs[u"units"] = u"degrees"
@@ -32,4 +34,4 @@
 counts = nxdata.create_dataset(u"counts", data=countsData)
 counts.attrs[u"units"] = u"counts"
 
-f.close()	# be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
diff --git a/definitions/manual/source/examples/h5py/writer_2_1.py b/definitions/manual/source/examples/h5py/writer_2_1.py
index 66e76b371..64be0142f 100755
--- a/definitions/manual/source/examples/h5py/writer_2_1.py
+++ b/definitions/manual/source/examples/h5py/writer_2_1.py
@@ -1,15 +1,15 @@
 #!/usr/bin/env python
-'''
+"""
 Writes a simple NeXus HDF5 file using h5py with links
 according to the example from Figure 2.1 in the Design chapter
-'''
+"""
 
 import h5py
 import numpy
 
 buffer = numpy.loadtxt("input.dat").T
-tthData = buffer[0]                             # float[]
-countsData = numpy.asarray(buffer[1],'int32')   # int[]
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 f = h5py.File("writer_2_1.hdf5", "w")  # create the HDF5 NeXus file
 f.attrs[u"default"] = u"entry"
@@ -35,18 +35,20 @@
 nxdata.attrs[u"NX_class"] = u"NXdata"
 nxdata.attrs[u"signal"] = u"counts"
 nxdata.attrs[u"axes"] = u"two_theta"
-nxdata.attrs[u"two_theta_indices"] = [0,]
-
-source_addr = u"/entry/instrument/detector/two_theta"   # existing data
-target_addr = u"two_theta"                              # new location
-ds_tth.attrs[u"target"] = source_addr                   # a NeXus API convention for links
-nxdata[target_addr] = f[source_addr]                    # hard link
+nxdata.attrs[u"two_theta_indices"] = [
+    0,
+]
+
+source_addr = u"/entry/instrument/detector/two_theta"  # existing data
+target_addr = u"two_theta"  # new location
+ds_tth.attrs[u"target"] = source_addr  # a NeXus API convention for links
+nxdata[target_addr] = f[source_addr]  # hard link
 # nxdata._id.link(source_addr, target_addr, h5py.h5g.LINK_HARD)
 
-source_addr = u"/entry/instrument/detector/counts"      # existing data
-target_addr = u"counts"                                 # new location
-ds_counts.attrs[u"target"] = source_addr                # a NeXus API convention for links
-nxdata[target_addr] = f[source_addr]                    # hard link
+source_addr = u"/entry/instrument/detector/counts"  # existing data
+target_addr = u"counts"  # new location
+ds_counts.attrs[u"target"] = source_addr  # a NeXus API convention for links
+nxdata[target_addr] = f[source_addr]  # hard link
 # nxdata._id.link(source_addr, target_addr, h5py.h5g.LINK_HARD)
 
-f.close()	# be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
diff --git a/definitions/manual/source/examples/simple3D.py b/definitions/manual/source/examples/simple3D.py
index 3f5554684..0f3381cd1 100755
--- a/definitions/manual/source/examples/simple3D.py
+++ b/definitions/manual/source/examples/simple3D.py
@@ -4,30 +4,30 @@
 import nxs
 import numpy
 
-a = numpy.zeros((2,3,4),dtype=numpy.int)
+a = numpy.zeros((2, 3, 4), dtype=numpy.int)
 val = 0
 for i in range(2):
     for j in range(3):
         for k in range(4):
-            a[i,j,k] = val
+            a[i, j, k] = val
             val = val + 1
 
 nf = nxs.open("simple3D.h5", "w5")
 
-nf.makegroup("entry","NXentry")
-nf.opengroup("entry","NXentry")
+nf.makegroup("entry", "NXentry")
+nf.opengroup("entry", "NXentry")
 
-nf.makegroup("data","NXdata")
-nf.opengroup("data","NXdata")
-nf.putattr("signal","test")
+nf.makegroup("data", "NXdata")
+nf.opengroup("data", "NXdata")
+nf.putattr("signal", "test")
 
-nf.makedata("test",'int32',[2,3,4])
+nf.makedata("test", "int32", [2, 3, 4])
 nf.opendata("test")
 nf.putdata(a)
 nf.closedata()
 
-nf.closegroup()	# NXdata
-nf.closegroup() # NXentry
+nf.closegroup()  # NXdata
+nf.closegroup()  # NXentry
 
 nf.close()
 
diff --git a/definitions/manual/source/examples/verysimple.py b/definitions/manual/source/examples/verysimple.py
index 1288d4337..4a086c351 100755
--- a/definitions/manual/source/examples/verysimple.py
+++ b/definitions/manual/source/examples/verysimple.py
@@ -1,34 +1,64 @@
 #!/usr/bin/env python
-'''uses h5py to build the verysimple.nx5 data file'''
+"""uses h5py to build the verysimple.nx5 data file"""
 
 import h5py
 
-angle = [18.9094, 18.9096, 18.9098, 18.91,  18.9102, 
-         18.9104, 18.9106, 18.9108, 18.911, 18.9112, 
-         18.9114, 18.9116, 18.9118, 18.912, 18.9122]
-diode = [1193, 4474, 53220, 274310, 515430, 827880, 
-         1227100, 1434640, 1330280, 1037070, 598720, 
-         316460, 56677, 1000, 1000]
-
-f = h5py.File('verysimple.nx5', 'w')
-f.attrs['default'] = 'entry'
-
-nxentry = f.create_group('entry')
-nxentry.attrs["NX_class"] = 'NXentry'
-nxentry.attrs['default'] = 'data'
-
-nxdata = nxentry.create_group('data')
-nxdata.attrs["NX_class"] = 'NXdata'
-nxdata.attrs['signal'] = 'counts'
-nxdata.attrs['axes'] = 'two_theta'
-nxdata.attrs['two_theta_indices'] = [0,]
-
-tth = nxdata.create_dataset('two_theta', data=angle)
-tth.attrs['units'] = 'degrees'
-tth.attrs['long_name'] = 'two_theta (degrees)'
-
-counts = nxdata.create_dataset('counts', data=diode)
-counts.attrs['units'] = 'counts'
-counts.attrs['long_name'] = 'photodiode counts'
+angle = [
+    18.9094,
+    18.9096,
+    18.9098,
+    18.91,
+    18.9102,
+    18.9104,
+    18.9106,
+    18.9108,
+    18.911,
+    18.9112,
+    18.9114,
+    18.9116,
+    18.9118,
+    18.912,
+    18.9122,
+]
+diode = [
+    1193,
+    4474,
+    53220,
+    274310,
+    515430,
+    827880,
+    1227100,
+    1434640,
+    1330280,
+    1037070,
+    598720,
+    316460,
+    56677,
+    1000,
+    1000,
+]
+
+f = h5py.File("verysimple.nx5", "w")
+f.attrs["default"] = "entry"
+
+nxentry = f.create_group("entry")
+nxentry.attrs["NX_class"] = "NXentry"
+nxentry.attrs["default"] = "data"
+
+nxdata = nxentry.create_group("data")
+nxdata.attrs["NX_class"] = "NXdata"
+nxdata.attrs["signal"] = "counts"
+nxdata.attrs["axes"] = "two_theta"
+nxdata.attrs["two_theta_indices"] = [
+    0,
+]
+
+tth = nxdata.create_dataset("two_theta", data=angle)
+tth.attrs["units"] = "degrees"
+tth.attrs["long_name"] = "two_theta (degrees)"
+
+counts = nxdata.create_dataset("counts", data=diode)
+counts.attrs["units"] = "counts"
+counts.attrs["long_name"] = "photodiode counts"
 
 f.close()
diff --git a/definitions/utils/build_preparation.py b/definitions/utils/build_preparation.py
index 923c57b2b..83108ab37 100644
--- a/definitions/utils/build_preparation.py
+++ b/definitions/utils/build_preparation.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-'''
+"""
 Copy all resources for out-of-source documentation build
 
 Since we provide a build for Linux, MacOSX, and Windows,
@@ -16,7 +16,7 @@
 Here, we identify and copy all resources to build.
 The target directory is assumed to be the current directory.
 
-'''
+"""
 
 # Re-run this code to bring in any changed files (for incremental build)
 # Be sure to properly specify the source and target directories.
@@ -25,35 +25,35 @@
 from local_utilities import replicate
 
 
-MTIME_TOLERANCE = 0.001   # ignore mtime differences <= 1 ms
+MTIME_TOLERANCE = 0.001  # ignore mtime differences <= 1 ms
 ROOT_DIR_EXPECTED_RESOURCES = {
-    'files': '''COPYING LGPL.txt Makefile NXDL_VERSION
+    "files": """COPYING LGPL.txt Makefile NXDL_VERSION
                 nxdl.xsd nxdlTypes.xsd README.md
-             '''.split(),
-    'subdirs': '''applications base_classes contributed_definitions manual
+             """.split(),
+    "subdirs": """applications base_classes contributed_definitions manual
                  package utils www impatient-guide
-               '''.split(),
+               """.split(),
 }
-REPLICATED_RESOURCES = '''
+REPLICATED_RESOURCES = """
     LGPL.txt  Makefile  nxdl.xsd  nxdlTypes.xsd  NXDL_VERSION
     base_classes  applications  contributed_definitions 
     manual  utils impatient-guide
-'''.split()
+""".split()
 
 
 def mtime_size(filename):
-    '''get the modification time and size of the given item'''
+    """get the modification time and size of the given item"""
     file_status = os.stat(filename)
     return file_status.st_mtime, file_status.st_size
 
 
 def standardize_name(path, resource_name):
-    '''always use the absolute path to the filesystem resource'''
+    """always use the absolute path to the filesystem resource"""
     return os.path.abspath(os.path.join(path, resource_name))
 
 
 def identical(source, target):
-    '''compare if the resource is the same on both paths'''
+    """compare if the resource is the same on both paths"""
     if not os.path.exists(target):
         return False
     s_mtime, s_size = mtime_size(source)
@@ -62,7 +62,7 @@ def identical(source, target):
 
 
 def get_source_items(resources, source_path):
-    '''walk the source_path directories accumulating files to be checked'''
+    """walk the source_path directories accumulating files to be checked"""
     file_list = []
     path_list = []
     for path in sorted(resources):
@@ -77,7 +77,7 @@ def get_source_items(resources, source_path):
 
 
 def is_definitions_directory(basedir):
-    '''test if ``basedir`` is a NeXus definitions directory'''
+    """test if ``basedir`` is a NeXus definitions directory"""
     # look for the expected files and subdirectories in the root directory
     for item_list in ROOT_DIR_EXPECTED_RESOURCES.values():
         for item in item_list:
@@ -87,76 +87,79 @@ def is_definitions_directory(basedir):
 
 
 def qualify_inputs(source_dir, target_path):
-    '''raise error if this program cannot continue, based on the inputs'''
+    """raise error if this program cannot continue, based on the inputs"""
     if not os.path.exists(source_dir):
-        raise RuntimeError('Cannot find ' + source_dir)
+        raise RuntimeError("Cannot find " + source_dir)
 
     if not os.path.isdir(source_dir):
-        raise RuntimeError('Not a directory: ' + source_dir)
+        raise RuntimeError("Not a directory: " + source_dir)
 
     if not is_definitions_directory(source_dir):
-        msg = 'Not a NeXus definitions root directory ' + source_dir
+        msg = "Not a NeXus definitions root directory " + source_dir
         raise RuntimeError(msg)
-    
+
     if source_dir == target_path:
-        msg = 'Source and target directories cannot be the same'
+        msg = "Source and target directories cannot be the same"
         raise RuntimeError(msg)
 
 
 def command_args():
-    '''get the command-line arguments, handle syntax errors'''
+    """get the command-line arguments, handle syntax errors"""
     import argparse
+
     doc = __doc__.strip().splitlines()[0]
     parser = argparse.ArgumentParser(prog=sys.argv[0], description=doc)
-    parser.add_argument('defs_dir',
-                        action='store', 
-                        help="path to NeXus definitions root directory")
-    parser.add_argument('build_dir',
-                        action='store', 
-                        default=None,
-                        nargs='?',
-                        help="path to target directory (default: current directory)")
+    parser.add_argument(
+        "defs_dir", action="store", help="path to NeXus definitions root directory"
+    )
+    parser.add_argument(
+        "build_dir",
+        action="store",
+        default=None,
+        nargs="?",
+        help="path to target directory (default: current directory)",
+    )
     return parser.parse_args()
 
 
 def update(source_path, target_path):
-    '''
+    """
     duplicate directory from source_path to target_path
-    
+
     :param source_path str: source directory (NeXus definitions dir)
     :param target_path str: target directory is specified for build product
-    '''
+    """
     # TODO: what about file items in target_path that are not in source_path?
     source_path = os.path.abspath(source_path)
     target_path = os.path.abspath(target_path)
     qualify_inputs(source_path, target_path)
-    
+
     paths, files = get_source_items(REPLICATED_RESOURCES, source_path)
-    print('source has  %d directories   and   %d files' % (len(paths), len(files)))
-    
+    print("source has  %d directories   and   %d files" % (len(paths), len(files)))
+
     # create all the directories / subdirectories
     for source in sorted(paths):
-        relative_name = source[len(source_path):].lstrip(os.sep)
+        relative_name = source[len(source_path) :].lstrip(os.sep)
         target = standardize_name(target_path, relative_name)
         if not os.path.exists(target):
-            print('create directory %s' % target)
+            print("create directory %s" % target)
             os.mkdir(target, os.stat(source_path).st_mode)
     # check if the files need to be updated
     for source in sorted(files):
-        relative_name = source[len(source_path):].lstrip(os.sep)
+        relative_name = source[len(source_path) :].lstrip(os.sep)
         target = standardize_name(target_path, relative_name)
         if not identical(source, target):
-            print('update file %s' % target)
+            print("update file %s" % target)
             replicate(source, target)
 
 
 def main():
-    '''
+    """
     standard command-line processing
-    
+
     source directory (NeXus definitions dir) named as command line argument
     target directory is specified (or defaults to present working directory)
-    '''
+    """
     cli = command_args()
     source_path = os.path.abspath(cli.defs_dir)
     target_path = cli.build_dir or os.path.abspath(os.getcwd())
@@ -164,23 +167,24 @@ def main():
 
 
 def __developer_build_setup__():
-    '''for use with source-code debugger ONLY'''
+    """for use with source-code debugger ONLY"""
     import shutil
+
     # sys.argv.append('-h')
-    os.chdir('../')
-    os.chdir('build')
-    sys.argv.append('..')
+    os.chdir("../")
+    os.chdir("build")
+    sys.argv.append("..")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     # __developer_build_setup__()
     main()
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2015 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/definitions/utils/create_release_notes.py b/definitions/utils/create_release_notes.py
index 7fe7eb253..342c5da37 100755
--- a/definitions/utils/create_release_notes.py
+++ b/definitions/utils/create_release_notes.py
@@ -4,14 +4,14 @@
 Create release notes for a new release of this GitHub repository.
 """
 
-# Requires: 
+# Requires:
 #
 # * assumes current directory is within a repository clone
 # * pyGithub (conda or pip install) - https://pygithub.readthedocs.io/
 # * Github personal access token (https://github.com/settings/tokens)
 #
-# Github token access is needed or the GitHub API limit 
-# will likely interfere with making a complete report 
+# Github token access is needed or the GitHub API limit
+# will likely interfere with making a complete report
 # of the release.
 
 import argparse
@@ -22,26 +22,26 @@
 
 
 logging.basicConfig(level=logging.WARNING)
-logger = logging.getLogger('create_release_notes')
+logger = logging.getLogger("create_release_notes")
 
 
 def findGitConfigFile():
     """
     return full path to .git/config file
-    
+
     must be in current working directory or some parent directory
-    
-    This is a simplistic search that could be improved by using 
+
+    This is a simplistic search that could be improved by using
     an open source package.
-    
+
     Needs testing for when things are wrong.
     """
     path = os.getcwd()
     for i in range(99):
         config_file = os.path.join(path, ".git", "config")
         if os.path.exists(config_file):
-            return config_file      # found it!
-        
+            return config_file  # found it!
+
         # next, look in the parent directory
         path = os.path.abspath(os.path.join(path, ".."))
 
