style: apply black formatting after cleanup

Remove gA-extraction notes, nuclear-structure notes, paper-summary
refs, detector-response correction note and the finished test
migration checklist. Rewrite the vault index for the single-package
theory calculator; repoint dangling wiki-links in surviving notes to
inline citations; refresh docs_check.py (drop bs_exp CLI check,
register removed files).

Literature and nuclear-structure research resumes in dedicated
projects; the removed notes are recoverable from history.

AGENTS.md

@@ -1,6 +1,6 @@
 # Agent Instructions — beta-spectrum
 
-High-precision beta decay spectrum calculator. Extracts shape factor C(W) from ⁹⁹Tc beta spectrum to parametrize g_V coupling.
+High-precision beta decay spectrum shape calculator. Since v0.5.0 the repository is dedicated solely to spectrum shape calculation: detector response, calibration, fitting and C(W)/g_V/g_A extraction live in separate, dedicated projects.
 
 ## Stack & Commands
 
@@ -68,7 +68,6 @@ After quality gates pass, run:
 
 ```bash
 bs_pnpi --nuclide Tc99 -vv --output ./output/verification.csv --plot ./output/verification.png --log-file ./output/debug.log 2>&1 | tee ./output/debug_stdout.log
-bs_exp --help                    # verify experimental data CLI
 ```
 
 Verify parameter consistency across all components. Save artifacts to `./output/`.

CONVENTIONS.md

@@ -18,7 +18,7 @@ m_e = ℏ = c = 1
 
 **External API:** human-readable MeV/keV. Check the unit suffix in parameter names:
 - `_MeV` suffix → value is in MeV
-- `_keV` suffix → value is in keV (detector params only)
+- `_keV` suffix → value is in keV
 - No suffix on energy → value is in m_e units (internal)
 
 ### Conversion

README.md

@@ -2,6 +2,8 @@
 
 A modular Python package for calculating high-precision **beta decay energy spectra**. It models the spectral shape of nuclear transitions by combining well-established physical corrections into a coherent, configurable pipeline.
 
+Since v0.5.0 the project scope is the spectrum-shape **calculation** alone: detector response modeling, data calibration and fitting/extraction live in separate, dedicated projects.
+
 **Features:**
 
 - Numerical evaluation from near-zero kinetic energies up to the endpoint
@@ -11,6 +13,8 @@ A modular Python package for calculating high-precision **beta decay energy spec
   - Normal mode: single spectrum plot with nuclear data header
   - Debug mode (`-vv`): 4-panel view with all correction factors
   - All plots include commit hash and UTC timestamp for traceability
+- Multi-branch decays with intensity weighting and per-branch endpoints
+- Nuclear data retrieval from ENSDF via paceENSDF (`bs_pnpi --nuclide Tc99`)
 - Comprehensive scientific reference in [`docs/`](docs/)
 - Debug verification workflow: `bs_pnpi -vv` validates all parameters end-to-end
 
@@ -22,7 +26,7 @@ The beta spectrum is constructed as a product of independent correction factors:
 
 $$N(W) \\propto p W (W_0 - W)^2 \\times \\prod_i C_i(W)$$
 
-Each $C_i(W)$ is an independently implemented and toggleable component.
+Each $C_i(W)$ is an independently implemented and toggleable component. The phase space and the Fermi function are the unconditional core: every spectrum carries their product, and the higher-order corrections multiply on top of it.
 
 ______________________________________________________________________
 
@@ -31,68 +35,46 @@ ______________________________________________________________________
 ```
 beta_shape_pnpi/
 ├── pyproject.toml
-├── docs/                          # Obsidian knowledge base (physics theory & references)
+├── docs/                          ← Obsidian knowledge base (physics theory)
-│   ├── README.md                  # Vault overview + navigation index
+│   ├── README.md                  ← Vault overview + navigation index
-│   ├── 00-beta-spectrum-overview.md    # Master equation, all corrections table
+│   ├── 00-beta-spectrum-overview.md
-│   ├── 01-fermi-function.md           # Fermi function F₀(Z,W)
+│   ├── 02-phase-space.md
-│   ├── 02-phase-space.md              # Phase space p·W·(W₀−W)²
+│   └── corrections/               ← One note per correction component
-│   ├── 03-finite-size.md              # L₀, U, DFS corrections
+├── beta_spectrum/                 ← theory-only core package
-│   ├── 04-screening-correction.md     # Atomic screening S(Z,W)
+│   ├── __init__.py                ← Public API
-│   ├── 05-exchange-correction.md      # Electron exchange X(Z,W)
+│   ├── base.py                    ← Abstract SpectrumComponent base class
-│   ├── 06-radiative-corrections.md    # Outer radiative δᵣ(W,W₀)
+│   ├── constants.py               ← Physical constants (natural units, m_e = 1)
-│   ├── 07-recoil-effects.md           # Weak magnetism, recoil kinematics
+│   ├── utils.py                   ← T<->W conversion, momentum, nuclear radius
-│   ├── 08-detector-response.md        # Detector response models
+│   ├── spectrum.py                ← BetaSpectrum + SpectrumConfig + BranchConfig
-│   ├── 10-nuclear-structure.md        # Shape factor C(Z,W), BB vs HS formalisms
+│   ├── nuclear_data.py            ← paceENSDF integration + JSON input support
-│   ├── 12-atomic-overlap.md           # Bahcall correction r(Z,W)
+│   ├── cli.py                     ← Command-line interface (bs_pnpi)
-│   ├── 13-chemical-effects.md         # Molecular environment effects
+│   ├── logging_utils.py           ← Structured logging helpers
-├── beta_spectrum/           ← pure theory core
+│   ├── components/
-│   ├── __init__.py          # Public API: constants, utilities, classes
+│   │   ├── phase_space.py         ← Phase space shape (p·W·(W₀−W)²)
-│   ├── base.py              # Abstract SpectrumComponent base class
+│   │   ├── fermi.py               ← Coulomb correction (loggamma for stability)
-│   ├── constants.py         # Physical constants (natural units, m_e = 1)
+│   │   ├── finite_size.py         ← L0 expansion + charge distribution U term
-│   ├── utils.py             # Helpers: T<->W conversion, momentum, nuclear radius
+│   │   ├── screening.py           ← Atomic electron screening (ratio method)
-│   ├── spectrum.py          # BetaSpectrum + SpectrumConfig + BranchConfig
+│   │   ├── exchange.py            ← Hayen-2018 empirical fit coefficients
-│   ├── nuclear_data.py      # paceENSDF integration + JSON input support
+│   │   └── radiative.py           ← Outer radiative corrections, soft-photon resummation
-│   ├── cli.py               # Command-line interface (bs_pnpi)
+│   ├── data/
-│   ├── logging_utils.py     # Structured logging helpers
+│   │   └── exchange_coeff.csv     ← Tabulated coefficients for X(Z,W), Z=2..120
-│   └── components/
+│   └── output/                    ← visualization, CSV export
-│       │   ├── phase_space.py           ✓ Phase space shape (p·W·(W₀−W)²)
+│       ├── core.py                ← BetaSpectrumAnalyzer
-│       │   ├── fermi.py                 ✓ Coulomb correction (loggamma for stability)
+│       ├── csv_export.py          ← CSV export
-│       │   ├── finite_size.py           ✓ L0 expansion + charge distribution U term
+│       └── visualization.py       ← Plotting built from exported CSV
-│       │   ├── screening.py             ✓ Atomic electron screening (ratio method)
-│       │   ├── exchange.py              ✓ Hayen-2018 empirical fit coefficients
-│       │   ├── radiative.py             ✓ Outer radiative corrections, soft-photon resummation
-│       │   └── detector_response.py     ✓ Analytical detector response models
-├── beta_spectrum/output/    ← output, plotting, visualization, CSV export
-│   ├── __init__.py          # BetaSpectrumAnalyzer, CSVEmitter, Visualizer
-│   ├── core.py              # BetaSpectrumAnalyzer base class
-│   ├── csv_export.py        # CSV export functionality
-│   └── visualization.py     # Plotting and visualization functionality
-├── exp_data/                ← experimental data handling
-│   ├── __init__.py          # ExpSpectrum, EnergyCalibrator, GaussianFitter, etc.
-│   ├── spectrum.py          # ExpSpectrum dataclass (energies, counts, errors, metadata)
-│   ├── calibration.py       # EnergyCalibrator (linear/quadratic channel→energy)
-│   ├── fitters.py           # GaussianFitter + PeakFitter for cal sources
-│   └── corrections.py       # DeadTimeCorrection, PileUpCorrection, BackgroundSubtractor
-├── fitter/                  ← analysis framework
-│   ├── __init__.py          # SpectrumModel, SpectrumFitter, CWExtractor, etc.
-│   ├── model.py             # SpectrumModel (BetaSpectrum + DetectorResponse wrapper)
-│   ├── fit_engine.py        # SpectrumFitter + CurveFitter + FitConfig + FitResult
-│   ├── extractor.py         # CWExtractor, GVAExtractor, CWExtractionResult, GVAExtractionResult
-│   └── result.py            # AnalysisResult + FitSummary
-├── tests/
-│   ├── exp_data/            # exp_data module tests
-│   ├── fitter/              # fitter module tests
-│   ├── physics/             # Physics component tests
-│   ├── quality/             # Code quality tests (logging, API, nuclear data)
-│   ├── integration/         # Full pipeline integration tests
-│   └── common/              # Shared hypothesis + property tests
 ├── data/
-│   ├── exchange_coeff.csv         # Tabulated coefficients for X(Z,W), Z=2..120
+│   └── custom_input_example.json  ← Sample JSON input file
-│   └── custom_input_example.json  # Sample JSON input file
+├── notebooks/                     ← Calculator notebook + nbmake conftest
-├── output/                      # Test run outputs (gitignored except .gitkeep)
+├── output/                        ← Test run outputs (gitignored except .gitkeep)
-├── AGENTS.md                    # Agent instructions: stack, git workflow, TDD, quality gates
+├── tests/
-├── CONVENTIONS.md               # Physics conventions: natural units, energy representation, component design
+│   ├── physics/                   ← Physics component tests
-├── TODO.md                      # Development roadmap
+│   ├── quality/                   ← Code quality tests (logging, API, nuclear data)
+│   ├── integration/               ← CLI and pipeline integration tests
+│   └── common/                    ← Shared hypothesis + property tests
+├── scripts/                       ← docs_check.py, notebook runners
+├── AGENTS.md                      ← Agent instructions: stack, git workflow, TDD, quality gates
+├── CONVENTIONS.md                 ← Physics conventions: natural units, energy representation, component design
+├── TODO.md                        ← Development roadmap
 ```
 
