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Updates for NMLv2.3 #96

Merged
merged 92 commits into from
Sep 20, 2023
Merged

Updates for NMLv2.3 #96

merged 92 commits into from
Sep 20, 2023

Commits on Apr 4, 2016

  1. workaround for problematic cnexp numerics

    @borismarin
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  2. using preexistent logic for checking Ca dependency

    @borismarin
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Commits on Apr 11, 2016

  1. explicit args for rates method; refactored Ca logic

    @borismarin
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Commits on Apr 12, 2016

  1. rearranging mod derivative blocks to please nrnoc parser

    @borismarin
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  2. Merge remote-tracking branch 'origin/development' into integrationMethod

    @borismarin
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  3. rearranging mod derivative blocks to please nrnoc parser

    @borismarin
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Commits on Aug 29, 2017

  1. Merge branch 'development' into integrationMethod

    @borismarin
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Commits on Aug 30, 2017

  1. Merge branch 'development' into integrationMethod

    @borismarin
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Commits on Nov 10, 2021

  1. Add ci

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Commits on Apr 26, 2022

  1. Initial EDEN writer

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  2. EDEN export fix

    @pgleeson
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Commits on May 12, 2022

  1. To v1.9.0 for NeuroML v2.3

    @pgleeson
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Commits on Jun 10, 2022

  1. Another option for finding compiled mod files

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Commits on Jun 14, 2022

  1. Increase chancks on locations for generated neuron libraries

    @pgleeson
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Commits on Jun 29, 2022

  1. Update options for export of json from netpyne

    @pgleeson
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  2. Update netpyne export

    @pgleeson
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Commits on Aug 1, 2022

  1. Update README.md

    @pgleeson
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  2. Temp disable sbml validation

    @pgleeson
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Commits on Aug 2, 2022

  1. Merge pull request #83 from NeuroML/test_sbml_fix 

    Temp disable sbml validation
    @pgleeson
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  2. Put back in test on sbml validity

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Commits on Aug 8, 2022

  1. Merge branch 'development' into experimental

    @pgleeson
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Commits on Aug 15, 2022

  1. Mainly whitespace changes from atom

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Commits on Oct 13, 2022

  1. Merge branch 'development' into experimental

    @pgleeson
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Commits on Oct 14, 2022

  1. fix(mac): check for libnrnmech.dylib on macs 

    Fixes #85
    @sanjayankur31
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Commits on Oct 19, 2022

  1. Merge pull request #86 from NeuroML/fix/issue-85 

    fix(mac): check for `libnrnmech.dylib` on macs
    @pgleeson
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  2. Merge branch 'development' into test_sbml_fix

    @pgleeson
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Commits on Nov 2, 2022

  1. Bwetter handling of np exec

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  2. Use getMembraneProperties(cell) & formatting

    @pgleeson
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  3. Improved netpyne json handling

    @pgleeson
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Commits on Nov 8, 2022

  1. Add variable to mod file to record current dens specific to that ion … 

    …channel

Add test on nrn unit conversions
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Commits on Nov 9, 2022

  1. More tests on units

    @pgleeson
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  2. Merge branch 'development' into experimental 

    * development:
  More tests on units
  Add variable to mod file to record current dens specific to that ion channel
  Improved netpyne json handling
  Use getMembraneProperties(cell) & formatting
  Bwetter handling of np exec
  fix(mac): check for `libnrnmech.dylib` on macs
    @pgleeson
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Commits on Nov 10, 2022

  1. Correcting units for Neuron saving of channel cond/current

    @pgleeson
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Commits on Nov 22, 2022

  1. chore(process-manager): add new NEURON release versions

    @sanjayankur31
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  2. feat(process-manager): check PATH folders for NEURON executables also 

    `NEURON_HOME` gets priority if it is defined, but if it is not, also
check `PATH` in addition to other common folders on Mac/Linux.
    @sanjayankur31
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  3. Support __SIMULATOR__ & __TIMESTAMP__ in report files for nrn/npyne

    @pgleeson
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  4. Merge branch 'experimental' into feat/check-PATH 

    * experimental:
  Support __SIMULATOR__ & __TIMESTAMP__ in report files for nrn/npyne
  Correcting units for Neuron saving of channel cond/current
  Add ci
    @pgleeson
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  5. Tweak of path finding

    @pgleeson
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  6. Merge branch 'development' into test_sbml_fix 

    * development:
  More tests on units
  Add variable to mod file to record current dens specific to that ion channel
  Improved netpyne json handling
  Use getMembraneProperties(cell) & formatting
  Bwetter handling of np exec
    @pgleeson
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  7. Merge pull request #88 from NeuroML/test_sbml_fix 

    Test sbml fix
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Commits on Nov 23, 2022

  1. Merge branch 'feat/check-PATH' into experimental 

    * feat/check-PATH:
  Tweak of path finding
  feat(process-manager): check PATH folders for NEURON executables also
  chore(process-manager): add new NEURON release versions
    @pgleeson
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  2. Merge pull request #89 from NeuroML/experimental 

    Correcting units for Neuron saving of channel cond/current
    @pgleeson
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Commits on Dec 6, 2022

  1. Improved handling nrn simulations with spaces

    @pgleeson
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  2. Tweaking output text

    @pgleeson
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Commits on Dec 8, 2022

  1. fix(check-PATH): split using colon, not semi-colon

    @sanjayankur31
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  2. Merge pull request #90 from NeuroML/fix/path-colon-not-semi 

    fix(check-PATH): split using colon, not semi-colon
    @sanjayankur31
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Commits on Feb 8, 2023