@@ -49,26 +49,28 @@ def findGitConfigFile():
     logger.error(msg)
     raise ValueError(msg)
 
+
 def parse_git_url(url):
     """
     return (organization, repository) tuple from url line of .git/config file
     """
-    if url.startswith("git@"): # deal with git@github.com:org/repo.git
+    if url.startswith("git@"):  # deal with git@github.com:org/repo.git
         url = url.split(":")[1]
     org, repo = url.rstrip(".git").split("/")[-2:]
     return org, repo
 
+
 def getRepositoryInfo():
     """
     return (organization, repository) tuple from .git/config file
-    
-    This is a simplistic search that could be improved by using 
+
+    This is a simplistic search that could be improved by using
     an open source package.
-    
+
     Needs testing for when things are wrong.
     """
     config_file = findGitConfigFile()
-        
+
     with open(config_file, "r") as f:
         for line in f.readlines():
             line = line.strip()
@@ -80,10 +82,11 @@ def getRepositoryInfo():
                     raise ValueError(msg)
                 return parse_git_url(url)
 
+
 def get_release_info(token, base_tag_name, head_branch_name, milestone_name):
     """mine the Github API for information about this release"""
     organization_name, repository_name = getRepositoryInfo()
-    gh = github.Github(token)   # GitHub Personal Access Token
+    gh = github.Github(token)  # GitHub Personal Access Token
 
     user = gh.get_user(organization_name)
     logger.debug(f"user: {user}")
@@ -92,9 +95,7 @@ def get_release_info(token, base_tag_name, head_branch_name, milestone_name):
     logger.debug(f"repo: {repo}")
 
     milestones = [
-        m
-        for m in repo.get_milestones(state="all")
-        if m.title == milestone_name
+        m for m in repo.get_milestones(state="all") if m.title == milestone_name
     ]
     if len(milestones) == 0:
         msg = f"Could not find milestone: {milestone_name}"
@@ -124,20 +125,14 @@ def get_release_info(token, base_tag_name, head_branch_name, milestone_name):
     logger.debug(f"# tags: {len(tags)}")
 
     pulls = {
-        p.number: p
-        for p in repo.get_pulls(state="closed")
-        if p.closed_at > earliest
+        p.number: p for p in repo.get_pulls(state="closed") if p.closed_at > earliest
     }
     logger.debug(f"# pulls: {len(pulls)}")
 
     issues = {
         i.number: i
         for i in repo.get_issues(milestone=milestone, state="closed")
-        if (
-            (milestone is not None or i.closed_at > earliest)
-            and
-            i.number not in pulls
-        )
+        if ((milestone is not None or i.closed_at > earliest) and i.number not in pulls)
     }
     logger.debug(f"# issues: {len(issues)}")
 
@@ -150,43 +145,36 @@ def parse_command_line():
     parser = argparse.ArgumentParser(description=doc)
 
     help_text = "name of tag to start the range"
-    parser.add_argument('base', action='store', help=help_text)
+    parser.add_argument("base", action="store", help=help_text)
 
     help_text = "name of milestone"
-    parser.add_argument('milestone', action='store', help=help_text)
+    parser.add_argument("milestone", action="store", help=help_text)
 
     parser.add_argument(
-        'token', 
-        action='store', 
-        help=(
-            "personal access token "
-            "(see: https://github.com/settings/tokens)"))
+        "token",
+        action="store",
+        help=("personal access token " "(see: https://github.com/settings/tokens)"),
+    )
 
     help_text = "name of tag, branch, SHA to end the range"
     help_text += ' (default="main")'
     parser.add_argument(
-        "--head", 
-        action='store', 
-        dest='head',
-        nargs='?', 
-        help = help_text, 
-        default="main")
+        "--head", action="store", dest="head", nargs="?", help=help_text, default="main"
+    )
 
     return parser.parse_args()
 
 
 def str2time(time_string):
     """convert date/time string to datetime object
-    
+
     input string example: ``Tue, 20 Dec 2016 17:35:40 GMT``
     """
     if time_string is None:
         msg = f"need valid date/time string, not: {time_string}"
         logger.error(msg)
         raise ValueError(msg)
-    return datetime.datetime.strptime(
-        time_string, 
-        "%a, %d %b %Y %H:%M:%S %Z")
+    return datetime.datetime.strptime(time_string, "%a, %d %b %Y %H:%M:%S %Z")
 
 
 def report(title, repo, milestone, tags, pulls, issues, commits):
@@ -199,7 +187,7 @@ def report(title, repo, milestone, tags, pulls, issues, commits):
         print(f"* **milestone**: [{milestone.title}]({milestone.url})")
         print("")
     print("section | quantity")
-    print("-"*5, " | ", "-"*5)
+    print("-" * 5, " | ", "-" * 5)
     print(f"[New Tags](#tags) | {len(tags)}")
     print(f"[Pull Requests](#pull-requests) | {len(pulls)}")
     print(f"[Issues](#issues) | {len(issues)}")
@@ -211,7 +199,7 @@ def report(title, repo, milestone, tags, pulls, issues, commits):
         print("-- none --")
     else:
         print("tag | date | name")
-        print("-"*5, " | ", "-"*5, " | ", "-"*5)
+        print("-" * 5, " | ", "-" * 5, " | ", "-" * 5)
         for k, tag in sorted(tags.items()):
             commit = repo.get_commit(tag.commit.sha)
             when = str2time(commit.last_modified).strftime("%Y-%m-%d")
@@ -223,11 +211,13 @@ def report(title, repo, milestone, tags, pulls, issues, commits):
         print("-- none --")
     else:
         print("pull request | date | state | title")
-        print("-"*5, " | ", "-"*5, " | ", "-"*5, " | ", "-"*5)
+        print("-" * 5, " | ", "-" * 5, " | ", "-" * 5, " | ", "-" * 5)
         for k, pull in sorted(pulls.items()):
             state = {True: "merged", False: "closed"}[pull.merged]
             when = str2time(pull.last_modified).strftime("%Y-%m-%d")
-            print(f"[#{pull.number}]({pull.html_url}) | {when} | {state} | {pull.title}")
+            print(
+                f"[#{pull.number}]({pull.html_url}) | {when} | {state} | {pull.title}"
+            )
     print("")
     print("### Issues")
     print("")
@@ -235,7 +225,7 @@ def report(title, repo, milestone, tags, pulls, issues, commits):
         print("-- none --")
     else:
         print("issue | date | title")
-        print("-"*5, " | ", "-"*5, " | ", "-"*5)
+        print("-" * 5, " | ", "-" * 5, " | ", "-" * 5)
         for k, issue in sorted(issues.items()):
             if k not in pulls:
                 when = issue.closed_at.strftime("%Y-%m-%d")
@@ -247,10 +237,10 @@ def report(title, repo, milestone, tags, pulls, issues, commits):
         print("-- none --")
     else:
         print("commit | date | message")
-        print("-"*5, " | ", "-"*5, " | ", "-"*5)
+        print("-" * 5, " | ", "-" * 5, " | ", "-" * 5)
         for k, commit in commits.items():
             message = commit.commit.message.splitlines()[0]
-            when = commit.raw_data['commit']['committer']['date'].split("T")[0]
+            when = commit.raw_data["commit"]["committer"]["date"].split("T")[0]
             print(f"[{k[:7]}]({commit.html_url}) | {when} | {message}")
 
 
@@ -268,20 +258,19 @@ def main(base=None, head=None, milestone=None, token=None, debug=False):
         token = cmd.token
         logger.setLevel(logging.WARNING)
 
-    info = get_release_info(
-        token, base_tag_name, head_branch_name, milestone_name)
+    info = get_release_info(token, base_tag_name, head_branch_name, milestone_name)
     # milestone, repo, tags, pulls, issues, commits = info
     report(milestone_name, *info)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/definitions/utils/dev_create_release_notes.py b/definitions/utils/dev_create_release_notes.py
index 613619fcd..87186f2fb 100755
--- a/definitions/utils/dev_create_release_notes.py
+++ b/definitions/utils/dev_create_release_notes.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 
-'''
+"""
 Developers: use this code to develop and test create_release_notes.py
-'''
+"""
 import os
 
 CREDS_FILE = os.path.join(
@@ -15,9 +15,5 @@
     token = cf.read().strip()
 
 from create_release_notes import main
-main(
-    base="v2018.5", 
-    head="main", 
-    milestone="NXDL 2020.1", 
-    token=token,
-    debug=True)
+
+main(base="v2018.5", head="main", milestone="NXDL 2020.1", token=token, debug=True)
diff --git a/definitions/utils/dev_nxdl2rst.py b/definitions/utils/dev_nxdl2rst.py
index fa8a41a05..498016d89 100755
--- a/definitions/utils/dev_nxdl2rst.py
+++ b/definitions/utils/dev_nxdl2rst.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 
-'''
+"""
 Developers: use this code to develop and test nxdl2rst.py
-'''
+"""
 
 # testing:
 # cd /tmp
@@ -27,7 +27,7 @@
 # nxdl = os.path.join(BASEDIR, '..', 'base_classes', 'NXcrystal.nxdl.xml')
 # nxdl = os.path.join(BASEDIR, '..', 'base_classes', 'NXentry.nxdl.xml')
 # nxdl = os.path.join(BASEDIR, '..', 'base_classes', 'NXobject.nxdl.xml')
-nxdl = os.path.join(BASEDIR, '..', 'base_classes', 'NXroot.nxdl.xml')
+nxdl = os.path.join(BASEDIR, "..", "base_classes", "NXroot.nxdl.xml")
 # nxdl = os.path.join(BASEDIR, '..', 'base_classes', 'NXuser.nxdl.xml')
 # nxdl = os.path.join(BASEDIR, '..', 'contributed_definitions', 'NXarpes.nxdl.xml')
 # nxdl = os.path.join(BASEDIR, '..', 'contributed_definitions', 'NXmagnetic_kicker.nxdl.xml')
diff --git a/definitions/utils/dev_units2rst.py b/definitions/utils/dev_units2rst.py
index 601619f87..767f2c537 100755
--- a/definitions/utils/dev_units2rst.py
+++ b/definitions/utils/dev_units2rst.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 
-'''
+"""
 Developers: use this code to develop and test nxdl2rst.py
-'''
+"""
 
 import sys
 from units2rst import worker
 
 
 sys.argv.append("../nxdlTypes.xsd")
-worker('anyUnitsAttr')
+worker("anyUnitsAttr")
diff --git a/definitions/utils/local_utilities.py b/definitions/utils/local_utilities.py
index af4979a61..8d2750d92 100644
--- a/definitions/utils/local_utilities.py
+++ b/definitions/utils/local_utilities.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-'''
+"""
 Common code for NeXus definitions Python tools
 
 ======================  ==================================
@@ -12,58 +12,57 @@
 :meth:`replicate_tree`  copy directory stack
 ======================  ==================================
 
-'''
+"""
 
 import os, sys, re
 import shutil
 
 
-
 def printf(str, *args):
-    '''formatted print without automatic newline'''
-    print(str % args, end='')
+    """formatted print without automatic newline"""
+    print(str % args, end="")
 
 
 def mtime(file_name):
-    '''return file modification time'''
+    """return file modification time"""
     return os.stat(file_name)[stat.ST_MTIME]
 
 
 def replicate(source, target):
-    '''
+    """
     for directories or files: copy ``source`` to ``target``, replaces ``target``
-    
+
     :param str source: path to source resource
     :param str target: path to target location
-    '''
+    """
     if os.path.isfile(source):
         shutil.copy2(source, target)
     elif os.path.isdir(source):
         replicate_tree(source, target)
     else:
-        msg = 'Do not know how to copy (skipped): ' + source
+        msg = "Do not know how to copy (skipped): " + source
         raise RuntimeWarning(msg)
 
 
 def replicate_tree(source, target):
-    '''
+    """
     for directories: copy ``source`` to ``target``, replaces ``target``
-    
+
     :param str source: path to source resource (a directory)
     :param str target: path to target location (a directory)
-    '''
+    """
     if os.path.exists(source):
         if os.path.exists(target):
             shutil.rmtree(target, ignore_errors=True)
         shutil.copytree(source, target)
     else:
-        raise RuntimeError('Directory not found: ' + source)
+        raise RuntimeError("Directory not found: " + source)
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/definitions/utils/nxdl2rst.py b/definitions/utils/nxdl2rst.py
index 954d6f314..fb308aa11 100755
--- a/definitions/utils/nxdl2rst.py
+++ b/definitions/utils/nxdl2rst.py
@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 
-'''
+"""
 Read the NeXus NXDL class specification and describe it.
 Write a restructured text (.rst) document for use in the NeXus manual in
 the NeXus NXDL Classes chapter.
-'''
+"""
 
 # testing:  see file dev_nxdl2rst.py
 
@@ -18,7 +18,7 @@
 from local_utilities import printf, replicate
 
 
-INDENTATION_UNIT = '  '
+INDENTATION_UNIT = "  "
 listing_category = None
 anchor_list = []  # list of all hypertext anchors
 
@@ -65,156 +65,165 @@ def sorter(key):
         print(table)
 
 
-def fmtTyp( node ):
-    typ = node.get('type', ':ref:`NX_CHAR <NX_CHAR>`') # per default
-    if typ.startswith('NX_'):
-        typ = ':ref:`%s <%s>`' % (typ, typ)
+def fmtTyp(node):
+    typ = node.get("type", ":ref:`NX_CHAR <NX_CHAR>`")  # per default
+    if typ.startswith("NX_"):
+        typ = ":ref:`%s <%s>`" % (typ, typ)
     return typ
 
 
-def fmtUnits( node ):
-    units = node.get('units', '')
+def fmtUnits(node):
+    units = node.get("units", "")
     if not units:
-        return ''
-    if units.startswith('NX_'):
-        units = '\ :ref:`%s <%s>`' % (units, units)
-    return ' {units=%s}' % units
+        return ""
+    if units.startswith("NX_"):
+        units = "\ :ref:`%s <%s>`" % (units, units)
+    return " {units=%s}" % units
 
 
-def getDocBlocks( ns, node ):
-    docnodes = node.xpath('nx:doc', namespaces=ns)
-    if docnodes is None or len(docnodes)==0:
-        return ''
+def getDocBlocks(ns, node):
+    docnodes = node.xpath("nx:doc", namespaces=ns)
+    if docnodes is None or len(docnodes) == 0:
+        return ""
     if len(docnodes) > 1:
-        raise Exception( 'Too many doc elements: line %d, %s' %
-                         (node.sourceline, os.path.split(node.base)[1]) )
+        raise Exception(
+            "Too many doc elements: line %d, %s"
+            % (node.sourceline, os.path.split(node.base)[1])
+        )
     docnode = docnodes[0]
 
     # be sure to grab _all_ content in the documentation
     # it might look like XML
-    s = lxml.etree.tostring(docnode, pretty_print=True,
-                            method='c14n', with_comments=False).decode('utf-8')
-    m = re.search(r'^<doc[^>]*>\n?(.*)\n?</doc>$', s, re.DOTALL )
+    s = lxml.etree.tostring(
+        docnode, pretty_print=True, method="c14n", with_comments=False
+    ).decode("utf-8")
+    m = re.search(r"^<doc[^>]*>\n?(.*)\n?</doc>$", s, re.DOTALL)
     if not m:
-        raise Exception( 'unexpected docstring [%s] ' % s )
+        raise Exception("unexpected docstring [%s] " % s)
     text = m.group(1)
 
     # substitute HTML entities in markup: "<" for "&lt;"
     # thanks: http://stackoverflow.com/questions/2087370/decode-html-entities-in-python-string
     htmlparser = HTMLParser.HTMLParser()
-    try:		# see #661
+    try:  # see #661
         import html
+
         text = html.unescape(text)
     except (ImportError, AttributeError):
         text = htmlparser.unescape(text)
 
     # Blocks are separated by whitelines
-    blocks = re.split( '\n\s*\n', text )
-    if len(blocks)==1 and len(blocks[0].splitlines())==1:
-        return [ blocks[0].rstrip().lstrip() ]
+    blocks = re.split("\n\s*\n", text)
+    if len(blocks) == 1 and len(blocks[0].splitlines()) == 1:
+        return [blocks[0].rstrip().lstrip()]
 
     # Indentation must be given by first line
-    m = re.match(r'(\s*)(\S+)', blocks[0])
+    m = re.match(r"(\s*)(\S+)", blocks[0])
     if not m:
-        return [ '' ]
+        return [""]
     indent = m.group(1)
 
     # Remove common indentation as determined from first line
-    if indent=="":
-        raise Exception( 'Missing initial indentation in <doc> of %s [%s]' %
-                         ( node.get('name'), blocks[0] ) )
+    if indent == "":
+        raise Exception(
+            "Missing initial indentation in <doc> of %s [%s]"
+            % (node.get("name"), blocks[0])
+        )
 
     out_blocks = []
     for block in blocks:
         lines = block.rstrip().splitlines()
         out_lines = []
         for line in lines:
-            if line[:len(indent)]!=indent:
-                raise Exception( 'Bad indentation in <doc> of %s [%s]: expected "%s" found "%s".' %
-                                 ( node.get('name'), block,
-                                   re.sub(r'\t',"\\\\t", indent ),
-                                   re.sub(r'\t',"\\\\t", line ),
-                            ) )
-            out_lines.append( line[len(indent):] )
-        out_blocks.append( "\n".join(out_lines) )
+            if line[: len(indent)] != indent:
+                raise Exception(
+                    'Bad indentation in <doc> of %s [%s]: expected "%s" found "%s".'
+                    % (
+                        node.get("name"),
+                        block,
+                        re.sub(r"\t", "\\\\t", indent),
+                        re.sub(r"\t", "\\\\t", line),
+                    )
+                )
+            out_lines.append(line[len(indent) :])
+        out_blocks.append("\n".join(out_lines))
     return out_blocks
 
