1039 Add functions for the Person to choose whether to comply to mask,test and isolation

[khoanguyen-dev]

Changes and Information

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

• Add a file for different NPI types
• The compliance levels are presented as a member vector in the Person class.
• Add functions to set and get compliance levels in the Person class.
• Add different functions to check wether a Person is complying to these NPIs.

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

• See World::migration for apply_mask_intervention()
• See TestingStrategy::run_strategy for apply_test_intervention()
• See Person::get_tested for apply_isolation_intervention()

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

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

Run on (8 X 24.121 MHz CPU s) CPU Caches: L1 Data 64 KiB (x8) L1 Instruction 128 KiB (x8) L2 Unified 4096 KiB (x2) Load Average: 2.98, 4.30, 4.88

• Main branch

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Benchmark Time CPU Iterations

abm_benchmark/abm_benchmark_50k 2247 ms 2242 ms 1 abm_benchmark/abm_benchmark_100k 4691 ms 4619 ms 1 abm_benchmark/abm_benchmark_200k 8577 ms 8299 ms 1

• 1039 branch

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Benchmark Time CPU Iterations

abm_benchmark/abm_benchmark_50k 2044 ms 2040 ms 1 abm_benchmark/abm_benchmark_100k 4169 ms 4098 ms 1 abm_benchmark/abm_benchmark_200k 8243 ms 8168 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 #1039 Closes #503

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 98.59155% with 1 line in your changes missing coverage. Please review.

Project coverage is 96.54%. Comparing base (cb5affd) to head (990fe6b). Report is 15 commits behind head on main.

Files with missing lines	Patch %	Lines
cpp/models/abm/model.cpp	96.96%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1040      +/-   ##
==========================================
+ Coverage   96.42%   96.54%   +0.11%     
==========================================
  Files         132      135       +3     
  Lines       11061    10906     -155     
==========================================
- Hits        10666    10529     -137     
+ Misses        395      377      -18     

Flag	Coverage Δ
	96.54% <98.59%> (?)

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[reneSchm]

I just noticed that the compliance vector looks very much like a parameter, especially with the getter/setter. We could think about putting it into a Person specific ParameterSet, as well as probably m_age or the random-group/hour variables; but probably in another PR.

[khoanguyen-dev]

For your comment @DavidKerkmann (https://github.com/SciCompMod/memilio/pull/1040#discussion_r1678913362): I realised that the testing_scheme_2 is not actually active so at one time the second person agrees to test but it's not performed. I have now added some more comments to clarify the number of draws.

[mknaranja]

@reneSchm @DavidKerkmann pls always check (and "check") reviewer boxes above.