Fix out-of-order crashes in notebooks

[kwabenantim]

Description
Notebooks crash routinely when some cells are run out-of-order.

To Do

• Reproduce problem.
• Investigate possible solutions for preventing out-of-order execution e.g. group things together in functions.
• Hide some functionality behind the scenes from users e.g. chaste.init(), SetupNotebookTest() etc.
• Gently recover from errors if out-of-order crashes cannot be avoided.
• Add additional tests if necessary.

[kwabenantim]

Can't seem to reproduce this now after most notebook crashes seem to have been fixed by #21.
Closing this issue now, but might reopen if these crashes resurface.