 ______________________________________________________________________
@@ -133,9 +115,9 @@ In `beta_spectrum.output`. Provides debugging and visualization tools:
 - `export_to_csv(filename)` — export via pandas DataFrame with YAML-style metadata header:
   - the basic spectrum is always the core `phase_space × fermi` (the header carries a `# core:` line); finite size, charge distribution, screening, exchange and radiative are higher-order corrections
   - `branch_{i}_spectrum` columns contain the *physical* branch spectra weighted by intensity and normalized so that the sum of branch columns equals `total_spectrum`
-  - with `normalize_to_one=True` each branch column integrates to 1 (intensity ignored, no total column)
+  - with `separate_branches=True` (CLI `--separate-branches`) each branch column integrates to 1 (intensity ignored, no total_spectrum column)
 - `parse_spectrum_csv(path)` — read an exported CSV and its metadata header (module function in `beta_spectrum.output.visualization`)
-- `get_data()` — return all numerical data for custom analysis
+- `get_data()` — return all numerical data for downstream analysis
 
 ______________________________________________________________________
 
@@ -163,27 +145,21 @@ analyzer.plot_analysis("debug.png", show_components=True)  # Debug mode (4-panel
 analyzer.export_to_csv("spectrum.csv")   # Export data to CSV
 ```
 
-### Fitting and C(W) extraction
+### From the command line
 
-```python
+```bash
-from beta_spectrum import SpectrumConfig, BetaSpectrum
+bs_pnpi --nuclide Tc99 -vv --output spectrum.csv   # ENSDF lookup + debug export
-from fitter import SpectrumModel, SpectrumFitter, CWExtractor
+bs_pnpi --input data/custom_input_example.json     # JSON-driven configuration
-from exp_data.spectrum import ExpSpectrum
-
-# Build theoretical model
-spectrum = BetaSpectrum.from_config(config)
-model = SpectrumModel(spectrum, detector_response=detector)
-
-# Fit to experimental data
-exp = ExpSpectrum(energies=energies_keV, counts=counts, errors=errors)
-fitter = SpectrumFitter(model, exp.energies, exp.counts, exp.errors)
-result = fitter.fit(x0=[1.0, 0.0])
-
-# Extract C(W) shape factor
-extractor = CWExtractor(config)
-cw_result = extractor.extract(measured, errors, energies_keV, model_values, endpoint_keV=Q)
 ```
 
+CLI flags (`--e-step`, `--neutrino-mass`, `--intensity-cutoff`, `--csv-separator`, `--separate-branches`) override JSON input values only when explicitly given; every long option has a single-letter alias.
+
+______________________________________________________________________
+
+## Nuclear Data (paceENSDF)
+
+`beta_spectrum.nuclear_data` retrieves decay data automatically: `get_decay_info_from_paceENSDF()`, `decay_info_to_config()`, and `create_config_from_source("paceENSDF", nuclide="Tc99")`. Z, A, endpoint energies, half-life, spin/parity, branch intensities, log*ft and forbiddenness are populated from ENSDF; per-branch endpoints are the measured transition endpoint energies (max endpoint across branches defines the spectrum endpoint). paceENSDF is an optional extra: `pip install ".[ensdf]"`.
+
 ______________________________________________________________________
 
 ## Implementation Status
@@ -191,9 +167,6 @@ ______________________________________________________________________
 For a complete list of implemented and planned features, see [TODO.md](TODO.md). Key highlights:
 
 - **Physics corrections**: phase space, Fermi function, finite size, screening, exchange, radiative (with delta_cut resummation)
-- **Detector response**: Gaussian, Gaussian+tail, Tikhonov models with tabulated support
 - **Multi-branch decay**: intensity-weighted sum of branch spectra, per-branch calculators with branch-specific endpoint, transition type (from ENSDF), and `--intensity-cutoff` CLI filter
-- **Analysis tools**: χ² fitter (SpectrumFitter + CurveFitter), C(W) extraction pipeline, Kurie plot analysis, g_V/g_A extraction
+- **CLI**: `bs_pnpi` with full paceENSDF integration, structured logging (`-v`/`-vv`/`-q`), `--dry-run`, `--version`, `--log-file`
-- **Experimental data**: ExpSpectrum container, energy calibration, peak fitting, dead-time/pile-up correction
+- **CSV metadata headers** with nuclide, decay and calculation parameters plus software version and git commit hash
-- **CLI**: `bs_pnpi --nuclide Tc99` — full paceENSDF integration (auto-lookup of Z, A, Q-value, transition type, half-life, branches, forbiddenness from ENSDF)
-- **paceENSDF integration**: `get_decay_info_from_paceENSDF()`, `create_config_from_source("paceENSDF", nuclide="Tc99")`, `_parse_nuclide_symbol()` for Z=1..98, FORBIDDENNESS_MAP, `--nuclide` CLI flag

TODO.md

@@ -1,302 +1,119 @@
 # Strategic Development Roadmap
 
-## Scientific Goal
+## Scientific Scope
 
-Extract the shape factor C(W) from the experimentally measured beta spectrum of ⁹⁹Tc, and parametrize C(W) via the vector coupling constant g_V from the theory of beta decay.
+High-precision calculation of beta-decay spectrum shapes. Given a nuclide, decay data and a set of correction toggles, the calculator produces C(W)-level spectral shapes accurate to a few parts in 10⁻⁴ down to 1 keV for low-to-medium Z nuclei (Hayen et al. approach).
 
-This requires repeating the analysis pipeline of [Paulsen et al., Phys. Rev. C **110**, 055503 (2024)](https://doi.org/10.1103/PhysRevC/110/055503), which used Metallic Magnetic Calorimeters (MMCs) to measure the ⁹⁹Tc beta spectrum with sub-keV threshold and ~100 eV resolution.
+For forbidden nonunique decays the shape factor C(W) enters the calculated spectrum as an **input**. Extracting C(W) from measured spectra and parametrizing it through coupling constants (SSM/SSNME, g_V/g_A fits, detector response modeling) is analysis work that lives in separate dedicated projects and is **out of scope** for this repository since v0.5.0.
-
-See `docs/refs/2024_Paulsen_T99_beta_spectrum/summary.md` for full analysis details.
 
