Fix sphinx config

Since notebook was moved to /notebooks, notebook for howtouse page was not loading the data from correct place

docs/source/conf.py

@@ -1,35 +1,44 @@
 # -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
-#
-# This file does only contain a selection of the most common options. For a
-# full list see the documentation:
-# http://www.sphinx-doc.org/en/master/config
+
+import os
+import shutil
+import sys
 
 # -- Path setup --------------------------------------------------------------
 
 # 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.
-#
-import os
-import sys
-import shutil
 sys.path.insert(0, os.path.abspath('../../')) 	# Reference the root directory so autodocs can find the python modules
 
-# Copy the example notebook, change %matplotlib to inline and change directory so that paths still work
+# Copy the example notebook into the docs source
 shutil.copyfile('../../notebooks/example_notebook.ipynb', 'howtouse.ipynb')
+
+# Open file
 with open('howtouse.ipynb') as f:
-    newText=f.read().replace('%matplotlib tk', r'%matplotlib inline\n%cd -q ../../')
-newText=newText.replace('DefDAP Example notebook', r'How to use')
-newText=newText.replace('This notebook', r'These pages')
+    old_text = f.read()
+
+# change %matplotlib to inline
+new_text = old_text.replace('%matplotlib tk', r'%matplotlib inline')
+
+# change directory so that paths still work
+new_text = new_text.replace('../tests/data/testDataEBSD', r'../../tests/data/testDataEBSD')
+new_text = new_text.replace('../tests/data/', r'../../tests/data/')
+
+# Change title to 'How to use'
+new_text = new_text.replace('DefDAP Example notebook', r'How to use')
+new_text = new_text.replace('This notebook', r'These pages')
+
+# Write back to notebook
 with open('howtouse.ipynb', "w") as f:
-    f.write(newText)
+    f.write(new_text)
 
 # -- Project information -----------------------------------------------------
 
 project = 'DefDAP'
-copyright = '2020, Mechanics of Microstructures Group at The University of Manchester'
+copyright = '2023, Mechanics of Microstructures Group at The University of Manchester'
 author = 'Michael D. Atkinson, Rhys Thomas, João Quinta da Fonseca'
 
 
@@ -81,7 +90,6 @@ def get_version():
 """
 
 napoleon_use_param = True
-#set_type_checking_flag = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -98,11 +106,7 @@ def get_version():
 # The master toctree document.
 master_doc = 'index'
 
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
+# The language for content autogenerated by Sphinx
 language = 'en'
 
 # List of patterns, relative to source directory, that match files and
@@ -138,16 +142,6 @@ def get_version():
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# The default sidebars (for documents that don't match any pattern) are
-# defined by theme itself.  Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
-#
-# html_sidebars = {}
-
 
 # -- Options for HTMLHelp output ---------------------------------------------