Many changes to code base
This merge request includes the following changes/updates:
- new testing methods to increase test coverage
- compressed gif image sizes
- fixes for Sphinx autodocs
- completion of docstrings in all modules
- migrated utility functions from init.py to Helpers.py
- added support for input hydrodynamic meshes as NumPy .npz files
- added conversion functions for output HDF5 files to .vtk (mesh) or .csv (particles) files
- some improvements to class variable setter/getter functions
Closes #10 (closed) #11 (closed) #12 (closed) Includes checklist items in #6