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Changes for NeuroML v2.3.1 release #120

Merged
merged 31 commits into from
Aug 20, 2024
Merged

Changes for NeuroML v2.3.1 release #120

merged 31 commits into from
Aug 20, 2024

Commits on Sep 22, 2023

  1. To v1.10.0

    @pgleeson
    pgleeson committed Sep 22, 2023
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Commits on Dec 20, 2023

  1. feat(nrnwriter): also handle ChannelDensityNonUniformNernst

    @sanjayankur31
    sanjayankur31 committed Dec 20, 2023
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Commits on Dec 21, 2023

  1. Merge pull request #109 from NeuroML/feat/channeldensitynonuniformnernst 

    feat(nrnwriter): also handle ChannelDensityNonUniformNernst
    @pgleeson
    pgleeson authored Dec 21, 2023
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Commits on Feb 12, 2024

  1. Add functionality to save file outputs of sed-ml

    @pgleeson
    pgleeson committed Feb 12, 2024
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  2. Generates valid sed-ml

    @pgleeson
    pgleeson committed Feb 12, 2024
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Commits on Feb 13, 2024

  1. Merge pull request #111 from NeuroML/experimental 

    Add functionality to save file outputs of sed-ml
    @pgleeson
    pgleeson authored Feb 13, 2024
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Commits on Feb 15, 2024

  1. feat(dlems-keywords): add cvode related keywords

    @sanjayankur31
    sanjayankur31 committed Feb 15, 2024
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  2. feat(netpyne-template): update to include cvode bits

    @sanjayankur31
    sanjayankur31 committed Feb 15, 2024
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  3. feat(dlems-writer): add bits for handling cvode in NEURON

    @sanjayankur31
    sanjayankur31 committed Feb 15, 2024
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  4. fix(netpyne): improve logic for cvode in generated script

    @sanjayankur31
    sanjayankur31 committed Feb 15, 2024
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Commits on Feb 22, 2024

  1. Merge pull request #112 from NeuroML/feat/netpyne-cvode 

    netpyne: expose cvode bits from LEMS
    @pgleeson
    pgleeson authored Feb 22, 2024
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Commits on Apr 18, 2024

  1. fix(sedml): sanitise report id in sedml export 

    fixes #114
    @sanjayankur31
    sanjayankur31 committed Apr 18, 2024
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  2. fix(sedml): make variable ids unique for data generators 

    Otherwise biosimulations errors;

```
Multiple objects have the following ids:\n      -
hhpop_0_bioPhys1_membraneProperties_KConductances_KConductance_n_q\n
- hhpop_0_bioPhys1_membraneProperties_NaConductances_NaConductance_h_q\n
  -
  hhpop_0_bioPhys1_membraneProperties_NaConductances_NaConductance_m_q\n
  - hhpop_0_v\n      - time""
```
    @sanjayankur31
    sanjayankur31 committed Apr 18, 2024
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  3. fix(sedml): also make data set ids in reports unique 

    Otherwise biosimulations errs with:

```
Multiple objects have the following ids:\n      - time
```
    @sanjayankur31
    sanjayankur31 committed Apr 18, 2024
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  4. fix(sedml): also make time id unique

    @sanjayankur31
    sanjayankur31 committed Apr 18, 2024
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  5. Merge pull request #115 from NeuroML/feat/sed-ml-id-fix 

    sedml fixes for biosimulations
    @pgleeson
    pgleeson authored Apr 18, 2024
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Commits on May 1, 2024

  1. Test on java 21

    @pgleeson
    pgleeson committed May 1, 2024
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  2. Just test on macos-12 for now...

    @pgleeson
    pgleeson committed May 1, 2024
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  3. Back to windows-2019

    @pgleeson
    pgleeson committed May 1, 2024
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  4. Merge pull request #116 from NeuroML/experimental 

    Test on java 21
    @pgleeson
    pgleeson authored May 1, 2024
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Commits on May 31, 2024

  1. Fixes to Neuron and Netpyne to handle case where cell has external mo… 

    …rphology/biophysicalProperties
    @pgleeson
    pgleeson committed May 31, 2024
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Commits on Jun 4, 2024

  1. Added check EXT_MORPH_BIOPHYS_CELL_MODEL, just passing on Neuron & Netne

    @pgleeson
    pgleeson committed Jun 4, 2024
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Commits on Jun 11, 2024

  1. Eden supports external morphology/bioPhys

    @pgleeson
    pgleeson committed Jun 11, 2024
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  2. To v1.10.1

    @pgleeson
    pgleeson committed Jun 11, 2024
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  3. Bump year in docs

    @pgleeson
    pgleeson committed Jun 11, 2024
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  4. Merge pull request #117 from NeuroML/experimental 

    To v1.10.1; Adds support for external morphology/biophysProps in cell element for Neuron/NetPyNE
    @pgleeson
    pgleeson authored Jun 11, 2024
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Commits on Jun 13, 2024

  1. Check if cell is CELL_2CA_POOLS_COMP_TYPE

    @pgleeson
    pgleeson committed Jun 13, 2024
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Commits on Jun 18, 2024

  1. Merge pull request #118 from NeuroML/experimental 

    Check if cell is CELL_2CA_POOLS_COMP_TYPE
    @pgleeson
    pgleeson authored Jun 18, 2024
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Commits on Jul 4, 2024

  1. Add location of neuron when pip installed on Binder

    @pgleeson
    pgleeson committed Jul 4, 2024
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Commits on Jul 31, 2024

  1. Add more info on namespaces in SED-ML export

    @pgleeson
    pgleeson committed Jul 31, 2024
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  2. Merge pull request #119 from NeuroML/experimental 

    Add location of neuron when pip installed on Binder
    @pgleeson
    pgleeson authored Jul 31, 2024
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