Upgrade sphinx and nbsphinx

Python/Module3_IntroducingNumpy/AdvancedIndexing.md

@@ -402,7 +402,7 @@ Use boolean array-indexing and NumPy's [logical functions](https://docs.scipy.or
 <!-- #endregion -->
 
 <!-- #region -->
-#### Converting a Boolean Index-Array to Integer index-arrays: numpy.where
+### Converting a Boolean Index-Array to Integer index-arrays: numpy.where
 The function [numpy.where](https://docs.scipy.org/doc/numpy/reference/generated/numpy.where.html) can be used to take a boolean-valued array, and produce the *tuple* of index-arrays that access the `True` entries of that array, via integer array indexing (discussed at the beginning of this section).
 
 ```python

Python/Module5_OddsAndEnds/WorkingWithFiles.md

@@ -14,7 +14,7 @@ jupyter:
 
 <!-- #raw raw_mimetype="text/restructuredtext" -->
 .. meta::
-   :description: Topic: Working with aths and files, Difficulty: Medium, Category: Section
+   :description: Topic: Working with paths and files, Difficulty: Medium, Category: Section
    :keywords: open file, read file, pathlib, join directory, context manager, close file, rb, binary file, utf-8, encoding, pickle, numpy, load, archive, npy, npz, pkl, glob, read lines, write, save
 <!-- #endraw -->
 
@@ -283,6 +283,8 @@ data/*.txt
 
 The `pathlib` module provides convenient functionality for globbing files. Once we have a `Path` object, we can simply call `glob()` on it and pass in a glob string. This will return a [generator](http://www.pythonlikeyoumeanit.com/Module2_EssentialsOfPython/Generators_and_Comprehensions.html#Introducing-Generators) that will yield each of the globbed files.
 
+<!-- #region -->
+
 ``` python
 # glob all of the text files in the present directory
 # that start with 'test' and end with '.txt'
@@ -303,6 +305,8 @@ The `pathlib` module provides convenient functionality for globbing files. Once
 ...         pass
 ```
 
+<!-- #endregion -->
+
 For more details on globbing, see [the documentation](https://docs.python.org/3/library/pathlib.html#pathlib.Path.glob).
 
 <div class="alert alert-info">

Python/changes.rst

@@ -7,6 +7,13 @@ in reverse chronological order. All previous releases should still be available
 on pip.
 
 
+----------
+2020-04-11
+----------
+
+Updated some of the "backend" technologies behind PLYMI: upgraded sphinx and nbsphinx.
+
+
 ----------
 2020-04-02
 ----------

Python/conf.py

@@ -31,46 +31,46 @@
 # 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.intersphinx',
-    'nbsphinx',
-    'sphinx.ext.todo',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.githubpages']
-
-import jupytext
+extensions = [
+    "sphinx.ext.intersphinx",
+    "nbsphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.githubpages",
+]
 
 nbsphinx_custom_formats = {
-    '.md': lambda s: jupytext.reads(s, '.md'),
+    '.md': ['jupytext.reads', {'fmt': 'md'}],
 }
 
 nbsphinx_allow_errors = False
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'Python Like You Mean It'
-copyright = '2019, Ryan Soklaski'
-author = 'Ryan Soklaski'
-html_title = 'Python Like You Mean It'
+project = "Python Like You Mean It"
+copyright = "2019, Ryan Soklaski"
+author = "Ryan Soklaski"
+html_title = "Python Like You Mean It"
 
 # 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 = '1.4'
+version = "1.4"
 # The full version, including alpha/beta/rc tags.
-release = '1.4.1'
+release = "1.4.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -82,10 +82,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = True
@@ -98,10 +98,13 @@
 #
 html_theme = "sphinx_rtd_theme"
 
+
 def setup(app):
-    app.add_stylesheet('my_theme.css')
-    app.add_javascript("https://www.googletagmanager.com/gtag/js?id=UA-115029372-1")
-    app.add_javascript("gtag.js")
+    app.add_css_file("my_theme.css")
+    app.add_js_file("https://www.googletagmanager.com/gtag/js?id=UA-115029372-1")
+    app.add_js_file("gtag.js")
+
+
 # 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.
@@ -111,28 +114,28 @@ def setup(app):
 # 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"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
 #
 # This is required for the alabaster theme
 # refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
 html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-        'donate.html',
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+        "donate.html",
     ]
 }
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'BPLYMI'
+htmlhelp_basename = "BPLYMI"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -141,15 +144,12 @@ def setup(app):
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -159,8 +159,7 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'BPLYMI.tex', 'BPython Like You Mean It',
-     'Ryan Soklaski', 'manual'),
+    (master_doc, "BPLYMI.tex", "BPython Like You Mean It", "Ryan Soklaski", "manual")
 ]
 
 
@@ -169,8 +168,7 @@ def setup(app):
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'bfundamentalsofpython', 'BPython Like You Mean It',
-     [author], 1)
+    (master_doc, "bfundamentalsofpython", "BPython Like You Mean It", [author], 1)
 ]
 
 
@@ -180,13 +178,17 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'BPLYMI', 'BPython Like You Mean It',
-     author, 'BPLYMI', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "BPLYMI",
+        "BPython Like You Mean It",
+        author,
+        "BPLYMI",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
 
 
-
-
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {"https://docs.python.org/": None}