fix: resolve 4 fatal bugs — json_to_config, create_config_from_source, Am-241 constant, CLI positional args

beta_spectrum/cli.py

@@ -22,6 +22,7 @@ from __future__ import annotations
 
 import argparse
 import sys
+from pathlib import Path
 
 from beta_spectrum.logging_utils import LoggingConfig, setup_logging
 from beta_spectrum.spectrum import SpectrumConfig
@@ -52,8 +53,18 @@ def _build_parser() -> argparse.ArgumentParser:
         version=f"%(prog)s {__import__('beta_spectrum').__version__}",
     )
 
-    # Source selection (mutually exclusive)
+    # Source selection (positional or flag)
-    source_group = parser.add_mutually_exclusive_group(required=True)
+    parser.add_argument(
+        "source",
+        nargs="?",
+        default=None,
+        help="Nuclide symbol (e.g. 'Tc99') or JSON file path. "
+        "Can also use --nuclide <symbol> or --input <file>. "
+        "Auto-detected: .json extension → JSON input, otherwise → paceENSDF.",
+    )
+
+    # Source selection flags (backward compatible, mutually exclusive)
+    source_group = parser.add_mutually_exclusive_group(required=False)
     source_group.add_argument(
         "--nuclide",
         type=str,
@@ -171,12 +182,36 @@ def _run(args: argparse.Namespace) -> None:
     logger.info("bs_pnpi starting...")
     logger.debug("Verbosity: %s | Log file: %s", log_level, args.log_file or "none")
 
+    # Resolve source: positional arg takes precedence, then flags
+    source_value = args.source
+    if source_value is None and args.nuclide:
+        source_value = args.nuclide
+    elif source_value is None and args.input:
+        source_value = args.input
+    elif source_value is not None:
+        # Auto-detect from positional argument
+        if source_value.endswith(".json") or Path(source_value).exists():
+            source_value = source_value
+        # else: keep as-is (nuclide symbol)
+
+    if source_value is None:
+        logger.error(
+            "Required: specify nuclide or JSON file "
+            "(e.g., 'bs_pnpi Tc99' or 'bs_pnpi --nuclide Tc99')"
+        )
+        sys.exit(1)
+
+    # Determine source type
+    if source_value.endswith(".json"):
+        source_type = "json"
+    else:
+        source_type = "paceENSDF"
+
     # Build config
-    source_type: str
     config: SpectrumConfig
-    if args.nuclide:
+    if source_type == "paceENSDF":
-        logger.info("Source: paceENSDF nuclide=%s", args.nuclide)
+        logger.info("Source: paceENSDF nuclide=%s", source_value)
-        decay_info = get_decay_info_from_paceENSDF(args.nuclide, "beta_minus")
+        decay_info = get_decay_info_from_paceENSDF(source_value, "beta_minus")
 
         # Normalize branch intensities to sum to 1.0
         if decay_info.branches:
@@ -208,24 +243,21 @@ def _run(args: argparse.Namespace) -> None:
             else:
                 config = create_config_from_source(
                     "paceENSDF",
-                    nuclide=args.nuclide,
+                    nuclide=source_value,
                     e_step_MeV=args.e_step,
+                    intensity_cutoff=args.intensity_cutoff,
                 )
         else:
             config = create_config_from_source(
                 "paceENSDF",
-                nuclide=args.nuclide,
+                nuclide=source_value,
                 e_step_MeV=args.e_step,
+                intensity_cutoff=args.intensity_cutoff,
             )
-        source_type = "paceENSDF"
-    elif args.input:
-        logger.info("Source: JSON file=%s", args.input)
-        data = load_json_input(args.input)
-        config = json_to_config(data)
-        source_type = "json"
     else:
-        logger.error("No source specified (use --nuclide or --input)")
+        logger.info("Source: JSON file=%s", source_value)
-        sys.exit(1)
+        data = load_json_input(source_value)
+        config = json_to_config(data)
 
     # Dry run: display resolved config and exit
     if args.dry_run:
@@ -318,13 +350,8 @@ def _print_dry_run_output(config, source_type: str) -> None:
     else:
         print("Mode: single-branch")
 
