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@DavidKerkmann DavidKerkmann commented Jul 21, 2025

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.

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

@DavidKerkmann DavidKerkmann linked an issue Jul 21, 2025 that may be closed by this pull request
2 tasks
@DavidKerkmann DavidKerkmann marked this pull request as draft July 21, 2025 13:25
@DavidKerkmann DavidKerkmann requested a review from jubicker July 21, 2025 13:26
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Minor additions to how infections work Implement infectionratefromviralshed
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