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Release Notes

Version 0.0.7

This release focuses on structural refactoring to improve codebase organization, specifically grouping morphology and integrator components into dedicated sub-packages (braincell.morph and braincell.quad).

Refactoring & Code Organization

  • Morphology Sub-package (braincell.morph)

    • Moved and renamed morphology-related modules into braincell/morph/:
      • _morphology.py -> morph/_morphology.py
      • _morphology_branch_tree.py -> morph/_branch_tree.py
      • _morphology_from_asc.py -> morph/_from_asc.py
      • _morphology_from_swc.py -> morph/_from_swc.py
      • _morphology_utils.py -> morph/_utils.py

  • Integrator Sub-package (braincell.quad)

    • Moved all integrator and solver modules into braincell/quad/:
      • _integrator*.py files moved to braincell/quad/.
    • This improves the clarity of the top-level namespace.

Documentation

  • Structure Updates
    • Updated API documentation to reflect the new module structure.
    • Simplified index.rst and reorganized API reference pages.
    • Updated copyright to reflect membership in the BrainX Ecosystem.

CI/CD

  • Workflow Updates
    • Bumped versions for actions/checkout, upload-artifact, and download-artifact.

Version 0.0.6

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

Version 0.0.5

This release brings significant performance improvements, new integration methods, enhanced morphology support, expanded documentation, and modernized packaging infrastructure.

New Features

  • Pallas Kernel Acceleration (#51)

    • Added Pallas kernel support for voltage solver to accelerate multi-compartment simulations
    • Introduced optimized triangular matrix computation with GPU/CPU backend support
    • Added debug kernels for Pallas backend testing

  • Backward Euler Solver (#49)

    • Added backward Euler integration method for improved numerical stability
    • Enhanced integration infrastructure with new solver options

  • Morphology Enhancements (#41, #46, #51)

    • Added support for immutable sections
    • Implemented DHS (Diagonal Hines Solver) support
    • Added lazy loading of networkx for better performance
    • Improved morphology branch tree handling and documentation
    • Enhanced ASC/SWC file support for morphology loading

Performance Improvements

  • Sodium Channel Integration (da6697f, 7f91bbe, 7c218f1)

    • Refactored sodium integration from backward Euler to RK4 solver for better accuracy
    • Updated population size handling in simulations
    • Optimized voltage solver performance

  • Integration System Refactoring (#47)

    • Refactored integrators to get time from brainstate.environ for better consistency
    • Streamlined solver logic and improved code structure

Documentation

  • Expanded Chinese Documentation (#45)

    • Added comprehensive Chinese language documentation
    • Included advanced tutorial examples and API references

  • New Documentation Structure (#40, #42)

    • Added quickstart guides, tutorials, and advanced tutorials
    • Reorganized documentation for better navigation
    • Enhanced code documentation and type hints (#44)

Infrastructure & Dependencies

  • Packaging Modernization

    • Migrated from setup.py to modern pyproject.toml-only configuration
    • Updated license format to SPDX identifier (Apache-2.0)
    • Improved package metadata and dependency specifications

  • Dependencies

    • Added brainpy>=3.0.0 as core dependency
    • Added braintools>=0.1.0 for enhanced tooling
    • Updated CI/CD configurations for Python 3.13 support

  • CI/CD Updates

    • Added Python 3.13 support (#50, #48)
    • Updated GitHub Actions: setup-python from 5 to 6, checkout from 4 to 5

Code Quality

  • Refactoring & Improvements (#44)
    • Improved external current registration and error handling
    • Enhanced type hints across the codebase
    • Better code organization and readability

Examples & Testing

  • Added linear solver test notebooks
  • Enhanced Golgi model simulation examples
  • Updated example scripts for better demonstration of features

Version 0.0.4

Previous release with core functionality.

Version 0.0.1

The first release of the project.