pyfieldml 0.4.0

A modern pure-Python implementation of FieldML 0.5 with evaluation engine and biomechanics model zoo.

pyfieldml

A modern, pure-Python implementation of FieldML 0.5 with a full evaluation engine, interop bridges (meshio, PyVista, XDMF, scikit-fem, OpenSim-adjacent), and a curated biomechanics model zoo.

FieldML is the Physiome Project's declarative markup language for representing mathematical fields over discrete meshes — used across computational physiology (cardiac, musculoskeletal, respiratory modeling). The original C++ FieldML-API has been effectively unmaintained since 2015. pyfieldml is an independent reimplementation that brings FieldML into the modern scientific-Python ecosystem.

Status: design phase. The approved design spec lives at docs/superpowers/specs/2026-04-18-pyfieldml-design.md. Implementation plan and phased build are next.

What it will do (v1.0)

• Full FieldML 0.5 read + write, round-trip validated against the C++ reference test suite
• Legacy read of FieldML 0.3 and 0.4 (auto up-conversion to 0.5)
• Evaluation engine with Lagrange (orders 1–2) and cubic Hermite-with-scaling bases
• Field.evaluate(element, xi), vectorized Field.sample(points), Jacobians
• High-level builders: add_lagrange_mesh, add_fiber_field, add_material_field, add_landmark_set, …
• Interop: meshio (two-way), PyVista (doc.plot(), doc.explore()), XDMF, scikit-fem, OpenSim-compatible asset export
• CLI: pyfieldml inspect | validate | convert | plot | lint | diff
• Curated model zoo: pyfieldml.datasets.load_femur(), load_rectus_femoris(), load_myocardium()
• Docs site with jupyter-lite in-browser runnable notebooks
• JOSS paper submitted alongside v1.0

License

Apache 2.0. See LICENSE and NOTICE.

Install

pip install pyfieldml

Development:

git clone https://github.com/kchemorion/pyfieldml
cd pyfieldml
uv sync --extra dev
uv run pytest

Quickstart

import pyfieldml as fml

doc = fml.read("model.fieldml")
print(doc.source_version)          # "0.5.0", "0.4", "0.3"
doc.validate()                     # XSD validation
doc.write("roundtripped.fieldml")

Phase 0 ships I/O and DOM-level round-trip. The semantic object model, evaluation engine, interop bridges, and model zoo arrive in later phases — see the design spec and plans.

Acknowledgments

pyfieldml is an independent Python reimplementation inspired by and validated against the C++ FieldML-API. Credit to its original authors — Caton Little, Alan Wu, Richard Christie, Andrew Miller, and Auckland Uniservices Ltd / the Auckland Bioengineering Institute — and to the Physiome Project community that maintains the FieldML specification.