do some refactoring using pycharm
more refactoring using pycharm
Merge remote-tracking branch 'origin/master' into refactor
reformat the optimize folder using pycharm
reformat potentials using pycharm
reformat systems using pycharm
reformat accept_tests using pycharm
reformat amber module using pycharm
reformat landscape module using pycharm
reformat transition_states module using pycharm
reformat utils module using pycharm
reformat examples using pycharm
Merge pull request #90 from js850/refactor

do a lot of small refactoring using pycharm