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Updates for NMLv2.3 #206

Merged
merged 132 commits into from
Sep 20, 2023
Merged

Updates for NMLv2.3 #206

merged 132 commits into from
Sep 20, 2023

Commits on Nov 10, 2021

  1. Add ci

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Commits on Apr 26, 2022

  1. Some jnmleden tests

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  2. Remove failing test

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  3. Add script specifically for omv tests

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  4. Install omv

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  5. One more eden test

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Commits on May 12, 2022

  1. To NeuroML v2.3

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Commits on Jun 1, 2022

  1. Initial test on fractional example

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Commits on Jun 6, 2022

  1. Restructure fract cond example to make clearer

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  2. Need to update spike times...

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Commits on Jun 7, 2022

  1. Further tidied up fractional cond example

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  2. Test fractional on nrn

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  3. Better testing times

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Commits on Jul 26, 2022

  1. feat: make MembraneProperties extend BaseWithoutId

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  2. feat: make SpikeThresh extend BaseWithoutId

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  3. feat: make SpecificCapacitance extend BaseWithoutId

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  4. feat: make InitMembPotential extend BaseWithoutId

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  5. feat: make Resistivity extend BaseWithoutId

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  6. fix: use complexContent for extension in MembraneProperties

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  7. fix: use complexContent to extend Resistivity

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  8. feat: make SynapticConnection extend BaseWithoutId

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  9. feat: make BlockMechanism extend BaseWithoutId

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Commits on Jul 27, 2022

  1. chore: reformat

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Commits on Aug 1, 2022

  1. Merge pull request #189 from NeuroML/feat/check-extends 

    Update schema to correctly make components extend some base class
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  2. fix: correct case 

    `BaseWithoutId` not `BaseWithoutID`
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  3. Merge pull request #190 from NeuroML/fix/correct-case 

    Fix/correct case
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  4. ci: disable fail-fast, update matrices

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  5. ci: limit to ubuntu

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  6. ci: fix runs-on

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  7. Merge pull request #191 from NeuroML/feat/update-ci-matrices-fast-fail 

    ci: disable fail-fast
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Commits on Aug 5, 2022

  1. feat: make IntracellularProperties extend BaseWithoutId

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  2. feat: make Property extend BaseWithoutId

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  3. feat: make Annotation extend BaseWithoutId

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  4. feat: make Constant extend BaseWithoutId

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  5. feat: make Exposure extend BaseWithoutId

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  6. feat: make NamedDimensionalType extend BaseWithoutId

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  7. feat: make NamedDimensionalVariable extend BaseWithoutId

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  8. feat: make Q10ConductanceScaling extend BaseWithoutId

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  9. feat: make HHRate extend BaseWithoutId

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  10. feat: make HHVariable extend BaseWithoutId

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  11. feat: make HHTime extend BaseWithoutId

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  12. feat: make PlasticityMechanism extend BaseWithoutId

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  13. feat: make SegmentParent extend BaseWithoutId

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  14. feat: make Point3DWithDiam extend BaseWithoutId

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  15. feat: make ProximalDetails extend BaseWithoutId

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  16. feat: make DistalDetails extend BaseWithoutId

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  17. feat: make Member extend BaseWithoutId

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  18. feat: make Include extend BaseWithoutId

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  19. feat: make Path extend BaseWithoutId

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  20. feat: make SubTree extend BaseWithoutId

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  21. feat: make SegmentEndPoint extend BaseWithoutId

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  22. feat: make InhomogeneousValue extend BaseWithoutId

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  23. feat: make Species extend Base

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  24. feat: make ExtracellularPropertiesLocal extend Base

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  25. feat: make SpaceStructure extend BaseWithoutId

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  26. feat: make Layout extend BaseWithoutId

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  27. feat: make UnstructuredLayout extend BaseWithoutId

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  28. feat: make RandomLayout extend BaseWithoutId

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  29. feat: make GridLayout extend BaseWithoutId

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  30. feat: make Instance extend BaseWithoutId

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  31. feat: make Location extend BaseWithoutId

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  32. feat: make ExplicitInput extend BaseWithoutId

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  33. feat: make Input extend BaseNonNegativeIntegerId

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Commits on Aug 8, 2022

  1. Merge branch 'development' into experimental

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Commits on Aug 12, 2022

  1. Merge pull request #193 from NeuroML/fix/intracellular-properties-sho… 

    …uld-extend-basewithoutid

Fix/intracellular properties should extend basewithoutid
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Commits on Aug 15, 2022

  1. Merge pull request #192 from NeuroML/fix/intracellular-properties-sho… 

    …uld-extend-basewithoutid

feat: make lots of elements extend BaseWithoutId (or other bases)
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Commits on Aug 17, 2022

  1. feat!: remove neuroLexId from BaseWithoutId

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  2. feat!: add neuroLexId to IonChannelScalable

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  3. feat!: add neuroLexId to IonChannelKS

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  4. feat!: add neuroLexId to BaseSynapse

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  5. feat!: add neuroLexId to BaseCell

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  6. feat! add neuroLexId to Segment

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  7. feat!: add neuroLexId to SegmentGroup

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  8. feat!: add neuroLexId to Network

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  9. feat!: add neuroLexId to Population