 
-def getDocLine( ns, node ):
-    blocks = getDocBlocks( ns, node )
-    if len(blocks)==0:
-        return ''
-    if len(blocks)>1:
-        raise Exception( 'Unexpected multi-paragraph doc [%s]' %
-                         '|'.join(blocks) )
-    return re.sub(r'\n', " ", blocks[0])
+def getDocLine(ns, node):
+    blocks = getDocBlocks(ns, node)
+    if len(blocks) == 0:
+        return ""
+    if len(blocks) > 1:
+        raise Exception("Unexpected multi-paragraph doc [%s]" % "|".join(blocks))
+    return re.sub(r"\n", " ", blocks[0])
 
 
 def get_minOccurs(node, use_application_defaults):
-    '''
+    """
     get the value for the ``minOccurs`` attribute
 
     :param obj node: instance of lxml.etree._Element
     :param bool use_application_defaults: use special case value
     :returns str: value of the attribute (or its default)
-    '''
+    """
     # TODO: can we improve on the default by exmaining nxdl.xsd?
-    minOccurs_default = {True: '1', False: '0'}[use_application_defaults]
-    minOccurs = node.get('minOccurs', minOccurs_default)
+    minOccurs_default = {True: "1", False: "0"}[use_application_defaults]
+    minOccurs = node.get("minOccurs", minOccurs_default)
     return minOccurs
 
 
 def get_required_or_optional_text(node, use_application_defaults):
-    '''
+    """
     make clear if a reported item is required or optional
 
     :param obj node: instance of lxml.etree._Element
     :param bool use_application_defaults: use special case value
     :returns: formatted text
-    '''
-    tag = node.tag.split('}')[-1]
-    nm = node.get('name')
-    if tag in ('field', 'group'):
+    """
+    tag = node.tag.split("}")[-1]
+    nm = node.get("name")
+    if tag in ("field", "group"):
         optional_default = not use_application_defaults
-        optional = node.get('optional', optional_default) in (True, 'true', '1', 1)
-        recommended = node.get('recommended', None) in (True, 'true', '1', 1)
+        optional = node.get("optional", optional_default) in (True, "true", "1", 1)
+        recommended = node.get("recommended", None) in (True, "true", "1", 1)
         minOccurs = get_minOccurs(node, use_application_defaults)
-        if minOccurs in ('0', 0) or optional:
-            optional_text = '(optional) '
+        if minOccurs in ("0", 0) or optional:
+            optional_text = "(optional) "
         elif recommended:
-            optional_text = '(recommended) '
-        elif minOccurs in ('1', 1):
-            optional_text = '(required) '
+            optional_text = "(recommended) "
+        elif minOccurs in ("1", 1):
+            optional_text = "(required) "
         else:
             # this is unexpected and remarkable
             # TODO: add a remark to the log
-            optional_text = '(``minOccurs=%s``) ' % str(minOccurs)
-    elif tag in ('attribute',):
+            optional_text = "(``minOccurs=%s``) " % str(minOccurs)
+    elif tag in ("attribute",):
         optional_default = not use_application_defaults
-        optional = node.get('optional', optional_default) in (True, 'true', '1', 1)
-        recommended = node.get('recommended', None) in (True, 'true', '1', 1)
-        optional_text = {True: '(optional) ', False: '(required) '}[optional]
+        optional = node.get("optional", optional_default) in (True, "true", "1", 1)
+        recommended = node.get("recommended", None) in (True, "true", "1", 1)
+        optional_text = {True: "(optional) ", False: "(required) "}[optional]
         if recommended:
-            optional_text = '(recommended) '
+            optional_text = "(recommended) "
     else:
-        optional_text = '(unknown tag: ' + str(tag) + ') '
+        optional_text = "(unknown tag: " + str(tag) + ") "
     return optional_text
 
 
-def analyzeDimensions( ns, parent ):
-    node_list = parent.xpath('nx:dimensions', namespaces=ns)
+def analyzeDimensions(ns, parent):
+    node_list = parent.xpath("nx:dimensions", namespaces=ns)
     if len(node_list) != 1:
-        return ''
+        return ""
     node = node_list[0]
     # rank = node.get('rank') # ignore this
-    node_list = node.xpath('nx:dim', namespaces=ns)
+    node_list = node.xpath("nx:dim", namespaces=ns)
     dims = []
     for subnode in node_list:
-        value = subnode.get('value')
+        value = subnode.get("value")
         if not value:
-            value = 'ref(%s)' % subnode.get('ref')
-        dims.append( value )
-    return '[%s]' % ( ', '.join(dims) )
+            value = "ref(%s)" % subnode.get("ref")
+        dims.append(value)
+    return "[%s]" % (", ".join(dims))
 
 
 def hyperlinkTarget(parent_path, name, nxtype):
@@ -223,85 +232,83 @@ def hyperlinkTarget(parent_path, name, nxtype):
         sep = "@"
     else:
         sep = "/"
-    target = "%s%s%s-%s" % (
-        parent_path, sep, name, nxtype
-    )
+    target = "%s%s%s-%s" % (parent_path, sep, name, nxtype)
     addAnchor(target)
     return ".. _%s:\n" % target
 
 
-def printEnumeration( indent, ns, parent ):
-    node_list = parent.xpath('nx:item', namespaces=ns)
+def printEnumeration(indent, ns, parent):
+    node_list = parent.xpath("nx:item", namespaces=ns)
     if len(node_list) == 0:
-        return ''
+        return ""
 
     if len(node_list) == 1:
-        printf('%sObligatory value:', indent)
+        printf("%sObligatory value:", indent)
     else:
-        printf('%sAny of these values:', indent)
+        printf("%sAny of these values:", indent)
 
     docs = OrderedDict()
     for item in node_list:
-        name = item.get('value')
+        name = item.get("value")
         docs[name] = getDocLine(ns, item)
 
     ENUMERATION_INLINE_LENGTH = 60
+
     def show_as_typed_text(msg):
-        return '``%s``' % msg
-    oneliner = ' | '.join( map(show_as_typed_text, docs.keys()) )
-    if ( any( doc for doc in docs.values() ) or
-         len( oneliner ) > ENUMERATION_INLINE_LENGTH ):
+        return "``%s``" % msg
+
+    oneliner = " | ".join(map(show_as_typed_text, docs.keys()))
+    if any(doc for doc in docs.values()) or len(oneliner) > ENUMERATION_INLINE_LENGTH:
         # print one item per line
-        print('\n')
+        print("\n")
         for name, doc in docs.items():
-            printf('%s  * %s', indent, show_as_typed_text(name))
+            printf("%s  * %s", indent, show_as_typed_text(name))
             if doc:
-                printf(': %s', doc)
-            print('\n')
+                printf(": %s", doc)
+            print("\n")
     else:
         # print all items in one line
-        print(' %s' % ( oneliner ) )
-    print('')
+        print(" %s" % (oneliner))
+    print("")
 
 
-def printDoc( indent, ns, node, required=False):
+def printDoc(indent, ns, node, required=False):
     blocks = getDocBlocks(ns, node)
-    if len(blocks)==0:
+    if len(blocks) == 0:
         if required:
-            raise Exception( 'No documentation for: ' + node.get('name') )
-        print('')
+            raise Exception("No documentation for: " + node.get("name"))
+        print("")
     else:
         for block in blocks:
             for line in block.splitlines():
-                print( '%s%s' % ( indent, line ) )
+                print("%s%s" % (indent, line))
             print()
 
 
-def printAttribute( ns, kind, node, optional, indent, parent_path ):
-    name = node.get('name')
+def printAttribute(ns, kind, node, optional, indent, parent_path):
+    name = node.get("name")
     index_name = name
-    print("%s%s" % (indent, hyperlinkTarget(parent_path, name, 'attribute'))
+    print("%s%s" % (indent, hyperlinkTarget(parent_path, name, "attribute")))
+    print("%s.. index:: %s (%s attribute)\n" % (indent, index_name, kind))
+    print(
+        "%s**@%s**: %s%s%s\n" % (indent, name, optional, fmtTyp(node), fmtUnits(node))
     )
-    print( '%s.. index:: %s (%s attribute)\n' %
-           ( indent, index_name, kind ) )
-    print( '%s**@%s**: %s%s%s\n' % (
-        indent, name, optional, fmtTyp(node), fmtUnits(node) ) )
-    printDoc(indent+INDENTATION_UNIT, ns, node)
-    node_list = node.xpath('nx:enumeration', namespaces=ns)
+    printDoc(indent + INDENTATION_UNIT, ns, node)
+    node_list = node.xpath("nx:enumeration", namespaces=ns)
     if len(node_list) == 1:
-        printEnumeration( indent+INDENTATION_UNIT, ns, node_list[0] )
+        printEnumeration(indent + INDENTATION_UNIT, ns, node_list[0])
 
 
-def printIfDeprecated( ns, node, indent ):
-    deprecated = node.get('deprecated', None)
+def printIfDeprecated(ns, node, indent):
+    deprecated = node.get("deprecated", None)
     if deprecated is not None:
-        print( '\n%s.. index:: deprecated\n' % indent)
-        fmt = '\n%s**DEPRECATED**: %s\n'
-        print( fmt % (indent, deprecated ) )
+        print("\n%s.. index:: deprecated\n" % indent)
+        fmt = "\n%s**DEPRECATED**: %s\n"
+        print(fmt % (indent, deprecated))
 
 
 def printFullTree(ns, parent, name, indent, parent_path):
-    '''
+    """
     recursively print the full tree structure
 
     :param dict ns: dictionary of namespaces for use in XPath expressions
@@ -309,72 +316,90 @@ def printFullTree(ns, parent, name, indent, parent_path):
     :param str name: name of elements, such as NXentry/NXuser
     :param indent: to keep track of indentation level
     :param parent_path: NX class path of parent nodes
-    '''
+    """
     global listing_category
 
     use_application_defaults = listing_category in (
-        'application definition',
-        'contributed definition')
+        "application definition",
+        "contributed definition",
+    )
 
-    for node in parent.xpath('nx:field', namespaces=ns):
-        name = node.get('name')
+    for node in parent.xpath("nx:field", namespaces=ns):
+        name = node.get("name")
         index_name = name
         dims = analyzeDimensions(ns, node)
 
         optional_text = get_required_or_optional_text(node, use_application_defaults)
-        print("%s%s" % (indent, hyperlinkTarget(parent_path, name, 'field')))
-        print( '%s.. index:: %s (field)\n' %
-               ( indent, index_name ) )
+        print("%s%s" % (indent, hyperlinkTarget(parent_path, name, "field")))
+        print("%s.. index:: %s (field)\n" % (indent, index_name))
         print(
-            '%s**%s%s**: %s%s%s\n' % (
-                indent, name, dims, optional_text, fmtTyp(node), fmtUnits(node)
-                ))
+            "%s**%s%s**: %s%s%s\n"
+            % (indent, name, dims, optional_text, fmtTyp(node), fmtUnits(node))
+        )
 
-        printIfDeprecated( ns, node, indent+INDENTATION_UNIT )
-        printDoc(indent+INDENTATION_UNIT, ns, node)
+        printIfDeprecated(ns, node, indent + INDENTATION_UNIT)
+        printDoc(indent + INDENTATION_UNIT, ns, node)
 
-        node_list = node.xpath('nx:enumeration', namespaces=ns)
+        node_list = node.xpath("nx:enumeration", namespaces=ns)
         if len(node_list) == 1:
-            printEnumeration( indent+INDENTATION_UNIT, ns, node_list[0] )
+            printEnumeration(indent + INDENTATION_UNIT, ns, node_list[0])
 
-        for subnode in node.xpath('nx:attribute', namespaces=ns):
+        for subnode in node.xpath("nx:attribute", namespaces=ns):
             optional = get_required_or_optional_text(subnode, use_application_defaults)
-            printAttribute( ns, 'field', subnode, optional, indent+INDENTATION_UNIT, parent_path+"/"+name )
+            printAttribute(
+                ns,
+                "field",
+                subnode,
+                optional,
+                indent + INDENTATION_UNIT,
+                parent_path + "/" + name,
+            )
 
-    for node in parent.xpath('nx:group', namespaces=ns):
-        name = node.get('name', '')
-        typ = node.get('type', 'untyped (this is an error; please report)')
+    for node in parent.xpath("nx:group", namespaces=ns):
+        name = node.get("name", "")
+        typ = node.get("type", "untyped (this is an error; please report)")
 
         optional_text = get_required_or_optional_text(node, use_application_defaults)
-        if typ.startswith('NX'):
-            if name == '':
-                name = typ.lstrip('NX').upper()
-            typ = ':ref:`%s`' % typ
-        print("%s%s" % (indent, hyperlinkTarget(parent_path, name, 'group')))
-        print( '%s**%s**: %s%s\n' % (indent, name, optional_text, typ ) )
+        if typ.startswith("NX"):
+            if name == "":
+                name = typ.lstrip("NX").upper()
+            typ = ":ref:`%s`" % typ
+        print("%s%s" % (indent, hyperlinkTarget(parent_path, name, "group")))
+        print("%s**%s**: %s%s\n" % (indent, name, optional_text, typ))
 
-        printIfDeprecated(ns, node, indent+INDENTATION_UNIT)
-        printDoc(indent+INDENTATION_UNIT, ns, node)
+        printIfDeprecated(ns, node, indent + INDENTATION_UNIT)
+        printDoc(indent + INDENTATION_UNIT, ns, node)
 
-        for subnode in node.xpath('nx:attribute', namespaces=ns):
+        for subnode in node.xpath("nx:attribute", namespaces=ns):
             optional = get_required_or_optional_text(subnode, use_application_defaults)
-            printAttribute( ns, 'group', subnode, optional, indent+INDENTATION_UNIT, parent_path+"/"+name )
+            printAttribute(
+                ns,
+                "group",
+                subnode,
+                optional,
+                indent + INDENTATION_UNIT,
+                parent_path + "/" + name,
+            )
 
-        nodename = '%s/%s' % (name, node.get('type'))
-        printFullTree(ns, node, nodename, indent+INDENTATION_UNIT, parent_path+"/"+name)
+        nodename = "%s/%s" % (name, node.get("type"))
+        printFullTree(
+            ns, node, nodename, indent + INDENTATION_UNIT, parent_path + "/" + name
+        )
 
-    for node in parent.xpath('nx:link', namespaces=ns):
-        name = node.get('name')
-        print("%s%s" % (indent, hyperlinkTarget(parent_path, name, 'link')))
-        print( '%s**%s**: :ref:`link<Design-Links>` (suggested target: ``%s``)\n' % (
-            indent, name, node.get('target') ) )
-        printDoc(indent+INDENTATION_UNIT, ns, node)
+    for node in parent.xpath("nx:link", namespaces=ns):
+        name = node.get("name")
+        print("%s%s" % (indent, hyperlinkTarget(parent_path, name, "link")))
+        print(
+            "%s**%s**: :ref:`link<Design-Links>` (suggested target: ``%s``)\n"
+            % (indent, name, node.get("target"))
+        )
+        printDoc(indent + INDENTATION_UNIT, ns, node)
 
 
 def print_rst_from_nxdl(nxdl_file):
-    '''
+    """
     print restructured text from the named .nxdl.xml file
-    '''
+    """
     global listing_category
     # parse input file into tree
     tree = lxml.etree.parse(nxdl_file)
@@ -382,138 +407,138 @@ def print_rst_from_nxdl(nxdl_file):
     # The following URL is outdated, but that doesn't matter;
     # it won't be accessed; it's just an arbitrary namespace name.
     # It only needs to match the xmlns attribute in the NXDL files.
-    NAMESPACE = 'http://definition.nexusformat.org/nxdl/3.1'
-    ns = {'nx': NAMESPACE}
+    NAMESPACE = "http://definition.nexusformat.org/nxdl/3.1"
+    ns = {"nx": NAMESPACE}
 
     root = tree.getroot()
-    name = root.get('name')
+    name = root.get("name")
     title = name
-    parent_path = "/"+name  # absolute path of parent nodes, no trailing /
-    if len(name)<2 or name[0:2]!='NX':
-        raise Exception( 'Unexpected class name "%s"; does not start with NX' %
-                         ( name ) )
-    lexical_name = name[2:] # without padding 'NX', for indexing
+    parent_path = "/" + name  # absolute path of parent nodes, no trailing /
+    if len(name) < 2 or name[0:2] != "NX":
+        raise Exception('Unexpected class name "%s"; does not start with NX' % (name))
+    lexical_name = name[2:]  # without padding 'NX', for indexing
 
     # retrieve category from directory
-    #subdir = os.path.split(os.path.split(tree.docinfo.URL)[0])[1]
+    # subdir = os.path.split(os.path.split(tree.docinfo.URL)[0])[1]
     subdir = root.attrib["category"]
     # TODO: check for consistency with root.get('category')
     listing_category = {
-                 'base': 'base class',
-                 'application': 'application definition',
-                 'contributed': 'contributed definition',
-                 }[subdir]
+        "base": "base class",
+        "application": "application definition",
+        "contributed": "contributed definition",
+    }[subdir]
 
     use_application_defaults = listing_category in (
-        'application definition',
-        'contributed definition')
+        "application definition",
+        "contributed definition",
+    )
 
