A list of non-urgent but important enhancements for future consideration

[wehs7661]

Here we list todos that are not currently urgent but could be important for future work:

• Re-examine previously written tests to see if there are better ways to test the functions. Presumably a lot of tests could be made more rigorous/meaningful using unittest.mock. test_analyze_traj.py should be free from this since most of its tests have just been written recently.
• Examine the code in msm_analysis.py and write unit tests for its functionalities. Expand its functionalities if necessary.