fix(scripts): list min/max calls, typed mains, drop unused header reads

notebooks/01-beta-spectrum-calculator.ipynb

@@ -94,8 +94,6 @@
     "    endpoint_MeV=0.294,\n",
     "    transition_type=\"F2\",\n",
     "    e_step_MeV=0.001,\n",
-    "    use_phase_space=True,\n",
-    "    use_fermi=True,\n",
     "    use_screening=True,\n",
     "    use_finite_size=True,\n",
     "    use_charge_dist=True,\n",
@@ -410,13 +408,16 @@
     }
    ],
    "source": [
+    "multi_analyzer = BetaSpectrumAnalyzer(multi_spectrum, multi_config)\n",
+    "\n",
     "fig, ax = plt.subplots(figsize=(12, 6))\n",
     "ax.plot(T_keV, total, \"k-\", linewidth=2.5, label=\"Total spectrum\")\n",
     "\n",
-    "branch_spectra = multi_spectrum.get_branch_normalized_spectra(W)\n",
-    "for i, bs in enumerate(branch_spectra):\n",
-    "    ax.plot(T_keV, bs, alpha=0.6, linewidth=1.5,\n",
-    "            label=\"Branch {} (E0={:.0f} keV)\".format(i+1, branches[i].endpoint_MeV*1000))\n",
+    "# Physical branch spectra: core (phase_space x fermi) x all enabled corrections\n",
+    "for i, b in enumerate(branches):\n",
+    "    physical = multi_analyzer.physical_branch_spectrum(i)\n",
+    "    ax.plot(T_keV, physical, alpha=0.6, linewidth=1.5,\n",
+    "            label=\"Branch {} (E0={:.0f} keV)\".format(i+1, b.endpoint_MeV*1000))\n",
     "\n",
     "for i, b in enumerate(branches):\n",
     "    br_end_keV = W_to_T(T_to_W(b.endpoint_MeV))\n",
@@ -430,7 +431,7 @@
     "ax.set_xlim(0, W0_max_keV)\n",
     "ax.grid(True, alpha=0.3)\n",
     "plt.tight_layout()\n",
-    "plt.show()"
+    "plt.show()\n"
    ]
   },
   {
@@ -541,8 +542,8 @@
     }
    ],
    "source": [
-    "analyzer = BetaSpectrumAnalyzer(multi_spectrum, multi_config)\n",
-    "analyzer.plot_analysis(show_components=True)"
+    "analyzer = multi_analyzer\n",
+    "analyzer.plot_analysis(show_components=True)\n"
    ]
   },
   {

notebooks/exp_calibration.ipynb

@@ -81,11 +81,7 @@
     "\n",
     "# Detect header size from file\n",
     "def detect_header_size(filepath):\n",
-    "    \"\"\"Detect MCA header size by checking for binary pattern.\"\"\"\n",
-    "    with open(filepath, 'rb') as f:\n",
-    "        header = f.read(128)\n",
-    "    # Check if first 32 bytes look like a header (small ints)\n",
-    "    # and bytes 32-128 also look like header\n",
+    "    \"\"\"Detect MCA header size from the file size.\"\"\"\n",
     "    # Simple heuristic: if file is exactly 32 + 4096*4 = 16412, header=32\n",
     "    # If file is 128 + 4096*4 = 16512, header=128\n",
     "    import os\n",
@@ -97,11 +93,7 @@
     "    elif size == expected_128:\n",
     "        return 128\n",
     "    else:\n",
-    "        # Try to detect by checking if byte 32 looks like an int\n",
-    "        with open(filepath, 'rb') as f:\n",
-    "            f.seek(32)\n",
-    "            test = f.read(4)\n",
-    "            return 32  # default\n",
+    "        return 32  # default\n",
     "\n",
     "# --- Raw run spectrum ---\n",
     "header_size = detect_header_size(RAW_FILE)\n",

scripts/analyze_raw.py

@@ -17,6 +17,7 @@ from __future__ import annotations
 
 import sys
 from pathlib import Path
+from typing import cast
 
 import numpy as np
 from scipy.stats import linregress
@@ -101,7 +102,10 @@ def estimate_endpoint_from_counts(
 
     # Linear fit: K = a + b * E, endpoint = -a/b
     try:
-        slope, intercept, r_val, _, _ = linregress(E_sel, K)[:5]
+        lin = cast("tuple[float, float, float, float, float]", linregress(E_sel, K))
+        slope = lin[0]
+        intercept = lin[1]
+        r_val = lin[2]
         if slope < 0 and abs(r_val) > 0.3:
             endpoint = -intercept / slope
             # Clamp to reasonable range (Q ± 100 keV)
@@ -129,7 +133,7 @@ def compute_regional_rates(counts: np.ndarray, energies_keV: np.ndarray) -> dict
     }
 