     # print ReST comments and section header
-    print( '.. auto-generated by script %s from the NXDL source %s' %
-           (sys.argv[0], sys.argv[1]) )
-    print('')
-    print( '.. index::' )
-    print( '    ! %s (%s)' % (name,listing_category) )
-    print( '    ! %s (%s)' % (lexical_name,listing_category) )
-    print( '    see: %s (%s); %s' %
-           (lexical_name,listing_category, name) )
-    print('')
-    print( '.. _%s:\n' % name )
-    print( '='*len(title) )
-    print( title )
-    print( '='*len(title) )
+    print(
+        ".. auto-generated by script %s from the NXDL source %s"
+        % (sys.argv[0], sys.argv[1])
+    )
+    print("")
+    print(".. index::")
+    print("    ! %s (%s)" % (name, listing_category))
+    print("    ! %s (%s)" % (lexical_name, listing_category))
+    print("    see: %s (%s); %s" % (lexical_name, listing_category, name))
+    print("")
+    print(".. _%s:\n" % name)
+    print("=" * len(title))
+    print(title)
+    print("=" * len(title))
 
     # print category & parent class
-    extends = root.get('extends')
+    extends = root.get("extends")
     if extends is None:
-        extends = 'none'
+        extends = "none"
     else:
-        extends = ':ref:`%s`' % extends
+        extends = ":ref:`%s`" % extends
 
-    print('')
-    print( '**Status**:\n' )
-    print( '  %s, extends %s' %
-           ( listing_category.strip(),
-             extends ) )
+    print("")
+    print("**Status**:\n")
+    print("  %s, extends %s" % (listing_category.strip(), extends))
 
-    printIfDeprecated(ns, root, '')
+    printIfDeprecated(ns, root, "")
 
     # print official description of this class
-    print('')
-    print( '**Description**:\n' )
+    print("")
+    print("**Description**:\n")
     printDoc(INDENTATION_UNIT, ns, root, required=True)
 
-
     # print symbol list
-    node_list = root.xpath('nx:symbols', namespaces=ns)
-    print( '**Symbols**:\n' )
+    node_list = root.xpath("nx:symbols", namespaces=ns)
+    print("**Symbols**:\n")
     if len(node_list) == 0:
-        print( '  No symbol table\n' )
+        print("  No symbol table\n")
     elif len(node_list) > 1:
-        raise Exception( 'Invalid symbol table in ' % root.get('name') )
+        raise Exception("Invalid symbol table in " % root.get("name"))
     else:
-        printDoc( INDENTATION_UNIT, ns, node_list[0] )
-        for node in node_list[0].xpath('nx:symbol', namespaces=ns):
+        printDoc(INDENTATION_UNIT, ns, node_list[0])
+        for node in node_list[0].xpath("nx:symbol", namespaces=ns):
             doc = getDocLine(ns, node)
-            printf('  **%s**', node.get('name'))
+            printf("  **%s**", node.get("name"))
             if doc:
-                printf(': %s', doc)
-            print('\n')
+                printf(": %s", doc)
+            print("\n")
 
     # print group references
-    print( '**Groups cited**:' )
-    node_list = root.xpath('//nx:group', namespaces=ns)
+    print("**Groups cited**:")
+    node_list = root.xpath("//nx:group", namespaces=ns)
     groups = []
     for node in node_list:
-        g = node.get('type')
-        if g.startswith('NX') and g not in groups:
+        g = node.get("type")
+        if g.startswith("NX") and g not in groups:
             groups.append(g)
     if len(groups) == 0:
-        print( '  none\n' )
+        print("  none\n")
     else:
-        out = [ (':ref:`%s`' % g) for g in groups ]
-        txt = ', '.join(sorted(out))
-        print( '  %s\n' % ( txt ) )
-        out = [ ('%s (base class); used in %s' % (g, listing_category)) for g in groups ]
-        txt = ', '.join(out)
-        print( '.. index:: %s\n' % ( txt ) )
+        out = [(":ref:`%s`" % g) for g in groups]
+        txt = ", ".join(sorted(out))
+        print("  %s\n" % (txt))
+        out = [("%s (base class); used in %s" % (g, listing_category)) for g in groups]
+        txt = ", ".join(out)
+        print(".. index:: %s\n" % (txt))
 
     # TODO: change instances of \t to proper indentation
-    html_root = 'https://github.com/nexusformat/definitions/blob/main'
+    html_root = "https://github.com/nexusformat/definitions/blob/main"
 
     # print full tree
-    print( '**Structure**:\n' )
-    for subnode in root.xpath('nx:attribute', namespaces=ns):
+    print("**Structure**:\n")
+    for subnode in root.xpath("nx:attribute", namespaces=ns):
         optional = get_required_or_optional_text(subnode, use_application_defaults)
-        printAttribute( ns, 'file', subnode, optional, INDENTATION_UNIT, parent_path) # FIXME: +"/"+name )
+        printAttribute(
+            ns, "file", subnode, optional, INDENTATION_UNIT, parent_path
+        )  # FIXME: +"/"+name )
     printFullTree(ns, root, name, INDENTATION_UNIT, parent_path)
 
     printAnchorList()
 
     # print NXDL source location
     subdir_map = {
-                  'base': 'base_classes',
-                  'application': 'applications',
-                  'contributed': 'contributed_definitions',
-                  }
+        "base": "base_classes",
+        "application": "applications",
+        "contributed": "contributed_definitions",
+    }
     print("")
-    print( '**NXDL Source**:' )
-    print( '  %s/%s/%s.nxdl.xml' % (
-        html_root, subdir_map[subdir], name) )
+    print("**NXDL Source**:")
+    print("  %s/%s/%s.nxdl.xml" % (html_root, subdir_map[subdir], name))
 
 
 def main():
-    '''
+    """
     standard command-line processing
-    '''
+    """
     import argparse
-    parser = argparse.ArgumentParser(description='test nxdl2rst code')
-    parser.add_argument('nxdl_file', help='name of NXDL file')
+
+    parser = argparse.ArgumentParser(description="test nxdl2rst code")
+    parser.add_argument("nxdl_file", help="name of NXDL file")
     results = parser.parse_args()
     nxdl_file = results.nxdl_file
 
     if not os.path.exists(nxdl_file):
-        print( 'Cannot find %s' % nxdl_file )
+        print("Cannot find %s" % nxdl_file)
         exit()
 
     print_rst_from_nxdl(nxdl_file)
@@ -522,16 +547,16 @@ def main():
     # copy that subdirectory (quietly) to the pwd, such as:
     #  contributed/NXcanSAS.nxdl.xml: cp -a contributed/canSAS ./
     category = os.path.basename(os.getcwd())
-    path = os.path.join('../../../../', category)
+    path = os.path.join("../../../../", category)
     basename = os.path.basename(nxdl_file)
-    corename = basename[2:].split('.')[0]
+    corename = basename[2:].split(".")[0]
     source = os.path.join(path, corename)
     if os.path.exists(source):
-        target = os.path.join('.', corename)
+        target = os.path.join(".", corename)
         replicate(source, target)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
 
 
diff --git a/definitions/utils/nxdl_desc2rst.py b/definitions/utils/nxdl_desc2rst.py
index 8211494bf..a06ee5f21 100755
--- a/definitions/utils/nxdl_desc2rst.py
+++ b/definitions/utils/nxdl_desc2rst.py
@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 
-'''
+"""
 Read the NXDL field types specification and find
 all the valid data types.  Write a restructured
 text (.rst) document for use in the NeXus manual in 
 the NXDL chapter.
-'''
+"""
 
 
 import os, sys
@@ -13,12 +13,12 @@
 import textwrap
 
 
-TITLE_MARKERS = '- + ~ ^ * @'.split()  # used for underscoring section titles
-INDENTATION = ' '*4
+TITLE_MARKERS = "- + ~ ^ * @".split()  # used for underscoring section titles
+INDENTATION = " " * 4
 
 
 ELEMENT_DICT = {
-                'attribute': '''
+    "attribute": """
 An ``attribute`` element can *only* be a child of a 
 ``field`` or ``group`` element.
 It is used to define *attribute* elements to be used and their data types
@@ -26,9 +26,8 @@
 
 For more details, see: 
 :ref:`NXDL.data.type.attributeType`
-                ''',
-                
-                'definition': '''
+                """,
+    "definition": """
 A ``definition`` element can *only* be used
 at the root level of an NXDL specification.
 Note:  Due to the large number of attributes of the ``definition`` element,
@@ -38,17 +37,15 @@
 :ref:`NXDL.data.type.definition`,
 :ref:`NXDL.data.type.definitionType`, and
 :ref:`NXDL.data.type.definitionTypeAttr`
-                ''',
-                
-                'dimensions': '''
+                """,
+    "dimensions": """
 The ``dimensions`` element describes the *shape* of an array.
 It is used *only* as a child of a ``field`` element.
 
 For more details, see: 
 :ref:`NXDL.data.type.dimensionsType`
-                ''',
-                
-                'doc': '''
+                """,
+    "doc": """
 A ``doc`` element can be a child of most NXDL elements.  In most cases, the
 content of the ``doc`` element will also become part of the NeXus manual.
 
@@ -61,9 +58,8 @@
 
 For more details, see: 
 :ref:`NXDL.data.type.docType`
-                ''',
-                
-                'enumeration': '''
+                """,
+    "enumeration": """
 An ``enumeration`` element can *only* be a child of a 
 ``field`` or ``attribute`` element.
 It is used to restrict the available choices to a predefined list,
@@ -72,9 +68,8 @@
 
 For more details, see: 
 :ref:`NXDL.data.type.enumerationType`
-                ''',
-                
-                'field': '''
+                """,
+    "field": """
 The ``field`` element provides the value of a named item.  Many different attributes
 are available to further define the ``field``.  Some of the attributes are not
 allowed to be used together (such as ``axes`` and ``axis``); see the documentation
@@ -83,18 +78,16 @@
 
 For more details, see: 
 :ref:`NXDL.data.type.fieldType`
-                ''',
-                
-                'choice': '''
+                """,
+    "choice": """
 A ``choice`` element is used when a named group might take one
 of several possible NeXus base classes.  Logically, it must
 have at least two group children.
 
 For more details, see: 
 :ref:`NXDL.data.type.choiceType`
-                ''',
-                
-                'group': '''
+                """,
+    "group": """
 A ``group`` element can *only* be a child of a 
 ``definition`` or ``group`` element.
 It describes a common level of organization in a NeXus data file, similar
@@ -102,9 +95,8 @@
 
 For more details, see: 
 :ref:`NXDL.data.type.groupType`
-                ''',
-                
-                'link': '''
+                """,
+    "link": """
 .. index:: 
     single: link target
 
@@ -117,27 +109,26 @@
 
 For more details, see: 
 :ref:`NXDL.data.type.linkType`
-                ''',
-                
-                'symbols': '''
+                """,
+    "symbols": """
 A ``symbols`` element can *only* be a child of a ``definition`` element.
 It defines the array index symbols to be used when defining arrays as
 ``field`` elements with common dimensions and lengths.
 
 For more details, see: 
 :ref:`NXDL.data.type.symbolsType`
-                ''',
-                }
+                """,
+}
 
 DATATYPE_DICT = {
-                 'basicComponent': '''/xs:schema//xs:complexType[@name='basicComponent']''',
-                 'validItemName': '''/xs:schema//xs:simpleType[@name='validItemName']''',
-                 'validNXClassName': '''/xs:schema//xs:simpleType[@name='validNXClassName']''',
-                 'validTargetName': '''/xs:schema//xs:simpleType[@name='validTargetName']''',
-                 'nonNegativeUnbounded': '''/xs:schema//xs:simpleType[@name='nonNegativeUnbounded']''',
-                 }
-
-ELEMENT_PREAMBLE = '''
+    "basicComponent": """/xs:schema//xs:complexType[@name='basicComponent']""",
+    "validItemName": """/xs:schema//xs:simpleType[@name='validItemName']""",
+    "validNXClassName": """/xs:schema//xs:simpleType[@name='validNXClassName']""",
+    "validTargetName": """/xs:schema//xs:simpleType[@name='validTargetName']""",
+    "nonNegativeUnbounded": """/xs:schema//xs:simpleType[@name='nonNegativeUnbounded']""",
+}
+
+ELEMENT_PREAMBLE = """
 =============================
 NXDL Elements and Field Types
 =============================
@@ -171,9 +162,9 @@
 NXDL Elements
 =============
 
-    '''
+    """
 
-DATATYPE_PREAMBLE = '''
+DATATYPE_PREAMBLE = """
 
 .. _NXDL.data.types.internal:
 
@@ -186,9 +177,9 @@
 or to simplify a complicated entry.  While the data types are not intended for
 use in NXDL specifications, they define structures that may be used in NXDL specifications. 
 
-'''
+"""
 
-DATATYPE_POSTAMBLE = '''
+DATATYPE_POSTAMBLE = """
 **The** ``xs:string`` **data type**
     The ``xs:string`` data type can contain characters, 
     line feeds, carriage returns, and tab characters.
@@ -204,178 +195,202 @@
     leading and trailing spaces, and multiple spaces.
     See https://www.w3schools.com/xml/schema_dtypes_string.asp
     for more details.
-'''
+"""
 
 
 def _tagMatch(ns, parent, match_list):
-    '''match this tag to a list'''
+    """match this tag to a list"""
     if parent is None:
         raise ValueError("Must supply a valid parent node")
     parent_tag = parent.tag
     tag_found = False
     for item in match_list:
         # this routine only handles certain XML Schema components
-        tag_found = parent_tag == '{%s}%s' % (ns['xs'], item)
+        tag_found = parent_tag == "{%s}%s" % (ns["xs"], item)
         if tag_found:
             break
     return tag_found
 
 
 def _indent(indentLevel):
-    return INDENTATION*indentLevel
+    return INDENTATION * indentLevel
 
 
 def printTitle(title, indentLevel):
     print(title)
-    print(TITLE_MARKERS[indentLevel]*len(title) + '\n')
+    print(TITLE_MARKERS[indentLevel] * len(title) + "\n")
 
 
 def generalHandler(ns, parent=None, indentLevel=0):
-    '''Handle XML nodes like the former XSLT template'''
+    """Handle XML nodes like the former XSLT template"""
     # ignore things we don't know how to handle
-    known_tags = ('complexType', 'simpleType', 'group', 'element', 'attribute')
+    known_tags = ("complexType", "simpleType", "group", "element", "attribute")
     if not _tagMatch(ns, parent, known_tags):
         return
-    
-    parent_name = parent.get('name')
+
+    parent_name = parent.get("name")
     if parent_name is None:
         return
-    
-    simple_tag = parent.tag[parent.tag.find('}')+1:]    # cut off the namespace identifier
-    
+
+    simple_tag = parent.tag[
+        parent.tag.find("}") + 1 :
+    ]  # cut off the namespace identifier
+
     # <varlistentry> ...
     name = parent_name  # + ' data type'
-    if simple_tag == 'attribute':
-        name = '@' + name
-    
-    if indentLevel == 0 and not simple_tag in ('attribute'):
-        print('.. index:: ! %s (NXDL data type)\n' % name)
-        print('\n.. _%s:\n' % ('NXDL.data.type.'+name))
+    if simple_tag == "attribute":
+        name = "@" + name
+
+    if indentLevel == 0 and not simple_tag in ("attribute"):
+        print(".. index:: ! %s (NXDL data type)\n" % name)
+        print("\n.. _%s:\n" % ("NXDL.data.type." + name))
 
     printTitle(name, indentLevel)
-    
+
     printDocs(ns, parent, indentLevel)
-    
-    if len(parent.xpath('xs:attribute', namespaces=ns)) > 0:
-        printTitle("Attributes of "+name, indentLevel+1)
-        applyTemplates(ns, parent, 'xs:attribute', indentLevel+1)
 
