fixes run's single method

[IAlibay]

Fixes #82

Changes:

• input arguments now reflects the changes made to read_molecule_file in #84
• Writing of pKa file is now optional (default behaviour has been kept). This will be particularly useful downstream where we would just want to have access to the MoleculeContainer object.
• new test_run file specific for testing run.

Notes:

• Tests in test_run overlap a lot with test_streamio, strictly speaking I could probably ditch part of test_streamio as it's implicitly tested. However in some ways it might be good to have the two run in parallel to make sure that some change in run.single isn't introducing new behaviour. Either way would work, but it might not be that big a deal with the tests running as fast as they currently do?

To do:

• Add in a test for the logger warning.

[codecov[bot]]

Codecov Report

Merging #85 into master will increase coverage by 1.89%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master      #85      +/-   ##
==========================================
+ Coverage   70.41%   72.30%   +1.89%     
==========================================
  Files          25       25              
  Lines        4140     4127      -13     
==========================================
+ Hits         2915     2984      +69     
+ Misses       1225     1143      -82     

Impacted Files	Coverage Δ
propka/input.py	62.65% <ø> (-0.23%)	:arrow_down:
propka/run.py	68.57% <100.00%> (+68.57%)	:arrow_up:
propka/ligand_pka_values.py	20.28% <0.00%> (-2.25%)	:arrow_down:
propka/coupled_groups.py	75.48% <0.00%> (-0.47%)	:arrow_down:
propka/vector_algebra.py	58.15% <0.00%> (-0.45%)	:arrow_down:
propka/bonds.py	60.48% <0.00%> (-0.32%)	:arrow_down:
propka/version.py	63.15% <0.00%> (-0.28%)	:arrow_down:
propka/protonate.py	88.42% <0.00%> (-0.18%)	:arrow_down:
propka/conformation_container.py	83.40% <0.00%> (-0.15%)	:arrow_down:
propka/group.py	76.38% <0.00%> (+1.71%)	:arrow_up:
... and 5 more

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[orbeckst]

Also, awesome test coverage... isn't it nice when one commit increases overall coverage by 2%!