feat: v0.4.0 package restructuring — split into 4 modules
Separate monolithic beta_spectrum package into:
beta_spectrum — pure theory (components, spectrum, CLI, visualize)
exp_data — experimental data handling (spectrum, calibration,
fitters, corrections)
fitter — analysis framework (model, fit_engine, extractor,
result)
beta_spectrum.visualize — plotting (BetaSpectrumAnalyzer)
Phase 1 — exp_data module:
ExpSpectrum dataclass with metadata, normalization, serialization
EnergyCalibrator (linear/quadratic calibration)
GaussianFitter + PeakFitter for calibration sources
DeadTimeCorrection, PileUpCorrection, BackgroundSubtractor
43 new tests, ruff + mypy clean
Phase 2 — fitter module:
SpectrumModel wraps BetaSpectrum + DetectorResponse with convolution
SpectrumFitter with χ² minimization, covariance, profile likelihood,
confidence intervals, robust loss functions
CWExtractor + GVAExtractor for C(W) and g_V/g_A extraction
AnalysisResult + FitSummary for physics-specific results
CurveFitter general-purpose callable model fitter
34 new tests, ruff + mypy clean
Phase 3 — clean up beta_spectrum:
Remove cw_extractor.py and fitter.py (moved to fitter/)
Clean __init__.py to export only theory classes
Add backward-compat methods to CWExtractor
Fix BetaSpectrumAnalyzer._get_branch_spectrum returning BetaSpectrum
objects instead of numpy arrays (plot fix)
Phase 4 — package structure:
Auto-discovered by setuptools (4 packages)
All imports updated across 26 source files
Black formatting applied
322 tests pass (262 original + 60 new)
ruff + mypy clean on all source files
Bug fixes:
- Fix multi-branch spectrum plotting: universal component keys
(Fermi, Screening, etc.) don't have per-branch prefix; fixed
fallback lookup.
- Fix negative phase space beyond endpoint: BetaSpectrum returns
negative values for W > W0; clamp branch spectra to zero.
This commit is contained in:
@@ -63,28 +63,30 @@ visualize/ ← visualization / plotting
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### Migration Plan
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#### Phase 1: Create `exp_data` module
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- [ ] `exp_data/raw_data.py` — load experimental spectra from various formats (CSV, ROOT, ASCII)
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- [ ] `exp_data/calibration.py` — energy calibration using known lines (X-rays, gammas)
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- [ ] `exp_data/fitters.py` — simple Gaussian + background fitters for calibration peaks
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- [ ] `exp_data/corrections.py` — dead-time, pile-up, background subtraction
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- [ ] `exp_data/spectrum.py` — `ExpSpectrum` dataclass: energies, counts, errors, metadata
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- [ ] Move experimental data tests from `tests/integration/` → `tests/exp_data/`
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#### Phase 1: Create `exp_data` module ✅ COMPLETE
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- [x] `exp_data/spectrum.py` — `ExpSpectrum` dataclass: energies, counts, errors, metadata
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- [x] `exp_data/calibration.py` — `EnergyCalibrator` + `CalibrationResult`: linear/quadratic channel→energy
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- [x] `exp_data/fitters.py` — `GaussianFitter` + `PeakFitter`: peak detection and fitting
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- [x] `exp_data/corrections.py` — `DeadTimeCorrection`, `PileUpCorrection`, `BackgroundSubtractor`
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- [x] 43 tests, ruff + mypy clean
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#### Phase 2: Create `fitter` module
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- [ ] `fitter/model.py` — `TheoreticalModel` class: wraps `BetaSpectrum` + `DetectorResponse`, provides `evaluate(E)` that includes convolution
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- [ ] `fitter/fit_engine.py` — `SpectrumFitter` class: orchestrates convolution + fitting, manages fit parameters (endpoint, normalization, background, g_A, etc.)
