1132 Rename public members of IDE model

[annawendler]

Changes and Information

• m_transitions was renamed to transitions
• m_populations was renamed to populations
• m_total_confirmed_cases was renamed to total_confirmed_cases
• Arguments of model constructor were partially renamed for better understanding

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Closes #1132

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.98%. Comparing base (0c4965a) to head (79bd228).
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1173      +/-   ##
==========================================
+ Coverage   96.97%   96.98%   +0.01%     
==========================================
  Files         148      148              
  Lines       13718    13782      +64     
==========================================
+ Hits        13303    13367      +64     
  Misses        415      415              

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[annawendler]

I changed the name m_transitions to flows because it is in line with our simulation functions where we also use the term flow. The term transition (e.g. in transition_idx) still occurs in some places when we are referring to the transitions themselves and not to the number of individuals transitioning from one compartment to another.

[lenaploetzke]

Nice work! Please consider especially to rename the InfectionTransisitons and the TransitionDistributions consistent to the flows TimeSeries.

[lenaploetzke]

Best solution for now 👍