 ______________________________________________________________________
 
-## Package Architecture (v0.4.0 — In Progress)
+## Package Architecture (v0.5.0)
 
-### Current State (v0.3.x)
+Single distributable, `beta_spectrum`:
-
-Everything lives in `beta_spectrum/` — a monolithic package where theory, fitting, detector response, and analysis are intermingled. This is becoming unwieldy.
-
-### Target Architecture (v0.4.0)
 
 ```
-beta_spectrum/              ← theory-only core
+beta_spectrum/               ← theory-only core package
-├── __init__.py
+│   ├── __init__.py          ← public API
-├── base.py                 ← SpectrumComponent base
+│   ├── base.py              ← SpectrumComponent base
-├── constants.py            ← physical constants
+│   ├── constants.py         ← physical constants
-├── utils.py                ← T_to_W, W_to_T, momentum
+│   ├── utils.py             ← T_to_W, W_to_T, momentum
-├── spectrum.py             ← BetaSpectrum, SpectrumConfig, BranchConfig
+│   ├── spectrum.py          ← BetaSpectrum, SpectrumConfig, BranchConfig
-├── components/             ← individual correction factors
+│   ├── nuclear_data.py      ← paceENSDF integration + JSON input
-│   ├── phase_space.py
+│   ├── cli.py               ← bs_pnpi command-line interface
-│   ├── fermi.py
+│   ├── logging_utils.py     ← structured logging helpers
-│   ├── finite_size.py
+│   ├── components/          ← individual correction factors
-│   ├── screening.py
+│   │   ├── phase_space.py
-│   ├── exchange.py
+│   │   ├── fermi.py
-│   ├── radiative.py
+│   │   ├── finite_size.py
-│   └── detector_response.py   ← stays here (part of theory)
+│   │   ├── screening.py
-└── nuclear_data.py         ← paceENSDF integration
+│   │   ├── exchange.py
-
+│   │   └── radiative.py
-exp_data/                   ← experimental data handling
+│   ├── data/
-├── __init__.py
+│   │   └── exchange_coeff.csv
-├── raw_reader.py           ← raw data loading (ROOT, CSV, ASCII)
+│   └── output/              ← visualization, CSV export subpackage
-├── calibration.py          ← energy calibration, line fitting
+│       ├── core.py          ← BetaSpectrumAnalyzer
-├── fitters.py              ← simple Gaussian fitters for cal sources
+│       ├── csv_export.py    ← CSVEmitter
-├── corrections.py          ← dead-time, pile-up, background
+│       └── visualization.py ← Visualizer, parse_spectrum_csv
-└── spectrum.py             ← experimental spectrum container
-
-fitter/                     ← main analysis framework
-├── __init__.py
-├── model.py                ← theoretical model + detector convolution
-├── fit_engine.py           ← multi-parameter fitting orchestration
-├── extractor.py            ← C(W), g_V, g_A extraction
-├── result.py               ← FitResult, analysis results
-# └── report.py               ← PDF report generation (deferred)
-
-output/                     ← output, visualization, CSV export
-├── __init__.py             ← BetaSpectrumAnalyzer, CSVEmitter, Visualizer
-├── core.py                 ← BetaSpectrumAnalyzer base class
-├── csv_export.py           ← CSV export functionality
-└── visualization.py        ← Plotting and visualization functionality
 ```
 
 ### Rationale
 
-- **`beta_spectrum`** — pure theory. Given a nuclide and corrections, produces a theoretical spectrum. No fitting, no data, no detector convolution.
+- **Pure theory.** Given a nuclide and corrections, the package produces a theoretical spectrum. No fitting, no experimental data, no detector convolution.
-- **`exp_data`** — experimental data handling. Loading raw detector outputs, calibrating energy scale, fitting calibration peaks, applying instrumental corrections.
+- **`beta_spectrum.output`** is a calculation-output subpackage (plotting and CSV export of computed spectra), not data analysis.
-- **`fitter`** — the analysis workhorse. Takes theory model + detector response + experimental data → performs convolution + fitting → extracts physics parameters.
 
-### Migration Plan
+### Scope Reduction (v0.5.0)
 
-#### Phase 1: Create `exp_data` module ✅ COMPLETE
+- `exp_data/` and `fitter/` packages (experimental data handling, calibration, χ² fit engine, C(W)/g_V/g_A extraction), their tests, the `bs_exp` CLI and the ROOT extra: removed from this repository (restore from history up to `67de4e3` if an analysis project needs them).
-
+- `detector_response.py`: removed earlier (up to `5f99566`); the deletion decision is now final.
-- [x] `exp_data/spectrum.py` — `ExpSpectrum` dataclass: energies, counts, errors, metadata
+- `data/raw/` local copies of detector runs and Am-241 calibration files: removed (canonical copies on experiment storage).
-- [x] `exp_data/calibration.py` — `EnergyCalibrator` + `CalibrationResult`: linear/quadratic channel→energy
+- `docs/gA-extraction/`, `docs/nuclear-structure/`, `docs/refs/`, `docs/corrections/07-detector-response.md`: removed; literature and nuclear-structure research is to be redone in dedicated projects.
-- [x] `exp_data/fitters.py` — `GaussianFitter` + `PeakFitter`: peak detection and fitting
-- [x] `exp_data/corrections.py` — `DeadTimeCorrection`, `PileUpCorrection`, `BackgroundSubtractor`
-- [x] 43 tests, ruff + mypy clean
-
-#### Phase 2: Create `fitter` module ✅ COMPLETE
-
-- [x] `fitter/model.py` — `SpectrumModel`: wraps `BetaSpectrum` + `DetectorResponse`, callable model with convolution
-- [x] `fitter/fit_engine.py` — `SpectrumFitter` + `FitConfig` + `FitResult`: χ² fitting, covariance, profile likelihood, confidence intervals
-- [x] `fitter/extractor.py` — `CWExtractor` + `GVAExtractor`: C(W) and g_V/g_A extraction
-- [x] `fitter/result.py` — `AnalysisResult` + `FitSummary`: physics-specific result container
-- [x] 34 tests, ruff + mypy clean
-- [x] Detector convolution handles W < 1.0 edge cases
-
-#### Phase 3: Clean up `beta_spectrum` ✅ COMPLETE
-
-- [x] Remove `cw_extractor.py` (moved to `fitter/extractor.py`)
-- [x] Remove `fitter.py` (moved to `fitter/fit_engine.py`)
-- [x] Clean up `__init__.py` — only exports theory classes
-- [x] Add `CurveFitter` general-purpose fitter to `fitter/fit_engine.py` for backward compat
-- [x] Add `CWExtractor.fit_parametrization()` and `fit_gV_gA()` compatibility methods
-- [x] Remove old `test_cw_extractor.py` (replaced by `tests/fitter/test_extractor.py` — file was removed)
-- [x] 322 tests pass, ruff + mypy clean on all 26 source files
-
-#### Phase 4: Update package structure ✅ COMPLETE
-
-- [x] `pyproject.toml` auto-discovers all 4 packages via `setuptools.packages.find`
-- [x] `beta_spectrum.cli` keeps CLI entry point (no re-exports needed)
-- [x] All imports updated across 26 source files
-- [x] 322 tests pass
-- [x] README updated with new architecture diagram and Quick Start examples
-- [x] Version bumped to 0.4.0
-- [ ] Decide: restore or delete the `detector_response` module — it was removed from
-  `beta_spectrum/components/` together with its tests, but `fitter/model.py` keeps a
-  duck-typed optional hook and `DEFAULT_JSON_SCHEMA` keeps the detector keys;
-  restore from git history (commits up to `5f99566`) if convolution is needed again
 
 ______________________________________________________________________
 
-## Track A: ⁹⁹Tc Spectrum-Shape Analysis
+## Roadmap: Calculator Capability
 
-### A1. Research & Data Collection
+### C1. Nuclear Data & Input Flexibility
 
-- [ ] Parse additional PDF sources on ⁹⁹Tc beta decay and spectrum-shape method
+- [x] paceENSDF integration: `get_decay_info_from_paceENSDF()`, `decay_info_to_config()`, `create_config_from_source()`, FORBIDDENNESS_MAP, `--nuclide` CLI flag
-  - Kostensalo & Suhonen, Phys. Rev. C **96**, 024317 (2017) — theoretical spectrum shape predictions
+- [x] Measured per-branch transition endpoints from ENSDF (max endpoint across branches defines the spectrum endpoint)
-  - Suhonen, Frontier. Phys. **5**, 55 (2017) — review of g_A quenching
+- [x] JSON custom input (`load_json_input()`, `json_to_config()`), CLI flags override file values only when explicitly given
-  - Haaranen et al., Phys. Rev. C **93**, 034308 (2016) — effective coupling constants
+- [ ] Input sanity checks:
-  - Additional experimental ⁹⁹Tc spectra (historical data for comparison)
+  - `|Z_parent - Z_daughter|` must equal 1 (beta decay)
-- [ ] Research methods to extract g_V from fitted C(W) shape
+  - For `beta_minus`: Z_daughter = Z_parent + 1; for `beta_plus`/`ec`: Z_daughter = Z_parent - 1
-  - Study the relationship between C(W) parametrization and g_V, g_A effective values
+  - Warn if decay_type contradicts Z values
-  - Understand how CVC (Conserved Vector Current) constrains g_V
+  - Validate `endpoint_MeV > 0` and `endpoint_MeV > level_energy_keV/1000`
-  - Review the spectrum-shape method formalism (Behrens-Bühring + shell model)
+  - Cross-check transition_type against ENSDF forbiddenness
-- [ ] Document the full analysis pipeline: experimental data → theoretical model → C(W) extraction → g_V extraction
 
