Fix pep8 issues

Should now pass Travis tests.
Address most of @wasade's comments

Most notably, DistanceMatrix.from_file has been almost completely rewritten to
be clearer and more robust to comments and empty lines.
Address @wasade's remaining issues

Notably, DistanceMatrix.to_file has 50-75% reduction in runtime since it now uses numpy.asarray to convert float values to string values.
Fix trailing whitespace pylint warnings