982 Make NPI delay implementation a parameter, set it and harmonize model advance functions

[mknaranja]

Changes and Information

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

• Rename delay_lockdown and make it a DynamicNPIsImplementationDelay Parameter
• Harmonize SECIR and SECIRVVS advance functions

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

• [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
• [ ] (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

Checks by code reviewer(s)

• [x] Corresponding issue(s) is/are linked and addressed
• [x] Code is clean of development artifacts (no deactivated or commented code lines, no debugging printouts, etc.)
• [x] Appropriate unit tests have been added, CI passes, code coverage and performance is acceptable (did not decrease)
• [x] 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).

[mknaranja]

@HenrZu @jubicker After I had reseen our delay_lockdown parameter on Thursday I directly made a first suggestion on how to improve it. There might be things missing like sampling, setting etc and tests are missing anyway. Could you have a look and take over?

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 99.50980% with 1 line in your changes missing coverage. Please review.

Project coverage is 96.47%. Comparing base (d4ed967) to head (5fcbb7e). Report is 4 commits behind head on main.

Files with missing lines	Patch %	Lines
cpp/models/ode_secir/model.h	96.29%	1 Missing :warning:

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #984      +/-   ##
==========================================
+ Coverage   96.44%   96.47%   +0.02%     
==========================================
  Files         135      135              
  Lines       11286    11369      +83     
==========================================
+ Hits        10885    10968      +83     
  Misses        401      401              

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[HenrZu]

@mknaranja @jubicker i have made some changes and added a few tests. Maybe one can verify/ review this further.

[jubicker]

@mknaranja @jubicker i have made some changes and added a few tests. Maybe one can verify/ review this further.

Looks good so far (only had some minor comments). But the merge conflicts should be resolved.