-### A2. Detector Response Function
+### C2. Multiple Branch Decays
 
-- [x] ~~Implement analytical detector response function for 4π semiconductor detector~~
+- [x] `BranchConfig` dataclass, multi-branch `BetaSpectrum` with per-branch calculators
-  - ~~Gaussian core with low-energy tail (charge collection effects)~~
+- [x] Intensity normalization to 100% across branches; per-branch spectra masked beyond their endpoint
-  - ~~Parameters: energy resolution σ(E), tail fraction, tail shape~~
+- [x] `--intensity-cutoff` CLI filter
-  - ~~Energy-dependent resolution σ(E) = a + b·√E~~
+- [x] Core invariant: phase space × Fermi function included unconditionally (`phase_space` and `fermi` have no toggles)
-  - ~~Implemented: Gaussian, Gaussian+tail, Tikhonov models with energy-dependent resolution and Fano factor~~
+- [x] Physical branch spectra and universal factor in CSV export; `--separate-branches` normalization mode
-- [x] ~~Implement convolution routines~~
-  - ~~Convolve theoretical spectrum with detector response for comparison to data~~
-  - ~~Implemented: convolve() with tabulated response support~~
-- [ ] Monte Carlo simulation (GEANT4) — out of scope for this project but noted for future
-  - Full detector geometry simulation
-  - Energy loss in source, dead layers, absorber
-  - Response matrix for unfolding (as done in Paulsen et al. with EGSNRC)
 
-### A3. Data Processing & Analysis
+### C3. Recoil and Weak Magnetism
 
-- [ ] Data processing pipeline for 1-hour run spectra
+Theory documented in `docs/corrections/06-recoil.md`; implementation pending.
-  - Background subtraction
-  - Energy calibration (using known X-ray/gamma lines)
-  - Dead-time correction
-  - Pulse pile-up correction
-- [ ] Endpoint fitting and energy calibration
-  - Kurie plot analysis for endpoint determination
-  - Polynomial calibration using known spectral lines
-  - Linearity correction across energy range
-- [ ] Data quality assessment procedures
-  - Residual analysis (data vs model)
-  - χ²/ndf evaluation
-  - Consistency checks across multiple runs
-  - Statistical combination of long-exposure spectra
 
-### A4. Fitter for C(W) Extraction
+- [ ] Implement recoil correction (R_N, Q terms, weak magnetism) as a `SpectrumComponent`
 
-- [x] ~~Implement fitter routine to extract experimental C(W) from data~~
+### C4. Beta+ / Electron Capture Support
-  - ~~χ² minimization: theoretical spectrum (with all corrections) vs measured spectrum~~
-  - ~~Free parameters: C(W) shape parameters, endpoint energy, normalization, background~~
-  - ~~Covariance matrix and uncertainty propagation~~
-  - ~~Implemented: `CurveFitter` with `least_squares` optimization, `FitResult` with covariance, chi2, residuals~~
-- [x] ~~Parametrize C(W) in terms of g_V (and g_A)~~
-  - ~~Fit C(W) data to theoretical parametrization~~
-  - ~~Extract g_V^eff and g_A^eff from the fit~~
-  - ~~Compare with Paulsen et al. results: g_A^eff = 0.574(36), g_V^eff = 0.376(5)~~
-  - ~~Implemented: `CWExtractor` with Kurie plot analysis, parametrized fitting, g_V/g_A extraction~~
-- [ ] Systematic uncertainty analysis
-  - Vary correction implementations within uncertainties
-  - Test sensitivity to detector response model
-  - Background model dependence
 
-______________________________________________________________________
+- [ ] Fermi function sign change for positrons
+- [ ] Radiative corrections for β⁺ (Sirlin corrections differ for e⁻ vs e⁺)
+- [ ] Screening correction for positrons (different atomic interaction)
+- [ ] Exchange correction (negligible for β⁺ but check)
 
-## Track B: Package Usability Improvements
+### C5. Neutrino Spectrum Support
 
-### B1. Nuclear Data Integration
+- [ ] Convenience analyser methods for plotting neutrino spectra (convert electron spectrum, plot both scaled)
+- [ ] Neutrino radiative correction h(W̃, W0) per Sirlin 2011; conversion f_ν(W_ν) = f_e(W̃) · [1 + (α/2π)(h − g)]
 
-- [x] ~~paceENSDF integration for automated nuclear data retrieval~~
+### C6. Neutrino Mass Effects
-  - ~~`get_decay_info_from_paceENSDF(nuclide, decay_type)` — retrieves Q-value, half-life, spin/parity, branches, forbiddenness from ENSDF~~
-  - ~~`decay_info_to_config()` — converts DecayInfo to SpectrumConfig with branch support~~
-  - ~~`create_config_from_source("paceENSDF", nuclide="Tc99")` — one-liner config creation~~
-  - ~~`_parse_nuclide_symbol()` — parses "Tc99" → (Tc, 43, 99) with full Z lookup for Z=1..98~~
-  - ~~`_resolve_decay_index()` — finds correct decay index (ground state by default)~~
-  - ~~`_get_decay_mode_symbol()` — maps beta_minus→BM, beta_plus/ec→ECBP~~
-  - ~~FORBIDDENNESS_MAP — translates paceENSDF codes (0A, 1F, 2F, …) to transition_type~~
-  - ~~CLI `--nuclide Tc99` uses paceENSDF automatically~~
-  - ~~Branch intensities, log_ft, level energies, transition types all populated from ENSDF~~
-  - ~~Tested with Tc99 (2 branches, F2) and Co60 (multi-branch)~~
 
-### B2. Input Flexibility
+Implemented: `neutrino_mass_MeV` config field, modified phase space factor √(1 − m_ν²/(W₀−W)²), `--neutrino-mass` CLI option.
 
-- [x] ~~Generalize parameter inputs via custom input file (YAML/JSON)~~
+- [ ] Document which corrections need m_ν as an additional input parameter
-  - ~~Declare isotope, transition type, detector parameters~~
+- [ ] Study impact on radiative corrections (mass singularities)
-  - ~~Toggle corrections on/off per-component~~
-  - ~~Reproducible calculation configurations~~
-  - ~~Implemented: `load_json_input()`, `json_to_config()`, `DEFAULT_JSON_SCHEMA` with full detector param support, CLI `--input` flag~~
-- [x] ~~Retrieve parameters directly from ENSDF database~~
-  - ~~Auto-populate W0, Z, A, transition type from isotope name~~
-  - ~~Reduce manual configuration errors~~
-  - ~~Implemented: `get_decay_info_from_paceENSDF()` returns DecayInfo with Z_parent, Z_daughter, A_number, endpoint_MeV, transition_type, forbiddenness_code, half_life, branches; CLI `--nuclide` uses this automatically~~
 
-### B3. Multiple Branch Decays
+### C7. Automated Report Generation
 
-- [x] ~~Add support for multiple branch decays~~
+- [ ] Procedurally generated PDF report for a calculation:
-  - ~~Calculate total spectral shape weighted by branch intensities~~
+  - Parameter table (nuclide, decay data, enabled corrections, version, commit)
-  - ~~Handle decays with significant branching to excited states~~
-  - ~~Sum contributions from all branches with proper weighting~~
-  - ~~Implemented: `BranchConfig` dataclass, multi-branch `BetaSpectrum` with per-branch calculators~~
-  - ~~Branch data from paceENSDF: intensity, endpoint (Q-value - excitation energy), transition type~~
-  - ~~Intensity normalization to 100% across all branches~~
-  - ~~CSV export: total spectrum, per-branch spectra, per-branch components (PhaseSpace, Radiative), universal components (Fermi, Screening, etc.)~~
-  - ~~Plot: total spectrum + individual branches with legend (transition type, endpoint energy)~~
-  - ~~Debug plot: vertical layout with per-branch panels, universal components panel~~
-  - ~~Energy grid extends to max branch endpoint, per-branch spectra masked beyond their endpoint~~
-  - ~~Single-branch = trivial case of multi-branch (no separate mode)~~
-  - ~~Per-branch transition types extracted from ENSDF (not defaulting to 'A')~~
-  - ~~`--intensity-cutoff` CLI option to filter out negligible branches~~
-  - ~~Branch spectra plotted as raw (un-normalized) contributions so total = sum of branches~~
-
-### B4. Beta+ Decay Support
-
-- [ ] Modify corrections to support β⁺ decays
-  - Fermi function sign change for positrons
-  - Radiative corrections for β⁺ (Sirlin corrections differ for e⁻ vs e⁺)
-  - Screening correction for positrons (different atomic interaction)
-  - Exchange correction (negligible for β⁺ but check)
-
-### B5. Neutrino Spectrum Support
-
-- [ ] Add convenience analyser methods for plotting neutrino spectra
-  - Convert electron spectrum to neutrino spectrum
-  - Plot both on same figure with proper scaling
-- [ ] Adopt corrections that differ for neutrino spectrum
-  - Implement neutrino radiative correction h(W̃, W0) per Sirlin 2011
-  - Conversion formula: f_ν(W_ν) = f_e(W̃) · [1 + (α/2π)(h − g)]
-  - Neutrino-specific corrections (no Fermi function, different radiative terms)
-
-### B6. Neutrino Mass Effects
-
-- [ ] Implement option to produce spectra with non-zero neutrino mass
-  - Modify phase space: (W0 − W)² → (W0 − W)² · √(1 − m_ν²/(W0−W)²)
-  - Add kink feature near endpoint for spectral distortion
-  - Useful for neutrino mass search applications
-- [ ] Research and document implications of significant neutrino mass
-  - Which corrections need m_ν as input parameter?
-  - Impact on radiative corrections (mass singularities)
-  - Impact on endpoint fitting procedures
-
-### B7. Automated Report Generation
-
-- [ ] Implement extensive procedurally generated PDF report
-  - Comprehensive details of the calculation
   - Component plots (phase space, Fermi, each correction factor)
   - Total spectrum with all corrections applied
-  - Residual analysis, fit quality metrics
-  - Parameter table with uncertainties
   - References to theoretical sources
-- [ ] Extend report generation to fitters
-  - Fit results with covariance matrix
-  - Parameter correlations
-  - Confidence intervals
-  - Goodness-of-fit statistics
 
