Improved comments in gap_junction Pynest examples #623

Merged
merged 3 commits into from Jan 9, 2017

Conversation

Projects
None yet
2 participants
@janhahne
Contributor

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.

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

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.

@heplesser

heplesser Jan 7, 2017

Contributor

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)

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

Just "in Hahne et al. (2015)"

@heplesser

heplesser Jan 7, 2017

Contributor

Just "in Hahne et al. (2015)"

@heplesser

@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})

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

Why have you removed all the wfr_ options here?

@heplesser

heplesser Jan 7, 2017

Contributor

Why have you removed all the wfr_ options here?

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

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

"Two neuron example" (no plural s)

@heplesser

heplesser Jan 7, 2017

Contributor

"Two neuron example" (no plural s)

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

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

See above.

@heplesser

heplesser Jan 7, 2017

Contributor

See above.

This comment has been minimized.

@janhahne

janhahne Jan 8, 2017

Contributor

@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).

@janhahne

janhahne Jan 8, 2017

Contributor

@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).

This comment has been minimized.

@heplesser

heplesser Jan 9, 2017

Contributor

OK.

@heplesser

heplesser Jan 9, 2017

Contributor

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]`

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

Full stop or colon at end of line missing.

@heplesser

heplesser Jan 7, 2017

Contributor

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

This comment has been minimized.

@heplesser

heplesser Jan 7, 2017

Contributor

Fullstop or colon missing.

@heplesser

heplesser Jan 7, 2017

Contributor

Fullstop or colon missing.

@janhahne

This comment has been minimized.

Show comment
Hide comment
@janhahne

janhahne Jan 8, 2017

Contributor

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

Contributor

janhahne commented Jan 8, 2017

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

@heplesser

This comment has been minimized.

Show comment
Hide comment
@heplesser

heplesser Jan 9, 2017

Contributor

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

Contributor

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

1 check passed

continuous-integration/travis-ci/pr The Travis CI build passed
Details

@janhahne janhahne deleted the janhahne:improve_comments branch Jan 9, 2017

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment