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