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:

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

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.39%. Comparing base (b184797) to head (a62966d).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1518      +/-   ##
==========================================
- Coverage   97.40%   97.39%   -0.02%     
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  Files         190      190              
  Lines       16866    16866              
==========================================
- Hits        16428    16426       -2     
- Misses        438      440       +2     

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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?

[HenrZu]

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?

Great points, thank you.

Regarding the first point. Internally, PyYAML directly converts null to Python’s None as null is the yaml syntax for no value. None would be read in as "None".