Version 0.0.8

Compatible with latest brainevent.

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.

What's Changed

• ⬆️ Bump actions/upload-artifact from 4 to 5 by @dependabot[bot] in #57
• ⬆️ Bump actions/download-artifact from 4 to 6 by @dependabot[bot] in #58
• ⬆️ Bump actions/checkout from 5 to 6 by @dependabot[bot] in #59
• ⬆️ Bump actions/upload-artifact from 5 to 6 by @dependabot[bot] in #60
• ⬆️ Bump actions/download-artifact from 6 to 7 by @dependabot[bot] in #61
• ⬆️ Bump styfle/cancel-workflow-action from 0.12.1 to 0.13.0 by @dependabot[bot] in #62
• Refactor morphology and integrators into morph/quad subpackages by @chaoming0625 in #63

Full Changelog: v0.0.6...v0.0.7

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

What's Changed

• Add morphology representation and splitting solvers by @TLDSZ in #28
• Simplify HH neuron and simulation by @chaoming0625 in #31
• Refactor documentation by @chaoming0625 in #32
• Refactor diffrax integration into step methods by @chaoming0625 in #33
• Refactor integrators and morphology; add implicit diffrax by @chaoming0625 in #34
• Add independent exp euler solver; refactor and update examples by @chaoming0625 in #35
• Add synapse models; refactor channels/integrators; reorganize examples by @chaoming0625 in #36
• Refactor and modernize example scripts by @chaoming0625 in #37
• Refactor morphology/MultiCompartment for ASC/SWC; add staggered solver by @chaoming0625 in #39
• Add Documentation Structure: Quickstart, Tutorials, and Advanced Tutorials by @YangJesse in #40
• Finished updating documentation; no modifications made to braincell code. by @YangJesse in #42
• Standardize Units, Refactor Current Handling, and Enhance Examples by @chaoming0625 in #44
• Refactor morphology; add immutable sections and DHS support by @chaoming0625 in #41
• Expand Chinese documentation; add advanced examples & API refs by @chaoming0625 in #45
• Refactor morphology branch tree: lazy load networkx and improve doc by @chaoming0625 in #46
• Refactor integrators: Get time from brainstate.environ by @chaoming0625 in #47
• ⬆️ Bump actions/checkout from 4 to 5 by @dependabot[bot] in #48
• Add Backward Euler solver; refactor integrations & morphology by @chaoming0625 in #49
• ⬆️ Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #50
• Accelerate voltage solver with Pallas kernels; update morphology by @chaoming0625 in #51
• Finished the english version of documents. by @YangJesse in #52
• Compatible with brainstate>=0.2.0 by @chaoming0625 in #53

New Contributors

• @dependabot[bot] made their first contribution in #48

Full Changelog: v0.0.1...v0.0.5

Version 0.0.1

This release is the basic feature about braincell. It supports modeling of single-compartment neurons. (The full support for multi-compartment models will come in the next release).

New Features

• Hierarchical structure for neuron - ion - channel.
• Single compartment neuron modeling.
• Numerical integration.

What's Changed

• fix tests by @chaoming0625 in #2
• New style to define the model by @chaoming0625 in #3
• Fix setup.py by @chaoming0625 in #4
• update package access by @chaoming0625 in #5
• Support for multi-compartmental neurons by @chaoming0625 in #6
• update doc by @chaoming0625 in #7
• Add example for conductance fitting of a three-compartment neuron by @chaoming0625 in #8
• Update by @chaoming0625 in #9
• fix bugs by @chaoming0625 in #10
• Swl by @TLDSZ in #11
• Support numerical integration using diffrax by @chaoming0625 in #12
• Swl by @TLDSZ in #13
• add more channel params by @TLDSZ in #14
• add the rest channels and fix bugs by @TLDSZ in #15
• fix bugs by @TLDSZ in #16
• add examples for fitting with Adam optimizer by @chaoming0625 in #18
• Fix gradient fitting by @chaoming0625 in #19
• add a neuron fitting example by @chaoming0625 in #20
• update code to compatible with brainstate>=0.1.0 by @chaoming0625 in #21
• Standardize integration methods by @chaoming0625 in #24
• fix ICav31_Ma2020 bug by @chaoming0625 in #22
• support exponential euler integration by @chaoming0625 in #25
• renaming package to braincell by @chaoming0625 in #26
• Update code by @chaoming0625 in #27
• Refactor integration functions to use exprel for improved numerical… by @chaoming0625 in #29

New Contributors

• @chaoming0625 made their first contribution in #2

Full Changelog: https://github.com/chaobrain/braincell/commits/v0.0.1