946 implement generalized linear chain trick

[lenaploetzke]

Changes and Information

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

• Added a GLCT-SECIR model (generalized linear chain trick model) that allows to use phase-type distributed stay times in the compartments.
• Added tests.
• Moved calculate_compartments function from the LCT model to the lct_infection_state such that the GLCT model can use the function as well.

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

Merge Request - Guideline Checklist

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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 Markdown files if necessary)
• 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 #946.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.98%. Comparing base (0962eb0) to head (6a612dc).
Report is 6 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1058      +/-   ##
==========================================
+ Coverage   96.59%   96.98%   +0.39%     
==========================================
  Files         137      142       +5     
  Lines       11057    11868     +811     
==========================================
+ Hits        10680    11510     +830     
+ Misses        377      358      -19     

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[annawendler]

This is a very cool model! I think it would benefit from adding more documentation to make it easier to understand.

[annawendler]

Looks good, just some comments regarding spelling :)