nestml 8.3.0__py3-none-any.whl

nestml-8.3.0.data/data/doc/citing.rst

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+Citing NESTML
+=============
+
+If you use NESTML in your work, please cite one or more of the following publications.
+
+In general, please cite the software release that you are using. In case you wish to refer to specific features of the processing toolchain, please cite the relevant scientific publication.
+
+
+Software releases
+-----------------
+
+Charl Linssen, Pooja N. Babu, Andreas Rogalski, Bernhard Rumpe and Abigail Morrison (2025). **NESTML 8.2.0.** Zenodo. `doi:10.5281/zenodo.16537793 <https://doi.org/10.5281/zenodo.16537793>`_.
+
+Charl Linssen, Pooja N. Babu, Bernhard Rumpe and Abigail Morrison (2025). **NESTML 8.1.0.** Zenodo. `doi:10.5281/zenodo.16537793 <https://doi.org/10.5281/zenodo.16537793>`_.
+
+Charl Linssen, Pooja N. Babu, Bernhard Rumpe and Abigail Morrison (2025). **NESTML 8.0.2.** Zenodo. `doi:10.5281/zenodo.15771528 <https://doi.org/10.5281/zenodo.15771528>`_.
+
+Charl Linssen, Pooja N. Babu, Bernhard Rumpe and Abigail Morrison (2025). **NESTML 8.0.1.** Zenodo. `doi:10.5281/zenodo.15292719 <https://doi.org/10.5281/zenodo.15292719>`_.
+
+Charl Linssen, Pooja N. Babu, Younes Bouhadjar, Leander Ewert, Willem Wybo, Melissa Lober, Florian Feller, Bernhard Rumpe and Abigail Morrison (2024). **NESTML 8.0.0.** Zenodo. `doi:10.5281/zenodo.12191059 <https://doi.org/10.5281/zenodo.12191059>`_.
+
+Charl A.P. Linssen, Pooja N. Babu, Bernhard Rumpe and Abigail Morrison (2024). **NESTML 7.0.1.** Zenodo. `doi:10.5281/zenodo.10966350 <https://doi.org/10.5281/zenodo.10966350>`_.
+
+Charl A.P. Linssen, Pooja N. Babu, Jochen M. Eppler, Leander Ewert, Krzysztof Blaszczyk, Willem Wybo, Beck Strohmer, Bernhard Rumpe and Abigail Morrison (2023). **NESTML 7.0.0.** Zenodo. `doi:10.5281/zenodo.10125416 <https://doi.org/10.5281/zenodo.10125416>`_.
+
+Charl A.P. Linssen, Pooja N. Babu, Levin Schmidt, Tom Tetzlaff, Maryada, Mohamed Ayssar Benelhedi, Jochen M. Eppler, Bernhard Rumpe and Abigail Morrison (2023). **NESTML 6.0.0.** Zenodo. `doi:10.5281/zenodo.8380365 <https://doi.org/10.5281/zenodo.8380365>`_.
+
+Charl A.P. Linssen, Pooja N. Babu, Jingxuan He,  Jochen Martin Eppler, Bernhard Rumpe and Abigail Morrison (2022). **NESTML 5.1.0.** Zenodo. `doi:10.5281/zenodo.7071624 <https://doi.org/10.5281/zenodo.7071624>`_.