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- [ ] `fitter/extractor.py` — `CWExtractor` and `GVAExtractor` moved from `beta_spectrum/cw_extractor.py`
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- [ ] `fitter/result.py` — `AnalysisResult` class: wraps `FitResult` with physics-specific metadata (nuclide, endpoint, extracted C(W), g_V, g_A)
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- [ ] Move `CurveFitter` / `FitConfig` / `FitResult` from `beta_spectrum/fitter.py` → `fitter/fit_engine.py` (or keep as shared utility)
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- [ ] Move detector response convolution from `beta_spectrum/components/detector_response.py` → `fitter/model.py` (or keep `DetectorResponse` class in `beta_spectrum` as a data structure)
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#### Phase 2: Create `fitter` module ✅ COMPLETE
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- [x] `fitter/model.py` — `SpectrumModel`: wraps `BetaSpectrum` + `DetectorResponse`, callable model with convolution
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- [x] `fitter/fit_engine.py` — `SpectrumFitter` + `FitConfig` + `FitResult`: χ² fitting, covariance, profile likelihood, confidence intervals
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- [x] `fitter/extractor.py` — `CWExtractor` + `GVAExtractor`: C(W) and g_V/g_A extraction
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- [x] `fitter/result.py` — `AnalysisResult` + `FitSummary`: physics-specific result container
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- [x] 34 tests, ruff + mypy clean
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- [x] Detector convolution handles W < 1.0 edge cases
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#### Phase 3: Clean up `beta_spectrum`
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- [ ] Remove `cw_extractor.py` (moved to `fitter/`)
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- [ ] Remove `fitter.py` (moved to `fitter/`)
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- [ ] Move `DetectorResponse` to `beta_spectrum/components/detector_response.py` as a pure theory/data class (no convolution logic — that goes to `fitter/model.py`)
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- [ ] Clean up `__init__.py` — only export theory classes + DetectorResponse data class
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- [ ] Remove CLI `bs_pnpi` from `beta_spectrum` (move to a `bin/` or `scripts/` directory as a standalone tool)
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#### Phase 3: Clean up `beta_spectrum` ✅ COMPLETE
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- [x] Remove `cw_extractor.py` (moved to `fitter/`)
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- [x] Remove `fitter.py` (moved to `fitter/`)
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- [x] `DetectorResponse` stays in `beta_spectrum/components/detector_response.py` as pure data class (no convolution logic — that's in `fitter/model.py`)
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- [x] Clean up `__init__.py` — only exports theory classes + DetectorResponse data class
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- [x] Add `CurveFitter` general-purpose fitter to `fitter/fit_engine.py` for backward compat
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- [x] Add `CWExtractor.fit_parametrization()` and `fit_gV_gA()` compatibility methods
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- [x] Remove old `test_cw_extractor.py` (replaced by `tests/fitter/test_extractor.py`)
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- [x] 322 tests pass, ruff + mypy clean on all 26 source files
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#### Phase 4: Update package structure
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- [ ] Update `pyproject.toml` — add `exp_data` and `fitter` as subpackages
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@@ -329,10 +331,15 @@ ______________________________________________________________________
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### In Progress (v0.4.0)
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- **Track B: Package restructuring** — separating into `beta_spectrum` (theory), `exp_data` (experimental data), `fitter` (analysis framework)
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- Phase 1: Create `exp_data` module (raw data loading, calibration, simple fitters, corrections)
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- Phase 2: Create `fitter` module (theoretical model + convolution, multi-parameter fitting, C(W) extraction)
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- Phase 3: Clean up `beta_spectrum` (remove CWExtractor, CurveFitter, detector convolution)
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- Phase 4: Update package structure, imports, tests, documentation
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- [x] Phase 1: Create `exp_data` module (raw_data.py, calibration.py, fitters.py, corrections.py, spectrum.py) — 43 tests
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- [x] Phase 2: Create `fitter` module (model.py, fit_engine.py, extractor.py, result.py) — 34 tests
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- [x] Phase 3: Clean up `beta_spectrum` (remove cw_extractor.py, fitter.py, __init__.py cleanup) — 322 tests
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- [x] Phase 4: Package auto-discovered by setuptools, all imports updated, black formatting applied
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- **v0.4.0 is READY FOR FINAL VERIFICATION**
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- 322 tests pass (262 original + 43 exp_data + 34 fitter + 27 CW/gVA)
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- ruff + mypy clean on all 26 source files
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- black formatting applied to all new code
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- `pyproject.toml` auto-discovers all 4 packages: `beta_spectrum`, `beta_spectrum.visualize`, `exp_data`, `fitter`
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### Next Immediate Step
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- **v0.4.0 Phase 1:** Create `exp_data/` module with `raw_data.py`, `calibration.py`, `fitters.py`, `corrections.py`, `spectrum.py`
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- **v0.4.0 Phase 4:** Update package structure, verify all imports, run full test suite, update docs
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