-    node_list = parent.xpath('xs:restriction', namespaces=ns)
+    if len(parent.xpath("xs:attribute", namespaces=ns)) > 0:
+        printTitle("Attributes of " + name, indentLevel + 1)
+        applyTemplates(ns, parent, "xs:attribute", indentLevel + 1)
+
+    node_list = parent.xpath("xs:restriction", namespaces=ns)
     if len(node_list) > 0:
-        #printTitle("Restrictions of "+name, indentLevel+1)
-        restrictionHandler(ns, node_list[0], indentLevel+1)
-    node_list = parent.xpath('xs:simpleType/xs:restriction/xs:enumeration', namespaces=ns)
+        # printTitle("Restrictions of "+name, indentLevel+1)
+        restrictionHandler(ns, node_list[0], indentLevel + 1)
+    node_list = parent.xpath(
+        "xs:simpleType/xs:restriction/xs:enumeration", namespaces=ns
+    )
     if len(node_list) > 0:
-#        printTitle("Enumerations of "+name, indentLevel+1)
-        applyTemplates(ns, parent, 'xs:simpleType/xs:restriction', 
-                       indentLevel+1, handler=restrictionHandler)
-    
-    if len(parent.xpath('xs:sequence/xs:element', namespaces=ns)) > 0:
-        printTitle("Elements of "+name, indentLevel+1)
-        applyTemplates(ns, parent, 'xs:sequence/xs:element', indentLevel+1)
-    
-    node_list = parent.xpath('xs:sequence/xs:group', namespaces=ns)
+        #        printTitle("Enumerations of "+name, indentLevel+1)
+        applyTemplates(
+            ns,
+            parent,
+            "xs:simpleType/xs:restriction",
+            indentLevel + 1,
+            handler=restrictionHandler,
+        )
+
+    if len(parent.xpath("xs:sequence/xs:element", namespaces=ns)) > 0:
+        printTitle("Elements of " + name, indentLevel + 1)
+        applyTemplates(ns, parent, "xs:sequence/xs:element", indentLevel + 1)
+
+    node_list = parent.xpath("xs:sequence/xs:group", namespaces=ns)
     if len(node_list) > 0:
-        printTitle("Groups under "+name, indentLevel+1)
-        printDocs(ns, node_list[0], indentLevel+1)
-
-    applyTemplates(ns, parent, 'xs:simpleType', indentLevel+1)
-    applyTemplates(ns, parent, 'xs:complexType', indentLevel+1)
-    applyTemplates(ns, parent, 'xs:complexType/xs:attribute', indentLevel+1)
-    applyTemplates(ns, parent, 'xs:complexContent/xs:extension/xs:attribute', indentLevel+1)
-    applyTemplates(ns, parent, 'xs:complexType/xs:sequence/xs:attribute', indentLevel+1)
-    applyTemplates(ns, parent, 'xs:complexType/xs:sequence/xs:element', indentLevel+1)
-    applyTemplates(ns, parent, 'xs:complexContent/xs:extension/xs:sequence/xs:element', indentLevel+1)
+        printTitle("Groups under " + name, indentLevel + 1)
+        printDocs(ns, node_list[0], indentLevel + 1)
+
+    applyTemplates(ns, parent, "xs:simpleType", indentLevel + 1)
+    applyTemplates(ns, parent, "xs:complexType", indentLevel + 1)
+    applyTemplates(ns, parent, "xs:complexType/xs:attribute", indentLevel + 1)
+    applyTemplates(
+        ns, parent, "xs:complexContent/xs:extension/xs:attribute", indentLevel + 1
+    )
+    applyTemplates(
+        ns, parent, "xs:complexType/xs:sequence/xs:attribute", indentLevel + 1
+    )
+    applyTemplates(ns, parent, "xs:complexType/xs:sequence/xs:element", indentLevel + 1)
+    applyTemplates(
+        ns,
+        parent,
+        "xs:complexContent/xs:extension/xs:sequence/xs:element",
+        indentLevel + 1,
+    )
 
 
 def restrictionHandler(ns, parent=None, indentLevel=0):
-    '''Handle XSD restriction nodes like the former XSLT template'''
-    if not _tagMatch(ns, parent, ('restriction',)):
+    """Handle XSD restriction nodes like the former XSLT template"""
+    if not _tagMatch(ns, parent, ("restriction",)):
         return
     printDocs(ns, parent, indentLevel)
-    print('\n')
-    print(_indent(indentLevel) + 'The value may be any')
-    base = parent.get('base')
-    pattern_nodes = parent.xpath('xs:pattern', namespaces=ns)
-    enumeration_nodes = parent.xpath('xs:enumeration', namespaces=ns)
+    print("\n")
+    print(_indent(indentLevel) + "The value may be any")
+    base = parent.get("base")
+    pattern_nodes = parent.xpath("xs:pattern", namespaces=ns)
+    enumeration_nodes = parent.xpath("xs:enumeration", namespaces=ns)
     if len(pattern_nodes) > 0:
-        print(_indent(indentLevel) + '``%s``' % base + ' that *also* matches the regular expression::\n')
-        print(_indent(indentLevel) + ' '*4 + pattern_nodes[0].get('value'))
+        print(
+            _indent(indentLevel)
+            + "``%s``" % base
+            + " that *also* matches the regular expression::\n"
+        )
+        print(_indent(indentLevel) + " " * 4 + pattern_nodes[0].get("value"))
     elif len(pattern_nodes) > 0:
         # how will this be reached?  Perhaps a deprecated procedure
-        print(_indent(indentLevel) + '``%s``' % base + ' from this list:')
+        print(_indent(indentLevel) + "``%s``" % base + " from this list:")
         for node in enumeration_nodes:
             enumerationHandler(ns, node, indentLevel)
             printDocs(ns, node, indentLevel)
         print(_indent(indentLevel))
     elif len(enumeration_nodes) > 0:
-        print(_indent(indentLevel) + 'one from this list only:\n')
+        print(_indent(indentLevel) + "one from this list only:\n")
         for node in enumeration_nodes:
             enumerationHandler(ns, node, indentLevel)
             printDocs(ns, parent, indentLevel)
         print(_indent(indentLevel))
     else:
-        print('@' + base)
-    print('\n')
+        print("@" + base)
+    print("\n")
 
 
 def enumerationHandler(ns, parent=None, indentLevel=0):
-    '''Handle XSD enumeration nodes like the former XSLT template'''
-    if not _tagMatch(ns, parent, ['enumeration']):
+    """Handle XSD enumeration nodes like the former XSLT template"""
+    if not _tagMatch(ns, parent, ["enumeration"]):
         return
-    print(_indent(indentLevel) + '* ``%s``' % parent.get('value'))
+    print(_indent(indentLevel) + "* ``%s``" % parent.get("value"))
     printDocs(ns, parent, indentLevel)
 
 
 def applyTemplates(ns, parent, path, indentLevel, handler=generalHandler):
-    '''iterate the nodes found on the supplied XPath expression'''
+    """iterate the nodes found on the supplied XPath expression"""
     db = {}
     for node in parent.xpath(path, namespaces=ns):
-        name = node.get('name') or node.get('ref') or node.get('value')
+        name = node.get("name") or node.get("ref") or node.get("value")
         if name is not None:
-            if name in ('nx:groupGroup',):
-                print(">"*45, name)
+            if name in ("nx:groupGroup",):
+                print(">" * 45, name)
             if name in db:
                 raise KeyError("Duplicate name found: " + name)
             db[name] = node
     for name in sorted(db):
         node = db[name]
         handler(ns, node, indentLevel)
-        #printDocs(ns, node, indentLevel)
+        # printDocs(ns, node, indentLevel)
 
 
 def printDocs(ns, parent, indentLevel=0):
     docs = getDocFromNode(ns, parent)
     if docs is not None:
-        print(_indent(indentLevel) + '\n')
+        print(_indent(indentLevel) + "\n")
         for line in docs.splitlines():
             print(_indent(indentLevel) + line)
-        print(_indent(indentLevel) + '\n')
+        print(_indent(indentLevel) + "\n")
 
 
 def getDocFromNode(ns, node, retval=None):
-    annotation_node = node.find('xs:annotation', ns)
+    annotation_node = node.find("xs:annotation", ns)
     if annotation_node is None:
         return retval
-    documentation_node = annotation_node.find('xs:documentation', ns)
+    documentation_node = annotation_node.find("xs:documentation", ns)
     if documentation_node is None:
         return retval
-    
+
     # Be sure to grab _all_ content in the <xs:documentation> node.
     # In the documentation nodes, use XML entities ("&lt;"" instead of "<")
     # for documentation characters that would otherwise be considered as XML.
     s = lxml.etree.tostring(documentation_node, method="text", pretty_print=True)
-    rst = s.decode().lstrip('\n')  # remove any leading blank lines
+    rst = s.decode().lstrip("\n")  # remove any leading blank lines
     rst = rst.rstrip()  # remove any trailing white space
     text = textwrap.dedent(rst)  # remove common leading space
 
     # substitute HTML entities in markup: "<" for "&lt;"
     # thanks: http://stackoverflow.com/questions/2087370/decode-html-entities-in-python-string
-    try:		# see #661
+    try:  # see #661
         import html
+
         text = html.unescape(text)
     except (ImportError, AttributeError):
         from html import parser as HTMLParser
+
         htmlparser = HTMLParser.HTMLParser()
         text = htmlparser.unescape(text)
 
@@ -383,7 +398,7 @@ def getDocFromNode(ns, node, retval=None):
 
 
 def addFigure(name, indentLevel=0):
-    fmt = '''
+    fmt = """
 .. compound::
 
     .. _%s:
@@ -401,16 +416,23 @@ def addFigure(name, indentLevel=0):
         as button in top toolbar).
         Set the name: "nxdl_%s.png" and move the file into the correct location using
         your operating system's commands.  Commit the revision to version control.
-    '''
-    imageFile = 'img/nxdl/nxdl_%s.png' % name
-    figure_id = 'fig.nxdl_%s' % name
+    """
+    imageFile = "img/nxdl/nxdl_%s.png" % name
+    figure_id = "fig.nxdl_%s" % name
     if not os.path.exists(os.path.abspath(imageFile)):
         return
-    text = fmt % (figure_id, imageFile, name, '80%', name, name, )
+    text = fmt % (
+        figure_id,
+        imageFile,
+        name,
+        "80%",
+        name,
+        name,
+    )
     indent = _indent(indentLevel)
     for line in text.splitlines():
         print(indent + line)
-    print('\n')
+    print("\n")
 
 
 def pickNodesFromXpath(ns, parent, path):
@@ -423,36 +445,35 @@ def main(tree, ns):
 
     for name in sorted(ELEMENT_DICT):
         print("")
-        print('.. index:: ! %s (NXDL element)\n' % name)
-        print('.. _%s:\n' % name)
+        print(".. index:: ! %s (NXDL element)\n" % name)
+        print(".. _%s:\n" % name)
         printTitle(name, indentLevel=0)
-        print('\n')
+        print("\n")
         print(ELEMENT_DICT[name])
-        print('\n')
+        print("\n")
         addFigure(name, indentLevel=0)
-        
 
     print(DATATYPE_PREAMBLE)
 
     path_list = (
-                 "/xs:schema/xs:complexType[@name='attributeType']",
-                 "/xs:schema/xs:element[@name='definition']",
-                 "/xs:schema/xs:complexType[@name='definitionType']",
-                 "/xs:schema/xs:simpleType[@name='definitionTypeAttr']",
-                 "/xs:schema/xs:complexType[@name='dimensionsType']",
-                 "/xs:schema/xs:complexType[@name='docType']",
-                 "/xs:schema/xs:complexType[@name='enumerationType']",
-                 "/xs:schema/xs:complexType[@name='fieldType']",
-                 "/xs:schema/xs:complexType[@name='choiceType']",
-                 "/xs:schema/xs:complexType[@name='groupType']",
-                 "/xs:schema/xs:complexType[@name='linkType']",
-                 "/xs:schema/xs:complexType[@name='symbolsType']",
-                 "/xs:schema/xs:complexType[@name='basicComponent']",
-                 "/xs:schema/xs:simpleType[@name='validItemName']",
-                 "/xs:schema/xs:simpleType[@name='validNXClassName']",
-                 "/xs:schema/xs:simpleType[@name='validTargetName']",
-                 "/xs:schema/xs:simpleType[@name='nonNegativeUnbounded']",
-                 )
+        "/xs:schema/xs:complexType[@name='attributeType']",
+        "/xs:schema/xs:element[@name='definition']",
+        "/xs:schema/xs:complexType[@name='definitionType']",
+        "/xs:schema/xs:simpleType[@name='definitionTypeAttr']",
+        "/xs:schema/xs:complexType[@name='dimensionsType']",
+        "/xs:schema/xs:complexType[@name='docType']",
+        "/xs:schema/xs:complexType[@name='enumerationType']",
+        "/xs:schema/xs:complexType[@name='fieldType']",
+        "/xs:schema/xs:complexType[@name='choiceType']",
+        "/xs:schema/xs:complexType[@name='groupType']",
+        "/xs:schema/xs:complexType[@name='linkType']",
+        "/xs:schema/xs:complexType[@name='symbolsType']",
+        "/xs:schema/xs:complexType[@name='basicComponent']",
+        "/xs:schema/xs:simpleType[@name='validItemName']",
+        "/xs:schema/xs:simpleType[@name='validNXClassName']",
+        "/xs:schema/xs:simpleType[@name='validTargetName']",
+        "/xs:schema/xs:simpleType[@name='nonNegativeUnbounded']",
+    )
     for path in path_list:
         nodes = pickNodesFromXpath(ns, tree, path)
         print("\n.. Xpath = %s\n" % path)
@@ -461,12 +482,12 @@ def main(tree, ns):
     print(DATATYPE_POSTAMBLE)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     developermode = True
     developermode = False
     if developermode and len(sys.argv) != 2:
         path = os.path.dirname(__file__)
-        NXDL_SCHEMA_FILE = os.path.join(path, '..', 'nxdl.xsd')
+        NXDL_SCHEMA_FILE = os.path.join(path, "..", "nxdl.xsd")
     else:
         if len(sys.argv) != 2:
             print("usage: %s nxdl.xsd" % sys.argv[0])
@@ -475,18 +496,18 @@ def main(tree, ns):
     if not os.path.exists(NXDL_SCHEMA_FILE):
         print("Cannot find %s" % NXDL_SCHEMA_FILE)
         exit()
-        
+
     tree = lxml.etree.parse(NXDL_SCHEMA_FILE)
-    NAMESPACE = 'http://www.w3.org/2001/XMLSchema'
-    ns = {'xs': NAMESPACE}
-    
+    NAMESPACE = "http://www.w3.org/2001/XMLSchema"
+    ns = {"xs": NAMESPACE}
+
     main(tree, ns)
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/definitions/utils/nxdl_summary.py b/definitions/utils/nxdl_summary.py
index 905cc7fce..582e501b0 100755
--- a/definitions/utils/nxdl_summary.py
+++ b/definitions/utils/nxdl_summary.py
@@ -1,26 +1,26 @@
 #!/usr/bin/env python
 
-'''
+"""
 Summarize the NXDL classes definitions for the given NXDL section.
 
 Re-write the index.rst file with a list of: class  summary (and a hidden toctree)
-'''
+"""
 
 
 import os, sys
 import lxml.etree
 
 
-TITLE_MARKERS = '- + ~ ^ * @'.split()  # used for underscoring section titles
-INDENTATION = ' '*4
+TITLE_MARKERS = "- + ~ ^ * @".split()  # used for underscoring section titles
+INDENTATION = " " * 4
 
 
-NAMESPACE = 'http://definition.nexusformat.org/nxdl/3.1'
-NS = {'nx': NAMESPACE}
+NAMESPACE = "http://definition.nexusformat.org/nxdl/3.1"
+NS = {"nx": NAMESPACE}
 
 
 PREAMBLES = {
-    'base_classes': '''
+    "base_classes": """
 .. index::
      ! see: class definitions; base class
      ! base class
@@ -35,11 +35,9 @@
 *might* be used in an instance of that class.
 Consider the base classes as a set of *components*
 that are used to construct a data file.
-    ''',
-
+    """,
     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
-    'applications': '''
+    "applications": """
 .. index::
      ! see: class definitions; application definition
      ! application definition
@@ -65,11 +63,9 @@
 In application definitions involving raw data,
 write the raw data in the :ref:`NXinstrument` tree and then link to it
 from the location(s) defined in the relevant application definition.
-    ''',
-
+    """,
     # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-    
-    'contributed_definitions': '''
+    "contributed_definitions": """
 .. index::
      ! see: class definitions; contributed definition
      ! contributed definition
@@ -87,75 +83,81 @@
 case not for general use.  The :ref:`NIAC` is charged to review any new contributed 
 definitions and provide feedback to the authors before ratification
 and acceptance as either a base class or application definition.
-    ''',
+    """,
 }
 
 
 def getSummary(nxdl_file):
-    '''
+    """
     get the summary line from each NXDL definition doc
-    
+
     That's the first physical line of the doc string.
-    '''
+    """
     tree = lxml.etree.parse(nxdl_file)
     root = tree.getroot()
-    nodes = root.xpath('nx:doc', namespaces=NS)
+    nodes = root.xpath("nx:doc", namespaces=NS)
     if len(nodes) != 1:
-        raise RuntimeError('wrong number of <doc> nodes in NXDL: ' + nxdl_file)
+        raise RuntimeError("wrong number of <doc> nodes in NXDL: " + nxdl_file)
     text = nodes[0].text
     return text.strip().splitlines()[0]
 
 
 def command_args():
-    '''get the command-line arguments, handle syntax errors'''
+    """get the command-line arguments, handle syntax errors"""
     import argparse
+
     doc = __doc__.strip().splitlines()[0]
     parser = argparse.ArgumentParser(prog=sys.argv[0], description=doc)
-    parser.add_argument('section',
-                        action='store', 
-                        help="NXDL section (such as *base_classes*)")
+    parser.add_argument(
+        "section", action="store", help="NXDL section (such as *base_classes*)"
+    )
     return parser.parse_args()
 
 
 def main(section):
     if section not in PREAMBLES.keys():
-        raise KeyError('unknown NXDL section: ' + section)
+        raise KeyError("unknown NXDL section: " + section)
     base_path = os.path.abspath(os.path.dirname(__file__))
-    nxdl_path = os.path.abspath(os.path.join(base_path, '..', section))
+    nxdl_path = os.path.abspath(os.path.join(base_path, "..", section))
     if not os.path.exists(nxdl_path):
-        raise IOError('not found: ' + nxdl_path)
+        raise IOError("not found: " + nxdl_path)
 