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  10. feat!: add neuroLexId to SynapticConnection

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  11. feat!: add neuroLexId to BaseConnection

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  12. Merge pull request #195 from NeuroML/feat/neurolexids 

    Feat/neurolexids
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  13. Merge pull request #194 from NeuroML/feat/neurolexids 

    Remove neuroLexId from BaseWithoutId and add it to individual ComponentType classes
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Commits on Aug 18, 2022

  1. Merge branch 'development' into experimental 

    * development:
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Commits on Sep 5, 2022

  1. Very old code, just updating so it won't throw an error in py3...

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  2. Merge pull request #197 from NeuroML/experimental 

    Fix non py3 code
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Commits on Sep 27, 2022

  1. feat: document Izhikevich2007Cell

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  2. feat: document adExIafCell

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  3. feat: add full ref to pinskyRinzelCA3Cell

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  4. Merge pull request #199 from NeuroML/feat/document-more-component-types 

    Feat/document more component types
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Commits on Nov 7, 2022

  1. Save more in ex15

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Commits on Nov 9, 2022

  1. Add test on recorded cond density

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Commits on Nov 23, 2022

  1. Update ci.yml

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  2. Merge branch 'development' into experimental 

    * development:
  Update ci.yml
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  3. Merge pull request #201 from NeuroML/experimental 

    Add test on recorded cond density
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Commits on Jan 25, 2023

  1. chore: update copyright year

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Commits on Jan 26, 2023

  1. numpy<=1.23.0 

    See OpenSourceBrain/osb-model-validation#91
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  2. Merge branch 'development' of github.com:NeuroML/NeuroML2 into develo… 

    …pment
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Commits on Feb 23, 2023

  1. Test on java 19

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  2. Merge pull request #204 from NeuroML/experimental 

    Test on java 19
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Commits on Mar 23, 2023

  1. Update README.md

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Commits on Apr 4, 2023

  1. Remove warning

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Commits on Apr 14, 2023

  1. Ignore arm64 dir

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Commits on May 3, 2023

  1. feat(schema): add OnStart

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  2. feat(schema): add OnEvent

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  3. feat(schema): add OnCondition

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  4. feat(schema): add Regime

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  5. chore: lint and format

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  6. feat(schema): add DerivedParameter

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  7. fix(schema): remove stary line

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  8. feat(schema): add DerivedParameter to ComponentType

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  9. Merge pull request #205 from NeuroML/feat/include-lems-elements 

    Includes LEMS dynamics elements that are used in the NeuroML core type definitions into the schema
    @pgleeson
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  10. Merge branch 'master' into development

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Commits on Aug 7, 2023

  1. Update README.md

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Commits on Aug 9, 2023

  1. Regenerated html versions of lems docs, not that they're used much

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  2. fix(cells.xml): match proximal/distal properties to schema 

    fixes #211
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  3. chore: regenerate cells.html

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Commits on Aug 23, 2023

  1. Merge pull request #212 from NeuroML/fix/issue-211 

    fix(cells.xml): match proximal/distal properties to schema
    @pgleeson
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  2. Adding a unit which Neuron may need to use

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  3. Merge branch 'experimental' of github.com:NeuroML/NeuroML2 into exper… 

    …imental
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  4. chore(componenttypes): add Meta

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  5. Many tests updated with more exact tolerances 

    Makes it easier to see if there is even a tiny change in behaviour of
simulators
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Commits on Sep 6, 2023

  1. Updated preferred units for Neuron 

    Add dimension to current in silent syn
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Commits on Sep 7, 2023

  1. feat(schema): add simple type to restrict component reference paths 

    The regex says that the path must be a string that:

- may start with a `/`
- followed by any number of the following strings optionally suffixed
  with a `/`
  - `../`
  - `./`
  - `[0-9]`
  - a string with the first letter as an alphanumberic letter, followed
    by any number of alphanumeric + `_` letters
    @sanjayankur31
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Commits on Sep 8, 2023

  1. Update NEURON preferred Units for idealGasConstantDims

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  2. Merge pull request #214 from NeuroML/feat/add-meta-to-sim 

    chore(componenttypes): add `Meta`
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Commits on Sep 10, 2023

  1. feat(comp-ref-path): limit path to known possibilities

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Commits on Sep 11, 2023

  1. Merge pull request #216 from NeuroML/feat/add-path-regex 

    feat(schema): add simple type to restrict component reference paths
    @pgleeson
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  2. Merge pull request #215 from NeuroML/experimental 

    Mainly updates to units preferred in neuron mod file generation
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Commits on Sep 20, 2023

  1. Add hindmarshRose1984Cell to core cells & schema

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  2. Formatted and updated docs from lems

    @pgleeson
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  3. Merge pull request #217 from NeuroML/experimental 

    Add hindmarshRose1984Cell to core cells & schema
    @pgleeson
    pgleeson authored Sep 20, 2023
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  4. To v1.9.1

    @pgleeson
    pgleeson committed Sep 20, 2023
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  5. Update GHA versions

    @pgleeson
    pgleeson committed Sep 20, 2023
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  6. Specify java distribution

    @pgleeson
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  7. Merge pull request #218 from NeuroML/experimental 

    To v1.9.1
    @pgleeson
    pgleeson authored Sep 20, 2023
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