Update Documentation

[PythonFZ]

#548 fixed some urgent RTD issue but left open:

• When running make html I get the following error (and a lot of warnings about missing docstrings which we will resolve over time)

WARNING: autodoc: failed to import module 'setup'; the following exception was raised:
...
  File "/tikhome/fzills/PycharmProjects/MLSuite/setup.py", line 5, in <module>
    with open("README.md", "r") as fh:
FileNotFoundError: [Errno 2] No such file or directory: 'README.md'

A few things that I noticed when reading through the documenation:

• We use both pip and pip3 and because python2 is EOL for quite some time, I would propose to stick with only unsing pip

• Pages to be (temporarly) removed because they are empty: Phonon Spectrum, Isothermal compressibility, Tensor operations in MDSuite, Autocorrelation in MDSuite, Ensemble Average, Fluctuation dissipation theorem, GK relations, Einstein relations, Onsager coefficients and dynamics in MDSuite,

• Molten_salt_Comparisonstill uses data["NaCl"].data_dict

• pip should be lower-case everywhere

• setup.py proper use of pathlib