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Changes for NeuroML v2.3.1 release #120

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merged 31 commits into from
Aug 20, 2024
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c2f1276
To v1.10.0
pgleeson Sep 22, 2023
b8713b4
feat(nrnwriter): also handle ChannelDensityNonUniformNernst
sanjayankur31 Dec 20, 2023
6e409b5
Merge pull request #109 from NeuroML/feat/channeldensitynonuniformnernst
pgleeson Dec 21, 2023
2f2e2a7
Add functionality to save file outputs of sed-ml
pgleeson Feb 12, 2024
f6ad0c8
Generates valid sed-ml
pgleeson Feb 12, 2024
728c83f
Merge pull request #111 from NeuroML/experimental
pgleeson Feb 13, 2024
fe6009b
feat(dlems-keywords): add cvode related keywords
sanjayankur31 Feb 15, 2024
2aa6950
feat(netpyne-template): update to include cvode bits
sanjayankur31 Feb 15, 2024
d5b2eb9
feat(dlems-writer): add bits for handling cvode in NEURON
sanjayankur31 Feb 15, 2024
dacf1f3
fix(netpyne): improve logic for cvode in generated script
sanjayankur31 Feb 15, 2024
aa62f9b
Merge pull request #112 from NeuroML/feat/netpyne-cvode
pgleeson Feb 22, 2024
1e3948d
fix(sedml): sanitise report id in sedml export
sanjayankur31 Apr 18, 2024
d5aaa32
fix(sedml): make variable ids unique for data generators
sanjayankur31 Apr 18, 2024
f8a601f
fix(sedml): also make data set ids in reports unique
sanjayankur31 Apr 18, 2024
ce395cf
fix(sedml): also make time id unique
sanjayankur31 Apr 18, 2024
62cfdc8
Merge pull request #115 from NeuroML/feat/sed-ml-id-fix
pgleeson Apr 18, 2024
e6ef4de
Test on java 21
pgleeson May 1, 2024
2d0159a
Just test on macos-12 for now...
pgleeson May 1, 2024
faf1311
Back to windows-2019
pgleeson May 1, 2024
9accde5
Merge pull request #116 from NeuroML/experimental
pgleeson May 1, 2024
528e08a
Fixes to Neuron and Netpyne to handle case where cell has external mo…
pgleeson May 31, 2024
a335c3c
Added check EXT_MORPH_BIOPHYS_CELL_MODEL, just passing on Neuron & Netne
pgleeson Jun 4, 2024
c4d3ae9
Eden supports external morphology/bioPhys
pgleeson Jun 11, 2024
7f7590e
To v1.10.1
pgleeson Jun 11, 2024
11aabc9
Bump year in docs
pgleeson Jun 11, 2024
c0fe053
Merge pull request #117 from NeuroML/experimental
pgleeson Jun 11, 2024
e6981bf
Check if cell is CELL_2CA_POOLS_COMP_TYPE
pgleeson Jun 13, 2024
de789e6
Merge pull request #118 from NeuroML/experimental
pgleeson Jun 18, 2024
bf3a099
Add location of neuron when pip installed on Binder
pgleeson Jul 4, 2024
ae0ef92
Add more info on namespaces in SED-ML export
pgleeson Jul 31, 2024
c527321
Merge pull request #119 from NeuroML/experimental
pgleeson Jul 31, 2024
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fix(netpyne): improve logic for cvode in generated script
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sanjayankur31 committed Feb 15, 2024
commit dacf1f3fadf1672d7a1a29c4ecab0f7b2d051052
10 changes: 7 additions & 3 deletions src/main/java/org/lemsml/export/dlems/DLemsWriter.java
Original file line number Diff line number Diff line change
@@ -228,10 +228,14 @@ public String getMainScript() throws LEMSException, IOException
if (nrn_cvode == true)
{
g.writeStringField(DLemsKeywords.CVODE.get(), "true");
g.writeStringField(DLemsKeywords.ABS_TOL.get(), abs_tol);
g.writeStringField(DLemsKeywords.REL_TOL.get(), rel_tol);

}
else
{
g.writeStringField(DLemsKeywords.CVODE.get(), "false");
}
/* set them to something even if not provided by user */
g.writeStringField(DLemsKeywords.ABS_TOL.get(), abs_tol);
g.writeStringField(DLemsKeywords.REL_TOL.get(), rel_tol);

int seed = DEFAULT_SEED;
if (simCpt.hasStringValue("seed"))
2 changes: 1 addition & 1 deletion src/main/resources/netpyne/run.vm
Original file line number Diff line number Diff line change
@@ -50,7 +50,7 @@ class NetPyNESimulation():
# cvode
if abs_tol is not None:
self.simConfig.cvode_active = True
self.simConfig.cvode_atol = $abs_tol
self.simConfig.cvode_atol = abs_tol
else:
self.simConfig.cvode_active = False

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