Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Removed iaf_neuron from docstring and documentation examples #626

Merged

Conversation

@stinebuu
Copy link
Contributor

stinebuu commented Jan 9, 2017

Changed iaf_neuron to iaf_psc_alpha in docstring examples and in documentation/examples. See #558 for a list. Also made sure PyNEST examples do not show deprecation warnings. This should fix #558.

topology/doc/user_manual_scripts/* is not changed, as this is done by #621 .

As discussed in #580, SLI examples are mostly left alone, though I have replaced iaf_neuron with iaf_psc_alpha.

Copy link
Member

Silmathoron left a comment

@stinebuu: thanks for doing this painful PR!
There are just a few changes that I think should be made, but it's good overall.

@heplesser I think you should have a look at nestmodule.cpp since I'm not too familiar with what's getting printed here...

@@ -267,7 +267,7 @@
"outputs": [],
"source": [
"def noise_params(V_mean, V_std, dt=1.0, tau_m=10., C_m=250.):\n",
" 'Returns mean and std for noise generator for parameters provided; defaults for iaf_neuron.'\n",
" 'Returns mean and std for noise generator for parameters provided.'\n",

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

Maybe leaving the explanation about the fact that tau_m=10., C_m=250. are the default values for the iaf_psc_alpha model could be useful...

@@ -21,7 +21,7 @@
*/

/* BeginDocumentation
Name: test_tsodyks_depressing - sli script for overall test of iaf_neuron model
Name: test_tsodyks_depressing - sli script for overall test of iaf_psc_exp model

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

Why is it not iaf_psc_alpha? (though I guess this should not be important)

This comment has been minimized.

Copy link
@stinebuu

stinebuu Jan 10, 2017

Author Contributor

The example already uses iaf_psc_exp, so I figured someone had changed the model and forgotten to update the comment. I did change it to iaf_psc_alpha first, and got confused when I couldn't find any ìaf_neurons in the actual example. I had the same reasoning with the example below, tsdoyks_facilitating.sli.

This comment has been minimized.

Copy link
@heplesser

heplesser Jan 10, 2017

Contributor

Actually, this example (and pretty much the other three tsodyks_* examples in examples/nest) are not in good shape. I suggest we remove all four sli examples here, we have proper Python examples for Tsodyks-style facilitation and depression.

@@ -21,7 +21,7 @@
*/

/* BeginDocumentation
Name: tsodyks_facilitating - sli script for overall test of iaf_neuron model
Name: tsodyks_facilitating - sli script for overall test of iaf_psc_exp model

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

This comment has been minimized.

Copy link
@heplesser

heplesser Jan 10, 2017

Contributor

See above.

SLI [3] [0] 2 PrintNetwork
+-[0] Subnet Dim=[12]
+- [1] iaf_psc_alpha
+- [2]...[11] iaf_cond_neuron

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

I think this should be iaf_cond_alpha

This comment has been minimized.

Copy link
@stinebuu

stinebuu Jan 10, 2017

Author Contributor

I must have been very focused on iaf_psc_alpha! Thanks for the review, I will look at it now.

+- lifb_cond_neuron [2]..(10)..[11]
+-[12] Subnet Dim=[2 5 6]
+- [1] iaf_psc_alpha
+- [2]...[11] iaf_cond_neuron

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create two 30x30 layers of iaf_neurons,
Create two 30x30 layers of iaf_psc_alphas,

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create two 30x30 layers of iaf_neurons with edge_wrap,
Create two 30x30 layers of iaf_psc_alphas with edge_wrap,

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create layer of 4x3 iaf_neurons, visualize
Create layer of 4x3 iaf_psc_alphas, visualize

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create layer of 12 freely placed iaf_neurons, visualize
Create layer of 12 freely placed iaf_psc_alphas, visualize

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create three layers of 4x3 iaf_neurons, each with different center.
Create three layers of 4x3 iaf_psc_alphas, each with different center.

This comment has been minimized.

Copy link
@Silmathoron

Silmathoron Jan 9, 2017

Member

see above

and int(...) to make sure we have integers.
Copy link
Member

Silmathoron left a comment

All good 👍

Copy link
Contributor

heplesser left a comment

@stinebuu Good job! I have added some suggestions for improvements.

'model': self.net_dict['neuron_model'],
'thread': thread
}, local_only=True
)[0]

This comment has been minimized.

Copy link
@heplesser

heplesser Jan 10, 2017

Contributor

@stinebuu I would not use the SuppressedDeprecationWarning here, but rather add a comment to explain that the next line will cause a deprecation warning.

@@ -21,7 +21,7 @@
*/

/* BeginDocumentation
Name: test_tsodyks_depressing - sli script for overall test of iaf_neuron model
Name: test_tsodyks_depressing - sli script for overall test of iaf_psc_exp model

This comment has been minimized.

Copy link
@heplesser

heplesser Jan 10, 2017

Contributor

Actually, this example (and pretty much the other three tsodyks_* examples in examples/nest) are not in good shape. I suggest we remove all four sli examples here, we have proper Python examples for Tsodyks-style facilitation and depression.

@@ -21,7 +21,7 @@
*/

/* BeginDocumentation
Name: tsodyks_facilitating - sli script for overall test of iaf_neuron model
Name: tsodyks_facilitating - sli script for overall test of iaf_psc_exp model

This comment has been minimized.

Copy link
@heplesser

heplesser Jan 10, 2017

Contributor

See above.

example saying a deprecation warning will be issued.
@stinebuu
Copy link
Contributor Author

stinebuu commented Jan 15, 2017

@heplesser I have now removed the tsodyks sli examples, removed SuppressedDeprecationWarning from the Potjans Python example, and added comments saying a deprecation warning will be issued. As in #580 I added a comment in the docstring as well. GetNodes appear in network.py, but to run the example you run example.py, so I added the comment in both scripts docstring.

@heplesser
Copy link
Contributor

heplesser commented Jan 15, 2017

@stinebuu Thank you! The checks in Travis failed due to a Travis problem. I have restarted the Travis builds. I also removed one extraneous comma from a comment using the online editor.

@heplesser heplesser merged commit 32fdfd8 into nest:master Jan 15, 2017
1 check passed
1 check passed
continuous-integration/travis-ci/pr The Travis CI build passed
Details
@stinebuu stinebuu deleted the stinebuu:fix558_deprecated_examples_and_functions branch Jan 17, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Linked issues

Successfully merging this pull request may close these issues.

3 participants
You can’t perform that action at this time.