More static typing

[speleo3]

• Parameters typing
• Options typing
• vector_algebra tests and refactoring
• Raise NotImplementedError from unused functions (of which some are broken if you try to run them)

[codecov]

Codecov Report

Attention: 56 lines in your changes are missing coverage. Please review.

Comparison is base (9d4b59c) 74.05% compared to head (abd3d05) 74.82%.

Files	Patch %	Lines
propka/hydrogens.py	0.00%	15 Missing ⚠️
propka/output.py	57.14%	15 Missing ⚠️
propka/ligand_pka_values.py	58.33%	5 Missing ⚠️
propka/group.py	75.00%	3 Missing ⚠️
propka/lib.py	93.18%	3 Missing ⚠️
propka/vector_algebra.py	91.66%	3 Missing ⚠️
propka/atom.py	94.73%	2 Missing ⚠️
propka/bonds.py	0.00%	2 Missing ⚠️
propka/parameters.py	97.89%	2 Missing ⚠️
propka/conformation_container.py	93.33%	1 Missing ⚠️
... and 5 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #177      +/-   ##
==========================================
+ Coverage   74.05%   74.82%   +0.77%     
==========================================
  Files          25       25              
  Lines        3943     4116     +173     
==========================================
+ Hits         2920     3080     +160     
- Misses       1023     1036      +13     

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