-### B8. CLI & Output Improvements
+### C8. CLI & Output Improvements
 
-- [x] Implement structured logging system
+- [ ] Auto-deduce `transition_type` from nuclear data (remove as explicit parameter where possible)
-  - Log to stdout with configurable verbosity levels (-v=INFO, -vv=DEBUG)
+- [ ] Auto-deduce `decay_type` from Z_parent vs Z_daughter difference
-  - Visualize workflow steps: data loading, parameter resolution, calculation progress
+- [x] Structured logging (`-v`, `-vv`, `-q`, `--log-file`)
-  - Log all used parameters: Z_parent, Z_daughter, A_number, endpoint, transition type, enabled corrections
+- [x] CSV metadata headers (ISO timestamp, nuclide, decay, calculation params, version, commit hash)
-  - Optional log file output with timestamped filename
+- [x] `--dry-run`, `--version`, single-letter aliases for every long option
-  - Integrate Python `logging` module with custom formatter
+- [x] Plots built from the exported CSV; commit hash + UTC timestamp stamps; normal/debug display modes
-- [x] Add metadata header to CSV output files
-  - Date and time of calculation (ISO 8601 format)
-  - Nuclide information: parent/daughter symbol, Z, A
-  - Decay/transition info: endpoint energy, transition type, forbiddenness
-  - Calculation parameters: energy step, enabled corrections, detector settings
-  - Software version and git commit hash (7 chars)
-  - Format: YAML-style comments at top of CSV file
-- [ ] Optimize CLI argument design and add sanity checks
-  - Auto-deduce `transition_type` from `decay_type` and nuclear data — remove as explicit CLI parameter
-  - Auto-deduce `decay_type` from Z_parent vs Z_daughter difference — remove as explicit CLI parameter
-  - Add sanity checks for custom input:
-    - `|Z_parent - Z_daughter|` must equal 1 (beta decay)
-    - For `beta_minus`: Z_daughter must be Z_parent + 1
-    - For `beta_plus`/`ec`: Z_daughter must be Z_parent - 1
-    - Warn if decay_type contradicts Z values (e.g., beta+ with Z_daughter > Z_parent)
-    - Validate endpoint_MeV > 0 and endpoint_MeV > level_energy_keV/1000
-    - Cross-check transition_type against ENSDF forbiddenness (if paceENSDF source)
-- [x] Add `--dry-run` option to validate input and display resolved parameters without calculation
-- [x] Add `--version` flag
-- [x] Add `-q/--quiet` flag to suppress terminal output
-- [x] Add `./output/` directory for debug verification artifacts (gitignored except `.gitkeep`)
-- [x] Add debug verification step to development workflow: `bs_pnpi -vv` with parameter consistency checks across all components, documented in DEVELOPMENT.md §4.5
-- [x] Add plot output with ID tracking (commit hash + UTC timestamp) and two display modes:
-  - Normal mode (default): single spectrum plot with nuclear data header
-  - Debug mode (-vv): 4-panel view with all correction factors and deviations
 
 ______________________________________________________________________
 
@@ -304,58 +121,46 @@ ______________________________________________________________________
 
 ### Additional Corrections
 
-Not implementing at this time. Additional corrections (weak magnetism, recoil kinematics, etc.) require a complex implementation with project-wide consequences. This is a far-future plan, irrelevant to the current ⁹⁹Tc analysis goal where the shape factor C(W) absorbs all unmodelled energy-dependent effects.
+Additional corrections beyond the implemented set require complex implementation with project-wide consequences; deferred as far-future work.
 
-### Nuclear Shape Factors C(Z,W)
+### Theoretical Shape Factors C(Z,W)
 
-Not implementing theoretical shape factor calculations. The entire point of this project is to **extract** C(W) from experimental data, not to compute it from nuclear theory (shell model, QRPA, etc.). Theoretical shape factor calculations require:
+Never computed here. Shell-model / QRPA transition densities and effective interactions belong to nuclear-structure codes; this repository treats C(W) as an input parameter of the spectrum model. The dedicated research into nuclear shape factors will be redone in separate projects.
-
-- Nuclear structure models (NUSHELLX, shell model codes)
-- One-body transition densities (OBTDs)
-- Coulomb displacement energy calculations
-- Multiple effective interactions
-
-These are handled by the nuclear physics community. Our role is to provide the analysis framework that extracts C(W) from data, then compare the extracted shape to theoretical predictions.
 
 ______________________________________________________________________
 
 ## Current Status
 
-**Version:** 0.3.1 → **In progress: 0.4.0 — Package restructuring**
+**Version:** v0.5.0 — theory-only scope reduction. Calculation logic unchanged from v0.4.1.
 
-### Completed (v0.3.x)
+### Completed (v0.3.x — theory core)
 
-- All theoretical corrections: phase space, Fermi function, finite size, screening, exchange, radiative (with delta_cut resummation)
+- All implemented theoretical corrections: phase space, Fermi function, finite size, screening, exchange, radiative (with delta_cut resummation)
-- Detector response module with analytical models (Gaussian, Gaussian+tail, Tikhonov), convolution API
-- χ² curve fitting framework (CurveFitter) with confidence intervals, profile likelihood, correlation analysis
-- C(W) shape factor extraction pipeline (CWExtractor) with Kurie plot analysis, parametrized fitting, g_V/g_A extraction
 - Multi-branch decay support (unified single/multi-branch)
-- CLI interface (`bs_pnpi`) with paceENSDF integration (`--nuclide`), structured logging (-v/-vv/-q), --dry-run, --version, --log-file
+- CLI (`bs_pnpi`) with paceENSDF integration, structured logging, `--dry-run`, `--version`, `--log-file`
 - CSV metadata headers with branch info
-- JSON input with full detector param support
+- paceENSDF `DecayInfo` retrieval (Z, A, endpoint, transition type, half-life, spin/parity, branches)
-- paceENSDF integration: `get_decay_info_from_paceENSDF()` returns DecayInfo with Z, A, endpoint, transition type, half-life, spin/parity, branches
-- Comprehensive test suite (262 tests, including 6 paceENSDF integration tests)
 - Notebook quality control with nbmake and auto-save plot hooks
-- Plot output: unified multi-branch approach, externalized headers, compact legends, consistent titles
+- Plot output: unified multi-branch approach, externalized headers, consistent titles
 
-### Completed (v0.4.0)
+### Completed (v0.4.0 — package split, later obsolete)
 
-- **Track B: Package restructuring** — separating into `beta_spectrum` (theory), `exp_data` (experimental data), `fitter` (analysis framework)
+- Interim split into `beta_spectrum` / `exp_data` / `fitter` packages
-  - [x] Phase 1: Create `exp_data` module (raw_data.py, calibration.py, fitters.py, corrections.py, spectrum.py) — 43 tests
+- Superseded by the v0.5.0 scope reduction: the analysis packages were removed entirely
-  - [x] Phase 2: Create `fitter` module (model.py, fit_engine.py, extractor.py, result.py) — 34 tests
+
-  - [x] Phase 3: Clean up `beta_spectrum` (remove cw_extractor.py, fitter.py, **init**.py cleanup) — 322 tests
+### Completed (v0.4.1 — normalization & CLI)
-  - [x] Phase 4: Package auto-discovered by setuptools, all imports updated, black formatting applied
+
-- **v0.4.0 is COMPLETE**
+- Core spectrum made unconditional (`phase_space × fermi`): core toggles removed, physical branch spectra in CSV export, plots built from the exported CSV
-  - 322 tests pass (262 original + 60 new)
+- Normalization audit fixes: lone surviving branch defines the spectrum, CLI options propagate through the JSON flow, positive-integral guard for both export modes, paceENSDF per-branch measured endpoints (Co60 fixed), single delegated paceENSDF config builder
-  - ruff + mypy clean on all 26 source files
+- CLI surface refresh: `--separate-branches` rename, single-letter aliases, dry-run cleanup, stale detector_* JSON schema keys removed
-  - black formatting applied to all new code
+
-  - `pyproject.toml` auto-discovers all 4 packages: `beta_spectrum`, `beta_spectrum.output`, `exp_data`, `fitter`
+### Completed (v0.5.0 — scope reduction)
-  - README updated with new architecture diagram and Quick Start examples
+
-  - Version bumped to 0.4.0
+- Removal of `exp_data/`, `fitter/`, raw detector data, analysis notebooks/scripts
+- Documentation rewrite to theory-only scope
+- 280 tests pass (theory-only suite), ruff + mypy clean
 
