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Removed iaf_neuron from docstring and documentation examples #626

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merged 13 commits into from Jan 15, 2017

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@stinebuu
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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.

@Silmathoron

@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...

Show outdated Hide outdated doc/model_details/noise_generator.ipynb
@@ -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",

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@Silmathoron

Silmathoron Jan 9, 2017

Contributor

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...

@Silmathoron

Silmathoron Jan 9, 2017

Contributor

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...

Show outdated Hide outdated examples/nest/tsodyks_depressing.sli
@@ -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

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@Silmathoron

Silmathoron Jan 9, 2017

Contributor

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

@Silmathoron

Silmathoron Jan 9, 2017

Contributor

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

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@stinebuu

stinebuu Jan 10, 2017

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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.

@stinebuu

stinebuu Jan 10, 2017

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.

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@heplesser

heplesser Jan 10, 2017

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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.

@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.

Show outdated Hide outdated examples/nest/tsodyks_facilitating.sli
@@ -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

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@Silmathoron

Silmathoron Jan 9, 2017

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see above

@Silmathoron

Silmathoron Jan 9, 2017

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see above

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@heplesser

heplesser Jan 10, 2017

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See above.

@heplesser

heplesser Jan 10, 2017

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See above.

Show outdated Hide outdated nestkernel/nestmodule.cpp
SLI [3] [0] 2 PrintNetwork
+-[0] Subnet Dim=[12]
+- [1] iaf_psc_alpha
+- [2]...[11] iaf_cond_neuron

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@Silmathoron

Silmathoron Jan 9, 2017

Contributor

I think this should be iaf_cond_alpha

@Silmathoron

Silmathoron Jan 9, 2017

Contributor

I think this should be iaf_cond_alpha

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@stinebuu

stinebuu Jan 10, 2017

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

@stinebuu

stinebuu Jan 10, 2017

Contributor

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

Show outdated Hide outdated nestkernel/nestmodule.cpp
+- lifb_cond_neuron [2]..(10)..[11]
+-[12] Subnet Dim=[2 5 6]
+- [1] iaf_psc_alpha
+- [2]...[11] iaf_cond_neuron

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@Silmathoron

Silmathoron Jan 9, 2017

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see above

@Silmathoron

Silmathoron Jan 9, 2017

Contributor

see above

Show outdated Hide outdated topology/examples/conncon_targets.py
@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create two 30x30 layers of iaf_neurons,
Create two 30x30 layers of iaf_psc_alphas,

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@Silmathoron

Silmathoron Jan 9, 2017

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see above

@Silmathoron

Silmathoron Jan 9, 2017

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see above

Show outdated Hide outdated topology/examples/connex_ew.py
@@ -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,

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@Silmathoron

Silmathoron Jan 9, 2017

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see above

@Silmathoron

Silmathoron Jan 9, 2017

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see above

Show outdated Hide outdated topology/examples/grid_iaf.py
@@ -22,7 +22,7 @@
'''
NEST Topology Module Example
Create layer of 4x3 iaf_neurons, visualize
Create layer of 4x3 iaf_psc_alphas, visualize

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@Silmathoron

Silmathoron Jan 9, 2017

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see above

@Silmathoron

Silmathoron Jan 9, 2017

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see above

Show outdated Hide outdated topology/examples/grid_iaf_irr.py
@@ -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

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@Silmathoron

Silmathoron Jan 9, 2017

Contributor

see above

@Silmathoron

Silmathoron Jan 9, 2017

Contributor

see above

Show outdated Hide outdated topology/examples/grid_iaf_oc.py
@@ -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.

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@Silmathoron

Silmathoron Jan 9, 2017

Contributor

see above

@Silmathoron

Silmathoron Jan 9, 2017

Contributor

see above

@Silmathoron

All good 👍

@heplesser

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

Show outdated Hide outdated pynest/examples/Potjans_2014/network.py
'model': self.net_dict['neuron_model'],
'thread': thread
}, local_only=True
)[0]

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@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.

@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.

Show outdated Hide outdated examples/nest/tsodyks_depressing.sli
@@ -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

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@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.

@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.

Show outdated Hide outdated examples/nest/tsodyks_facilitating.sli
@@ -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

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@heplesser

heplesser Jan 10, 2017

Contributor

See above.

@heplesser

heplesser Jan 10, 2017

Contributor

See above.

Removed tsodyks_*.sli examples. Added comments in Potjans_2014 PyNEST
example saying a deprecation warning will be issued.
@stinebuu

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stinebuu Jan 15, 2017

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@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.

Contributor

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.

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@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.

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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

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@stinebuu stinebuu deleted the stinebuu:fix558_deprecated_examples_and_functions branch Jan 17, 2017

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