Improve existing unit tests and overall code coverage

[wehs7661]

Before the next release (presumably 0.5.0), one of the action items is to improve the quality of existing unit tests and covered the untested functions. Here is a checklist for the modules to test. An item is checked only if the existing tests have been re-examined and new tests have been added (when necessary) to increase the code coverage.

• ensemble_EXE.py (finished at commit 09adb37)
• utils/utils.py (commits d83e5a)
• utils/gmx_parser.py
• analysis/analyze_matrix.py
• analysis/analyze_traj.py
• analysis/analyze_free_energy.py
• analysis/msm_analysis.py

Notably, there should not be a need to cover the CLIs and utils/exceptions.py. We do need to re-examine the CLIs to make sure they are all sufficiently compartmentalized, so I list them below as well.

• Compartmentalize run_EEXE.py
• Compartmentalize analyze_EEXe.py
• Compartmentalize explore_EEXE.py

[wehs7661]

Closing this issue now since some action items have become outdated, and the valid ones have been incorporated/restated in issue #41.