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@chaoming0625 chaoming0625 released this 13 Oct 15:06
· 2 commits to main since this release
v0.0.6
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This release focuses on major dependency updates, code modernization, and extensive refactoring to improve compatibility with the latest BrainPy ecosystem.

Breaking Changes

  • Dependency Version Updates
    • Updated brainstate from >=0.1.0 to >=0.2.0
    • Updated brainpy from >=3.0.0 to >=2.7.0
    • These updates may require users to upgrade their BrainPy ecosystem packages

Refactoring & Code Improvements

  • Core Architecture Simplification (2acd212)

    • Refactored HHTypedNeuron to use brainpy directly for better integration
    • Simplified _base.py with significant code reduction (221 insertions, 282 deletions)
    • Removed deprecated _integrator_diffrax.py module (29 lines removed)
    • Streamlined integrator implementations in _integrator_runge_kutta.py
    • Cleaned up _single_compartment.py and integration protocol

  • Parameter Initialization Migration (fa71171, a79c306, 18b053c, 77a11ac)

    • Migrated parameter initialization from brainstate.nn to braintools across the entire codebase
    • Updated parameter initialization in ion channels (calcium, potassium, sodium, hyperpolarization-activated)
    • Refactored parameter initialization in synapse models (markov)
    • Updated HTC and EINet classes to use braintools
    • Updated all example scripts and notebooks to use braintools for parameter initialization

  • API Migration (e84351a, bf50e6e)

    • Migrated from brainstate.nn to brainpy.state and braintools
    • Fixed _base errors in brainpy integration
    • Updated CurrentProj references across the codebase

Documentation

  • Updated Documentation (#54, 2acd212)
    • Updated braincell logo image
    • Refreshed tutorial notebooks (cell, channel, ion tutorials in both English and Chinese)
    • Updated advanced tutorial examples (sc02-sc05 notebooks)
    • Revised quickstart concepts documentation
    • Updated all documentation to reflect API changes and new parameter initialization patterns

Examples

  • Example Updates
    • Updated all example scripts to use new APIs:
      • SC01_fitting_a_hh_neuron.py
      • SC03_COBA_HH_2007_braincell.py
      • SC05_thalamus_single_compartment_neurons.py
      • SC06_unified_thalamus_model.py
      • SC07_Straital_beta_oscillation_2011.py
      • MC11_simple_dendrite_model.py
      • MC13_golgi_model/ simulations

CI/CD

  • Publishing Workflow Enhancement (2acd212)
    • Updated .github/workflows/Publish.yml with improved configuration

Code Statistics

  • Overall changes: 48 files changed, 1,307 insertions(+), 1,408 deletions(-)
  • Net reduction of ~100 lines while improving code quality and maintainability
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