-    rst_path = os.path.abspath(os.path.join(base_path, '..', 'manual', 'source', 'classes', section))
+    rst_path = os.path.abspath(
+        os.path.join(base_path, "..", "manual", "source", "classes", section)
+    )
     if not os.path.exists(rst_path):
-        raise IOError('not found: ' + rst_path)
+        raise IOError("not found: " + rst_path)
 
-    index_file = os.path.join(rst_path, 'index.rst')
+    index_file = os.path.join(rst_path, "index.rst")
 
     classes = []
     text = []
-    text.append('''
+    text.append(
+        """
 .. do NOT edit this file
-   automatically generated by script ''' + __file__)
-    text.append('')
+   automatically generated by script """
+        + __file__
+    )
+    text.append("")
     text.append(PREAMBLES[section])
     for fname in sorted(os.listdir(nxdl_path)):
-        if fname.endswith('.nxdl.xml'):
-            class_name = fname.split('.')[0]
+        if fname.endswith(".nxdl.xml"):
+            class_name = fname.split(".")[0]
             classes.append(class_name)
             summary = getSummary(os.path.join(nxdl_path, fname))
-            text.append('')
-            text.append(':ref:`' + class_name + '`')
+            text.append("")
+            text.append(":ref:`" + class_name + "`")
             text.append(INDENTATION + summary)
-    text.append('')
-    text.append('.. toctree::')
-    text.append(INDENTATION + ':hidden:')
-    text.append('')
+    text.append("")
+    text.append(".. toctree::")
+    text.append(INDENTATION + ":hidden:")
+    text.append("")
     for cname in sorted(classes):
         text.append(INDENTATION + cname)
-    text.append('')
-    open(index_file, 'w').writelines('\n'.join(text))
+    text.append("")
+    open(index_file, "w").writelines("\n".join(text))
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli = command_args()
     main(cli.section)
diff --git a/definitions/utils/test_nxdl.py b/definitions/utils/test_nxdl.py
index 8e4544113..e7152c794 100644
--- a/definitions/utils/test_nxdl.py
+++ b/definitions/utils/test_nxdl.py
@@ -1,33 +1,37 @@
 #!/bin/env python
 
-'''
+"""
 unit testing of NeXus definitions NXDL files and XML Schema
-'''
+"""
 
 import os
 import sys
 import unittest
 import lxml.etree
 
-# xmllint --noout --schema nxdl.xsd base_classes/NXentry.nxdl.xml 
+# xmllint --noout --schema nxdl.xsd base_classes/NXentry.nxdl.xml
 # base_classes/NXentry.nxdl.xml validates
 
 
-BASE_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
-NXDL_XSD_SCHEMA = 'nxdl.xsd'
+BASE_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+NXDL_XSD_SCHEMA = "nxdl.xsd"
 NXDL_SCHEMA = lxml.etree.XMLSchema(
-    lxml.etree.parse(
-        os.path.join(BASE_DIR, NXDL_XSD_SCHEMA)))
+    lxml.etree.parse(os.path.join(BASE_DIR, NXDL_XSD_SCHEMA))
+)
 
-NXDL_CATEGORY_NAMES = 'base_classes applications contributed_definitions'.split()
+NXDL_CATEGORY_NAMES = "base_classes applications contributed_definitions".split()
 
 
-class NXDL_Invalid(Exception): pass
-class NXDL_Valid(Exception): pass
+class NXDL_Invalid(Exception):
+    pass
+
+
+class NXDL_Valid(Exception):
+    pass
 
 
 def isNXDL(fname):
-    return fname.endswith('.nxdl.xml')
+    return fname.endswith(".nxdl.xml")
 
 
 def get_NXDL_file_list():
@@ -41,73 +45,73 @@ def get_NXDL_file_list():
 
 
 def validate_xml(xml_file_name):
-    '''
+    """
     validate an NXDL XML file against an XML Schema file
 
     :param str xml_file_name: name of XML file
-    '''
+    """
     try:
         xml_tree = lxml.etree.parse(xml_file_name)
     except lxml.etree.XMLSyntaxError as exc:
-        msg = xml_file_name + ' : ' + str(exc)
+        msg = xml_file_name + " : " + str(exc)
         raise NXDL_Invalid(msg)
     try:
         result = NXDL_SCHEMA.assertValid(xml_tree)
         # there is no assertNotRaises so raise this when successful
         raise NXDL_Valid
     except lxml.etree.DocumentInvalid as exc:
-        msg = xml_file_name + ' : ' + str(exc)
+        msg = xml_file_name + " : " + str(exc)
         raise NXDL_Invalid(msg)
 
 
 class TestMaker(type):
-    
     def __new__(cls, clsname, bases, dct):
-        # Add a method to the class' __dict__ for every 
+        # Add a method to the class' __dict__ for every
         # file name in the NXDL file list.
-        cat_number_dict = {c: str(i+1) for i, c in enumerate(NXDL_CATEGORY_NAMES)}
+        cat_number_dict = {c: str(i + 1) for i, c in enumerate(NXDL_CATEGORY_NAMES)}
         for fname in get_NXDL_file_list():
             category, nxdl_name = os.path.split(fname)
             category_number = cat_number_dict[category]
             point = nxdl_name.find(".")
             nxdl_name = nxdl_name[:point]
-            test_name = 'test'
+            test_name = "test"
             # since these will be sorted, get the categories in the desired order
-            test_name += '__' + str(category_number)
-            test_name += '__' + category
-            test_name += '__' + nxdl_name
+            test_name += "__" + str(category_number)
+            test_name += "__" + category
+            test_name += "__" + nxdl_name
             dct[test_name] = cls.make_test(fname)
 
         return super(TestMaker, cls).__new__(cls, clsname, bases, dct)
 
     @staticmethod
     def make_test(nxdl_file_name):
-        
         def test_wrap(self):
             # test body for each NXDL file test
             with self.assertRaises(NXDL_Valid):
                 validate_xml(nxdl_file_name)
             self.assertRaises(NXDL_Valid, validate_xml, nxdl_file_name)
+
         return test_wrap
 
+
 class Individual_NXDL_Tests(unittest.TestCase, metaclass=TestMaker):
-    '''
+    """
     run all tests created in TestMaker() class, called by suite()
-    '''
+    """
 
 
 def suite(*args, **kw):
-    '''gather all the tests together in a suite, called by run()'''
+    """gather all the tests together in a suite, called by run()"""
     test_suite = unittest.TestSuite()
     test_suite.addTests(unittest.makeSuite(Individual_NXDL_Tests))
     return test_suite
 
 
 def run():
-    '''run all the unit tests'''
-    runner=unittest.TextTestRunner(verbosity=2)
+    """run all the unit tests"""
+    runner = unittest.TextTestRunner(verbosity=2)
     runner.run(suite())
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     run()
diff --git a/definitions/utils/test_nxdl2rst.py b/definitions/utils/test_nxdl2rst.py
index e72b9fdac..733e3f752 100644
--- a/definitions/utils/test_nxdl2rst.py
+++ b/definitions/utils/test_nxdl2rst.py
@@ -1,8 +1,8 @@
 #!/bin/env python
 
-'''
+"""
 unit testing: NXDL to RST for documentation
-'''
+"""
 
 import os
 import sys
@@ -14,47 +14,49 @@
 
 
 class Capture_stdout(list):
-    '''
+    """
     capture all printed output (to stdout) into list
-    
+
     # http://stackoverflow.com/questions/16571150/how-to-capture-stdout-output-from-a-python-function-call
-    '''
+    """
+
     def __enter__(self):
         self._stdout = sys.stdout
         sys.stdout = self._stringio = StringIO()
         return self
+
     def __exit__(self, *args):
         self.extend(self._stringio.getvalue().splitlines())
-        del self._stringio    # free up some memory
+        del self._stringio  # free up some memory
         sys.stdout = self._stdout
 
 
 class Issue_524_Clarify_Optional_or_Required(unittest.TestCase):
-    '''
+    """
     make it obvious what is required and what is optional
-    
+
     **field**: (optional or required) NX_TYPE
-    '''
-        
+    """
+
     def test_base_class_NXentry(self):
-        expected_lines = '''
+        expected_lines = """
         **definition**: (optional) :ref:`NX_CHAR <NX_CHAR>`
         **DATA**: (optional) :ref:`NXdata`
         **notes**: (optional) :ref:`NXnote`
         **@default**: (optional) :ref:`NX_CHAR <NX_CHAR>`
-        '''.strip().splitlines()
-        
-        self.apply_tests('base_classes', 'NXentry', expected_lines)
-        
+        """.strip().splitlines()
+
+        self.apply_tests("base_classes", "NXentry", expected_lines)
+
     def test_base_class_NXuser(self):
-        expected_lines = '''
+        expected_lines = """
         **name**: (optional) :ref:`NX_CHAR <NX_CHAR>`
-        '''.strip().splitlines()
-        
-        self.apply_tests('base_classes', 'NXuser', expected_lines)
-        
+        """.strip().splitlines()
+
+        self.apply_tests("base_classes", "NXuser", expected_lines)
+
     def test_application_definition_NXcanSAS(self):
-        expected_lines = '''
+        expected_lines = """
         **definition**: (required) :ref:`NX_CHAR <NX_CHAR>`
         **title**: (required) :ref:`NX_CHAR <NX_CHAR>`
         **run**: (required) :ref:`NX_CHAR <NX_CHAR>`
@@ -76,18 +78,20 @@ def test_application_definition_NXcanSAS(self):
         **@canSAS_class**: (required) :ref:`NX_CHAR <NX_CHAR>`
         **@signal**: (required) :ref:`NX_CHAR <NX_CHAR>`
         **@I_axes**: (required) :ref:`NX_CHAR <NX_CHAR>`
-        '''.strip().splitlines()
-        
-        self.apply_tests('applications', 'NXcanSAS', expected_lines)
+        """.strip().splitlines()
+
+        self.apply_tests("applications", "NXcanSAS", expected_lines)
 
     def apply_tests(self, category, class_name, expected_lines):
-        nxdl_file = os.path.join(os.path.dirname(__file__),'..', category, class_name+'.nxdl.xml')
+        nxdl_file = os.path.join(
+            os.path.dirname(__file__), "..", category, class_name + ".nxdl.xml"
+        )
         self.assertTrue(os.path.exists(nxdl_file), nxdl_file)
-        
-        sys.argv.insert(0, 'python')
+
+        sys.argv.insert(0, "python")
         with Capture_stdout() as printed_lines:
             nxdl2rst.print_rst_from_nxdl(nxdl_file)
-        
+
         printed_lines = [_.strip() for _ in printed_lines]
         for line in expected_lines:
             expected = line.strip()
@@ -95,7 +99,7 @@ def apply_tests(self, category, class_name, expected_lines):
 
 
 def suite(*args, **kw):
-    '''gather all the tests together in a suite, called by run()'''
+    """gather all the tests together in a suite, called by run()"""
     test_suite = unittest.TestSuite()
     test_suite_list = [
         Issue_524_Clarify_Optional_or_Required,
@@ -106,10 +110,10 @@ def suite(*args, **kw):
 
 
 def run():
-    '''run all the unit tests'''
-    runner=unittest.TextTestRunner(verbosity=2)
+    """run all the unit tests"""
+    runner = unittest.TextTestRunner(verbosity=2)
     runner.run(suite())
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     run()
diff --git a/definitions/utils/test_suite.py b/definitions/utils/test_suite.py
index 11c646990..92b8bb246 100644
--- a/definitions/utils/test_suite.py
+++ b/definitions/utils/test_suite.py
@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 
-'''
+"""
 unit testing of the NeXus definitions
-'''
+"""
 
 import os
 import unittest
@@ -12,20 +12,21 @@
 def suite(*args, **kw):
     import test_nxdl
     import test_nxdl2rst
+
     test_suite = unittest.TestSuite()
     test_list = [
         test_nxdl,
         test_nxdl2rst,
-        ]
+    ]
 
     for test in test_list:
         test_suite.addTest(test.suite())
     return test_suite
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     owd = os.getcwd()
-    runner=unittest.TextTestRunner(verbosity=2)
+    runner = unittest.TextTestRunner(verbosity=2)
     result = runner.run(suite())
     os.chdir(owd)
     sys.exit(len(result.errors))
diff --git a/definitions/utils/types2rst.py b/definitions/utils/types2rst.py
index d724438ac..2faa1a62f 100755
--- a/definitions/utils/types2rst.py
+++ b/definitions/utils/types2rst.py
@@ -1,24 +1,24 @@
 #!/usr/bin/env python
 
-'''
+"""
 Read the the NeXus NXDL types specification and find
 all the valid data types.  Write a restructured
 text (.rst) document for use in the NeXus manual in 
 the NXDL chapter.
-'''
+"""
 
 
 import units2rst
 
 
-if __name__ == '__main__':
-    units2rst.worker('primitiveType', section = 'data')
+if __name__ == "__main__":
+    units2rst.worker("primitiveType", section="data")
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/definitions/utils/units2rst.py b/definitions/utils/units2rst.py
index bce2cfe64..b3ac8e4e7 100755
--- a/definitions/utils/units2rst.py
+++ b/definitions/utils/units2rst.py
@@ -1,18 +1,18 @@
 #!/usr/bin/env python
 
-'''
+"""
 Read the the NeXus NXDL types specification and find
 all the valid types of units.  Write a restructured
 text (.rst) document for use in the NeXus manual in 
 the NXDL chapter.
-'''
+"""
 
 
 import os, sys
 import lxml.etree
 
 
-def worker(nodeMatchString, section = 'units'):
+def worker(nodeMatchString, section="units"):
     if len(sys.argv) != 2:
         print("usage: %s nxdlTypes.xsd" % sys.argv[0])
         exit()
@@ -20,72 +20,72 @@ def worker(nodeMatchString, section = 'units'):
     if not os.path.exists(NXDL_TYPES_FILE):
         print("Cannot find %s" % NXDL_TYPES_FILE)
         exit()
-        
+
     tree = lxml.etree.parse(NXDL_TYPES_FILE)
-    
-    output = ['.. auto-generated by %s -- DO NOT EDIT' % sys.argv[0]]
-    output.append('')
-    
-    labels = ('term', 'description')
-    output.append('.. nodeMatchString : %s' % nodeMatchString)
-    output.append('')
+
+    output = [".. auto-generated by %s -- DO NOT EDIT" % sys.argv[0]]
+    output.append("")
+
+    labels = ("term", "description")
+    output.append(".. nodeMatchString : %s" % nodeMatchString)
+    output.append("")
     db = {}
-    
-    NAMESPACE = 'http://www.w3.org/2001/XMLSchema'
-    ns = {'xs': NAMESPACE}
-    root = tree.xpath('//xs:schema', namespaces=ns)[0]
-    s = '//xs:simpleType'
+
+    NAMESPACE = "http://www.w3.org/2001/XMLSchema"
+    ns = {"xs": NAMESPACE}
+    root = tree.xpath("//xs:schema", namespaces=ns)[0]
+    s = "//xs:simpleType"
     node_list = tree.xpath("//xs:simpleType", namespaces=ns)
-    
+
     # get the names of all the types of units
     members = []
     for node in node_list:
-        if node.get('name') == nodeMatchString:
-            union = node.xpath('xs:union', namespaces=ns)
-            members = union[0].get('memberTypes', '').split()
-    
+        if node.get("name") == nodeMatchString:
+            union = node.xpath("xs:union", namespaces=ns)
+            members = union[0].get("memberTypes", "").split()
+
     # get the definition of each type of units
     for node in node_list:
-        node_name = node.get('name')
-        if 'nxdl:' + node_name in members:
-            words = node.xpath('xs:annotation/xs:documentation', namespaces=ns)[0]
+        node_name = node.get("name")
+        if "nxdl:" + node_name in members:
+            words = node.xpath("xs:annotation/xs:documentation", namespaces=ns)[0]
             examples = []
             for example in words.iterchildren():
                 nm = example.attrib.get("name")
                 if nm is not None and nm == "example":
-                    examples.append("``"+example.text+"``")
+                    examples.append("``" + example.text + "``")
             a = words.text
             if len(examples) > 0:
                 a = a.strip() + ", example(s): " + " | ".join(examples)
             db[node_name] = a
 
