Further refine the unit tests of ensemble_md

[wehs7661]

Now the code coverage has been enhanced to 96%. However, we want to further refine the tests by accomplishing the following tasks, as listed in #41.

• Add unit tests for functionalities relevant to MT-REXEE, which are in replica_exchange_EE.py
  - [ ] 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.
• Re-examine the missed lines to push the code coverage as much as possible.
• Check if the warnings are actually harmless.
• Add a UserWarning to msm_analysis.py to reflect the fact that the script msm_analysis.py is still a work in progress and we are not planning to expand or test the module in the short term.

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Update: We have deferred the following task and noted it Issue #50

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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.38%. Comparing base (27320da) to head (5175648).
Report is 21 commits behind head on master.

❗ Current head 5175648 differs from pull request most recent head 7faf9cf. Consider uploading reports for the commit 7faf9cf to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #49      +/-   ##
==========================================
+ Coverage   96.10%   98.38%   +2.28%     
==========================================
  Files          10       10              
  Lines        1950     1921      -29     
==========================================
+ Hits         1874     1890      +16     
+ Misses         76       31      -45     

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[wehs7661]

The currently implemented unit tests could trigger 21 warnings when performed. 18 of them are either DeprecationWarning or MatplotlibDeprecation Warning, which are harmless for the short term. The other 3 are RuntimeWarning:

• Two of them are from the first test of _df_combine_adjacent in analyze_free_energy.py. They are harmless.
• The other is from the second test of traj2transmtx in analyze_traj.py. It is also harmless.

For more details please check the changes made here.