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Releases: chaobrain/braintrace

Version 0.1.2

25 Dec 13:54
@chaoming0625 chaoming0625
v0.1.2
ea7ae59

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Version 0.1.2 Latest
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Major Changes

Import Path Migration

  • Updated dependency from brainpy to brainpy.state: Migrated all imports to use the more specific brainpy.state module
    • Updated braintrace/nn/_readout.py: Changed neuron model imports from brainpy to brainpy.state
    • Updated all documentation notebooks (12 files): Concepts, RNN/SNN online learning, batching, state management, and graph visualization tutorials
    • Updated example scripts (4 files): COBA EI RSNN, SNN evaluation, feedforward conv SNN, and SNN models
    • Updated requirements.txt and pyproject.toml to specify brainpy-state as dependency
    • Total: 19 files changed with improved module structure and consistency

New Algorithms

  • Added PP-Prop (Pseudo-Prospective Propagation) algorithm: New eligibility trace algorithm in VJP-based methods
    • Added pp_prop to braintrace/_etrace_vjp/esd_rtrl.py
    • Updated docs/apis/algorithms.rst to include PP-Prop in algorithm documentation

Python 3.14 Support

  • Added Python 3.14 compatibility: Updated project metadata to officially support Python 3.14
    • Updated pyproject.toml classifiers to include Python 3.14

Bug Fixes

  • Fixed version info tuple creation: Corrected the version info structure in braintrace/__init__.py
    • Ensures proper version tuple formatting for compatibility checks

CI/CD Improvements

  • Updated GitHub Actions workflow: Bumped actions/upload-artifact from v5 to v6
    • Modernized CI/CD pipeline with latest GitHub Actions versions
    • Improved artifact upload reliability and performance

Documentation Updates

  • Updated documentation links: Refreshed links in concept documentation for better navigation
    • Updated docs/quickstart/concepts-en.ipynb (116 lines modified)
    • Updated docs/quickstart/concepts-zh.ipynb (104 lines modified)

Breaking Changes

Dependency Change:

  1. Dependency name change: The project now requires brainpy-state instead of brainpy
    • Update your requirements.txt or installation commands accordingly
# Old (0.1.1)
pip install brainpy

# New (0.1.2)
pip install brainpy-state
  1. Import path update: Update neuron model imports to use brainpy.state
# New (0.1.2)
from brainpy.state import IF, LIF, ALIF

Migration Guide

Update Dependencies

Replace brainpy with brainpy-state in your project dependencies:

pip uninstall brainpy
pip install brainpy-state

Update Import Statements

If you have custom code importing neuron models, update to use brainpy.state:

# Find and replace in your codebase
# from brainpy import → from brainpy.state import

Version

  • Bumped version from 0.1.1 to 0.1.2

What's Changed

  • update document link by @xinzhu-L in #52
  • ⬆️ Bump actions/upload-artifact from 5 to 6 by @dependabot[bot] in #53
  • update change 'import brainpy' to 'import brainpy.state' by @xinzhu-L in #54
  • Add pp_prop algorithm and support for Python 3.14 in project metadata by @chaoming0625 in #55

Full Changelog: v0.1.1...v0.1.2

Contributors

chaoming0625, dependabot, and xinzhu-L
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Version 0.1.1

02 Dec 03:56
@chaoming0625 chaoming0625
v0.1.1
4185ef9
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Version 0.1.1

Major Changes

Project Rename: BrainScale → BrainTrace

  • Renamed the entire project from brainscale to braintrace: This change reflects the project's focus on eligibility trace-based learning algorithms
    • Package directory renamed from brainscale/ to braintrace/
    • All internal imports updated from brainscale to braintrace
    • Updated all 95 files including source code, tests, documentation, and examples
    • Updated pyproject.toml with new project name and metadata
    • Updated README with new project branding and citation information

VJP-Based Eligibility Trace Algorithms

  • Added new VJP-based eligibility trace module (_etrace_vjp/): Comprehensive implementation of vector-Jacobian product based algorithms

