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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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.43%. Comparing base (b184797) to head (20b34d1).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1518      +/-   ##
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+ Coverage   97.40%   97.43%   +0.02%     
==========================================
  Files         190      190              
  Lines       16866    15963     -903     
==========================================
- Hits        16428    15553     -875     
+ Misses        438      410      -28     

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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".

[mknaranja]

There are some minor inconsistencies with formatting. Could we apply clang-format on the created files?

[mknaranja]

Thank you for all the continuous changes, I basically have three comments / questions that are remaining:

• Can we do clang-format on the generated files?
• We could probably also generate probabilities for transitions (to R vs to D), right?
• In the SEIRD model, we include D in the total population size for the denominator. The generator probably uses all compartments, right? It is probably to much right now to designate which states should go in the denominator but we should write a comment on this in the documentation and open an issue for this.

Otherwise, I only tested running and looked into the results. I haven't gone through the code line-by-line anymore.

[HenrZu]

Thank you for all the continuous changes, I basically have three comments / questions that are remaining:

* Can we do clang-format on the generated files?

* We could probably also generate probabilities for transitions (to R vs to D), right?

* In the SEIRD model, we include D in the total population size for the denominator. The generator probably uses all compartments, right? It is probably to much right now to designate which states should go in the denominator but we should write a comment on this in the documentation and open an issue for this.

Otherwise, I only tested running and looked into the results. I haven't gone through the code line-by-line anymore.

Thank you for the feedback.

1. Clang format is now run (optionally) after rendering.

2. Moved to Support probabilistic branching transitions in the model generator #1555

3. See addition in modelgenerator rst