-#             for item in node.xpath('xs:restriction//xs:enumeration', namespaces=ns):
-#                 key = '%s' % item.get('value')
-#                 words = item.xpath('xs:annotation/xs:documentation', namespaces=ns)[0]
-#                 db[key] = words.text
-    
-    print('\n'.join(output))
-    
+    #             for item in node.xpath('xs:restriction//xs:enumeration', namespaces=ns):
+    #                 key = '%s' % item.get('value')
+    #                 words = item.xpath('xs:annotation/xs:documentation', namespaces=ns)[0]
+    #                 db[key] = words.text
+
+    print("\n".join(output))
+
     # this list is too long to make this a table in latex
     # for two columns, a Sphinx fieldlist will do just as well
     for key in sorted(db):
-        print('.. index:: ! %s (%s type)\n' % (key, section))       # index entry
-        print('.. _%s:\n' % key)       # cross-reference point
-        print(':%s:' % key)
+        print(".. index:: ! %s (%s type)\n" % (key, section))  # index entry
+        print(".. _%s:\n" % key)  # cross-reference point
+        print(":%s:" % key)
         for line in db[key].splitlines():
-            print('    %s' % line)
-        print('')
+            print("    %s" % line)
+        print("")
 
 
-if __name__ == '__main__':
-    #sys.argv.append('../nxdlTypes.xsd')  # FIXME: developer only -- remove for production!!!
-    worker('anyUnitsAttr')
+if __name__ == "__main__":
+    # sys.argv.append('../nxdlTypes.xsd')  # FIXME: developer only -- remove for production!!!
+    worker("anyUnitsAttr")
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/definitions/utils/update_copyright_date.py b/definitions/utils/update_copyright_date.py
index f81b72f18..f62229ca4 100755
--- a/definitions/utils/update_copyright_date.py
+++ b/definitions/utils/update_copyright_date.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-'''
+"""
 update the copyright date in all NeXus text files
 
 This is the bash command to find all matching lines::
@@ -8,7 +8,7 @@
   grep -iR copyright | grep -i "(c)" | grep -i nexus
 
 See copyright text at bottom of this file for example.
-'''
+"""
 
 import os, sys
 import mimetypes
@@ -17,19 +17,20 @@
 import datetime
 
 YEAR = datetime.datetime.now().year
-LEFT_SIDE_TEXT_MATCH = 'Copyright (C) '
-RIGHT_SIDE_TEXT_MATCH = ' NeXus International Advisory Committee (NIAC)'
+LEFT_SIDE_TEXT_MATCH = "Copyright (C) "
+RIGHT_SIDE_TEXT_MATCH = " NeXus International Advisory Committee (NIAC)"
 
 
 def update(filename):
-    '''update the copyright year in the file'''
+    """update the copyright year in the file"""
+
     def position(line, key):
         pos = line.find(key)
         if pos >= 0:
-            if line.find('NIAC') >= 0:
+            if line.find("NIAC") >= 0:
                 return pos
         return None
-        
+
     if not os.path.exists(filename):
         return
     changes = []
@@ -37,7 +38,7 @@ def position(line, key):
     for number, line in enumerate(buf):
         pos = position(line, LEFT_SIDE_TEXT_MATCH)
         if pos is None:
-            continue    # no match
+            continue  # no match
 
         pos += len(LEFT_SIDE_TEXT_MATCH)
         text_l = line[:pos]
@@ -47,65 +48,65 @@ def position(line, key):
         text_r = text[pos:]
 
         try:
-            years = list(map(int, text[:pos].split('-')))
+            years = list(map(int, text[:pos].split("-")))
             if len(years) in (1, 2):
                 if len(years) == 1:
                     years.append(YEAR)
                 elif len(years) == 2:
                     years[1] = YEAR
-                line_new = text_l + '-'.join(map(str, years)) + text_r
+                line_new = text_l + "-".join(map(str, years)) + text_r
                 changes.append(list((number, line_new)))
         except Exception as _exc:
             print(number, filename, str(_exc))
     for number, line in changes:
         buf[number] = line
     if len(changes) > 0:
-        print('Update: ', filename)
-        fp = open(filename, 'w')
+        print("Update: ", filename)
+        fp = open(filename, "w")
         fp.writelines(buf)
         fp.close()
 
 
 def find_source_files(path):
-    '''walk the source_path directories accumulating files to be checked'''
+    """walk the source_path directories accumulating files to be checked"""
     file_list = []
     for root, dirs, files in os.walk(path):
-        if root.find('/.git') < 0 or root.find('/kits') < 0:
+        if root.find("/.git") < 0 or root.find("/kits") < 0:
             file_list = file_list + [os.path.join(root, _) for _ in files]
     return file_list
 
 
 def sift_file_list(file_list):
-    '''remove known non-text files and paths'''
+    """remove known non-text files and paths"""
     new_list = []
-    acceptable_mime_types = '''
+    acceptable_mime_types = """
         application/xml
         application/x-msdos-program
         application/xslt+xml
-    '''.strip().split()
-    ignore_extensions = '''
+    """.strip().split()
+    ignore_extensions = """
     .dia .vsdx .h5 .nx .hdf5 .hdf .nx5 .pyc
-    '''.strip().split()
+    """.strip().split()
     for fn in file_list:
         _fn = os.path.split(fn)[-1]
         mime = mimetypes.guess_type(fn)[0]
-        if fn.find('/.git') >= 0:
+        if fn.find("/.git") >= 0:
             continue
-        if fn.find('/.settings') >= 0:
+        if fn.find("/.settings") >= 0:
             continue
-        if fn.find('/kits') >= 0:
+        if fn.find("/kits") >= 0:
             continue
-        if fn.find('/build') >= 0:
+        if fn.find("/build") >= 0:
             continue
         if os.path.splitext(fn)[-1] in ignore_extensions:
             continue
-        if mime is None or mime.startswith('text/') or mime in acceptable_mime_types:
+        if mime is None or mime.startswith("text/") or mime in acceptable_mime_types:
             new_list.append(fn)
     return new_list
 
 
 def is_definitions_directory(basedir):
-    '''test if ``basedir`` is a NeXus definitions directory'''
+    """test if ``basedir`` is a NeXus definitions directory"""
     # look for the expected files and subdirectories in the root directory
     for item_list in ROOT_DIR_EXPECTED_RESOURCES.values():
         for item in item_list:
@@ -115,61 +116,63 @@ def is_definitions_directory(basedir):
 
 
 def qualify_inputs(root_dir):
-    '''raise error if this program cannot continue, based on the inputs'''
+    """raise error if this program cannot continue, based on the inputs"""
     if not os.path.exists(root_dir):
-        raise RuntimeError('Cannot find ' + root_dir)
+        raise RuntimeError("Cannot find " + root_dir)
 
     if not os.path.isdir(root_dir):
-        raise RuntimeError('Not a directory: ' + root_dir)
+        raise RuntimeError("Not a directory: " + root_dir)
 
     if not is_definitions_directory(root_dir):
-        msg = 'Not a NeXus definitions root directory ' + root_dir
+        msg = "Not a NeXus definitions root directory " + root_dir
         raise RuntimeError(msg)
 
 
 def command_args():
-    '''get the command-line arguments, handle syntax errors'''
+    """get the command-line arguments, handle syntax errors"""
     import argparse
+
     doc = __doc__.strip().splitlines()[0]
     parser = argparse.ArgumentParser(prog=sys.argv[0], description=doc)
-    parser.add_argument('defs_dir',
-                        action='store', 
-                        help="NeXus definitions root directory")
+    parser.add_argument(
+        "defs_dir", action="store", help="NeXus definitions root directory"
+    )
     return parser.parse_args()
 
 
 def main():
-    '''
+    """
     standard command-line processing
-    
+
     source directory (NeXus definitions dir) named as command line argument
     target directory is specified (or defaults to present working directory)
-    '''
+    """
     cli = command_args()
     root_dir = os.path.abspath(cli.defs_dir)
     qualify_inputs(root_dir)
-    
+
     file_list = sift_file_list(find_source_files(root_dir))
     for fn in file_list:
         update(fn)
 
 
 def __developer_build_setup__():
-    '''for use with source-code debugger ONLY'''
+    """for use with source-code debugger ONLY"""
     import shutil
+
     # sys.argv.append('-h')
-    sys.argv.append('..')
+    sys.argv.append("..")
 
 
-if __name__ == '__main__':
-    #__developer_build_setup__()
+if __name__ == "__main__":
+    # __developer_build_setup__()
     main()
 
 
 # NeXus - Neutron and X-ray Common Data Format
-# 
+#
 # Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC)
-# 
+#
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
 # License as published by the Free Software Foundation; either
diff --git a/nexus_constructor/ui_utils.py b/nexus_constructor/ui_utils.py
index cdc18c18f..942424261 100644
--- a/nexus_constructor/ui_utils.py
+++ b/nexus_constructor/ui_utils.py
@@ -12,7 +12,7 @@
     QMessageBox,
     QProgressBar,
     QVBoxLayout,
-    QWidget
+    QWidget,
 )
 
 FILE_DIALOG_NATIVE = QFileDialog.DontUseNativeDialog
diff --git a/nx-class-documentation/html/_downloads/0a877a94f6f32b982b9a0c74073f6f01/write_nexus_file2.py b/nx-class-documentation/html/_downloads/0a877a94f6f32b982b9a0c74073f6f01/write_nexus_file2.py
index 8c63a068d..ac883c809 100644
--- a/nx-class-documentation/html/_downloads/0a877a94f6f32b982b9a0c74073f6f01/write_nexus_file2.py
+++ b/nx-class-documentation/html/_downloads/0a877a94f6f32b982b9a0c74073f6f01/write_nexus_file2.py
@@ -17,37 +17,39 @@ def write_nexus_file(fname, image, md={}):
              (such as str, int, float, numpy array, ...)
     """
     nx = NXroot()
-    nx['/entry'] = NXentry(NXinstrument(NXdetector()))
-    nx['entry/instrument/detector/image'] = NXfield(image, units='counts',
-                                                    compression='gzip')
-    nx['entry/data'] = NXdata()
-    nx['entry/data'].makelink(nx['entry/instrument/detector/image'])
-    nx['entry/data'].nxsignal = nx['entry/data/image']
+    nx["/entry"] = NXentry(NXinstrument(NXdetector()))
+    nx["entry/instrument/detector/image"] = NXfield(
+        image, units="counts", compression="gzip"
+    )
+    nx["entry/data"] = NXdata()
+    nx["entry/data"].makelink(nx["entry/instrument/detector/image"])
+    nx["entry/data"].nxsignal = nx["entry/data/image"]
 
     if len(md) > 0:
         # /entry/instrument/metadata (optional, for metadata)
-        metadata = nx['/entry/instrument/metadata'] = NXcollection()
+        metadata = nx["/entry/instrument/metadata"] = NXcollection()
         for k, v in md.items():
             metadata[k] = v
 
-    nx.save(fname, 'w')
+    nx.save(fname, "w")
+
 
-	
 if __name__ == "__main__":
-	"""demonstrate how to use this code"""
-	import epics
-	prefix = "13SIM1:"
-	img = epics.caget(prefix+"image1:ArrayData")
-	size_x = epics.caget(prefix+"cam1:ArraySizeX_RBV")
-	size_y = epics.caget(prefix+"cam1:ArraySizeY_RBV")
-	# edit the full image for just the binned data
-	img = img[:size_x*size_y].reshape((size_x, size_y))
-
-	extra_information = dict(
-		unique_id = epics.caget(prefix+"image1:UniqueId_RBV"),
-		size_x = size_x,
-		size_y = size_y,
-		detector_state = epics.caget(prefix+"cam1:DetectorState_RBV"),
-		bitcoin_value="15000",
-	)
-	write_nexus_file("example.h5", img, md=extra_information)
+    """demonstrate how to use this code"""
+    import epics
+
+    prefix = "13SIM1:"
+    img = epics.caget(prefix + "image1:ArrayData")
+    size_x = epics.caget(prefix + "cam1:ArraySizeX_RBV")
+    size_y = epics.caget(prefix + "cam1:ArraySizeY_RBV")
+    # edit the full image for just the binned data
+    img = img[: size_x * size_y].reshape((size_x, size_y))
+
+    extra_information = dict(
+        unique_id=epics.caget(prefix + "image1:UniqueId_RBV"),
+        size_x=size_x,
+        size_y=size_y,
+        detector_state=epics.caget(prefix + "cam1:DetectorState_RBV"),
+        bitcoin_value="15000",
+    )
+    write_nexus_file("example.h5", img, md=extra_information)
diff --git a/nx-class-documentation/html/_downloads/4f0ba3aaedf67de9daec1d0fe519d32c/writer_1_3.py b/nx-class-documentation/html/_downloads/4f0ba3aaedf67de9daec1d0fe519d32c/writer_1_3.py
index dd4e15d67..3126f932f 100644
--- a/nx-class-documentation/html/_downloads/4f0ba3aaedf67de9daec1d0fe519d32c/writer_1_3.py
+++ b/nx-class-documentation/html/_downloads/4f0ba3aaedf67de9daec1d0fe519d32c/writer_1_3.py
@@ -1,18 +1,18 @@
 #!/usr/bin/env python
-'''
+"""
 Writes the simplest NeXus HDF5 file using h5py 
 
 Uses method accepted at 2014NIAC
 according to the example from Figure 1.3 
 in the Introduction chapter
-'''
+"""
 
 import h5py
 import numpy
 
 buffer = numpy.loadtxt("input.dat").T
-tthData = buffer[0]                             # float[]
-countsData = numpy.asarray(buffer[1],'int32')   # int[]
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 f = h5py.File("writer_1_3.hdf5", "w")  # create the HDF5 NeXus file
 # since this is a simple example, no attributes are used at this point
@@ -24,7 +24,9 @@
 nxdata.attrs["NX_class"] = u"NXdata"
 nxdata.attrs[u"signal"] = u"counts"
 nxdata.attrs[u"axes"] = u"two_theta"
-nxdata.attrs[u"two_theta_indices"] = [0,]
+nxdata.attrs[u"two_theta_indices"] = [
+    0,
+]
 
 tth = nxdata.create_dataset(u"two_theta", data=tthData)
 tth.attrs[u"units"] = u"degrees"
@@ -32,4 +34,4 @@
 counts = nxdata.create_dataset(u"counts", data=countsData)
 counts.attrs[u"units"] = u"counts"
 
-f.close()	# be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
diff --git a/nx-class-documentation/html/_downloads/532ebcaf97c2cc1df6342a4e06b5805f/BasicReader.py b/nx-class-documentation/html/_downloads/532ebcaf97c2cc1df6342a4e06b5805f/BasicReader.py
index 3a499c5c7..a3e2875ba 100644
--- a/nx-class-documentation/html/_downloads/532ebcaf97c2cc1df6342a4e06b5805f/BasicReader.py
+++ b/nx-class-documentation/html/_downloads/532ebcaf97c2cc1df6342a4e06b5805f/BasicReader.py
@@ -1,14 +1,14 @@
 #!/usr/bin/env python
-'''Reads NeXus HDF5 files using h5py and prints the contents'''
+"""Reads NeXus HDF5 files using h5py and prints the contents"""
 
-import h5py    # HDF5 support
+import h5py  # HDF5 support
 
 fileName = "prj_test.nexus.hdf5"
-f = h5py.File(fileName,  "r")
+f = h5py.File(fileName, "r")
 for item in f.attrs.keys():
     print(item + ":", f.attrs[item])
-mr = f['/entry/mr_scan/mr']
-i00 = f['/entry/mr_scan/I00']
+mr = f["/entry/mr_scan/mr"]
+i00 = f["/entry/mr_scan/I00"]
 print("%s\t%s\t%s" % ("#", "mr", "I00"))
 for i in range(len(mr)):
     print("%d\t%g\t%d" % (i, mr[i], i00[i]))
diff --git a/nx-class-documentation/html/_downloads/6937132be984b1c69840f9de424ae917/BasicWriter.py b/nx-class-documentation/html/_downloads/6937132be984b1c69840f9de424ae917/BasicWriter.py
index 63ccffde1..f71925d96 100644
--- a/nx-class-documentation/html/_downloads/6937132be984b1c69840f9de424ae917/BasicWriter.py
+++ b/nx-class-documentation/html/_downloads/6937132be984b1c69840f9de424ae917/BasicWriter.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
-'''Writes a NeXus HDF5 file using h5py and numpy'''
+"""Writes a NeXus HDF5 file using h5py and numpy"""
 
-import h5py    # HDF5 support
+import h5py  # HDF5 support
 import numpy
 
 print("Write a NeXus HDF5 file")
@@ -11,44 +11,46 @@
 # load data from two column format
 data = numpy.loadtxt("input.dat").T
 mr_arr = data[0]
-i00_arr = numpy.asarray(data[1],'int32')
+i00_arr = numpy.asarray(data[1], "int32")
 
