SpectraFit-Core

High-performance numerical curve fitting — a Rust kernel with analytical Jacobians, Pydantic-typed schemas, and a self-auditing benchmark that audits its own credibility against independent oracles (lmfit, JAX, scipy) and NIST StRD certified values.

Status: beta (0.1.1). APIs and the benchmark contract may still change before the stable 1.0 release. See LIMITATIONS.md for disclosed gaps.

Documentation: https://anselmoo.github.io/SpectraFit-Core/ — start with Installation and Quickstart.

What is this?

SpectraFit-Core fits spectroscopic and general nonlinear models with a Rust Levenberg–Marquardt / trust-region core, exposed to Python through a PyO3 wheel and a Pydantic schema mirror. Its distinguishing feature is a trustworthy benchmark: rather than asking you to take its speed/accuracy claims on faith, it ships a dashboard that verifies its own numbers (independent parity oracle, timing-isolation guards, render-truth provenance, NIST StRD validation) and visibly discloses what it has not verified.

Installation

pip install spectrafit-core   # or: uv add spectrafit-core

To build from source (Rust toolchain + maturin required):

git clone https://github.com/Anselmoo/SpectraFit-Core.git
cd SpectraFit-Core
uv sync --extra benchmark   # dev tooling is a dependency-group, installed by default
uv run maturin develop

In a source checkout, uv run pytest runs the full test suite.

Quick start

Fit a single Gaussian peak to synthetic data, using only the public spectrafit_core API (verified to run — see Quickstart for the full walkthrough):

import numpy as np
from spectrafit_core import MeasurementData, compose, fit, gaussian

# Synthetic "measured" data: a Gaussian peak plus a little noise.
x = np.linspace(-5, 5, 200)
y = 3.0 * np.exp(-0.5 * ((x - 0.5) / 1.2) ** 2) + np.random.default_rng(0).normal(
    0, 0.05, x.size
)

# Build the model graph: one Gaussian node with initial guesses.
graph = compose([gaussian("peak1", amplitude=1.0, center=0.0, sigma=1.0)]).build()

# Run the fit.
result = fit(graph, MeasurementData(x=x.tolist(), y=y.tolist()))

print(result.parameters)  # fitted amplitude/center/sigma, keyed "peak1.<param>"
print(result.r_squared)  # goodness of fit

This is deterministic (seeded RNG) and recovers the true amplitude/center/sigma (3.0, 0.5, 1.2) to within about one standard error, with r_squared ≈ 0.998:

{'peak1.sigma': ParameterResult(value=1.2024163241228947, ..., stderr=0.004211511681961483),
 'peak1.center': ParameterResult(value=0.49756589193680784, ..., stderr=0.004211469158787863),
 'peak1.amplitude': ParameterResult(value=2.997594452290324, ..., stderr=0.00909249987508253)}
0.9979075074894731

The block above is reformatted for readability: print emits it as one long line, and dict ordering is an implementation detail — your keys may appear in a different order. The values are what matter, and they are reproducible: the example seeds its RNG.

Benchmark

The benchmark (python/oracles/) fits the same problems with spectrafit (the Rust kernel under test) and five reference backends: lmfit, jax/optimistix and three scipy.optimize.least_squares methods (lm, trf, dogbox).

• Cases: a deterministic catalogue defined in python/oracles/cases.py (CATEGORY_REGISTRY: easy, complex, scaling, lineshapes, reality, edge, optfn, fixed, tied). Every case can be opened on its own in the report.
• Showcases: a 3-D fit with the native gaussian_nd kernel and a joint multi-spectrum fit with GlobalFitGraph (shared centres and widths, per-spectrum amplitudes).
• Data flow: benchmark run → results.json (the BenchReport contract) → FastAPI → the React app in web/. poe report_html bundles the same report into one offline file.
• Report: Standing shows what was measured, without a verdict; Evidence shows every backend on every case, side by side.

uv run poe benchmark         # full run → results.json + manifest.json
uv run poe benchmark_quick   # lean reps, fast local iteration
uv run poe serve             # serve the latest report over FastAPI (http://localhost:8000)
uv run poe benchmark_gate    # spectrafit-vs-lmfit regression gate on the latest run

# or the CLI directly
PYTHONPATH=python uv run python -m oracles.cli run --reps 10 --mc 30
PYTHONPATH=python uv run python -m oracles.cli gate

Each run writes its own folder:

.spectrafit_reports/<category>/<YYYY-MM-DD>_run_NNN/
  results.json     # the BenchReport contract payload (served by the FastAPI app)
  manifest.json    # run metadata + headline stats (geomean speedup, max |Δr²|, win-rate)
.spectrafit_reports/index.json   # all runs, newest first

The latest run resolves via oracles.reports.latest_results(category).

Regression gate

benchmark_gate (and CI) always checks three axes — spectrafit must not become slower than lmfit overall (geomean speedup < 1×), must not break accuracy parity (max |Δr²| > 1e-3 on the LM-family cases; the multimodal optfn/global category is excluded since two stochastic global optimizers legitimately reach different optima), and must not regress any backend's convergence. Up to four more axes are appended only when their backing evidence exists (self-perf, model-selection, σ-calibration, speed inference) — the gate is never a fixed axis count. See Why SpectraFit-Core, "A benchmark that verifies itself" section, for the full axis-by-axis description.

Web report

uv run poe serve   # serve the latest report over FastAPI (in another shell)

cd web && npm install
npm run dev        # dev server; proxies /api → http://localhost:8000 (the FastAPI app)
npm run build      # production build → dist/ (fetches /api/report at runtime)
npm run test       # vitest: render all views from fixtures, no browser/API (alias: npm run smoke)
npm run contract   # regenerate src/openapi.gen.ts from the live /openapi.json

Self-contained HTML — one command builds the extension, runs the benchmark, and bundles a single, deployable report.html (all JS/CSS inlined, the report inlined as window.__BENCH__) that opens offline with no server:

uv run poe report_html   # → .spectrafit_reports/benchmark/<run>/report.html (one file, tens of MB;
                          # size scales with the backend roster and case catalog)

The Python contract (oracles.bench_contract) is the single source of truth. The FastAPI app publishes it as OpenAPI, and npm run contract generates the TypeScript types from that schema, so engine and UI cannot drift apart.

Adding a model or case

The benchmark is registry-driven (see Extending SpectraFit-Core): register one PeakModel in oracles.models, reference its key from a CaseSpec/CaseFamily in oracles.cases. After a contract change, regenerate the TS types from the live OpenAPI schema: uv run poe serve then cd web && npm run contract.

Contributing

Contributions of any size are welcome — issues and pull requests here; see CONTRIBUTING.md for development setup, conventions, and the PR process. SpectraFit-Core is also developed on the MPCDF GitLab; changes from both places are kept in sync automatically.

Citing

If you use SpectraFit-Core in academic work, please cite it via CITATION.cff (GitHub's "Cite this repository" button reads it). Every release is archived on Zenodo; the concept DOI 10.5281/zenodo.23043544 always resolves to the latest version.

License

MIT © Anselm Hahn. See also CONTRIBUTING.md, CODE_OF_CONDUCT.md, and SECURITY.md.