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Improved comments in gap_junction Pynest examples #623

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merged 3 commits into from Jan 9, 2017

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@janhahne janhahne commented Jan 6, 2017

Improved comments (added additional information and markdown notation) in the gap-junction Pynest examples

http://www.nest-simulator.org/py_sample/gap_junctions_two_neurons/
http://www.nest-simulator.org/py_sample/gap_junctions_inhibitory_network/

to increase readability on the NEST homepage.

Just a change of documentation, no change in functionality. @steffengraber or @heplesser, could you have a quick look? There is probably no need for a detailed review.

input of 500.0 Hz with synaptic weight JE = 300.0 pA and the same
delay d. In addition (60*500)/2 gap junctions are added randomly to the
network resulting in an average of 60 gap-junction connections per neuron.
This script simulates an inhibitory network of `500` Hodgkin-Huxley neurons.

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@heplesser

heplesser Jan 7, 2017
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I don't think that setting 500 in backticks will improve readability. I would use backticks only for actual code examples. This applies to the remainder of the text.

a stable synchronous state is reached.
This example is also used as test case 2 (see figure 9 and 10)
in the article Hahne et al. (2015)

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heplesser Jan 7, 2017
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Just "in Hahne et al. (2015)"

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@heplesser heplesser left a comment

@janhahne I think you did a nice job, but see my comments/questions.

'wfr_comm_interval': 1.0,
'wfr_tol': 0.0001,
'wfr_max_iterations': 15,
'wfr_interpolation_order': 3})

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heplesser Jan 7, 2017
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Why have you removed all the wfr_ options here?

@@ -22,27 +22,23 @@
"""
Gap Junctions: Two neurons example

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heplesser Jan 7, 2017
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"Two neuron example" (no plural s)

'wfr_comm_interval': 1.0,
'wfr_tol': 0.0001,
'wfr_max_iterations': 15,
'wfr_interpolation_order': 3})

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heplesser Jan 7, 2017
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See above.

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@janhahne

janhahne Jan 8, 2017
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@heplesser The wfr settings are now discussed in the general gap junction documentation ( http://nest-simulator.org/simulations-with-gap-junctions/ ). The default settings are well chosen and from my point of view there is only little reason to change these settings. Until now the parameter were (re-)set to their defaults in the examples just to demonstrate how the parameters are set. For anyone just looking at the examples it might however of course be useful to have this code lines here.

After further considerations I reintroducted the settings in one of the examples (the network example).

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heplesser Jan 9, 2017
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OK.

an accurate gap junction between both neurons
In order to create the `gap_junction` connection we employ the `all_to_all`
connection rule: Gap junctions are bidirectional connections, therefore we
need to connect `neuron[0]` to `neuron[1]` and `neuron[1]` to `neuron[0]`

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heplesser Jan 7, 2017
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Full stop or colon at end of line missing.

{'model': 'gap_junction', 'weight': 0.5})

"""
Finally we start the simulation and plot the membrane potentials of
both neurons

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heplesser Jan 7, 2017
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Fullstop or colon missing.

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@janhahne janhahne commented Jan 8, 2017

@heplesser Thank you for the careful look! I pushed some improvements.

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@heplesser heplesser commented Jan 9, 2017

Since this is just a minor documentation update, I merge without second review.

@heplesser heplesser merged commit e817ee2 into nest:master Jan 9, 2017
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@janhahne janhahne deleted the janhahne:improve_comments branch Jan 9, 2017
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