Housekeeping

[kwabenantim]

Description
Tidy up repository.

To Do

• Remove unused files/directories such as:
  • dynamic/wrapper_generators/generate_wrapper_code_old.py
  • dynamic/wrappers/preload/
  • .travis.yml
  • Everything in infra/conda except chaste, vtk, and xsd because most dependencies are now on conda-forge.
  • apps/
  • src/tutorial/
  • doc/tutorials/Python/TestCellSorting/results_from_time_0
  • doc/tutorials/.ipynb_checkpoints/
• Clean up code:
  • Remove namespace py=pybind11 etc. from headers.
  • Add #include <pybind11/pybind11.h> in headers.
  • Group and sort includes.
  • Do code formatting.
  • Fix wrapper guard naming e.g. AbstractCaUpdateRule3_hpp__pyplusplus_wrapper doesn't correspond to filename AbstractCaUpdateRule3.cppwg.hpp, and pyplusplus is no longer used for wrapper generation.
  • To clarify purpose of typedefs, use only where required e.g. typedef AbstractCaUpdateRule<2> AbstractCaUpdateRule2 is necessary for the PYBIND11_OVERLOAD macro but not elsewhere.