+
+Charl A.P. Linssen, Pooja N. Babu, Ayssar Benelhedi, Robin De Schepper, Tanguy Fardet, Jochen Martin Eppler, Bernhard Rumpe and Abigail Morrison (2022). **NESTML 5.0.0.** Zenodo. `doi:10.5281/zenodo.5784175 <https://doi.org/10.5281/zenodo.5784175>`_.
+
+Pooja Nagendra Babu, Charl Linssen, Jochen Martin Eppler, Tobias Schulte to Brinke, Abolfazl Ziaeemehr, Tanguy Fardet, Younes Bouhadjar, Renato Duarte, Bernhard Rumpe and Abigail Morrison (2021). **NESTML 4.0.** Zenodo. `doi:10.5281/zenodo.4740083 <https://doi.org/10.5281/zenodo.4740083>`_.
+
+Charl Linssen, Bernhard Rumpe, Sebastian Berns, Tanguy Fardet, Konstantin Perun, Tobias Schulte to Brinke, Dennis Terhorst, Jochen M. Eppler and Abigail Morrison (2020). **NESTML 3.1.** Zenodo. `doi:10.5281/zenodo.3697733 <http://doi.org/10.5281/zenodo.3697733>`_.
+
+Konstantin Perun, Philip Traeder, Jochen Martin Eppler, Dimitri Plotnikov, Tammo Ippen, Tanguy Fardet, Guido Trensch, Sanin Aleksey, Inga Blundell and Jakob Jordan (2018) **NESTML 3.0.** Zenodo. `doi:10.5281/zenodo.1412608 <http://doi.org/10.5281/zenodo.1412608>`_.
+
+
+Scientific publications
+-----------------------
+
+Charl Linssen, Pooja N. Babu, Jochen M. Eppler, Luca Koll, Bernhard Rumpe and Abigail Morrison (2025) **NESTML: a generic modeling language and code generation tool for the simulation of spiking neural networks with advanced plasticity rules.** Front. Neuroinform. `doi:10.3389/fninf.2025.1544143 <https://doi.org/10.3389/fninf.2025.1544143>`_.
+
+Inga Blundell, Dimitri Plotnikov, Jochen Martin Eppler and Abigail Morrison (2018) **Automatically selecting a suitable integration scheme for systems of differential equations in neuron models.** Front. Neuroinform. `doi:10.3389/fninf.2018.00050 <https://doi.org/10.3389/fninf.2018.00050>`_.
+
+Konstantin Perun, Bernhard Rumpe, Dimitri Plotnikov, Guido Trensch, Jochen Martin Eppler, Inga Blundell and Abigail Morrison (2018). **Reengineering NestML with Python and MontiCore** (Version 2.4). Zenodo. `doi:10.5281/zenodo.1319653 <http://doi.org/10.5281/zenodo.1319653>`_.
+
+Dimitri Plotnikov, Bernhard Rumpe, Inga Blundell, Tammo Ippen, Jochen Martin Eppler and Abigail Morrison (2016). **NESTML: a modeling language for spiking neurons.** In Modellierung 2016, March 2-4 2016, Karlsruhe, Germany. 93–108. `doi:10.5281/zenodo.1412345 <http://doi.org/10.5281/zenodo.1412345>`_.

