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Introduce trainer module and refactor public APIs and docs (#68)
* Add new regularization classes and corresponding tests for ElasticNet, Huber, Group Lasso, Total Variation, Max Norm, Entropy, Orthogonal, Spectral Norm, and various prior distributions * Add trainer module with training framework and progress bar utilities * Update test descriptions for fit_hyper parameter in regularization tests * delete braintools.param module * refactor: reorganize imports and enhance module documentation for clarity and usability * bump: update version to 0.1.7 * refactor: update import statement for matfile module
1 parent 206c5ec commit db019e3

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‎braintools/__init__.py‎

Lines changed: 53 additions & 19 deletions
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# ==============================================================================
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__version__ = "0.1.6"
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__version__ = "0.1.7"
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__version_info__ = tuple(map(int, __version__.split(".")))
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from . import conn
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from . import input
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from . import metric
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from . import optim
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from . import param
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from . import quad
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from . import surrogate
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from . import trainer
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from . import tree
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from . import visualize
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from ._spike_encoder import *
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from ._spike_encoder import __all__ as encoder_all
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from ._spike_operation import *
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from ._spike_operation import __all__ as operation_all
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from ._spike_encoder import (
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LatencyEncoder,
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RateEncoder,
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PoissonEncoder,
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PopulationEncoder,
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BernoulliEncoder,
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DeltaEncoder,
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StepCurrentEncoder,
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SpikeCountEncoder,
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TemporalEncoder,
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RankOrderEncoder,
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)
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from ._spike_operation import (
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spike_bitwise_or,
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spike_bitwise_and,
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spike_bitwise_iand,
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spike_bitwise_not,
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spike_bitwise_xor,
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spike_bitwise_ixor,
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spike_bitwise,
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)
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__all__ = [
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'conn',
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'input',
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'init',
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'file',
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'metric',
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'visualize',
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'optim',
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'tree',
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'quad',
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'surrogate',
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'param',
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] + encoder_all + operation_all
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'conn',
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'input',
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'init',
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'file',
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'metric',
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'visualize',
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'optim',
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'trainer',
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'tree',
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'quad',
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'surrogate',
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del encoder_all, operation_all
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'LatencyEncoder',
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'RateEncoder',
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'PoissonEncoder',
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'PopulationEncoder',
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'BernoulliEncoder',
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'DeltaEncoder',
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'StepCurrentEncoder',
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'SpikeCountEncoder',
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'TemporalEncoder',
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'RankOrderEncoder',
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'spike_bitwise_or',
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'spike_bitwise_and',
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'spike_bitwise_iand',
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'spike_bitwise_not',
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'spike_bitwise_xor',
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'spike_bitwise_ixor',
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'spike_bitwise',
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]

‎braintools/conn/__init__.py‎

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Original file line numberDiff line numberDiff line change
@@ -98,23 +98,187 @@
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"""
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from ._base import *
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from ._base import __all__ as base_all
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from ._biological import *
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from ._biological import __all__ as biological_all
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from ._compartment import *
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from ._compartment import __all__ as comp_all
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from ._kernel import *
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from ._kernel import __all__ as kernel_all
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from ._random import *
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from ._random import __all__ as point_all
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from ._regular import *
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from ._regular import __all__ as regular_all
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from ._spatial import *
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from ._spatial import __all__ as spatial_all
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from ._topological import *
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from ._topological import __all__ as topological_all
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__all__ = base_all + comp_all + kernel_all + point_all + spatial_all + topological_all + biological_all + regular_all
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del base_all, comp_all, kernel_all, point_all, spatial_all, topological_all, biological_all
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del regular_all
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# Base classes and utilities
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from ._base import (
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ConnectionResult,
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Connectivity,
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PointConnectivity,
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MultiCompartmentConnectivity,
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ScaledConnectivity,
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CompositeConnectivity,
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)
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# Biological patterns
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from ._biological import (
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ExcitatoryInhibitory,
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)
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# Multi-compartment connectivity
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from ._compartment import (
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# Compartment type constants
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SOMA,
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BASAL_DENDRITE,
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APICAL_DENDRITE,
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AXON,
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# Basic compartment patterns
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CompartmentSpecific,
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AllToAllCompartments,
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# Anatomical targeting patterns
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SomaToDendrite,
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AxonToSoma,
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DendriteToSoma,
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AxonToDendrite,
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DendriteToDendrite,
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# Morphology-aware patterns
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ProximalTargeting,
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DistalTargeting,
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BranchSpecific,
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MorphologyDistance,
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# Dendritic patterns
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DendriticTree,
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BasalDendriteTargeting,
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ApicalDendriteTargeting,
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DendriticIntegration,
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# Axonal patterns
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AxonalProjection,
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AxonalBranching,
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AxonalArborization,
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TopographicProjection,
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# Synaptic patterns
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SynapticPlacement,
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SynapticClustering,
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# Custom patterns
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CustomCompartment,
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)
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# Kernel-based connectivity
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from ._kernel import (
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Conv2dKernel,
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GaussianKernel,
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GaborKernel,
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DoGKernel,
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MexicanHat,
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SobelKernel,
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LaplacianKernel,
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CustomKernel,
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)
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# Random connectivity patterns
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from ._random import (
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Random,
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FixedProb,
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ClusteredRandom,
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)
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# Regular patterns
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from ._regular import (
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AllToAll,
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OneToOne,
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)
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# Spatial connectivity patterns
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from ._spatial import (
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DistanceDependent,
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Gaussian,
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Exponential,
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Ring,
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Grid2d,
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RadialPatches,
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)
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# Topological patterns
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from ._topological import (
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SmallWorld,
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ScaleFree,
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Regular,
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ModularRandom,
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ModularGeneral,
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HierarchicalRandom,
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CorePeripheryRandom,
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)
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__all__ = [
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# Base classes
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'ConnectionResult',
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'Connectivity',
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'PointConnectivity',
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'MultiCompartmentConnectivity',
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'ScaledConnectivity',
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'CompositeConnectivity',
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# Biological patterns
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'ExcitatoryInhibitory',
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# Compartment constants
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'SOMA',
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'BASAL_DENDRITE',
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'APICAL_DENDRITE',
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'AXON',
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# Multi-compartment patterns
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'CompartmentSpecific',
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'AllToAllCompartments',
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'SomaToDendrite',
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'AxonToSoma',
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'DendriteToSoma',
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'AxonToDendrite',
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'DendriteToDendrite',
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'ProximalTargeting',
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'DistalTargeting',
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'BranchSpecific',
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'MorphologyDistance',
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'DendriticTree',
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'BasalDendriteTargeting',
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'ApicalDendriteTargeting',
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'DendriticIntegration',
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'AxonalProjection',
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'AxonalBranching',
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'AxonalArborization',
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'TopographicProjection',
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'SynapticPlacement',
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'SynapticClustering',
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'CustomCompartment',
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# Kernel patterns
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'Conv2dKernel',
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'GaussianKernel',
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'GaborKernel',
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'DoGKernel',
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'MexicanHat',
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'SobelKernel',
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'LaplacianKernel',
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'CustomKernel',
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# Random patterns
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'Random',
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'FixedProb',
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'ClusteredRandom',
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# Regular patterns
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'AllToAll',
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'OneToOne',
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# Spatial patterns
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'DistanceDependent',
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'Gaussian',
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'Exponential',
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'Ring',
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'Grid2d',
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'RadialPatches',
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# Topological patterns
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'SmallWorld',
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'ScaleFree',
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'Regular',
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'ModularRandom',
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'ModularGeneral',
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'HierarchicalRandom',
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'CorePeripheryRandom',
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]

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