    • base.py: Core base classes and utilities for VJP operations (671 lines)
    • d_rtrl.py: Diagonal Real-Time Recurrent Learning implementation (756 lines)
    • esd_rtrl.py: Efficient Sparse Diagonal RTRL implementation (847 lines)
    • hybrid.py: Hybrid approaches combining multiple techniques (604 lines)
    • graph_executor.py: Graph-based execution for VJP computations
    • misc.py: Miscellaneous utilities including matrix spectrum normalization

  • Refactored VJP algorithm structure: Migrated from monolithic _etrace_vjp_algorithms.py (2,888 lines) to modular architecture

    • Better separation of concerns
    • Improved testability with dedicated test files (d_rtrl_test.py, esd_rtrl_test.py, graph_executor_test.py)

Logo and Branding

  • Updated logo format from JPG to PNG for consistency
  • Updated logo across documentation

Breaking Changes

Package Rename:

  1. Import path change: All imports must now use braintrace instead of brainscale
# Old (0.1.0)
import brainscale
from brainscale import EligibilityTrace
from brainscale.nn import Linear, GRUCell

# New (0.1.1)
import braintrace
from braintrace import EligibilityTrace
from braintrace.nn import Linear, GRUCell
  1. Installation: Package name changed from brainscale to braintrace
# Old
pip install brainscale

# New
pip install braintrace

Migration Guide

Update Import Statements

Replace all occurrences of brainscale with braintrace:

# Find and replace in your codebase
# brainscale → braintrace

VJP Algorithm Usage

The new VJP-based algorithms are now available through the modular interface:

from braintrace._etrace_vjp import d_rtrl, esd_rtrl, hybrid

Version

  • Bumped version from 0.1.0 to 0.1.1
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Version 0.1.0

13 Oct 15:05
@chaoming0625 chaoming0625
v0.1.0
3ef0e92
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Version 0.1.0

Major Changes

State Management Refactoring

  • Renamed ETraceState to HiddenState: All eligibility trace state management now uses the more general HiddenState naming convention

    • Updated across _etrace_algorithms.py, _etrace_concepts.py, _state_managment.py
    • Added deprecation warnings for ETraceState to guide users to brainstate.HiddenState
    • Updated all documentation and examples to reflect the new naming

  • Renamed ETraceGroupState to HiddenGroupState: Improved consistency in hidden state handling

    • Updated in _etrace_compiler_hidden_group.py
    • Added deprecation warnings for backward compatibility

  • Added deprecation handling: Implemented __getattr__ in main __init__.py to provide helpful warnings when using deprecated names:

    • ETraceState → brainstate.HiddenState
    • ETraceGroupState → brainstate.HiddenGroupState
    • ETraceTreeState → brainstate.HiddenTreeState

Neural Network Module Reorganization

  • Consolidated neural network modules: Removed standalone neuron, synapse, and activation modules, migrating them to brainstate and brainpy ecosystems

    • Deleted files:
      • brainscale/nn/_neurons.py (IF, LIF, ALIF now in brainpy.state)
      • brainscale/nn/_synapses.py (Expon, Alpha, DualExpon, STP, STD now in brainpy.state)
      • brainscale/nn/_elementwise.py (activation functions now in brainstate.nn)
      • brainscale/nn/_poolings.py (pooling layers now in brainstate.nn)

  • Renamed _rate_rnns.py to _rnn.py: Simplified module naming for better clarity

  • Added comprehensive deprecation warnings in nn.__getattr__: Automatically redirects users to the correct modules:

    • Neuron models (IF, LIF, ALIF) → brainpy.state
    • Synapse models (Expon, Alpha, DualExpon, STP, STD) → brainpy.state
    • Activation functions (ReLU, Sigmoid, etc.) → brainstate.nn
    • Pooling layers (MaxPool, AvgPool, etc.) → brainstate.nn
    • Dropout layers → brainstate.nn

API Improvements

  • Normalization parameter standardization: Renamed normalized_shape to in_size across all normalization layers for consistency

    • Updated in _normalizations.py for LayerNorm, GroupNorm, InstanceNorm, etc.
    • Improved clarity and consistency with other layer APIs