 ### Next Immediate Step
 
-- **Track A: ⁹⁹Tc spectrum-shape analysis** — start real data processing pipeline
+- C1 input sanity checks (decay/Z consistency, endpoint validation)
-  - Data processing pipeline for experimental runs
+- C3 recoil & weak magnetism correction implementation
-  - Endpoint fitting and energy calibration
-  - Systematic uncertainty analysis

beta_spectrum/__init__.py

@@ -52,4 +52,4 @@ __all__ = [
     "DEFAULT_JSON_SCHEMA",
 ]
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"

beta_spectrum/cli.py

@@ -65,12 +65,14 @@ def _build_parser() -> argparse.ArgumentParser:
     # Source selection flags (backward compatible, mutually exclusive)
     source_group = parser.add_mutually_exclusive_group(required=False)
     source_group.add_argument(
+        "-N",
         "--nuclide",
         type=str,
         help="Nuclide symbol for paceENSDF lookup (e.g. 'Tc99', 'Co60'). "
         "Retrieves decay parameters from the ENSDF database via paceENSDF.",
     )
     source_group.add_argument(
+        "-i",
         "--input",
         type=str,
         metavar="FILE",
@@ -79,20 +81,27 @@ def _build_parser() -> argparse.ArgumentParser:
 
     # Common parameters
     parser.add_argument(
+        "-s",
         "--e-step",
         type=float,
-        default=0.001,
+        default=None,
-        help="Energy step size in MeV (default: 0.001). All energies are in MeV throughout the toolkit.",
+        help="Energy step size in MeV (default: 0.001 for nuclide input; "
+        "for JSON input the file's e_step_MeV is used when the flag is "
+        "omitted). All energies are in MeV throughout the toolkit.",
     )
     parser.add_argument(
+        "-m",
         "--neutrino-mass",
         type=float,
-        default=0.0,
+        default=None,
-        help="Neutrino mass in MeV (default: 0.0). Set to non-zero value to include neutrino mass effects in phase space calculation.",
+        help="Neutrino mass in MeV (default: 0.0, or the JSON file's "
+        "neutrino_mass_MeV when omitted). Set to non-zero value to include "
+        "neutrino mass effects in phase space calculation.",
     )
 
     # Output
     parser.add_argument(
+        "-o",
         "--output",
         type=str,
         metavar="FILE",
@@ -101,6 +110,7 @@ def _build_parser() -> argparse.ArgumentParser:
 
     # Plotting
     parser.add_argument(
+        "-p",
         "--plot",
         type=str,
         metavar="FILE",
@@ -124,6 +134,7 @@ def _build_parser() -> argparse.ArgumentParser:
         help="Suppress all terminal output (only errors shown).",
     )
     log_group.add_argument(
+        "-L",
         "--log-file",
         type=str,
         metavar="PATH",
@@ -131,20 +142,23 @@ def _build_parser() -> argparse.ArgumentParser:
         "Log file is always opened in append mode at DEBUG level.",
     )
     log_group.add_argument(
+        "-d",
         "--dry-run",
         action="store_true",
         help="Validate input and display resolved configuration without computing spectrum.",
     )
     log_group.add_argument(
+        "-c",
         "--intensity-cutoff",
         type=float,
-        default=0.0,
+        default=None,
         metavar="FRAC",
         help="Minimum branch intensity fraction to include in the spectrum "
         "(default: 0.0 = include all branches). "
         "Branches below this threshold are excluded from the calculation and plots.",
     )
     log_group.add_argument(
+        "-V",
         "--csv-verbosity",
         type=str,
         default="full",
@@ -152,15 +166,20 @@ def _build_parser() -> argparse.ArgumentParser:
         help="CSV output verbosity: 'full' (all components) or 'concise' (total spectrum and normalized branch components only) (default: full)",
     )
     log_group.add_argument(
+        "-S",
         "--csv-separator",
         type=str,
-        default=",",
+        default=None,
         help="CSV column separator (default: ','). Use 'tab' for tab separation.",
     )
     log_group.add_argument(
-        "--normalize-to-one",
+        "-b",
+        "--separate-branches",
         action="store_true",
-        help="Normalize each branch to 1, ignoring intensity. In this case, total spectrum will not be produced (only energy and branch-wise spectra).",
+        default=None,
+        help="Emit separate branch spectra, each normalized to integrate to "
+        "1 (intensities ignored; no total_spectrum column). Default: total "
+        "spectrum with intensity-normalized branch columns.",
     )
 
     return parser
@@ -173,15 +192,10 @@ def _run(args: argparse.Namespace) -> None:
     from beta_spectrum.logging_utils import get_logger
     from beta_spectrum.nuclear_data import (
         create_config_from_source,
-        get_decay_info_from_paceENSDF,
         json_to_config,
         load_json_input,
     )
-    from beta_spectrum.spectrum import (
+    from beta_spectrum.spectrum import BetaSpectrum
-        BetaSpectrum,
-        BranchConfig,
-        SpectrumConfig,
-    )
     from beta_spectrum.output import BetaSpectrumAnalyzer
 
     # Determine logging level
@@ -230,66 +244,45 @@ def _run(args: argparse.Namespace) -> None:
     else:
         source_type = "paceENSDF"
 
-    # Build config
+    # Resolve optional CLI flags: None means "not provided". For paceENSDF
+    # they fall back to literal defaults; for JSON they let the file's own
+    # values through unless explicitly overridden.
+    e_step_MeV = 0.001 if args.e_step is None else float(args.e_step)
+    neutrino_mass_MeV = 0.0 if args.neutrino_mass is None else float(args.neutrino_mass)
+    intensity_cutoff = (
+        0.0 if args.intensity_cutoff is None else float(args.intensity_cutoff)
+    )
+    csv_separator = "," if args.csv_separator is None else args.csv_separator
+    separate_branches = bool(args.separate_branches)
+
+    # Build config — a single delegated path for every data source.
     config: SpectrumConfig
     if source_type == "paceENSDF":
         logger.info("Source: paceENSDF nuclide=%s", source_value)
-        decay_info = get_decay_info_from_paceENSDF(source_value, "beta_minus")
+        config = create_config_from_source(
-
+            "paceENSDF",
-        # Normalize branch intensities to sum to 1.0
+            nuclide=source_value,
-        if decay_info.branches:
+            e_step_MeV=e_step_MeV,
-            total_intensity = sum(b.intensity for b in decay_info.branches)
+            intensity_cutoff=intensity_cutoff,
-            if total_intensity > 0:
+            neutrino_mass_MeV=neutrino_mass_MeV,
-                branches = [
+            csv_separator=csv_separator,
-                    BranchConfig(
+            separate_branches=separate_branches,
-                        endpoint_MeV=(
+        )
-                            (decay_info.endpoint_MeV - b.level_energy_keV / 1000.0)
-                            if b.level_energy_keV > 0
-                            else decay_info.endpoint_MeV
-                        ),
-                        transition_type=b.transition_type,
-                        intensity=b.intensity / total_intensity,
-                    )
-                    for b in decay_info.branches
-                    if b.intensity / total_intensity >= args.intensity_cutoff
-                ]
-                config = SpectrumConfig(
-                    Z_parent=decay_info.Z_parent,
-                    Z_daughter=decay_info.Z_daughter,
-                    A_number=decay_info.A_number,
-                    endpoint_MeV=decay_info.endpoint_MeV,
-                    transition_type=decay_info.transition_type,
-                    e_step_MeV=args.e_step,
-                    neutrino_mass_MeV=args.neutrino_mass,
-                    branches=branches,
-                    intensity_cutoff=args.intensity_cutoff,
-                    csv_separator=args.csv_separator,
-                    normalize_to_one=args.normalize_to_one,
-                )
-            else:
-                config = create_config_from_source(
-                    "paceENSDF",
-                    nuclide=source_value,
-                    e_step_MeV=args.e_step,
-                    intensity_cutoff=args.intensity_cutoff,
-                    neutrino_mass_MeV=args.neutrino_mass,
-                    csv_separator=args.csv_separator,
-                    normalize_to_one=args.normalize_to_one,
-                )
-        else:
-            config = create_config_from_source(
-                "paceENSDF",
-                nuclide=source_value,
-                e_step_MeV=args.e_step,
-                intensity_cutoff=args.intensity_cutoff,
-                neutrino_mass_MeV=args.neutrino_mass,
-                csv_separator=args.csv_separator,
-                normalize_to_one=args.normalize_to_one,
-            )
     else:
         logger.info("Source: JSON file=%s", source_value)
         data = load_json_input(source_value)
         config = json_to_config(data)
+        # CLI flags override the JSON file values only when explicitly
+        # provided; unset flags keep the file's own values.
+        if args.e_step is not None:
+            config.e_step_MeV = e_step_MeV
+        if args.neutrino_mass is not None:
+            config.neutrino_mass_MeV = neutrino_mass_MeV
+        if args.intensity_cutoff is not None:
+            config.intensity_cutoff = intensity_cutoff
+        if args.csv_separator is not None:
+            config.csv_separator = csv_separator
+        config.separate_branches = separate_branches
 
