Add type annotations and mypy CI job

[speleo3]

Static type checking is becoming popular for serious Python projects. This PR adds a substantial amount of type annotations and a static type checking CI job with mypy.

Static type checking reveals lots of potential for cleanup and better design decisions, but this patch deliberately doesn't clean up anything. Cleanup could happen in follow-ups.

[codecov]

Codecov Report

Attention: 20 lines in your changes are missing coverage. Please review.

Comparison is base (ee89e36) 73.09% compared to head (035b827) 72.98%.

❗ Current head 035b827 differs from pull request most recent head 57d7c67. Consider uploading reports for the commit 57d7c67 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #172      +/-   ##
==========================================
- Coverage   73.09%   72.98%   -0.11%     
==========================================
  Files          25       25              
  Lines        3988     4017      +29     
==========================================
+ Hits         2915     2932      +17     
- Misses       1073     1085      +12     

Files	Coverage Δ
propka/calculations.py	100.00% <100.00%> (ø)
propka/input.py	98.09% <100.00%> (+0.01%)	⬆️
propka/molecular_container.py	92.85% <100.00%> (+0.33%)	⬆️
propka/bonds.py	55.55% <75.00%> (+0.15%)	⬆️
propka/group.py	76.96% <96.55%> (-0.02%)	⬇️
propka/vector_algebra.py	61.02% <95.45%> (+1.98%)	⬆️
propka/energy.py	90.33% <83.33%> (-0.66%)	⬇️
propka/atom.py	74.71% <83.33%> (-2.95%)	⬇️
propka/conformation_container.py	83.68% <82.60%> (-1.30%)	⬇️
propka/hydrogens.py	16.48% <66.66%> (+0.72%)	⬆️

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