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

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.47%. Comparing base (46f65b5) to head (c6fe442).

Additional details and impacted files

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##             main    #1518      +/-   ##
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+ Coverage   97.46%   97.47%   +0.01%     
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  Files         190      190              
  Lines       15966    15966              
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+ Hits        15561    15563       +2     
+ Misses        405      403       -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".

[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

[Copilot]

Pull request overview

Adds a new Model Generator to the memilio-generation Python package that can generate MEmilio ODE model C++ sources, pybind11 bindings, and a Python example from a YAML/TOML specification (via CLI or Python API), along with documentation and tests.

Changes:

• Introduces memilio.modelgenerator (schema, validation, generator, CLI) plus Jinja2 templates for C++/pybind/example outputs.
• Updates packaging/docs to split “Model Generator” vs “Bindings Generator” dependencies and document the new workflow.
• Adds example configs (SEIR/SEIRD, YAML+TOML) and comprehensive unit tests; adjusts CI to install the bindings extra for the generation package.

Reviewed changes

Copilot reviewed 24 out of 24 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
pycode/memilio-generation/tests/test_modelgenerator.py	New unit tests covering parsing/validation/rendering/patching/CLI behavior.
pycode/memilio-generation/README.md	Reframes package docs around two tools (bindings generator + model generator) and links to RTD pages.
pycode/memilio-generation/pyproject.toml	Adds model-generator runtime deps, moves libclang to optional bindings extra, registers memilio-modelgenerator script, includes templates as package data.
pycode/memilio-generation/memilio/modelgenerator/validator.py	New config validator collecting multiple errors into ValidationError.
pycode/memilio-generation/memilio/modelgenerator/templates/simulation_py.jinja2	Template for generated memilio.simulation.<namespace> Python shim importing the compiled module.
pycode/memilio-generation/memilio/modelgenerator/templates/pybindings_cpp.jinja2	Template for generated pybind11 module for the model.
pycode/memilio-generation/memilio/modelgenerator/templates/parameters_h.jinja2	Template for generated parameters.h including constraints and (optional) ContactPatterns.
pycode/memilio-generation/memilio/modelgenerator/templates/model_h.jinja2	Template for generated model.h implementing get_flows for infection/linear/custom transitions.
pycode/memilio-generation/memilio/modelgenerator/templates/model_cpp.jinja2	Minimal translation unit including the generated header.
pycode/memilio-generation/memilio/modelgenerator/templates/infection_state_h.jinja2	Template for generated infection state enum header.
pycode/memilio-generation/memilio/modelgenerator/templates/example_py.jinja2	Template for generated runnable Python example simulation script.
pycode/memilio-generation/memilio/modelgenerator/templates/CMakeLists_model_txt.jinja2	Template for per-model CMake target.
pycode/memilio-generation/memilio/modelgenerator/schema.py	New dataclass-based internal config representation.
pycode/memilio-generation/memilio/modelgenerator/generator.py	Core implementation: YAML/TOML loading, parsing, rendering, clang-format integration, and patching existing repo files.
pycode/memilio-generation/memilio/modelgenerator/cli.py	New CLI entrypoint (memilio-modelgenerator) with preview/write/force modes.
pycode/memilio-generation/memilio/modelgenerator/__init__.py	Exposes generator/schema/validator in the package namespace.
pycode/examples/modelgenerator/seird.yaml	Example SEIRD config (includes a custom transition).
pycode/examples/modelgenerator/seir.yaml	Example SEIR YAML config.
pycode/examples/modelgenerator/seir.toml	Example SEIR TOML config.
docs/source/python/m-modelgenerator.rst	Full documentation for the new Model Generator.
docs/source/python/m-generation.rst	Updates overview/install instructions to distinguish both tools and their dependencies.
docs/source/python/m-bindingsgenerator.rst	Adds dedicated docs page for the existing bindings generator content.
docs/source/cpp/model_creation.rst	Links C++ model creation docs to the new Model Generator page.
.github/actions/test-py/action.yml	CI: installs memilio-generation[bindings,dev] to ensure generation tests have libclang available.

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