nestml-8.3.0.data/data/doc/extending.rst

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+Extending NESTML
+################
+
+The NESTML toolchain is lightweight, modular and extensible.
+
+
+Internal workflow
+-----------------
+
+When NESTML is invoked, several steps are executed in sequence. First, the model(s) are parsed and validated. Then, depending on which target platform has been selected, transformations may occur, such as variable name rewriting in case of conflict with a keyword in the target language). The transformed models are then passed to the code generator, which combines them with a set of templates. Finally, an optional build stage compiles and builds the code, for example to yield a dynamically loadable library (``.so`` or ``.dll`` file).
+
+.. figure:: https://raw.githubusercontent.com/nest/nestml/main/doc/fig/internal_workflow.png
+   :alt: NESTML model(s) → Parsing and validation → Transform → (+ Templates) → Generate code (and build) → Executable (binary) code
+
+A more detailed description of the internal architecture of NESTML can be found in the following places:
+
+* Tammo Ippen, "NESTML - Creating a Neuron Modeling Language and Generating Efficient Code for the NEST Simulator with MontiCore". Master's thesis, RWTH Aachen University (2013) :download:`PDF <extending/Tammo_Ippen_Master_Thesis.pdf>`
+* Konstantin Perun, "Reengineering of NestML with Python". Master's thesis, RWTH Aachen University (2018) :download:`PDF <extending/Konstantin_Perun_Master_thesis.pdf>`
+* Dimitri Plotnikov, "NESTML - die Domänenspezifische Sprache für den NEST-Simulator Neuronaler Netzwerke im Human Brain Project". Doctoral thesis, RWTH Aachen University (2017) :download:`PDF <extending/Dimitri_Plotnikov_Doctoral_Thesis.pdf>`
+
+  * A condensed online English version is available: :doc:`pynestml_toolchain/index`
+
+
+API documentation
+-----------------
+
+API documentation is automatically generated from source code and can be browsed here: :mod:`pynestml` **module index**
+
+
+Running NESTML with custom templates
+------------------------------------
+
+NESTML generates model-specific code using a set of Jinja templates. The templates for each target platform are located in the `pynestml/codegeneration/resources_* <https://github.com/nest/nestml/tree/main/pynestml/codegeneration>`__ subdirectories. (For more information on code generation using templates, see :ref:`Section 3.1: AST Transformations and Code Generation`.) For example, for NEST, NESTML by default uses the templates in the directory `pynestml/codegeneration/resources_nest/point_neuron <https://github.com/nest/nestml/tree/main/pynestml/codegeneration/resources_nest/point_neuron>`__. These defaults are specified in the code generator within its default values dictionary (``_default_options``, see for instance https://github.com/nest/nestml/blob/main/pynestml/codegeneration/nest_code_generator.py).
+
+The default directory can be changed by specifying code generator options that override the default values. This can be done either by passing these options via the ``codegen_opts`` parameter of the NESTML Python API call to ``generate_target()``, or on the command line, through the ``--codegen_opts`` parameter to a JSON file. For example:
+
+.. code-block:: bash
+
+   nestml --input_path models/neurons/iaf_psc_exp_neuron.nestml --codegen_opts /home/nest/work/codegen_options.json
+
+An example ``codegen_options.json`` file for NEST could look as follows:
+
+.. code-block:: json
+
+   {
+        "templates":
+        {
+            "path": "/home/nest/work/custom_templates",
+            "model_templates": {
+                "neuron": ["@NEURON_NAME@.cpp.jinja2", "@NEURON_NAME@.h.jinja2"],
+                "synapse": ["@SYNAPSE_NAME@.h.jinja2"]
+            },
+            "module_templates": ["setup/CMakeLists.txt.jinja2",
+                                 "setup/@MODULE_NAME@.h.jinja2","setup/@MODULE_NAME@.cpp.jinja2"]
+        }
+   }
+
+The ``templates`` option in the JSON file contains information on the custom Jinja templates to be used for code generation.
+
+* The ``path`` option indicates the root directory of the custom Jinja templates.
+* The ``model_templates`` option indicates the names of the Jinja templates for neuron and synapse model(s) or relative path to a directory containing the neuron and synapse model(s) templates.
+* The ``module_templates`` option indicates the names or relative path to a directory containing the Jinja templates for the module.
+
+The escape sequence ``@NEURON_NAME@`` (resp. ``@SYNAPSE_NAME@``, ``@MODULE_NAME@``) will be replaced with the name of the neuron model (resp. synapse model or name of the module) during code generation.
+
+If a directory is given, the directory is recursively searched for templates (files ending in the ``.jinja2`` extension), for example:
+
+.. code-block:: python
+
+   codegen_opts = {"templates": {"module_templates": ["setup"]}}
+
+
+Adding a new target platform
+----------------------------
+
+* Add a new set of templates in a new directory under `pynestml/codegeneration/resources_* <https://github.com/nest/nestml/tree/main/pynestml/codegeneration>`__.
+* Implement a new code generator, for example based on the existing `nest_code_generator.py <https://github.com/nest/nestml/tree/main/pynestml/codegeneration/nest_code_generator.py>`_.
+* Optionally, implement a new builder, for example based on the existing `nest_builder.py <https://github.com/nest/nestml/tree/main/pynestml/codegeneration/nest_builder.py>`_.
+* Add the new target platform to the frontend in `pynestml_frontend.py <https://github.com/nest/nestml/blob/main/pynestml/frontend/pynestml_frontend.py>`__.

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