Merge pull request #83 from CardiacModelling/tweaks_to_message

Tweaks to messages and re-run notebooks; Reformat code with black

README.md

@@ -96,7 +96,7 @@ Congratulations!
 You landed at an altitude of 1309m.
   https://opentopomap.org/#marker=15/57.07019/-3.669487
 You are 31m from the nearest named hill top, "Ben Macdui",
-  ranked the 2d heighest in GB.
+  ranked the 2nd highest in GB.
   http://hillsummits.org.uk/htm_summit/518.htm
 ```
 

docs/source/conf.py

@@ -28,35 +28,35 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.viewcode',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
 ]
 
 # Autodoc defaults
 autodoc_default_options = {
-    'members': None,
-    'inherited-members': None,
+    "members": None,
+    "inherited-members": None,
 }
 
 # 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 = u'nevis'
-copyright = u'2022, University of Nottingham'
-author = u'"Where is Ben Nevis" authors'
+project = "nevis"
+copyright = "2022, University of Nottingham"
+author = '"Where is Ben Nevis" authors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -72,7 +72,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = 'en'
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -81,11 +81,11 @@
 
 # Suppress warnings about unused footnotes (i.e. citations of papers)
 suppress_warnings = [
-    'ref.footnote',
+    "ref.footnote",
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -96,33 +96,30 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # 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 = {
-
     # See: https://alabaster.readthedocs.io/en/latest/customization.html
-
     # Fixed sidebar is unusable: Doesn't have its own scrollbar!
     # 'fixed_sidebar': True,
-
-    'page_width': '1280px',
-    'sidebar_width': '320px',
+    "page_width": "1280px",
+    "sidebar_width": "320px",
 }
 
 # 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"]
 
 
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'Nevisdoc'
+htmlhelp_basename = "Nevisdoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -131,15 +128,12 @@
     # 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',
@@ -149,19 +143,21 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'Nevis.tex', u'nevis Documentation',
-     u'"Where is Ben Nevis" Authors', 'manual'),
+    (
+        master_doc,
+        "Nevis.tex",
+        "nevis Documentation",
+        '"Where is Ben Nevis" Authors',
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'nevis', u'nevis Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "nevis", "nevis Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -170,8 +166,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'nevis', u'nevis Documentation',
-     author, 'nevis', 'API docs for nevis.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "nevis",
+        "nevis Documentation",
+        author,
+        "nevis",
+        "API docs for nevis.",
+        "Miscellaneous",
+    ),
 ]
-

example.py

@@ -11,5 +11,4 @@
 nevis.download_os_terrain_50()
 
 # Create and store a figure
-nevis.write_test_figure('gb-small.png')
-
+nevis.write_test_figure("gb-small.png")

gb.py

@@ -37,15 +37,18 @@
 points = trajectory = None
 if False:
     import numpy as np
+
     ben = nevis.ben()
     points = []
     trajectory = [np.array(ben.grid)]
     for i in range(50):
         trajectory.append(
-            trajectory[-1] + (np.random.random(2) - 0.5) * 5e2 * i**1.5)
+            trajectory[-1] + (np.random.random(2) - 0.5) * 5e2 * i**1.5
+        )
         for j in range(10):
             points.append(
-                trajectory[-1] + (np.random.random(2) - 0.5) * 8e2 * i**1.5)
+                trajectory[-1] + (np.random.random(2) - 0.5) * 8e2 * i**1.5
+            )
     trajectory = np.array(trajectory)
     points = np.array(points)
 
@@ -59,8 +62,8 @@
 
 # Labels
 labels = {
-    'Ben Nevis': nevis.ben(),
-    'Holme Fen': nevis.fen(),
+    "Ben Nevis": nevis.ben(),
+    "Holme Fen": nevis.fen(),
 }
 
 # Load data
@@ -81,7 +84,6 @@
 )
 
 # Save plot, and check resulting image dimensions
-if not os.path.isdir('results'):
-    os.makedirs('results')
-nevis.save_plot('results/gb.png', fig, heights, verbose=True)
-
+if not os.path.isdir("results"):
+    os.makedirs("results")
+nevis.save_plot("results/gb.png", fig, heights, verbose=True)