TVB-2719 Fix build_ext warnings

[ayan-b]

This PR aims to remove the warning generated after running python setup.py build_ext --inplace.

Closes #19

[ayan-b]

I am not entirely sure why in some places char is used for int datatype (to save space maybe?) and if I should change them to get rid of the warnings.

[ayan-b]

@liadomide, this PR removes some of the warnings, they are -

• FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release!
• local variable 'distance' referenced before assignment.

Warnings not removed -

• numpy deprecated warning #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION", now if I add that macro the build fails altogether with error: ‘PyArrayObject’ {aka ‘struct tagPyArrayObject’} has no member named ‘dimensions’. Looks like someone else has also encountered the same error https://gitlab.kwant-project.org/kwant/kwant/-/merge_requests/251.
• char is used as an array index. An easy fix is changing the char datatype to int, however, I am not entirely sure if I should do that as the author may have some other intentions in his mind.

Also, I fixed some typos and moved a piece of code of both the functions local_gdist_matrix and compute_gdist to another function in this PR.