 
-def main():
+def main() -> None:
     """Main analysis pipeline."""
     data_dir = Path(__file__).parent.parent / "data" / "raw"
     output_dir = Path(__file__).parent.parent / "output"
@@ -168,8 +172,6 @@ def main():
     print("\nSubtracting consecutive runs...")
     individual_runs = []
     for i in range(1, len(cumulative_specs)):
-        parent_a = cumulative_specs[i].run_id
-        parent_b = cumulative_specs[i - 1].run_id
         diff = subtract_spectra(
             cumulative_a=cumulative_specs[i],
             cumulative_b=cumulative_specs[i - 1],
@@ -215,33 +217,52 @@ def main():
     print(f"\n{'=' * 60}")
     print(f"Analysis of {len(run_ids)} individual Tc-99 runs")
     print(f"{'=' * 60}")
-    print(f"Run range: {run_ids.min()} - {run_ids.max()}")
-    print(f"Total counts: {total_rates.min():.0f} - {total_rates.max():.0f}")
-    print(f"Low-energy fraction: {low_fractions.min():.3f} - {low_fractions.max():.3f}")
-    print(f"Endpoint estimate: {endpoints.min():.1f} - {endpoints.max():.1f} keV")
+    print(f"Run range: {min(run_ids)} - {max(run_ids)}")
+    print(f"Total counts: {min(total_rates):.0f} - {max(total_rates):.0f}")
+    print(
+        f"Low-energy fraction: {min(low_fractions):.3f} " f"- {max(low_fractions):.3f}"
+    )
+    print(f"Endpoint estimate: {min(endpoints):.1f} - {max(endpoints):.1f} keV")
 
     # Endpoint drift
     if len(run_ids) > 10:
-        slope, intercept, r_val, _, _ = linregress(run_ids, endpoints)
-        print(f"\nEndpoint drift: {slope:.3f} keV/run (R²={r_val**2:.4f})")
-        print(f"  Start (run 1): {intercept + slope * run_ids[0]:.1f} keV")
-        print(f"  End (run {run_ids[-1]}): {intercept + slope * run_ids[-1]:.1f} keV")
+        lin_e = cast(
+            "tuple[float, float, float, float, float]",
+            linregress(run_ids, endpoints),
+        )
+        slope_e = lin_e[0]
+        intercept_e = lin_e[1]
+        r_e = lin_e[2]
+        print(f"\nEndpoint drift: {slope_e:.3f} keV/run (R²={r_e ** 2:.4f})")
+        print(f"  Start (run 1): {intercept_e + slope_e * run_ids[0]:.1f} keV")
+        print(
+            f"  End (run {run_ids[-1]}): {intercept_e + slope_e * run_ids[-1]:.1f} keV"
+        )
 
     # Rate drift
-    slope, intercept, r_val, _, _ = linregress(run_ids, total_rates)
-    print(f"\nTotal count rate drift: {slope:.0f} counts/run (R²={r_val**2:.4f})")
+    lin_r = cast(
+        "tuple[float, float, float, float, float]", linregress(run_ids, total_rates)
+    )
+    slope_r = lin_r[0]
+    r_r = lin_r[2]
+    print(f"\nTotal count rate drift: {slope_r:.0f} counts/run (R²={r_r ** 2:.4f})")
 
     # 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"
-        )
-        for i in range(len(run_ids)):
+    try:
+        with open(results_file, "w") as f:
             f.write(
-                f"{run_ids[i]},{total_rates[i]:.0f},{low_rates[i]:.0f},"
-                f"{high_rates[i]:.0f},{low_fractions[i]:.4f},{endpoints[i]:.1f}\n"
+                "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},"
+                    f"{high_rates[i]:.0f},{low_fractions[i]:.4f},{endpoints[i]:.1f}\n"
+                )
+    except OSError as exc:
+        print(f"Cannot write {results_file}: {exc}")
+        raise SystemExit(1) from exc
     print(f"\nResults saved to {results_file}")
 
     # Plot

scripts/docs_check.py

@@ -471,7 +471,7 @@ CHECKS = [
 ]
 
 
-def main():
+def main() -> int:
     parser = argparse.ArgumentParser(description="Check documentation consistency")
     parser.add_argument(
         "--strict", action="store_true", help="Treat warnings as errors (exit 1)"