Add unit tests for replica_exchange_EE.py, the utils module and a part of the analysis module

[wehs7661]

In this PR, we aim to enhance the code coverage for the following scripts:

• replica_exchange_EE.py (not including functions relevant to MT-REXEE)
• utils/gmx_parser.py
• utils/utils.py
• analysis/analyze_traj.py

Note that scripts like utils/exceptions.py and analysis/analyze_matrix.py already have code coverages nearly 100%. Some future work include

• Adding unit tests for the following scripts:
  • analysis/analyze_free_energy.py
  • analysis/clustering.py
  • analysis/msm_anslysis.py
  • analysis/synthesize_data.py
• Adding regression tests for CLIs.
• Adding tests using MPI
• Adding tests relevant to multi-topology REXEE

[codecov]

Codecov Report

Attention: Patch coverage is 86.00000% with 21 lines in your changes are missing coverage. Please review.

Project coverage is 92.34%. Comparing base (4b409bd) to head (0f9952b).

Files	Patch %	Lines
ensemble_md/analysis/analyze_matrix.py	66.66%	8 Missing ⚠️
ensemble_md/replica_exchange_EE.py	73.91%	6 Missing ⚠️
ensemble_md/analysis/synthesize_data.py	83.33%	5 Missing ⚠️
ensemble_md/analysis/analyze_traj.py	96.96%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           master      #37       +/-   ##
===========================================
+ Coverage   52.95%   92.34%   +39.38%     
===========================================
  Files           7        8        +1     
  Lines        1571     1645       +74     
===========================================
+ Hits          832     1519      +687     
+ Misses        739      126      -613     

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