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Refactor conngen module to be a ConnBuilder #1830

Merged
merged 51 commits into from
Nov 23, 2020
Merged

Refactor conngen module to be a ConnBuilder #1830

merged 51 commits into from
Nov 23, 2020

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jougs
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@jougs jougs commented Nov 7, 2020 •
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This PR refactors the Connection Generator interface for NEST to be a regular ConnBuilder called conngen instead of being an extension module called conngen, which used to provide the CGConnect function. This addresses one of the action items of #1717.

jougs added 21 commits August 23, 2020 22:53
@jougs
Remove Python 2 workaround
b01620a
@jougs
Refactor conngen module functionality into a ConnBuilder
b03c0f3
@jougs
Update conngen_interface SLI example
43c201c
@jougs
Update SLI documentation for ConnGen related functions
b9bccbf
@jougs
Make strings consistent
7cc177a
@jougs
Update PyNEST example docstrings
2952250
@jougs
Remove ConnGen functions from PyNEST HL API
ea3dc97
@jougs
Update 2to3 conversion guide wrt Connect with a ConnGen
a202516
@jougs
Formatting
c06c383
@jougs
Protect from compilation in case libneurosim is not there
4d452e5
@jougs
Force Python 3 and monkey patch CSA build scripts
bea0530
@jougs
Export PYTHONPATH so csa is actually available
5aaaa10
@jougs
Replace old CGConnect to Connect with conngen rule and remove useless…
d286a1b 
… tests
@jougs
Formatting
9bc2d43
@jougs
Merge branch 'master' of github.com:nest/nest-simulator into refactor…
e4fff41 
…_conngen_module
@jougs
Update conngen documentation and move to connection management guide
bdd6340
@jougs
Fix build script for libneurosim
4c249c6
@jougs
Add library search path for CSA installation
23854c3
@jougs
Fix CSA tests
368b805
@jougs
Reorder initializers to avoid warning
8ee1ba0
@jougs
Remove debug output
e87dd5e
@jougs jougs self-assigned this Nov 7, 2020
@jougs jougs added I: Behavior changes Introduces changes that produce different results for some users S: Normal Handle this with default priority T: Maintenance Work to keep up the quality of the code and documentation. labels Nov 7, 2020
@jougs jougs added this to the NEST 3.0 milestone Nov 7, 2020
@jougs jougs mentioned this pull request Nov 9, 2020
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@stinebuu stinebuu self-requested a review November 9, 2020 08:55
@jougs jougs mentioned this pull request Nov 11, 2020
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sarakonradi
sarakonradi suggested changes Nov 12, 2020
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Thanks! I've added some documentation-related suggestions inline.

doc/guides/connection_management.rst Outdated
Comment on lines 208 to 209
library, NEST supports the Connection Generator Interface (`Djurfeldt
et al., 2014 <https://doi.org/10.3389/fninf.2014.00043>`_).
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Could we use an RST footnote reference instead, i.e., writing Connection Generator Interface [1]_ and adding a "References" section at the bottom?

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Good idea. Done in d5802c9.

examples/nest/conngen_interface.sli Outdated Show resolved Hide resolved
pynest/examples/csa_spatial_example.py Outdated Show resolved Hide resolved
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jougs commented Nov 13, 2020

@stinebuu, @sarakonradi: I've addressed all your points in my recent commits. Not sure if we really need the review by @hakonsbm. If you think we're good without, feel free to say so or remove the request of review.

@jougs jougs requested review from stinebuu and sarakonradi and removed request for hakonsbm November 13, 2020 13:33
stinebuu
stinebuu approved these changes Nov 13, 2020
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Thank you!

sarakonradi
sarakonradi approved these changes Nov 13, 2020
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LGTM!

@jougs jougs mentioned this pull request Nov 16, 2020
Merged
@stinebuu stinebuu merged commit 8f5a5fc into nest:master Nov 23, 2020
@hakonsbm hakonsbm mentioned this pull request Apr 14, 2021
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@jougs jougs mentioned this pull request Nov 22, 2021
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@jougs jougs deleted the refactor_conngen_module branch August 31, 2023 14:01
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@sarakonradi sarakonradi sarakonradi approved these changes

@stinebuu stinebuu stinebuu approved these changes

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I: Behavior changes Introduces changes that produce different results for some users S: Normal Handle this with default priority T: Maintenance Work to keep up the quality of the code and documentation.
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Status: Done
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@jougs @stinebuu @sarakonradi