Merge pull request #194 from NeuroML/feat/neuron-home

Document using `NEURON_HOME`

source/Userdocs/IzhikevichNetworkExample.md

@@ -12,7 +12,10 @@ We will create a small network of cells, simulate this network, and generate a p
 Spike times of neurons in 2 populations recorded from the simulation.
 ```
 
-The Python script used to create the model, simulate it, and generate this plot is below:
+The Python script used to create the model, simulate it, and generate this plot is below.
+Please note that this example uses the {ref}`NEURON <userdocs:neuron>` simulator to simulate the model.
+Please ensure that the `NEURON_HOME` environment variable is correctly set as noted {ref}`here <userdocs:neuron:envvar>`.
+
 ```{literalinclude} ./NML2_examples/izhikevich-network.py
 ----
 language: python

source/Userdocs/MultiCompartmentOLMexample.md

@@ -394,6 +394,9 @@ Level 10 network graph generated by pynml
 ```
 ## Simulating the model
 
+Please note that this example uses the {ref}`NEURON <userdocs:neuron>` simulator to simulate the model.
+Please ensure that the `NEURON_HOME` environment variable is correctly set as noted {ref}`here <userdocs:neuron:envvar>`.
+
 Now that we have declared and inspected our network model and all its components, we can proceed to simulate it.
 We do this in the `main` function:
 ```{literalinclude} ./NML2_examples/olm-example.py

source/Userdocs/Software/Tools/NEURON.md

@@ -5,6 +5,7 @@
 
 [NEURON](http://www.neuron.yale.edu/neuron) is a widely used simulation environment and is one of the main target platforms for a standard facilitating exchange of neuronal models.
 
+(userdocs:neuron:simulating)=
 ## Simulating NeuroML models in NEURON
 
 {ref}`jNeuroML <jneuroml>` or {ref}`pyNeuroML <pyNeuroML>` can be used to convert NeuroML2/LEMS models to NEURON. This involves pointing at a {ref}`LEMS Simulation file <userdocs:lemssimulation>` describing what to simulate, and using the `-neuron` option:
@@ -32,6 +33,28 @@ from pyneuroml.pynml import run_lems_with_jneuroml_neuron
 run_lems_with_jneuroml_neuron(lems_file_name)
 ```
 
+(userdocs:neuron:envvar)=
+## Setting the NEURON_HOME environment variable
+
+Since it is possible to install multiple versions of NEURON in different places, the NeuroML tools need to be told where the NEURON tools are.
+To do this, they look at the `NEURON_HOME` environment variable.
+This needs to hold the path to where the binary (`bin`) folder holding the NEURON tools such as `nrniv` are located.
+On Linux like systems, one can use `which` to find these tools and set the variable:
+
+``` {code-block} bash
+$ which nrniv
+~/.local/share/virtualenvs/neuroml-311-dev/bin/nrniv
+
+$ export NEURON_HOME="~/.local/share/virtualenvs/neuroml-311-dev/"
+```
+
+One can combine these commands together also:
+
+``` {code-block} bash
+$ export NEURON_HOME="$(dirname $(dirname $(which nrniv)))"
+```
+
+(userdocs:neuron:neuroconstruct)=
 ## Using neuroConstruct
 
 NEURON simulations can also be generated from NeuroML model components by {ref}`neuroConstruct <userdocs:supporting:apps:neuroconstruct>`, but most of this functionality is related to {ref}`NeuroML v1 <userdocs:neuromlv1>`.