fix: decay_info_to_config() now passes branches to SpectrumConfig; update docs for paceENSDF completion

- Fixed bug: decay_info_to_config() was dropping branches, causing
  create_config_from_source('paceENSDF') to return single-branch config
- Added BranchConfig import to nuclear_data.py
- Marked B1 (paceENSDF integration) as complete in TODO.md
- Updated README.md with paceENSDF details in Implementation Status
- Updated TODO.md Current Status with v0.3.1 notes

README.md

@@ -151,4 +151,5 @@ For a complete list of implemented and planned features, see [TODO.md](TODO.md).
 - **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, C(W) extraction pipeline, Kurie plot analysis
-- **CLI**: `bs_pnpi` with paceENSDF integration, structured logging, CSV metadata headers, branch info in dry-run and CSV output
+- **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

@@ -82,10 +82,17 @@ ______________________________________________________________________
 
 ### B1. Nuclear Data Integration
 
-- [ ] Add usage of `paceENSDF` package to retrieve nuclear data for decays
+- [x] ~~paceENSDF integration for automated nuclear data retrieval~~
-  - Q-values, half-lives, branch intensities, decay schemes
+  - ~~`get_decay_info_from_paceENSDF(nuclide, decay_type)` — retrieves Q-value, half-life, spin/parity, branches, forbiddenness from ENSDF~~
-  - Automated setup of W0, Z, A parameters from ENSDF
+  - ~~`decay_info_to_config()` — converts DecayInfo to SpectrumConfig with branch support~~
-  - Support for multiple isotopes without manual input
+  - ~~`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
 
@@ -218,9 +225,11 @@ ______________________________________________________________________
 
 ## Current Status
 
-**Version:** 0.3.1\
+**Version:** 0.3.1\n
-**Implemented:** Phase space, Fermi function, finite size, screening, exchange, radiative corrections (with delta_cut resummation). Detector response module with analytical models (Gaussian, Gaussian+tail, Tikhonov), convolution API, declarative config integration. χ² curve fitting framework (CurveFitter) with confidence intervals, profile likelihood, and correlation analysis. C(W) shape factor extraction pipeline (CWExtractor) with Kurie plot analysis, parametrized fitting, and g_V/g_A extraction. Multi-branch decay support with per-branch calculators and intensity-weighted sum. CLI interface (`bs_pnpi`) with paceENSDF integration, structured logging (-v/-vv/-q), --dry-run, --version, --log-file. CSV metadata headers with branch info. JSON input with full detector param support. Comprehensive test suite (226 tests). Notebook quality control with nbmake and auto-save plot hooks.
+**Implemented:** Phase space, Fermi function, finite size, screening, exchange, radiative corrections (with delta_cut resummation). Detector response module with analytical models (Gaussian, Gaussian+tail, Tikhonov), convolution API, declarative config integration. χ² curve fitting framework (CurveFitter) with confidence intervals, profile likelihood, and correlation analysis. C(W) shape factor extraction pipeline (CWExtractor) with Kurie plot analysis, parametrized fitting, and g_V/g_A extraction. Multi-branch decay support with per-branch calculators and intensity-weighted sum. CLI interface (`bs_pnpi`) with paceENSDF integration (`--nuclide`), structured logging (-v/-vv/-q), --dry-run, --version, --log-file. CSV metadata headers with branch info. JSON input with full detector param support. paceENSDF integration: `get_decay_info_from_paceENSDF()` returns DecayInfo with Z, A, endpoint, transition type (from forbiddenness), half-life, spin/parity, and full branch list; `decay_info_to_config()` converts to SpectrumConfig with branches; `create_config_from_source("paceENSDF", nuclide="Tc99")` one-liner; `_parse_nuclide_symbol()` for Z=1..98; FORBIDDENNESS_MAP; CLI `--nuclide` uses it automatically. Comprehensive test suite (262 tests, including 6 paceENSDF integration tests). Notebook quality control with nbmake and auto-save plot hooks.
 
