diff --git a/README.rst b/README.rst index eb96de9c..0f8f433d 100644 --- a/README.rst +++ b/README.rst @@ -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 ' -loadflags '-L ' mod + cp -r mods/ + export DATADIR=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')") + cp -r $DATADIR/mod/* mods/ + nrnivmodl -incflags '-I ' -loadflags '-L ' mods + +To use the Blue Brain open models, you can build `neurodamus-models `_. +It will also produce a handy `build_neurodamus.sh` script that calls `nrnivmodl` with all dependencies to compile your future mod files + +.. code-block:: sh + + build_neurodamus mods/ Examples ======== -Once installed, you should be able to find `neurodamus` in your path: +Once neurodamus is installed, you should be able to find the executable `neurodamus` in your path: .. code-block:: @@ -74,7 +84,7 @@ We hope to bring the same advantages to the launcher script soon. .. code-block:: sh - export NEURODAMUS_PYTHON=/neurodamus/data + export NEURODAMUS_PYTHON=$(python -c "import neurodamus; from pathlib import Path; print(Path(neurod)mus.__file__).parent / 'data')") export HOC_LIBRARY_PATH= srun -mpi -python $NEURODAMUS_PYTHON/init.py diff --git a/docs/architecture.rst b/docs/architecture.rst index 135b4f41..51afa00d 100644 --- a/docs/architecture.rst +++ b/docs/architecture.rst @@ -455,4 +455,4 @@ flags in the CLI of Neurodamus. Development ------------ -You can find more information `here `_. +You can find more information on the page :ref:`development.rst`. diff --git a/docs/development.rst b/docs/development.rst index fb88bebe..831427e2 100644 --- a/docs/development.rst +++ b/docs/development.rst @@ -1,3 +1,5 @@ +.. _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. diff --git a/docs/index.rst b/docs/index.rst index 06d0a2ef..f88a9b62 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,6 +19,7 @@ Contents Developer Documentation Developing a Custom Neurodamus Memory Load Balance Tutorial + More on Neurodamus Wiki Indices and tables