  • Enhanced input dimension validation: Improved error checking in convolutional layers to catch dimension mismatches early

  • Refactored imports for consistency: Updated all internal imports to use braintools for optimization and initialization utilities consistently across the codebase

Testing Infrastructure

  • Added comprehensive unit tests for neural network modules:
    • _conv_test.py: 868 lines of tests for convolutional layers (Conv1d, Conv2d, Conv3d, ConvTranspose)
    • _linear_test.py: 658 lines of tests for linear layers (Linear, Identity)
    • _normalizations_test.py: 695 lines of tests for normalization layers (LayerNorm, BatchNorm, GroupNorm, etc.)
    • _readout_test.py: 763 lines of tests for readout layers (LeakyRateReadout, LeakySpikeReadout)
    • _rnn_test.py: 710 lines of tests for RNN cells (VanillaRNNCell, GRUCell, LSTMCell, MGUCell, etc.)
    • Total: 3,694 lines of new test coverage

Documentation Updates

  • Streamlined API documentation: Updated docs/apis/nn.rst to remove redundant sections and enhance RNN overview
  • Updated tutorials and examples: All 16 tutorial notebooks and 11 example scripts updated to reflect new APIs:
    • Concepts tutorials (en/zh)
    • RNN and SNN online learning guides
    • Batching strategies documentation
    • ETrace state management examples
    • Graph visualization tutorials

Code Quality Improvements

  • Removed redundant docstrings: Cleaned up duplicate documentation in LeakyRateReadout and LeakySpikeReadout
  • Improved code organization: Streamlined __all__ definitions across all modules
  • Enhanced readability: Consistent import structure and better code formatting throughout

Dependency Updates

  • Updated requirements.txt: Refined dependency specifications to ensure compatibility with latest brainstate and brainpy versions
  • Updated pyproject.toml: Bumped version to 0.1.0 and updated project metadata

Breaking Changes

API Changes:

  1. State class renaming (with deprecation warnings):

    • ETraceState → Use brainstate.HiddenState instead
    • ETraceGroupState → Use brainstate.HiddenGroupState instead
    • ETraceTreeState → Use brainstate.HiddenTreeState instead

  2. Neural network component migration (with deprecation warnings):

    • Neuron models (IF, LIF, ALIF) → Use brainpy.state module
    • Synapse models (Expon, Alpha, etc.) → Use brainpy.state module
    • Activation functions → Use brainstate.nn module
    • Pooling layers → Use brainstate.nn module

  3. Normalization parameter rename:

    • normalized_shape → in_size (for LayerNorm, GroupNorm, etc.)

  4. Module file reorganization:

    • nn/_rate_rnns.py → nn/_rnn.py
    • Removed: _neurons.py, _synapses.py, _elementwise.py, _poolings.py

Migration Guide

For State Management:

# Old (0.0.11)
from brainscale import ETraceState, ETraceGroupState

# New (0.1.0)
from brainstate import HiddenState, HiddenGroupState

For Neural Network Components:

# Old (0.0.11)
from brainscale.nn import IF, LIF, Expon, ReLU, MaxPool2d

# New (0.1.0)
from brainpy.state import IF, LIF, Expon
from brainstate.nn import ReLU, MaxPool2d

For Normalization Layers:

# Old (0.0.11)
norm = LayerNorm(normalized_shape=(128,))

# New (0.1.0)
norm = LayerNorm(in_size=128)

Note: All deprecated APIs include automatic warnings that will guide you to the correct replacements. The old APIs will continue to work in 0.1.0 but will be removed in a future release.