  1. Update README.md

    @pgleeson
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Commits on Feb 23, 2023

  1. Test on java 19

    Padraig Gleeson committed Feb 23, 2023
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  2. Windows ci fix

    Padraig Gleeson committed Feb 23, 2023
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  3. Merge pull request #91 from NeuroML/experimental 

    Test on java 19
    @pgleeson
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  4. Add support for arm64 on mac with apple silicon

    Padraig Gleeson committed Feb 23, 2023
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Commits on Apr 1, 2023

  1. Merge branch 'integrationMethod' into development

    @borismarin
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Commits on Apr 4, 2023

  1. Revert num integration method changes

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Commits on May 3, 2023

  1. feat: remove getSegment from SpecificCapacitance and Resistivity

    @sanjayankur31
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  2. Merge branch 'master' into development

    @pgleeson
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  3. Test on win 2019

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  4. More windows-2019

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  5. Merge pull request #94 from NeuroML/feat/remove-get-segment 

    feat: remove `getSegment` from `SpecificCapacitance` and `Resistivity`
    @pgleeson
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  6. Merge pull request #95 from NeuroML/experimental 

    Stick to win 2019 for testing
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Commits on May 4, 2023

  1. Merge branch 'master' into experimental

    @pgleeson
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  2. Merge branch 'experimental' into development

    @pgleeson
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Commits on May 19, 2023

  1. feat(json-serializer): do not treat all as a special segment group 

    We treat it like any other group to populate a section list.
Instead, we create a `nrn_all` reserved section list that contains
all sections in it. If a user creates a `nrn_all` segment group in their
NeuroML representation, we throw an exception and ask them to use a
different name.

Fixes #99
    @sanjayankur31
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  2. chore: bump patch version to indicate bugfix

    @sanjayankur31
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Commits on May 26, 2023

  1. Merge pull request #101 from NeuroML/feat/99-treat-all-normal 

    Feat/99 treat all normal - test in experimental branch
    @pgleeson
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  2. Reverting to v1.9.0 

    @sanjayankur31 as all the other org.neuroml.x libs have the same version
num, it's best to update all at once or just before release to ensure
they are compatible. jNeuroML is easier to update and can be incremented
when this change for all is fully tested.
    @pgleeson
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Commits on May 30, 2023

  1. feat(neuron-writer): reserve all as a sectionlist/segment group 

    ... that *always* includes all segments.
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  2. Merge remote-tracking branch 'origin/experimental' into feat/99-treat… 

    …-all-normal
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  3. feat(json-serializer): do not include duplicate segments/sections in … 

    …"all"
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Commits on Jun 8, 2023

  1. feat(graphviz): prevent overlapping in generated graphs 

    This improves the generated graph when using other layouts

Reference: https://graphviz.org/docs/attrs/overlap/
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  2. chore(graphviz): remove extra new line

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Commits on Aug 7, 2023

  1. Merge pull request #104 from NeuroML/feat/99-treat-all-normal 

    Feat/99 treat all normal - test on experimental
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  2. Merge pull request #100 from NeuroML/feat/99-treat-all-normal 

    jsonserializer: Treat `all` as a normal subgroup, reserve and use `nrn_all` as list of all segments/sections
    @pgleeson
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Commits on Aug 8, 2023

  1. Merge branch 'feat/graphviz-no-overlap' into experimental

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  2. Merge pull request #102 from NeuroML/feat/graphviz-no-overlap 

    feat(graphviz): prevent overlapping in generated graphs
    @pgleeson
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  3. Merge branch 'development' into experimental

    @pgleeson
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Commits on Aug 23, 2023

  1. Small tweaks to sedml/sbml writers

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  2. feat(neuron-writer): use Meta to allow use of cvode

    @sanjayankur31
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  3. fix(neuron-writer): set default dt even when cvode is in use

    @sanjayankur31
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Commits on Aug 24, 2023

  1. feat(neuron-writer): include both cvode and standard integration 

    ... setting values for the cvode params enables it
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Commits on Aug 25, 2023

  1. fix(neuron-writer): don't resize recorder vector when using cvode

    @sanjayankur31
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  2. fix(neuron-writer): do not resize recording vector when using cvode

    @sanjayankur31
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Commits on Aug 29, 2023

  1. Update formatting of generated neuron code

    @pgleeson
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Commits on Sep 5, 2023

  1. Update Neuron units for capacitance (nF) & ensure dv/dt is units mV/ms 

    More general tidying generated mod files
    @pgleeson
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  2. Update pynn cell export

    @pgleeson
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  3. Update versions for github actions

    @pgleeson
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Commits on Sep 6, 2023

  1. Further updates to neuron units - tested across more models 

    Allows length and diameter when parameters in lems abstract cell to be
used for section in hoc
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Commits on Sep 8, 2023

  1. Uopdate neuron units for idealGasConstantDims

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  2. Merge pull request #105 from NeuroML/feat/nrn-cvode 

    feat(neuron-writer): use `Meta` to allow use of cvode
    @pgleeson
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Commits on Sep 12, 2023

  1. Merge pull request #107 from NeuroML/experimental 

    Update to use of units in mod files
    @pgleeson
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  2. Add distribution: 'temurin'

    @pgleeson
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Commits on Sep 20, 2023

  1. To v1.9.1

    @pgleeson
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  2. Merge pull request #108 from NeuroML/experimental 

    To v1.9.1
    @pgleeson
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