-    if config.use_detector_response:
+    # Detector response is a Phase 4 feature — not yet implemented
-        print(
+    print("Detector:   not configured (Phase 4)")
-            f"Detector:   {config.detector_model} (sigma={config.detector_sigma_a_keV} keV, "
-            f"tail={config.detector_tail_fraction})"
-        )
-    else:
-        print("Detector:   disabled")
     print("========================================")
 
 

beta_spectrum/nuclear_data.py

@@ -272,7 +272,7 @@ def _get_decay_mode_symbol(
     }
     if decay_type not in mapping:
         raise ValueError(
-            f"Unknown decay type '{decay_type}'. " f"Supported: {list(mapping.keys())}"
+            f"Unknown decay type '{decay_type}'. Supported: {list(mapping.keys())}"
         )
     return mapping[decay_type]
 
@@ -638,9 +638,6 @@ def json_to_config(data: Dict[str, Any]) -> SpectrumConfig:
         endpoint_MeV=float(data["endpoint_MeV"]),
         transition_type=str(data.get("transition_type", "A")),
         e_step_MeV=float(data.get("e_step_MeV", 0.001)),
-        detector_model=str(data.get("detector_model", "gaussian")),
-        detector_channel_energy_range=tuple(
-        ),
     )
 
 
@@ -685,8 +682,12 @@ def create_config_from_source(
         decay_type = kwargs.get("decay_type", "beta_minus")
         decay_index = kwargs.get("decay_index", None)
         e_step = kwargs.get("e_step_MeV", 0.001)
+        intensity_cutoff = kwargs.get("intensity_cutoff", 0.0)
         info = get_decay_info_from_paceENSDF(nuclide, decay_type, decay_index)
         return decay_info_to_config(
+            info,
+            e_step_MeV=e_step,
+            intensity_cutoff=intensity_cutoff,
         )
     elif source == "json":
         if not json_path:

exp_data/calibration.py

@@ -312,7 +312,7 @@ class EnergyCalibrator:
         filepath : str or Path
             Path to the Am-241 binary calibration file (CAM1.DAT or CAM2.DAT).
         known_energies : list of float, optional
-            Known Am-241 line energies in keV. Defaults to [13.8, 17.8, 26.3].
+            Known Am-241 line energies in keV. Defaults to [13.9, 17.8, 26.3, 59.54].
         n_channels : int
             Number of channels (default 4096).
 
@@ -352,8 +352,11 @@ class EnergyCalibrator:
         peak_counts = counts_search[peaks]
 
         # Known Am-241 gamma lines (keV)
+        # Am-241 decays to Np-237; Np K X-rays at 13.9 keV (Kα), 17.8 keV (Kβ),
+        # 20.8 keV (L-series); Np gamma at 26.3 keV; Np/Am gamma at 59.54 keV.
+        # Source: LNHb Table de Radionucléides, IAEA nuclear data.
         if known_energies is None:
-            known_energies = [13.0, 17.8, 26.3, 59.54]
+            known_energies = [13.9, 17.8, 26.3, 59.54]
 
         # Match peaks to known energies using a simpler, more robust
         # approach: find the two strongest peaks that span the largest

exp_data/raw_reader.py

@@ -151,7 +151,7 @@ def calibrate_from_am241(
         Path to the Am-241 binary file (CAM1.DAT or CAM2.DAT).
     known_peaks
         Mapping of energy_keV -> expected channel. If None, auto-detects
-        Am-241 peaks at 13.8, 17.8, 26.3 keV.
+        Am-241 peaks at 13.9, 17.8, 26.3 keV.
     n_channels
         Number of channels.
 
