From 03c5ee8f3df69da78899424c7d5fe078a7fb7c81 Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Tue, 5 Mar 2024 10:34:51 +0000 Subject: [PATCH] feat(pyneuroml): add info about extra subpackages fixes #196 --- source/Userdocs/Software/pyNeuroML.md | 29 ++++++++++++++++----------- 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/source/Userdocs/Software/pyNeuroML.md b/source/Userdocs/Software/pyNeuroML.md index 19cbeed1..408e6109 100644 --- a/source/Userdocs/Software/pyNeuroML.md +++ b/source/Userdocs/Software/pyNeuroML.md @@ -67,24 +67,29 @@ pip install pyneuroml By default, this will only install the minimal set of packages required to use pyNeuroML. To use pyNeuroML with specific {ref}`supporting tools `, please install them as required: -For {ref}`NEURON ` - ```{code-block} console -pip install NEURON +pip install pyneuroml[neuron] # for NEURON simulation backend +pip install pyneuroml[brian] # for Brian2 simulation backend +pip install pyneuroml[netpyne] # for NetPyNE simulation backend +pip install pyneuroml[povray] # for povray functions +pip install pyneuroml[hdf5] # for HDF5 support +pip install pyneuroml[analysis] # for analysis functions +pip install pyneuroml[tune] # for tuning/fitting functions +pip install pyneuroml[vispy] # for 3D interactive morphology plotting using vispy +pip install pyneuroml[plotly] # for interactive plotting with plotly +pip install pyneuroml[nsg] # pulls in pynsgr to use NSG +pip install pyneuroml[combine] # includes libsbml, libsedml +pip install pyneuroml[tellurium] # for Tellurium simulation backend +pip install pyneuroml[all] # installs all of the above +pip install pyneuroml[dev] # installs the above and other test related packages +pip install pyneuroml[doc] # for building documentation ``` -For compiling NEURON mod files, you also need a C compiler and the make utility installed on your computer. +Please note that for compiling NEURON mod files, you also need a C compiler and the `make` utility installed on your computer. Additionally, to run parallel simulations the [MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface) libraries are also needed. Please see the [NEURON installation documentation](https://www.neuron.yale.edu/neuron/download) for more information on installing NEURON on your computer. -{ref}`Brian `, {ref}`NetPyNE ` can also be similarly installed: - -``` -pip install netpyne -pip install brian2 -``` - -For more information, please refer to their respective documentations. +For more information on individual simulation backends, please refer to their respective documentations. (pyneuroml:install_fedora)= ### Installation on Fedora Linux