1442 Generic country Simulation

[HenrZu]

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

• Load contact data based on Prem et al., 2017
• Example ode_seir_contact_matrix_example.py runs a simulation for a specified country with real contact and population data
• The contact matrices are available for around 90 countries.

If need be, add additional information and what the reviewer should look out for in particular:

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• Tests are added for new functionality and a local test run was successful (with and without OpenMP)
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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.30%. Comparing base (7a332d8) to head (c9912e3).
⚠️ Report is 10 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1466      +/-   ##
==========================================
+ Coverage   97.29%   97.30%   +0.01%     
==========================================
  Files         186      187       +1     
  Lines       15961    16027      +66     
==========================================
+ Hits        15529    15595      +66     
  Misses        432      432              

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[mknaranja]

why do these functions start with "_"?

[HenrZu]

This is a convention in python that indicates that this function (or even a variabble) is only used internally in this file.

[mknaranja]

Thank you. Great addition. I went through it line by line with the debugger and checked here and there also for alternative if/else. I had some small comments + one bigger one for the aggregation of age groups.

I did not check if it works with a path provided and only briefly looked at the tests.

[mknaranja]

I think this is not correct. First, the rows (or columns; depending on the orientation from-to) should be multiplied with the group size (0-4: x, 5-14: y, ...). Then you can add and eventually you divide by the sum of x+y... Right?