1279 minor additions to how infections work

[DavidKerkmann]

Changes and Information

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

• Add InfectionRateFromViralShed parameter
• Rename infectivity functionality to viral shed functionality
• Removed distributions from viral shed parameters; this is not required to have
• Rework infection setup, initial stay duration is now drawn randomly when initialized somewhere in the middle of the infection

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

Merge Request - Guideline Checklist

Please check our git workflow. Use the draft feature if the Pull Request is not yet ready to review.

Checks by code author

• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
• New code adheres to coding guidelines
• No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• Tests are added for new functionality and a local test run was successful (with and without OpenMP)
• Appropriate documentation for new functionality has been added (Doxygen in the code and explanations in the online documentation)
• Proper attention to licenses, especially no new third-party software with conflicting license has been added
• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Benchmak results:
Main:

---------------------------------------------------------------------------
Benchmark                                 Time             CPU   Iterations
---------------------------------------------------------------------------
abm_benchmark/abm_benchmark_50k        3457 ms         3469 ms            1
abm_benchmark/abm_benchmark_100k       7463 ms         7391 ms            1
abm_benchmark/abm_benchmark_200k      14989 ms        14859 ms            1

This branch:

---------------------------------------------------------------------------
Benchmark                                 Time             CPU   Iterations
---------------------------------------------------------------------------
abm_benchmark/abm_benchmark_50k        3517 ms         3516 ms            1
abm_benchmark/abm_benchmark_100k       7016 ms         7031 ms            1
abm_benchmark/abm_benchmark_200k      14182 ms        14125 ms            1

Checks by code reviewer(s)

• Corresponding issue(s) is/are linked and addressed
• Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• No large data files added in the whole history of commits(files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
• On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

Closes #1279
Closes #1247

[codecov]

Codecov Report

❌ Patch coverage is 97.67442% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 97.37%. Comparing base (2755329) to head (c9d1989).
⚠️ Report is 8 commits behind head on main.

Files with missing lines	Patch %	Lines
cpp/models/abm/infection.cpp	96.90%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1320      +/-   ##
==========================================
+ Coverage   97.30%   97.37%   +0.07%     
==========================================
  Files         187      189       +2     
  Lines       16027    16560     +533     
==========================================
+ Hits        15595    16126     +531     
- Misses        432      434       +2     

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[DavidKerkmann]

Added benchmark results.

[DavidKerkmann]

I changed everything according to the comments.

[jubicker]

Looks good to me now. Maybe you can have a look at the CodeCov?