1167 Update some dependencies

[reneSchm]

Changes and Information

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

• Update minimum required cmake 3.11 -> 3.13
• Update spdlog 1.11.0 -> 1.15.0
• Update Eigen 3.3.9 -> 3.4.0
• Update JsonCpp 1.9.5 -> 1.9.6

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

• These updates help with support of recent compiler versions
• cmake 3.13 was already required by install in cpp/CMakeLists.txt:183, prior versions are unable to install targets from a subdirectory
• A newer spdlog version is required unless we want to silence several compiler warnings when including the library with gcc 14+. chose newest release, though we may use an older one if there is a reason for it
• Eigen 3.4.0 is newest release, but already 2 years old. It adds more compatibility with STL, e.g. iterators and initializer list support.
  • IMPORTANT: now including Eigen as system library to avoid several compiler warnings from within the library. could use several pragmas to silence each error individually instead
  • Eigen 4.0.0 may be available soon^(TM)
• JsonCpp 1.9.6 has several bugfixes, though we are not affected by these bugs (AFAIK)
• Check commits for steps taken to update the code to these versions. Updates are independent and can be selectively undone, if desired
  • changes to the serialization test are due to stricter is_container requirement, causing std::array to be serialized as tuple. deserialization of std::array was not supported anyways, so this is not a breaking change

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 #1167

[codecov]

Codecov Report

Attention: Patch coverage is 97.63314% with 4 lines in your changes missing coverage. Please review.

Project coverage is 96.97%. Comparing base (754675b) to head (af94264).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
cpp/memilio/compartments/compartmentalmodel.h	71.42%	2 Missing ⚠️
cpp/memilio/utils/logging.h	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1168      +/-   ##
==========================================
+ Coverage   96.95%   96.97%   +0.01%     
==========================================
  Files         148      148              
  Lines       13715    13718       +3     
==========================================
+ Hits        13298    13303       +5     
+ Misses        417      415       -2     

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[mknaranja]

@reneSchm Please update readmes :)

[mknaranja]

Thank you for the updates. I gave some more or less informed comments. Maybe check for them, update the readmes and then it should be OK.

[reneSchm]

Thanks for the review @mknaranja. Please check the "additional information for reviewers", in case you haven't.

I had made Eigen a system library, so we do not need to manually add compiler diagnostics. I hadn't removed them before your review (see here).

I also replaced mio::Vector by Eigen::VectorX (new in 3.4.0) in that commit, so it is more obvious that Vector is a Eigen type and not something we wrote ourselves.

[mknaranja]

Looks good. There is just one comment / discussion we should agree on.