     # Dry run: display resolved config and exit
     if args.dry_run:
@@ -373,7 +366,6 @@ def _print_dry_run_output(config, source_type: str) -> None:
         f"Nuclide:    {_decay_notation(config.Z_parent, config.Z_daughter, config.A_number)}"
     )
     print(f"Endpoint:   {config.endpoint_MeV * 1000:.1f} keV")
-    print(f"Transition: {config.transition_type}")
     print(f"e_step:     {config.e_step_MeV:.4f} MeV")
     print(f"neutrino_mass_MeV: {config.neutrino_mass_MeV:.6f}")
     print(f"Corrections: {', '.join(enabled) if enabled else 'none'}")
@@ -393,8 +385,6 @@ def _print_dry_run_output(config, source_type: str) -> None:
     else:
         print("Mode: single-branch")
 
-    # Detector response is a Phase 4 feature — not yet implemented
-    print("Detector:   not configured (Phase 4)")
     print("========================================")
 
 
@@ -516,10 +506,16 @@ def _decay_notation(Z_parent: int, Z_daughter: int, A: int) -> str:
     return f"{_nuclide_symbol(Z_parent, A)} -> {_nuclide_symbol(Z_daughter, A)}"
 
 
-def main() -> None:
+def main(argv: list[str] | None = None) -> None:
-    """Main entry point for the CLI."""
+    """Main entry point for the CLI.
+
+    Parameters
+    ----------
+    argv : list[str], optional
+        Explicit argument vector (for tests/embedding); None reads sys.argv.
+    """
     parser = _build_parser()
-    args = parser.parse_args()
+    args = parser.parse_args(argv)
 
     try:
         _run(args)

beta_spectrum/nuclear_data.py

@@ -96,6 +96,10 @@ class BranchInfo:
         log(ft) value for this branch.
     transition_type : str
         Forbiddenness classification for this branch (A, F1, F1U, F2, ...).
+    endpoint_MeV : float
+        Measured beta endpoint energy of this transition in MeV (ENSDF
+        column 7). 0.0 means "not provided": consumers fall back to
+        base-endpoint minus level-energy subtraction.
     """
 
     level_index: int
@@ -103,6 +107,7 @@ class BranchInfo:
     intensity: float
     log_ft: Optional[float]
     transition_type: str = "A"
+    endpoint_MeV: float = 0.0
 
 
 def _parse_nuclide_symbol(symbol: str) -> Tuple[str, int, int]:
@@ -384,24 +389,19 @@ def get_decay_info_from_paceENSDF(
 
     # Extract Q-value from ground state branch (state[7] = endpoint energy in keV)
     # and half-life from halflife_data
-    endpoint_keV = 0.0
     half_life_str = "unknown"
 
+    # The spectrum endpoint is the maximum measured transition endpoint
+    # across all branches (ENSDF column 7, keV). Selecting the ground
+    # state branch or the first branch is wrong whenever those branches
+    # are absent or non-maximal (e.g. Co60, whose first listed branch
+    # endpoint is below higher-level transition endpoints).
+    endpoint_keV = 0.0
     if beta_data:
-        for k, v in beta_data.items():
+        for _k, v in beta_data.items():
             for state in v:
-                if state[0] == 0:  # ground state branch
+                if len(state) > 7 and state[7] is not None:
-                    endpoint_keV = float(state[7])
+                    endpoint_keV = max(endpoint_keV, float(state[7]))
-                    break
-            if endpoint_keV > 0:
-                break
-
-        # No ground state branch — use first available branch
-        if endpoint_keV == 0.0:
-            for k, v in beta_data.items():
-                if v and len(v) > 0:
-                    endpoint_keV = float(v[0][7])
-                    break
 
     if halflife_data:
         for k, v in halflife_data.items():
@@ -447,6 +447,11 @@ def get_decay_info_from_paceENSDF(
                 intensity=float(state[9]) / 100.0,
                 log_ft=float(state[11]) if state[11] is not None else None,
                 transition_type=branch_transition_type,
+                endpoint_MeV=(
+                    float(state[7]) / 1000.0
+                    if len(state) > 7 and state[7] is not None
+                    else 0.0
+                ),
             )
             branches.append(branch)
 
@@ -472,7 +477,7 @@ def decay_info_to_config(
     intensity_cutoff: float = 0.0,
     neutrino_mass_MeV: float = 0.0,
     csv_separator: str = ",",
-    normalize_to_one: bool = False,
+    separate_branches: bool = False,
 ) -> SpectrumConfig:
     """
     Convert DecayInfo to a SpectrumConfig.
@@ -489,20 +494,28 @@ def decay_info_to_config(
         Neutrino mass in MeV.
     csv_separator : str
         CSV column separator.
-    normalize_to_one : bool
+    separate_branches : bool
-        If True, normalize each branch to 1, ignoring intensity.
+        If True, emit separate branch spectra, each normalized to
+        integrate to 1 (intensity ignored; no total spectrum column).
 
     Returns
     -------
     SpectrumConfig
         Configuration ready for BetaSpectrum.from_config().
     """
-    # Convert BranchInfo -> BranchConfig for SpectrumConfig
+    # Convert BranchInfo -> BranchConfig for SpectrumConfig. Per-branch
+    # endpoints are the measured transition endpoint energies when
+    # available; the base-endpoint minus level-energy subtraction is only
+    # a legacy fallback for hand-built DecayInfo objects without them.
     branches: Optional[List[BranchConfig]] = None
     if info.branches:
         branches = [
             BranchConfig(
-                endpoint_MeV=info.endpoint_MeV - b.level_energy_keV / 1000.0,
+                endpoint_MeV=(
+                    b.endpoint_MeV
+                    if b.endpoint_MeV > 0.0
+                    else info.endpoint_MeV - b.level_energy_keV / 1000.0
+                ),
                 transition_type=b.transition_type,
                 intensity=b.intensity,
             )
@@ -523,7 +536,7 @@ def decay_info_to_config(
         branches=branches,
         intensity_cutoff=intensity_cutoff,
         csv_separator=csv_separator,
-        normalize_to_one=normalize_to_one,
+        separate_branches=separate_branches,
     )
 
 
@@ -542,14 +555,6 @@ DEFAULT_JSON_SCHEMA = {
     "transition_type": "F2",
     "e_step_MeV": 0.001,
     "neutrino_mass_MeV": 0.0,
-    "detector_model": "gaussian",
-    "detector_sigma_a_keV": 1.0,
-    "detector_sigma_b": 0.0,
-    "detector_tail_fraction": 0.0,
-    "detector_tau_keV": 5.0,
-    "detector_fano_factor": 0.12,
-    "detector_n_channels": 4096,
-    "detector_channel_energy_range": [0.0, 0.35],
 }
 
 
@@ -615,8 +620,13 @@ def load_json_input(filepath: str) -> Dict[str, Any]:
     if not path.exists():
         raise FileNotFoundError(f"Input file not found: {filepath}")
 
-    with open(path, "r") as f:
+    try:
-        data = json.load(f)
+        with open(path, "r", encoding="utf-8") as f:
+            data = json.load(f)
+    except OSError as exc:
+        raise FileNotFoundError(f"Input file not readable: {filepath}") from exc
+    except json.JSONDecodeError as exc:
+        raise ValueError(f"Invalid JSON in input file {filepath}: {exc}") from exc
 
     # Fill in defaults for missing optional fields
     for key, default in DEFAULT_JSON_SCHEMA.items():
@@ -699,7 +709,7 @@ def create_config_from_source(
         intensity_cutoff = kwargs.get("intensity_cutoff", 0.0)
         neutrino_mass = kwargs.get("neutrino_mass_MeV", 0.0)
         csv_separator = kwargs.get("csv_separator", ",")
-        normalize_to_one = kwargs.get("normalize_to_one", False)
+        separate_branches = kwargs.get("separate_branches", False)
         info = get_decay_info_from_paceENSDF(nuclide, decay_type, decay_index)
         return decay_info_to_config(
             info,
@@ -707,7 +717,7 @@ def create_config_from_source(
             intensity_cutoff=intensity_cutoff,
             neutrino_mass_MeV=neutrino_mass,
             csv_separator=csv_separator,
-            normalize_to_one=normalize_to_one,
+            separate_branches=separate_branches,
         )
     elif source == "json":
         if not json_path:

beta_spectrum/output/csv_export.py

@@ -1,7 +1,7 @@
 """
 CSV export module — CSV export functionality for BetaSpectrumAnalyzer.
 
