Fix run manager bugs

[xuyuon]

Fixed a number of bugs:

1. The likelihood now should also take sample_transform and likelihood_transform
2. save_summary() no longer prints self.SNRs if the run is not an injection run.
3. save_summary() will switch back to the original output method after completing the summary file printing.
4. Fixed the issue where initialize_transforms() will drops the name in self.run.sample_transforms and run.likelihood_transforms

[thomasckng]

@xuyuon Feel free to merge it anytime