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Update PyNEST examples to use NEST 3 features #1534

Merged
merged 53 commits into from
May 17, 2021
Merged

Update PyNEST examples to use NEST 3 features #1534

merged 53 commits into from
May 17, 2021

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terhorstd
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addressing issues in #1504

@heplesser heplesser added I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) S: High Should be handled next T: Enhancement New functionality, model or documentation labels Apr 22, 2020
@heplesser heplesser added this to the NEST 3.0 milestone Apr 22, 2020
@sarakonradi sarakonradi mentioned this pull request Apr 24, 2020
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@terhorstd terhorstd linked an issue Apr 28, 2020 that may be closed by this pull request
Finalize PyNEST examples #1504
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@sarakonradi
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After discussing this with @terhorstd offline, we agreed to remove the 50-example checklist in #1504. I have now added a new list comprised of general aspects to inspect across the examples.

Most items are code-related. I am happy taking care of the last two points, as they are documentation-based.

@hakonsbm @abigailm Please feel free to tick further boxes that are done!

@sarakonradi
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Having discussed this offline, the most efficient way to go about the examples is to divide #1504 into several mini PRs and to rename this PR.

@terhorstd Could we turn off draft mode then? And shall we title this PR "Incorporate NEST 3 features into PyNEST examples"?

As @hakonsbm sent his PR to your branch, there are still some SetDefaults() that we should probably get rid of. I have added this point to the #1504 checklist.

@terhorstd terhorstd changed the title reworked code style in pynest/examples update PyNEST examples to used NEST 3 features May 20, 2020
@terhorstd terhorstd changed the title update PyNEST examples to used NEST 3 features update PyNEST examples to use NEST 3 features May 20, 2020
@terhorstd terhorstd marked this pull request as ready for review May 20, 2020 08:30
@sarakonradi sarakonradi mentioned this pull request May 20, 2020
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@terhorstd terhorstd removed a link to an issue May 20, 2020
Finalize PyNEST examples #1504
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stinebuu
stinebuu suggested changes May 22, 2020
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Thanks! I have some comments and suggestions.

pynest/examples/brunel_alpha_nest.py Outdated Show resolved Hide resolved
pynest/examples/brunel_delta_nest.py Outdated Show resolved Hide resolved
pynest/examples/brunel_exp_multisynapse_nest.py Outdated Show resolved Hide resolved
pynest/examples/clopath_synapse_spike_pairing.py Outdated Show resolved Hide resolved
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@stinebuu stinebuu linked an issue Mar 10, 2021 that may be closed by this pull request
Examples fail with voltage_trace has no attribute show #1964
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@heplesser
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@terhorstd Please remove pynest/examples/spatial/hill_tononi_Vp.py to resolve the conflict, it has been removed in master.

This was referenced Apr 26, 2021
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@terhorstd
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So, it's not all perfect, but most things work and some are explicitly split of into separate PRs, like the quantal synapse example. I expect more separate issues/PRs will appear, but they should then be handled on their own.

@jougs jougs requested review from jougs and removed request for jhnnsnk May 5, 2021 16:31
stinebuu
stinebuu reviewed May 11, 2021
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Thanks @terhorstd! I have just some small comments and suggested updates.

pynest/examples/brunel_alpha_nest.py Outdated Show resolved Hide resolved
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jougs
jougs approved these changes May 17, 2021
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Other than my 4 minor suggestions, I'm fine with this and approve on condition that you address them timely.

As I took over the review assignment from @jhnnsnk and can assert that all of @stinebuu's concerns have been addressed appropriately, my approval is also the second one required.

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jougs
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On second thought just seconds later, I decided to commit the suggestions myself and merge :-)

@jougs jougs merged commit 794d7eb into nest:master May 17, 2021
@terhorstd terhorstd changed the title update PyNEST examples to use NEST 3 features Update PyNEST examples to use NEST 3 features Jun 10, 2021
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@sarakonradi sarakonradi sarakonradi requested changes

@stinebuu stinebuu stinebuu approved these changes

@jhnnsnk jhnnsnk jhnnsnk requested changes

@jougs jougs jougs approved these changes

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@sarakonradi sarakonradi

Labels
I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) S: High Should be handled next T: Enhancement New functionality, model or documentation
Projects
Documentation
Status: Done
Milestone
NEST 3.0
Development

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Examples fail with voltage_trace has no attribute show
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@terhorstd @sarakonradi @jhnnsnk @jougs @heplesser @stinebuu @hakonsbm