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Bugfix for rxd reactions involving rxd parameters.#1933

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ramcdougal merged 6 commits into
neuronsimulator:masterfrom
adamjhn:rxd_parameter_fix
Aug 24, 2022
Merged

Bugfix for rxd reactions involving rxd parameters.#1933
ramcdougal merged 6 commits into
neuronsimulator:masterfrom
adamjhn:rxd_parameter_fix

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@adamjhn

@adamjhn adamjhn commented Jul 25, 2022

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@adamjhn adamjhn added bug rxd reaction-diffusion labels Jul 25, 2022
@adamjhn adamjhn requested a review from ramcdougal July 25, 2022 18:20
adamjhn added a commit to adamjhn/netpyne that referenced this pull request Jul 25, 2022
Parameters need to be added before reactions.
Parameter names should probably default to the key (in the same way as species and states).
Additional storing the hObj for rxd region geometry in netParams causing problems saving netParams, becuase the geometry objects are not JSON serializable.

Fix depends on NEURON pull request; neuronsimulator/nrn#1933
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✔️ 7475dd5 -> Azure artifacts URL

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✔️ f9d25ba -> Azure artifacts URL

Comment thread test/rxd/test_parameter_reaction.py Outdated

@ramcdougal ramcdougal left a comment

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LGTM

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Codecov Report

Merging #1933 (92c0990) into master (b46b452) will increase coverage by 0.03%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1933      +/-   ##
==========================================
+ Coverage   46.47%   46.50%   +0.03%     
==========================================
  Files         526      526              
  Lines      119212   119216       +4     
==========================================
+ Hits        55401    55439      +38     
+ Misses      63811    63777      -34     
Impacted Files Coverage Δ
share/lib/python/neuron/rxd/region.py 81.14% <100.00%> (+0.41%) ⬆️
share/lib/python/neuron/rxd/rxd.py 83.89% <100.00%> (+0.04%) ⬆️
share/lib/python/neuron/rxd/species.py 79.08% <0.00%> (+0.30%) ⬆️
share/lib/python/neuron/rxd/rate.py 69.64% <0.00%> (+2.38%) ⬆️
share/lib/python/neuron/rxd/rxdmath.py 59.81% <0.00%> (+3.55%) ⬆️
share/lib/python/neuron/rxd/reaction.py 74.04% <0.00%> (+3.81%) ⬆️

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✔️ 92c0990 -> Azure artifacts URL

@ramcdougal ramcdougal merged commit 1b76917 into neuronsimulator:master Aug 24, 2022
@ramcdougal ramcdougal deleted the rxd_parameter_fix branch August 24, 2022 23:57
@alexsavulescu alexsavulescu mentioned this pull request Dec 15, 2022
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4 participants