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Improve docs: link to Wiki and neurodamus-models
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WeinaJi committed Dec 4, 2024
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20 changes: 15 additions & 5 deletions README.rst
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Expand Up @@ -44,16 +44,26 @@ Install neurodamus
Build special with mod files
----------------------------
Once neuron and neurodamus are installed, you can build `special` with your mod files:

.. code-block:: sh
mkdir mods
cp -r mod-files-from-released-circuit mods/
cp -r neurodamus-install-prefix/share/mod/* mods/
nrnivmodl -incflags '-I <include-paths-of-our-dependencies>' -loadflags '-L <libs-paths-for-linking>' mod
cp -r <your-mod-files> mods/
export DATADIR=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')")
cp -r $DATADIR/mod/* mods/
nrnivmodl -incflags '-I <include-paths-of-our-dependencies>' -loadflags '-L <libs-paths-for-linking>' mods
To use the Blue Brain open models, you can build `neurodamus-models <https://github.com/blueBrain/neurodamus-models>`_.
It will also produce a handy `build_neurodamus.sh` script that calls `nrnivmodl` with all dependencies to compile your future mod files

.. code-block:: sh
build_neurodamus mods/
Examples
========
Once installed, you should be able to find `neurodamus` in your path:
Once neurodamus is installed, you should be able to find the executable `neurodamus` in your path:

.. code-block::
Expand All @@ -74,7 +84,7 @@ We hope to bring the same advantages to the launcher script soon.

.. code-block:: sh
export NEURODAMUS_PYTHON=<neurodamus_folder>/neurodamus/data
export NEURODAMUS_PYTHON=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')")
export HOC_LIBRARY_PATH=<hoc_files_folder>
srun <srun params> <your_built_special> -mpi -python $NEURODAMUS_PYTHON/init.py <neurodamus params>
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2 changes: 1 addition & 1 deletion docs/architecture.rst
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Expand Up @@ -455,4 +455,4 @@ flags in the CLI of Neurodamus.
Development
------------

You can find more information `here <development.rst>`_.
You can find more information on the page :ref:`development.rst`.
2 changes: 2 additions & 0 deletions docs/development.rst
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.. _development.rst:

How to develop / use a custom Neurodamus-py
===========================================
Neurodamus-py is a Python application. Therefore, all generic procedures on how to manage Python applications generally apply.
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1 change: 1 addition & 0 deletions docs/index.rst
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Expand Up @@ -19,6 +19,7 @@ Contents
Developer Documentation <architecture>
Developing a Custom Neurodamus <development>
Memory Load Balance Tutorial <memory_load_balance>
More on Neurodamus Wiki <https://github.com/BlueBrain/neurodamus/wiki>


Indices and tables
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