Skip to content

1512 Generate ODE models from yaml template #1518

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
HenrZu wants to merge 12 commits into
base: main
Choose a base branch
from
Open

1512 Generate ODE models from yaml template #1518

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
56d6bf6
first idea to generate ODE models from yaml template with jinja2, Tes…
HenrZu Mar 23, 2026
4598389
add toml support
reneSchm Mar 26, 2026
f0a6637
move into generation pkg, add example, yaml without ""
HenrZu Mar 30, 2026
1b18185
prevent overwrite of existing models (unless explicit allowed)
HenrZu Mar 30, 2026
9753bbc
typo template
HenrZu Mar 30, 2026
9166ed7
doc
HenrZu Mar 30, 2026
e70cf41
add simulation.py file for bindings
HenrZu Mar 30, 2026
340de4e
fix binding example
HenrZu Mar 30, 2026
71fb81c
[ci skip] Apply suggestions from code review
HenrZu Apr 7, 2026
2633302
[ci skip] review suggestions in doc
HenrZu Apr 7, 2026
d552a34
add support for list of compartments in foi
HenrZu Apr 7, 2026
e6a9b52
move model generator into memilio generation package, fix doc style, …
HenrZu Apr 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
29 changes: 25 additions & 4 deletions docs/source/python/m-generation.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,27 @@
MEmilio Generation
===================

.. note::

The ``memilio-generation`` package contains two independent tools:

* **Model Generator:** generates a C++ compartmental model with Python bindings from a YAML/TOML configuration file. See :doc:`m-modelgenerator`.
Comment thread
HenrZu marked this conversation as resolved.
* **Bindings Generator:** automatically generates Python bindings from existing C++ model source files using libclang. Described on this page.

.. toctree::
:maxdepth: 1
:hidden:

m-modelgenerator

.. _bindings-generator:
Copy link
Copy Markdown
Member

@mknaranja mknaranja Apr 18, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The bindings generator should also be placed in a subsection as the model generator


Bindings Generator
------------------

Comment thread
HenrZu marked this conversation as resolved.
Overview
~~~~~~~~

This package provides an automatic code generator for Python bindings of the MEmilio C++ library.
It enables the automatic generation of a part of the :doc:`Python Bindings <m-simulation>` that is common across multiple models.
For a particular example, see the SEIR model with its files `oseir.cpp <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-simulation/memilio/simulation/bindings/models/oseir.cpp>`_ and `oseir.py <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-simulation/memilio/simulation/oseir.py>`_.
Expand All @@ -13,7 +34,7 @@ The following figure from Chapter 5 outlines the workflow of the generator. Blue


Dependencies
----------
~~~~~~~~~~~~

The package uses the `Clang C++ library <https://clang.llvm.org/>`_ and the `LibClang Python library <https://libclang.readthedocs.io/en/latest/index.html>`_ to analyze the C++ code of a model. Both need to be installed and share the same version.

Expand All @@ -33,7 +54,7 @@ For a successful build, the development libraries for Python need to be installe
If you want to try a different version, set your `libclang` version under ``dependencies`` in the `pyproject.toml <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/pyproject.toml>`_ and change the clang command in ``create_ast`` in `ast.py <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/memilio/generation/ast.py>`_.

Usage
-----
~~~~~

During the installation the package creates a compilation database (compile_commands.json) for the models of the `MEmilio C++ Library <https://github.com/SciCompMod/memilio/blob/main/cpp/>`_.

Expand All @@ -59,7 +80,7 @@ To use the visualization run the command:


Visualization
-------------
~~~~~~~~~~~~~

The package contains a `Visualization class <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-generation/memilio/generation/graph_visualization.py>`_ to display the generated AST.
This allows you to visualize the abstract syntax tree (AST) of the C++ model in different ways:
Expand All @@ -83,7 +104,7 @@ This means that any nodes beyond the specified depth (e.g., all nodes at level 3
Notice that the visualization as a PNG file should not print the whole AST, as it is not possible to display the whole AST in a single image.

Development
-----------
~~~~~~~~~~~

When implementing new model features you can follow these steps:

Expand Down
Loading
Loading