@@ -175,7 +175,7 @@ def calibrate_from_am241(
     _peak_heights = props["peak_heights"]  # noqa: F841
 
     # Known Am-241 gamma lines (keV)
-    am241_lines = {13.8: None, 17.8: None, 26.3: None}
+    am241_lines = {13.9: None, 17.8: None, 26.3: None}
     if known_peaks:
         am241_lines = known_peaks
     else:
@@ -220,7 +220,7 @@ def read_am241_calibration(
     """
     filepath = Path(filepath)
 
-    # Am-241 known peaks (keV): 13.8, 17.8, 26.3, 59.54
+    # Am-241 known peaks (keV): 13.9, 17.8, 26.3, 59.54
     # The spectrum typically has a few prominent peaks
     with open(filepath, "rb") as f:
         _header = f.read(128)
@@ -232,7 +232,7 @@ def read_am241_calibration(
     metadata = {
         "source": "Am241",
         "calibration_type": "energy",
-        "known_peaks_keV": [13.8, 17.8, 26.3, 59.54],
+        "known_peaks_keV": [13.9, 17.8, 26.3, 59.54],
     }
 
     return ExpSpectrum(

scripts/analyze_raw.py

@@ -29,7 +29,7 @@ from exp_data.raw_reader import (
 )
 
 # Energy calibration from Am-241 source: E = offset + gain * channel
-# Determined automatically from known Am-241 gamma lines (13.8, 17.8, 26.3 keV)
+# Determined automatically from known Am-241 gamma lines (13.9, 17.8, 26.3 keV)
 CALIBRATION_FILE = "data/raw/CAM1.DAT"
 _calib_offset, _calib_gain = calibrate_from_am241(CALIBRATION_FILE)
 ENERGY_OFFSET = _calib_offset
@@ -234,7 +234,9 @@ def main():
     # Save results
     results_file = output_dir / "rate_analysis.csv"
     with open(results_file, "w") as f:
-        f.write("run,total_counts,low_energy_counts,high_energy_counts,low_fraction,endpoint_keV\n")
+        f.write(
+            "run,total_counts,low_energy_counts,high_energy_counts,low_fraction,endpoint_keV\n"
+        )
         for i in range(len(run_ids)):
             f.write(
                 f"{run_ids[i]},{total_rates[i]:.0f},{low_rates[i]:.0f},"
@@ -265,7 +267,9 @@ def main():
         # Endpoint
         axes[1, 0].plot(run_ids, endpoints, "r-", lw=1.5)
         axes[1, 0].axhline(
-            TC99_ENDPOINT, color="gray", ls="--",
+            TC99_ENDPOINT,
+            color="gray",
+            ls="--",
             label=f"Tc-99 Q ≈ {TC99_ENDPOINT} keV",
         )
         axes[1, 0].set_xlabel("Run number")

tests/quality/test_nuclear_data.py

@@ -202,7 +202,8 @@ class TestDecayInfoToConfig:
         assert abs(config.endpoint_MeV - 0.294) < 1e-6
         assert config.transition_type == "A"
 
-    def test_with_detector_response(self):
+    def test_with_e_step_and_cutoff(self):
+        """Verify e_step_MeV and intensity_cutoff kwargs are passed through."""
         info = DecayInfo(
             parent_symbol="Co60",
             Z_parent=27,
@@ -215,13 +216,30 @@ class TestDecayInfoToConfig:
             parent_J=0.0,
             parent_pi=1,
             half_life="y",
-            branches=[],
+            branches=[
+                BranchInfo(
+                    level_index=0,
+                    level_energy_keV=0.0,
+                    intensity=0.5,
+                    log_ft=5.0,
+                    transition_type="A",
+                ),
+                BranchInfo(
+                    level_index=1,
+                    level_energy_keV=10.0,
+                    intensity=0.3,
+                    log_ft=6.0,
+                    transition_type="A",
+                ),
+            ],
         )
-        config = decay_info_to_config(
+        config = decay_info_to_config(info, e_step_MeV=0.005, intensity_cutoff=0.4)
-            info, use_detector_response=True, e_step_MeV=0.005
-        )
-        assert config.use_detector_response is True
         assert config.e_step_MeV == 0.005
+        assert config.intensity_cutoff == 0.4
+        # Only branch with intensity >= 0.4 should be included
+        assert config.branches is not None
+        assert len(config.branches) == 1
+        assert config.branches[0].intensity == 0.5
 
 
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