1512 Generate ODE models from yaml template

[HenrZu]

Changes and Information

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

• Given a configuration template (yaml,toml), we generate the C++ source files and also the python bindings for this model (+ Python example)
• Can be started via CLI or Python file

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

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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 within the code (Doxygen) for new functionality has been added in the code.
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• (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.).
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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.40%. Comparing base (b184797) to head (db3d653).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   97.40%   97.40%           
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  Files         190      190           
  Lines       16866    16866           
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  Hits        16428    16428           
  Misses        438      438           

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[mknaranja]

Thank you very much for this great feature. So far I have only gone through the documentation. I will try to check functionality and core code more closely but this could maybe help to improve the documentation,

[mknaranja]

I get memilio-modelgenerator: command not found after pip install -e pycode/memilio-generation and memilio-modelgenerator pycode/examples/modelgenerator/seir.yaml ./

[kilianvolmer]

Thank you for writing this really good and extensive documentation! I added a few typo fixes. Apart from that I only have three minor concerns/suggestions:

• I think it is quite confusing to add null as indicator that there is no upper limit. Maybe this could be changed to None or something similar?
• Could you please add a sentence on reinstalling memilio-simulation for people who installed it using pypy?
• It took me a second to understand that Development and extension is not about a SEIR model as used in the documentation, but about new features for the generator. Could you maybe add one more sentence on that or move this section to a separate file?