Version

  • Bumped version from 0.0.11 to 0.1.0
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Version 0.0.11

09 Oct 03:11
@chaoming0625 chaoming0625
v0.0.11
ec5162a
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Version 0.0.11

Major Changes

Import Refactoring

  • Migrated imports from brainstate to braintools: All initialization-related imports now use braintools.init instead of brainstate.init

    • Updated imports in:
      • brainscale/nn/_neurons.py: Changed from brainstate import init to from braintools import init
      • brainscale/nn/_linear.py: Changed from brainstate import init to from braintools import init
      • brainscale/nn/_conv.py: Updated initialization imports
      • brainscale/nn/_synapses.py: Updated initialization imports
      • brainscale/nn/_readout.py: Updated initialization imports

  • Migrated neural network model imports from brainstate.nn to brainpy: Updated base classes for neuron models

    • IF, LIF, ALIF now inherit from brainpy instead of brainstate.nn
    • Maintained API compatibility while using the new brainpy backend

  • Updated functional API calls: Changed from brainstate.functional.sigmoid to brainstate.nn.sigmoid in RNN cells

Dependency Updates

  • Added brainpy as a required dependency in requirements.txt

Documentation Enhancements

  • Improved docstring formatting across the codebase:
    • Enhanced parameter documentation with proper type annotations using NumPy-style docstrings
    • Added missing "Returns" sections to property and method docstrings
    • Converted inline examples to proper "Examples" sections with code blocks
    • Updated documentation in:
      • brainscale/_etrace_algorithms.py: Enhanced EligibilityTrace and ETraceAlgorithm documentation
      • brainscale/_etrace_compiler_base.py: Improved parameter and return type documentation
      • brainscale/_etrace_compiler_module_info.py: Enhanced module documentation

Core Algorithm Updates

  • RNN State Management: Updated all RNN cells to use braintools.init.param for state initialization and reset
    • ValinaRNNCell: Updated init_state() and reset_state() methods
    • GRUCell: Updated state management and activation functions
    • CFNCell: Updated forget and input gate implementations
    • MGUCell: Updated minimal gated unit state handling

Test Updates

  • Refactored test imports: Updated test files to use new import paths
    • brainscale/_etrace_model_test.py: Updated with new import structure
    • brainscale/_etrace_vjp_algorithms_test.py: Aligned with new API

Version

  • Bumped version from 0.0.10 to 0.0.11

Files Changed (17 files)

  • .gitignore: Added new patterns
  • brainscale/__init__.py: Updated version number
  • brainscale/_etrace_algorithms.py: Enhanced documentation and imports
  • brainscale/_etrace_compiler_base.py: Improved documentation
  • brainscale/_etrace_compiler_graph.py: Minor updates
  • brainscale/_etrace_compiler_hidden_group.py: Minor updates
  • brainscale/_etrace_compiler_module_info.py: Enhanced documentation
  • brainscale/_etrace_model_test.py: Updated test imports
  • brainscale/_etrace_vjp_algorithms_test.py: Updated test imports
  • brainscale/_etrace_vjp_graph_executor.py: Updated imports
  • brainscale/nn/_conv.py: Migrated to braintools imports
  • brainscale/nn/_linear.py: Migrated to braintools imports
  • brainscale/nn/_neurons.py: Migrated to brainpy and braintools
  • brainscale/nn/_rate_rnns.py: Migrated to braintools and updated functional APIs
  • brainscale/nn/_readout.py: Updated imports
  • brainscale/nn/_synapses.py: Updated imports
  • requirements.txt: Added brainpy dependency

Breaking Changes

None. All changes maintain backward compatibility at the API level.

Migration Guide

If you have custom code using brainscale:

  • No changes required for end users
  • If extending brainscale internally, note that initialization utilities now come from braintools instead of brainstate

What's Changed

  • ⬆️ Bump actions/setup-python from 5 to 6 by @dependabot[bot] in #40
  • Modernize codebase and migrate ecosystem APIs by @oujago in #41
  • Migrate core APIs to BrainPy and BrainTools by @chaoming0625 in #42

New Contributors

Full Changelog: v0.0.10...v0.0.11

Contributors

chaoming0625, oujago, and dependabot
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Version 0.0.10

15 Sep 14:32
@chaoming0625 chaoming0625
v0.0.10
a7418fd
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Version 0.0.10

What's Changed

New Contributors

Full Changelog: https://github.com/chaobrain/brainscale/commits/v0.0.10

Contributors

chaoming0625 and dependabot
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