-**Completed:** A2 — detector response function and convolution routines. A4 — fitter routine and C(W) extraction pipeline. B2 — input flexibility (JSON input, ENSDF auto-population). B3 — multi-branch decay support (BranchConfig, per-branch calculators, intensity weighting, branch-aware CSV export and plotting, per-branch transition types from ENSDF, `--intensity-cutoff` CLI option, raw-value plotting where total = sum of branches). B8 — CLI & output improvements (logging, CSV headers, dry-run, version). B8.2 — CLI refinement: removed --mode, --transition-type, --decay-index flags; clarified units (MeV everywhere); enhanced logging (INFO shows components, DEBUG shows internals); CSV headers use element notation (Tc99 -> Ru99). B8.3 — debug verification framework: `./output/` directory for artifacts, development workflow step 4.5 with `-vv` parameter consistency checks across all components. B8.4 — plot output with ID tracking (commit hash + UTC timestamp) and two display modes (normal spectrum plot with nuclear data header; debug 4-panel view with all corrections).
+**Completed:** A2 — detector response function and convolution routines. A4 — fitter routine and C(W) extraction pipeline. B1 — paceENSDF integration (full nuclear data retrieval: Q-value, half-life, spin/parity, branches, forbiddenness, log_ft; CLI `--nuclide` auto-lookup). B2 — input flexibility (JSON input, ENSDF auto-population). B3 — multi-branch decay support (BranchConfig, per-branch calculators, intensity weighting, branch-aware CSV export and plotting, per-branch transition types from ENSDF, `--intensity-cutoff` CLI option, raw-value plotting where total = sum of branches). B8 — CLI & output improvements (logging, CSV headers, dry-run, version). B8.2 — CLI refinement: removed --mode, --transition-type, --decay-index flags; clarified units (MeV everywhere); enhanced logging (INFO shows components, DEBUG shows internals); CSV headers use element notation (Tc99 -> Ru99). B8.3 — debug verification framework: `./output/` directory for artifacts, development workflow step 4.5 with `-vv` parameter consistency checks across all components. B8.4 — plot output with ID tracking (commit hash + UTC timestamp) and two display modes (normal spectrum plot with nuclear data header; debug 4-panel view with all corrections).
+
+**Bug fix (v0.3.1):** Fixed `decay_info_to_config()` to pass branches to `SpectrumConfig` (was dropping them, causing `create_config_from_source("paceENSDF")` to return single-branch config). Added `BranchConfig` import to `nuclear_data.py`.
 
 **Next immediate step:** A3 — data processing pipeline for experimental spectra (background subtraction, energy calibration, dead-time correction, pulse pile-up correction).

beta_spectrum/nuclear_data.py

@@ -13,7 +13,7 @@ from dataclasses import dataclass
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple
 
-from beta_spectrum.spectrum import SpectrumConfig
+from beta_spectrum.spectrum import BranchConfig, SpectrumConfig
 
 # Mapping from paceENSDF forbiddenness codes to our transition_type
 FORBIDDENNESS_MAP: Dict[str, str] = {
@@ -470,6 +470,7 @@ def decay_info_to_config(
     info: DecayInfo,
     e_step_MeV: float = 0.001,
     use_detector_response: bool = False,
+    intensity_cutoff: float = 0.0,
 ) -> SpectrumConfig:
     """
     Convert DecayInfo to a SpectrumConfig.
@@ -482,12 +483,29 @@ def decay_info_to_config(
         Energy step size in MeV.
     use_detector_response : bool
         Whether to enable detector response convolution.
+    intensity_cutoff : float
+        Minimum branch intensity fraction to include.
 
     Returns
     -------
     SpectrumConfig
         Configuration ready for BetaSpectrum.from_config().
     """
+    # Convert BranchInfo -> BranchConfig for SpectrumConfig
+    branches: Optional[List[BranchConfig]] = None
+    if info.branches:
+        branches = [
+            BranchConfig(
+                endpoint_MeV=info.endpoint_MeV - b.level_energy_keV / 1000.0,
+                transition_type=b.transition_type,
+                intensity=b.intensity,
+            )
+            for b in info.branches
+            if b.intensity >= intensity_cutoff
+        ]
+        if not branches:
+            branches = None
+
     return SpectrumConfig(
         Z_parent=info.Z_parent,
         Z_daughter=info.Z_daughter,
@@ -496,6 +514,8 @@ def decay_info_to_config(
         transition_type=info.transition_type,
         e_step_MeV=e_step_MeV,
         use_detector_response=use_detector_response,
+        branches=branches,
+        intensity_cutoff=intensity_cutoff,
     )