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feat(pyneuroml): add info about extra subpackages
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fixes #196
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sanjayankur31 committed Mar 5, 2024
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Expand Up @@ -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 <userdocs:supporting:apps>`, please install them as required:

For {ref}`NEURON <userdocs:supporting:apps: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 <userdocs:supporting:apps:brian>`, {ref}`NetPyNE <userdocs:supporting:apps: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
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