-Column semantics (v0.4.0 onward):
+Column semantics (v0.4.1 onward):
 - The basic spectrum is ALWAYS core = phase_space x fermi; the Fermi function
   is a core spectrum component, never an optional correction. Higher-order
   corrections (finite size, charge distribution, screening, exchange,
@@ -12,14 +12,14 @@ Column semantics (v0.4.0 onward):
   (the total column itself is normalized to integrate to 1). In the legacy
   export branch columns contained only the per-branch phase-space x
   radiative product WITHOUT the Fermi function — physically wrong.
-- ``normalize_to_one`` mode: each branch column is normalized to
+- ``separate_branches`` mode: each branch column is normalized to
   integrate to 1 individually, intensity is ignored, no total column.
 """
 
 from __future__ import annotations
 
 from datetime import datetime, timezone
-from typing import TYPE_CHECKING, Dict, Optional
+from typing import TYPE_CHECKING, Dict
 
 import numpy as np
 import pandas as pd
@@ -62,7 +62,7 @@ class CSVEmitter:
         """
         components = analyzer.components
         config = analyzer.config
-        to_one = config.normalize_to_one
+        separate = config.separate_branches
         n_branches = analyzer._n_branches
 
         # Physical branch spectra: core(phase_space x fermi) x corrections.
@@ -127,9 +127,9 @@ class CSVEmitter:
         header_lines.append(f"# e_step: {config.e_step_MeV:.4f} MeV")
         header_lines.append(f"# n_points: {len(analyzer.energies_MeV)}")
 
-        if to_one:
+        if separate:
             header_lines.append(
-                "# branch normalization: to_one "
+                "# branch normalization: separate "
                 "(each branch integrates to 1, intensity ignored)"
             )
         else:
@@ -179,16 +179,17 @@ class CSVEmitter:
             "energy_MeV": analyzer.energies_MeV,
         }
 
-        integral: Optional[float] = None
+        # Positive-integral guard applies to BOTH normalization modes: a
-        if not to_one:
+        # degenerate spectrum must never be written (not even as zeros).
-            total_raw = analyzer.spectrum(analyzer.W)
+        total_raw = analyzer.spectrum(analyzer.W)
-            integral = float(np.trapezoid(total_raw, analyzer.energies_MeV))
+        integral = float(np.trapezoid(total_raw, analyzer.energies_MeV))
-            if integral <= 0.0:
+        if integral <= 0.0:
-                raise ValueError(
+            raise ValueError(
-                    "Total spectrum integral is non-positive: every branch "
+                "Total spectrum integral is non-positive: every branch "
-                    "is degenerate (check neutrino_mass vs branch endpoints "
+                "is degenerate (check neutrino_mass vs branch endpoints "
-                    "and intensity_cutoff)"
+                "and intensity_cutoff)"
-                )
+            )
+        if not separate:
             data["total_spectrum"] = total_raw / integral
 
         for i in range(n_branches):
@@ -198,27 +199,32 @@ class CSVEmitter:
             else:
                 col_name = f"branch_{key_i}_spectrum"
 
-            if to_one:
+            if separate:
                 area = float(np.trapezoid(physical[i], analyzer.energies_MeV))
                 if area > 0.0:
                     data[col_name] = physical[i] / area
                 else:
                     data[col_name] = np.zeros_like(physical[i])
             else:
-                assert integral is not None
                 intensity_i = analyzer._unified_branches[i].intensity
                 data[col_name] = physical[i] * intensity_i / integral
 
         if csv_verbosity == "full":
             # Per-branch component columns (factorized ingredients).
-            for i in range(n_branches):
+            # Only multi-branch mode carries per-branch factors: in single
-                for comp_name in ["PhaseSpace", "Radiative"]:
+            # mode the bare PhaseSpace/Radiative columns below already
-                    key = analyzer._get_component_key(i, comp_name)
+            # describe the single spectrum, and prefixed duplicates would
-                    if key in components:
+            # silently disagree with them once renamed.
-                        data[f"branch_{i + 1}_{comp_name}"] = components[key]
+            if analyzer._is_multi:
+                for i in range(n_branches):
+                    for comp_name in ["PhaseSpace", "Radiative"]:
+                        key = analyzer._get_component_key(i, comp_name)
+                        if key in components:
+                            data[f"branch_{i + 1}_{comp_name}"] = components[key]
 
             # Universal components (no prefix): Fermi plus universal
-            # higher-order corrections.
+            # higher-order corrections. In single mode the core factors
+            # (PhaseSpace, Radiative) also appear here unprefixed.
             for name, values in components.items():
                 if not name.startswith("branch_"):
                     data[name] = values

beta_spectrum/output/visualization.py

@@ -235,7 +235,6 @@ def _plot_spectra_view_from_df(
 ) -> Figure:
     """Plot total spectrum and per-branch spectra from CSV columns."""
     energies = df["energy_MeV"].to_numpy()
-    e_step_keV = (meta["e_step_MeV"] or 0.0) * 1000.0
 
     fig, ax = plt.subplots(figsize=(12, 7))
 
@@ -266,7 +265,7 @@ def _plot_spectra_view_from_df(
         )
 
     ax.set_xlabel(r"Electron kinetic energy $E$ [MeV]", fontsize=12)
-    ax.set_ylabel(f"Normalized Counts / {e_step_keV:.1f} keV", fontsize=12)
+    ax.set_ylabel(r"Normalized spectrum [MeV$^{-1}$]", fontsize=12)
     fig.suptitle(_spectrum_title(meta), fontsize=14, fontweight="bold")
     ax.set_yscale("log")
     ax.grid(True, alpha=0.3)
@@ -288,7 +287,6 @@ def _plot_debug_view_from_df(
 ) -> Figure:
     """Debug view (4 panels) built entirely from CSV columns."""
     energies = df["energy_MeV"].to_numpy()
-    e_step_keV = (meta["e_step_MeV"] or 0.0) * 1000.0
     active = _active_branches(meta)
 
     fig, axes = plt.subplots(4, 1, figsize=(12, 16), sharex=True)
@@ -318,7 +316,7 @@ def _plot_debug_view_from_df(
             label=f"Br. {b['index']} ({b['intensity'] * 100:.1f}%)",
         )
     ax.set_yscale("log")
-    ax.set_ylabel(f"Normalized Counts / {e_step_keV:.1f} keV", fontsize=10)
+    ax.set_ylabel(r"Normalized spectrum [MeV$^{-1}$]", fontsize=10)
     ax.set_title("Spectrum", fontsize=11)
     ax.grid(True, alpha=0.3)
     ax.legend(fontsize=8, loc="best", ncol=2)
@@ -331,6 +329,9 @@ def _plot_debug_view_from_df(
         ax.plot(energies, fermi_scaled, "r-", lw=1.5, label="Fermi", alpha=0.8)
     for color_i, b in enumerate(active):
         col = f"branch_{b['index']}_PhaseSpace"
+        if col not in df.columns:
+            # Single-branch CSVs carry the core factors unprefixed.
+            col = "PhaseSpace"
         if col not in df.columns:
             continue
         ps_vals = df[col].to_numpy()
@@ -374,6 +375,9 @@ def _plot_debug_view_from_df(
     ax = axes[3]
     for color_i, b in enumerate(active):
         col = f"branch_{b['index']}_Radiative"
+        if col not in df.columns:
+            # Single-branch CSVs carry the core factors unprefixed.
+            col = "Radiative"
         if col not in df.columns:
             continue
         ax.plot(

beta_spectrum/spectrum.py

@@ -57,9 +57,6 @@ class SpectrumConfig:
     """
     Configuration for beta spectrum calculation.
 
-    Supports declarative detector response specification:
-    to enable automatic detector smearing via convolve_with_detector().
-
     Supports multi-branch decay via the `branches` field. When branches are
     provided, the total spectrum is the intensity-weighted sum of individual
     branch spectra. Each branch has its own endpoint energy and transition type.
@@ -90,9 +87,10 @@ class SpectrumConfig:
 
     # CSV output options
     csv_separator: str = ","  # Default separator for CSV output
-    normalize_to_one: bool = (
+    separate_branches: bool = (
-        False  # If True, normalize each branch to 1, ignoring intensity
+        False  # If True: emit separate branch spectra, each normalized to
     )
+    # integrate to 1 (intensity ignored); no total spectrum column
 
 
 def _effective_single_fields(config: SpectrumConfig) -> Tuple[float, str]:

data/custom_input_example.json

@@ -5,14 +5,5 @@
     "A_number": 99,
     "endpoint_MeV": 0.294,
     "transition_type": "A",
-    "e_step_MeV": 0.001,
+    "e_step_MeV": 0.001
-    "use_detector_response": false,
-    "detector_model": "gaussian",
-    "detector_sigma_a_keV": 1.0,
-    "detector_sigma_b": 0.0,
-    "detector_tail_fraction": 0.0,
-    "detector_tau_keV": 5.0,
-    "detector_fano_factor": 0.12,
-    "detector_n_channels": 4096,
-    "detector_channel_energy_range": [0.0, 0.35]
 }