MAINT: Refactor setup.py cythonization

[bocklund]

• Move extension definitions out to the top level to make setup.py easier to read
• Add a dictionary of global compiler directives that currently just sets the language level to 3 (fixing a FutureWarning)
• Fixes a few cythonization warnings about typing indices

As of this PR, there's currently no warnings being emitted from the Cythonizing step. There's still some warnings in the compiling step but some (all?), like the deprecated NumPy API warnings, are out of our control.

[codecov]

Codecov Report

Merging #334 (f9670dd) into develop (fdd14be) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop     #334   +/-   ##
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  Coverage    84.55%   84.55%           
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  Files           45       45           
  Lines         4526     4526           
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  Hits          3827     3827           
  Misses         699      699           

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[richardotis]

Can the extra compiler and link arguments be removed? I think they are mostly (entirely?) irrelevant now.

[bocklund]

Can the extra compiler and link arguments be removed? I think they are mostly (entirely?) irrelevant now.

Looks like it! Removed.