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jaxfne v0.3.4: Chainable Tutorial Grammar

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@HNXJ HNXJ released this 26 May 15:22
· 585 commits to main since this release
v0.3.4
8662d1c

Release: May 26, 2026

Status: Stable, production-ready

What's New

Chainable Configuration Grammar

The public API uses an intuitive chainable pattern for building models:

cfg = jtfne.Configuration()
cfg = cfg.runtime(seed=7, dtype="float32", duration_ms=1000.0, dt_ms=0.1)
cfg = cfg.column("single_neuron", layers=["L2/3"], n=1)
cfg = cfg.cell_types({"E": 1.0})
cfg = cfg.connectivity()
cfg = cfg.set_emitter("izhikevich", "cortical_eig")
cfg = cfg.probes(["MUA-proxy", "source-proxy", "LFP-proxy"])

model = jtfne.construct(cfg)
signals = jtfne.simulate(model, duration_ms=1000.0, dt_ms=0.1, seed=7)

Validated Tutorials

Three v0.3.x core tutorials are fully validated:

  • v0.3.1: Single-neuron Izhikevich dynamics
  • v0.3.2: Parameter sweep exploration
  • v0.3.3: Two-neuron E/I coupling

Plus two Suite notebooks:

  • Suite No. 1: Computational biophysics foundations
  • Suite No. 2: Spectrolaminar network motifs

Optional Dependencies Handled Correctly

  • matplotlib is optional; core API does not require it
  • Visualization tests skip gracefully if matplotlib is unavailable
  • Install with pip install "jaxfne[viz]" for plotting support
  • Core CI/test suite passes without matplotlib

Documentation Updates

  • README.md updated with v0.3.4 grammar and PyPI links
  • Scope boundaries clarified
  • Installation docs reference v0.3.4
  • Quickstart shows current chainable API

Breaking Changes

None from v0.2.30. v0.3.4 is built on the stable v0.2.30 foundation with new tutorials and public grammar documentation.

Validation

  • Test suite: 1062 passed, 37 skipped
  • PyPI smoke test: PASS (install, import, grammar execution)
  • Tutorial execution: All 5 release notebooks execute successfully
  • Twine check: PASS (wheel and sdist)
  • GitHub Actions: Green on main

Install

pip install -U "jaxfne>=0.3.4"

Or with visualization:

pip install "jaxfne[viz]"

Scope & Limitations

jaxfne v0.3.4 is a computational scaffold, not a validated biological simulator:

  • Proxy readouts only — no solved Maxwell equations
  • No empirical calibration — simulation results are relative metrics
  • Tutorial-scale — examples demonstrate concepts, not biological ground truth
  • Optional visualization — figures are instructional aids

All outputs declare truth_mode: truth_safe_unverified and claim_level: computational_scaffold.

Next Steps

v0.3.4 is a stable checkpoint. Future v0.3.x work can focus on:

  • Additional tutorials (multi-area networks, plasticity)
  • Advanced visualization (Plotly interactivity)
  • Optimization workflows
  • Jaxley bridge enhancements

Package: Available on PyPI
Documentation: Read the Docs
Repository: GitHub

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