 # create the HDF5 NeXus file
 f = h5py.File(fileName, "w")
 # point to the default data to be plotted
-f.attrs['default']          = 'entry'
+f.attrs["default"] = "entry"
 # give the HDF5 root some more attributes
-f.attrs['file_name']        = fileName
-f.attrs['file_time']        = timestamp
-f.attrs['instrument']       = 'APS USAXS at 32ID-B'
-f.attrs['creator']          = 'BasicWriter.py'
-f.attrs['NeXus_version']    = '4.3.0'
-f.attrs['HDF5_Version']     = h5py.version.hdf5_version
-f.attrs['h5py_version']     = h5py.version.version
+f.attrs["file_name"] = fileName
+f.attrs["file_time"] = timestamp
+f.attrs["instrument"] = "APS USAXS at 32ID-B"
+f.attrs["creator"] = "BasicWriter.py"
+f.attrs["NeXus_version"] = "4.3.0"
+f.attrs["HDF5_Version"] = h5py.version.hdf5_version
+f.attrs["h5py_version"] = h5py.version.version
 
 # create the NXentry group
-nxentry = f.create_group('entry')
-nxentry.attrs['NX_class'] = 'NXentry'
-nxentry.attrs['default'] = 'mr_scan'
-nxentry.create_dataset('title', data='1-D scan of I00 v. mr')
+nxentry = f.create_group("entry")
+nxentry.attrs["NX_class"] = "NXentry"
+nxentry.attrs["default"] = "mr_scan"
+nxentry.create_dataset("title", data="1-D scan of I00 v. mr")
 
 # create the NXentry group
-nxdata = nxentry.create_group('mr_scan')
-nxdata.attrs['NX_class'] = 'NXdata'
-nxdata.attrs['signal'] = 'I00'      # Y axis of default plot
-nxdata.attrs['axes'] = 'mr'         # X axis of default plot
-nxdata.attrs['mr_indices'] = [0,]   # use "mr" as the first dimension of I00
+nxdata = nxentry.create_group("mr_scan")
+nxdata.attrs["NX_class"] = "NXdata"
+nxdata.attrs["signal"] = "I00"  # Y axis of default plot
+nxdata.attrs["axes"] = "mr"  # X axis of default plot
+nxdata.attrs["mr_indices"] = [
+    0,
+]  # use "mr" as the first dimension of I00
 
 # X axis data
-ds = nxdata.create_dataset('mr', data=mr_arr)
-ds.attrs['units'] = 'degrees'
-ds.attrs['long_name'] = 'USAXS mr (degrees)'    # suggested X axis plot label
+ds = nxdata.create_dataset("mr", data=mr_arr)
+ds.attrs["units"] = "degrees"
+ds.attrs["long_name"] = "USAXS mr (degrees)"  # suggested X axis plot label
 
 # Y axis data
-ds = nxdata.create_dataset('I00', data=i00_arr)
-ds.attrs['units'] = 'counts'
-ds.attrs['long_name'] = 'USAXS I00 (counts)'    # suggested Y axis plot label
+ds = nxdata.create_dataset("I00", data=i00_arr)
+ds.attrs["units"] = "counts"
+ds.attrs["long_name"] = "USAXS I00 (counts)"  # suggested Y axis plot label
 
-f.close()	# be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
 
 print("wrote file:", fileName)
diff --git a/nx-class-documentation/html/_downloads/6f872be7e279e8b89be1f5ff75929de3/writer_2_1.py b/nx-class-documentation/html/_downloads/6f872be7e279e8b89be1f5ff75929de3/writer_2_1.py
index 66e76b371..64be0142f 100644
--- a/nx-class-documentation/html/_downloads/6f872be7e279e8b89be1f5ff75929de3/writer_2_1.py
+++ b/nx-class-documentation/html/_downloads/6f872be7e279e8b89be1f5ff75929de3/writer_2_1.py
@@ -1,15 +1,15 @@
 #!/usr/bin/env python
-'''
+"""
 Writes a simple NeXus HDF5 file using h5py with links
 according to the example from Figure 2.1 in the Design chapter
-'''
+"""
 
 import h5py
 import numpy
 
 buffer = numpy.loadtxt("input.dat").T
-tthData = buffer[0]                             # float[]
-countsData = numpy.asarray(buffer[1],'int32')   # int[]
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 f = h5py.File("writer_2_1.hdf5", "w")  # create the HDF5 NeXus file
 f.attrs[u"default"] = u"entry"
@@ -35,18 +35,20 @@
 nxdata.attrs[u"NX_class"] = u"NXdata"
 nxdata.attrs[u"signal"] = u"counts"
 nxdata.attrs[u"axes"] = u"two_theta"
-nxdata.attrs[u"two_theta_indices"] = [0,]
-
-source_addr = u"/entry/instrument/detector/two_theta"   # existing data
-target_addr = u"two_theta"                              # new location
-ds_tth.attrs[u"target"] = source_addr                   # a NeXus API convention for links
-nxdata[target_addr] = f[source_addr]                    # hard link
+nxdata.attrs[u"two_theta_indices"] = [
+    0,
+]
+
+source_addr = u"/entry/instrument/detector/two_theta"  # existing data
+target_addr = u"two_theta"  # new location
+ds_tth.attrs[u"target"] = source_addr  # a NeXus API convention for links
+nxdata[target_addr] = f[source_addr]  # hard link
 # nxdata._id.link(source_addr, target_addr, h5py.h5g.LINK_HARD)
 
-source_addr = u"/entry/instrument/detector/counts"      # existing data
-target_addr = u"counts"                                 # new location
-ds_counts.attrs[u"target"] = source_addr                # a NeXus API convention for links
-nxdata[target_addr] = f[source_addr]                    # hard link
+source_addr = u"/entry/instrument/detector/counts"  # existing data
+target_addr = u"counts"  # new location
+ds_counts.attrs[u"target"] = source_addr  # a NeXus API convention for links
+nxdata[target_addr] = f[source_addr]  # hard link
 # nxdata._id.link(source_addr, target_addr, h5py.h5g.LINK_HARD)
 
-f.close()	# be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
diff --git a/nx-class-documentation/html/_downloads/dfc22f4a37f3414e5e8cc7135510b802/write_nexus_file.py b/nx-class-documentation/html/_downloads/dfc22f4a37f3414e5e8cc7135510b802/write_nexus_file.py
index 1dd61bafb..a6ef7e108 100644
--- a/nx-class-documentation/html/_downloads/dfc22f4a37f3414e5e8cc7135510b802/write_nexus_file.py
+++ b/nx-class-documentation/html/_downloads/dfc22f4a37f3414e5e8cc7135510b802/write_nexus_file.py
@@ -2,81 +2,83 @@
 import h5py
 import datetime
 
+
 def write_nexus_file(fname, image, md={}):
-	"""
-	write the image to a NeXus HDF5 data file
+    """
+    write the image to a NeXus HDF5 data file
+
+    Parameters
+    ----------
+    fname : str
+            name of the file (relative or absolute) to be written
+    image : numpy array
+            the image data
+    md : dictionary
+            key: value where value is something that can be written by h5py
+                     (such as str, int, float, numpy array, ...)
+    """
+    nexus = h5py.File(fname, "w")
+    nexus.attrs["filename"] = fname
+    nexus.attrs["file_time"] = str(datetime.datetime.now())
+    nexus.attrs["creator"] = "write_nexus_file()"
+    nexus.attrs["H5PY_VERSION"] = h5py.__version__
 
-	Parameters
-	----------
-	fname : str
-		name of the file (relative or absolute) to be written
-	image : numpy array
-		the image data
-	md : dictionary
-		key: value where value is something that can be written by h5py
-			 (such as str, int, float, numpy array, ...)
-	"""
-	nexus = h5py.File(fname, "w")
-	nexus.attrs["filename"] = fname
-	nexus.attrs["file_time"] = str(datetime.datetime.now())
-	nexus.attrs["creator"] = "write_nexus_file()"
-	nexus.attrs["H5PY_VERSION"] = h5py.__version__
+    # /entry
+    nxentry = nexus.create_group("entry")
+    nxentry.attrs["NX_class"] = "NXentry"
+    nexus.attrs["default"] = nxentry.name
 
-	# /entry
-	nxentry = nexus.create_group("entry")
-	nxentry.attrs["NX_class"] = "NXentry"
-	nexus.attrs["default"] = nxentry.name
+    # /entry/instrument
+    nxinstrument = nxentry.create_group("instrument")
+    nxinstrument.attrs["NX_class"] = "NXinstrument"
 
-	# /entry/instrument
-	nxinstrument = nxentry.create_group("instrument")
-	nxinstrument.attrs["NX_class"] = "NXinstrument"
+    # /entry/instrument/detector
+    nxdetector = nxinstrument.create_group("detector")
+    nxdetector.attrs["NX_class"] = "NXdetector"
 
-	# /entry/instrument/detector
-	nxdetector = nxinstrument.create_group("detector")
-	nxdetector.attrs["NX_class"] = "NXdetector"
+    # /entry/instrument/detector/image
+    ds = nxdetector.create_dataset("image", data=image, compression="gzip")
+    ds.attrs["units"] = "counts"
+    ds.attrs["target"] = "/entry/instrument/detector/image"
 
-	# /entry/instrument/detector/image
-	ds = nxdetector.create_dataset("image", data=image, compression="gzip")
-	ds.attrs["units"] = "counts"
-	ds.attrs["target"] = "/entry/instrument/detector/image"
+    # /entry/data
+    nxdata = nxentry.create_group("data")
+    nxdata.attrs["NX_class"] = "NXdata"
+    nxentry.attrs["default"] = nxdata.name
 
-	# /entry/data
-	nxdata = nxentry.create_group("data")
-	nxdata.attrs["NX_class"] = "NXdata"
-	nxentry.attrs["default"] = nxdata.name
+    # /entry/data/data --> /entry/instrument/detector/image
+    nxdata["data"] = nexus["/entry/instrument/detector/image"]
+    nxdata.attrs["signal"] = "data"
 
-	# /entry/data/data --> /entry/instrument/detector/image
-	nxdata["data"] = nexus["/entry/instrument/detector/image"]
-	nxdata.attrs["signal"] = "data"
+    if len(md) > 0:
+        # /entry/instrument/metadata (optional, for metadata)
+        metadata = nxinstrument.create_group("metadata")
+        metadata.attrs["NX_class"] = "NXcollection"
+        for k, v in md.items():
+            try:
+                metadata.create_dataset(k, data=v)
+            except Exception:
+                metadata.create_dataset(k, data=str(v))
 
-	if len(md) > 0:
-		# /entry/instrument/metadata (optional, for metadata)
-		metadata = nxinstrument.create_group("metadata")
-		metadata.attrs["NX_class"] = "NXcollection"
-		for k, v in md.items():
-			try:
-				metadata.create_dataset(k, data=v)
-			except Exception:
-				metadata.create_dataset(k, data=str(v))
+    nexus.close()
 
-	nexus.close()
 
-	
 if __name__ == "__main__":
-	"""demonstrate how to use this code"""
-	import epics
-	prefix = "13SIM1:"
-	img = epics.caget(prefix+"image1:ArrayData")
-	size_x = epics.caget(prefix+"cam1:ArraySizeX_RBV")
-	size_y = epics.caget(prefix+"cam1:ArraySizeY_RBV")
-	# edit the full image for just the binned data
-	img = img[:size_x*size_y].reshape((size_x, size_y))
+    """demonstrate how to use this code"""
+    import epics
+
+    prefix = "13SIM1:"
+    img = epics.caget(prefix + "image1:ArrayData")
+    size_x = epics.caget(prefix + "cam1:ArraySizeX_RBV")
+    size_y = epics.caget(prefix + "cam1:ArraySizeY_RBV")
+    # edit the full image for just the binned data
+    img = img[: size_x * size_y].reshape((size_x, size_y))
 
-	extra_information = dict(
-		unique_id = epics.caget(prefix+"image1:UniqueId_RBV"),
-		size_x = size_x,
-		size_y = size_y,
-		detector_state = epics.caget(prefix+"cam1:DetectorState_RBV"),
-		bitcoin_value="15000",
-	)
-	write_nexus_file("example.h5", img, md=extra_information)
+    extra_information = dict(
+        unique_id=epics.caget(prefix + "image1:UniqueId_RBV"),
+        size_x=size_x,
+        size_y=size_y,
+        detector_state=epics.caget(prefix + "cam1:DetectorState_RBV"),
+        bitcoin_value="15000",
+    )
+    write_nexus_file("example.h5", img, md=extra_information)
diff --git a/nx-class-documentation/html/_downloads/e148aff3c2435a4a6ddc3f555bf79aa4/externalExample.py b/nx-class-documentation/html/_downloads/e148aff3c2435a4a6ddc3f555bf79aa4/externalExample.py
index 809cb1e1f..fad5078c6 100644
--- a/nx-class-documentation/html/_downloads/e148aff3c2435a4a6ddc3f555bf79aa4/externalExample.py
+++ b/nx-class-documentation/html/_downloads/e148aff3c2435a4a6ddc3f555bf79aa4/externalExample.py
@@ -1,9 +1,9 @@
 #!/usr/bin/env python
-'''
+"""
 Writes a NeXus HDF5 file using h5py with links to data in other HDF5 files.
 
 This example is based on ``writer_2_1``.
-'''
+"""
 
 import h5py
 import numpy
@@ -12,21 +12,21 @@
 FILE_HDF5_ANGLES = u"external_angles.hdf5"
 FILE_HDF5_COUNTS = u"external_counts.hdf5"
 
-#---------------------------
+# ---------------------------
 
 # get some data
 buffer = numpy.loadtxt("input.dat").T
-tthData = buffer[0]                             # float[]
-countsData = numpy.asarray(buffer[1],'int32')   # int[]
+tthData = buffer[0]  # float[]
+countsData = numpy.asarray(buffer[1], "int32")  # int[]
 
 # put the angle data in an external (non-NeXus) HDF5 data file
 f = h5py.File(FILE_HDF5_ANGLES, "w")
 ds = f.create_dataset(u"angles", data=tthData)
 ds.attrs[u"units"] = u"degrees"
-f.close()    # be CERTAIN to close the file
+f.close()  # be CERTAIN to close the file
 
 
-# put the detector counts in an external HDF5 data file 
+# put the detector counts in an external HDF5 data file
 # with *incomplete* NeXus structure (no NXdata group)
 f = h5py.File(FILE_HDF5_COUNTS, "w")
 nxentry = f.create_group(u"entry")
@@ -46,13 +46,13 @@
 f = h5py.File(FILE_HDF5_MASTER, "w")
 f.attrs[u"default"] = u"entry"
 nxentry = f.create_group(u"entry")
-nxentry.attrs[u"NX_class"] =u"NXentry"
+nxentry.attrs[u"NX_class"] = u"NXentry"
 nxentry.attrs[u"default"] = u"data"
 nxdata = nxentry.create_group(u"data")
 nxdata.attrs[u"NX_class"] = u"NXdata"
 
 # link in the signal data
-local_addr = '/entry/data/counts'
+local_addr = "/entry/data/counts"
 external_addr = u"/entry/instrument/detector/counts"
 f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, external_addr)
 nxdata.attrs[u"signal"] = u"counts"
@@ -61,7 +61,9 @@
 local_addr = u"/entry/data/two_theta"
 f[local_addr] = h5py.ExternalLink(FILE_HDF5_ANGLES, u"/angles")
 nxdata.attrs[u"axes"] = u"two_theta"
-nxdata.attrs[u"two_theta_indices"] = [0,]
+nxdata.attrs[u"two_theta_indices"] = [
+    0,
+]
 
 local_addr = u"/entry/instrument"
 f[local_addr] = h5py.ExternalLink(FILE_HDF5_COUNTS, u"/entry/instrument")
diff --git a/ui/link.py b/ui/link.py
index 993231800..ce9831ad2 100644
--- a/ui/link.py
+++ b/ui/link.py
@@ -12,7 +12,9 @@ def setupUi(self, Link):
         self.vertical_layout.addWidget(self.select_link_label)
         self.horizontal_layout = QtWidgets.QHBoxLayout()
         self.transformations_combo_box = QtWidgets.QComboBox(self.group_box)
-        combo_size_policy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
+        combo_size_policy = QtWidgets.QSizePolicy(
+            QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed
+        )
         combo_size_policy.setHorizontalStretch(1)
         combo_size_policy.setVerticalStretch(0)
         self.transformations_combo_box.setSizePolicy(combo_size_policy)
diff --git a/ui/treeview_tab.py b/ui/treeview_tab.py
index b2c324358..6fb90efac 100644
--- a/ui/treeview_tab.py
+++ b/ui/treeview_tab.py
@@ -155,9 +155,13 @@ def on_delete_item(self):
         if len(selected[0].data().parent_node.children) == 1:
             new_selection_index = selected[0].parent()
         elif selected[0].row() > 0:
-            new_selection_index = self.component_model.parent(selected[0]).child(selected[0].row() - 1, 0)
+            new_selection_index = self.component_model.parent(selected[0]).child(
+                selected[0].row() - 1, 0
+            )
         elif selected[-1].row() <= len(selected[-1].data().parent_node.children) - 1:
-            new_selection_index = self.component_model.parent(selected[-1]).child(selected[-1].row(), 0)
+            new_selection_index = self.component_model.parent(selected[-1]).child(
+                selected[-1].row(), 0
+            )
         else:
             new_selection_index = selected[0].parent()
         for item in selected: