feat(cli): separate-branches rename, short aliases, clean dry-run

- --normalize-to-one renamed to --separate-branches (no alias; the
  name now describes the output choice: total spectrum with
  intensity-normalized branches vs separate branches, each
  normalized to unit area with intensities left to the data user).
  SpectrumConfig.normalize_to_one -> separate_branches, CSV header
  word to_one -> separate.
- every long option gains a single-letter alias: -N -i -s -m -o -p
  -L -d -c -V -S -b (only -v/-q existed before)
- dry-run drops the top-level Transition: line — the per-branch
  list below already reports each branch's transition type
- version bumped to 0.4.1 (pyproject, __version__, CSV semantics
  docstring, TODO roadmap entry)

README.md

@@ -132,7 +132,7 @@ 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
 
@@ -194,5 +194,5 @@ For a complete list of implemented and planned features, see [TODO.md](TODO.md).
 - **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
 - **Experimental data**: ExpSpectrum container, energy calibration, peak fitting, dead-time/pile-up correction
-- **CLI**: `bs_pnpi --nuclide Tc99` — full paceENSDF integration (auto-lookup of Z, A, Q-value, transition type, half-life, branches, forbiddenness from ENSDF); for JSON input the file's values are used and CLI flags (`--e-step`, `--neutrino-mass`, `--intensity-cutoff`, `--csv-separator`, `--normalize-to-one`) override them only when explicitly given
+- **CLI**: `bs_pnpi --nuclide Tc99` — full paceENSDF integration (auto-lookup of Z, A, Q-value, transition type, half-life, branches, forbiddenness from ENSDF); for JSON input the file's values are used and CLI flags (`--e-step`, `--neutrino-mass`, `--intensity-cutoff`, `--csv-separator`, `--separate-branches`) override them only when explicitly given; every long option has a single-letter alias (`-N`, `-i`, `-s`, `-m`, `-o`, `-p`, `-L`, `-d`, `-c`, `-V`, `-S`, `-b`)
 - **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; per-branch endpoints are the measured transition endpoint energies from ENSDF (max endpoint across branches defines the spectrum endpoint)

TODO.md

@@ -322,7 +322,7 @@ ______________________________________________________________________
 
 ## Current Status
 
-**Version:** 0.3.1 → **In progress: 0.4.0 — Package restructuring**
+**Version:** 0.4.0 → **v0.4.1 — CLI options refresh & normalization fixes** (released on `dev/core-fermi-csv`)
 
 ### Completed (v0.3.x)
 
@@ -354,6 +354,12 @@ ______________________________________________________________________
   - README updated with new architecture diagram and Quick Start examples
   - Version bumped to 0.4.0
 
+### Completed (v0.4.1)
+
+- Core spectrum made unconditional (`phase_space × fermi`): core toggles removed, physical branch spectra in CSV export, plots built from the exported CSV
+- 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
+- CLI surface refresh: `--normalize-to-one` renamed to `--separate-branches` (no alias), single-letter aliases for every option, dry-run drops the redundant top-level `Transition:` line, stale detector_* JSON schema keys removed
+
 ### Next Immediate Step
 
 - **Track A: ⁹⁹Tc spectrum-shape analysis** — start real data processing pipeline

beta_spectrum/__init__.py

@@ -52,4 +52,4 @@ __all__ = [
     "DEFAULT_JSON_SCHEMA",
 ]
 
-__version__ = "0.4.0"
+__version__ = "0.4.1"

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",
@@ -79,6 +81,7 @@ def _build_parser() -> argparse.ArgumentParser:
 
     # Common parameters
     parser.add_argument(
+        "-s",
         "--e-step",
         type=float,
         default=None,
@@ -87,6 +90,7 @@ def _build_parser() -> argparse.ArgumentParser:
         "omitted). All energies are in MeV throughout the toolkit.",
     )
     parser.add_argument(
+        "-m",
         "--neutrino-mass",
         type=float,
         default=None,
@@ -97,6 +101,7 @@ def _build_parser() -> argparse.ArgumentParser:
 
     # Output
     parser.add_argument(
+        "-o",
         "--output",
         type=str,
         metavar="FILE",
@@ -105,6 +110,7 @@ def _build_parser() -> argparse.ArgumentParser:
 
     # Plotting
     parser.add_argument(
+        "-p",
         "--plot",
         type=str,
         metavar="FILE",
@@ -128,6 +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",
@@ -135,11 +142,13 @@ 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=None,
@@ -149,6 +158,7 @@ def _build_parser() -> argparse.ArgumentParser:
         "Branches below this threshold are excluded from the calculation and plots.",
     )
     log_group.add_argument(
+        "-V",
         "--csv-verbosity",
         type=str,
         default="full",
@@ -156,16 +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=None,
         help="CSV column separator (default: ','). Use 'tab' for tab separation.",
     )
     log_group.add_argument(
-        "--normalize-to-one",
+        "-b",
+        "--separate-branches",
         action="store_true",
         default=None,
-        help="Normalize each branch to 1, ignoring intensity. In this case, total spectrum will not be produced (only energy and branch-wise spectra).",
+        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
@@ -239,7 +253,7 @@ def _run(args: argparse.Namespace) -> None:
         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
-    normalize_to_one = bool(args.normalize_to_one)
+    separate_branches = bool(args.separate_branches)
 
     # Build config — a single delegated path for every data source.
     config: SpectrumConfig
@@ -252,7 +266,7 @@ def _run(args: argparse.Namespace) -> None:
             intensity_cutoff=intensity_cutoff,
             neutrino_mass_MeV=neutrino_mass_MeV,
             csv_separator=csv_separator,
-            normalize_to_one=normalize_to_one,
+            separate_branches=separate_branches,
         )
     else:
         logger.info("Source: JSON file=%s", source_value)
@@ -268,7 +282,7 @@ def _run(args: argparse.Namespace) -> None:
             config.intensity_cutoff = intensity_cutoff
         if args.csv_separator is not None:
             config.csv_separator = csv_separator
-        config.normalize_to_one = normalize_to_one
+        config.separate_branches = separate_branches
 
     # Dry run: display resolved config and exit
     if args.dry_run:
@@ -352,7 +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'}")

beta_spectrum/nuclear_data.py

@@ -477,7 +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.
@@ -494,8 +494,9 @@ def decay_info_to_config(
         Neutrino mass in MeV.
     csv_separator : str
         CSV column separator.
-    normalize_to_one : bool
-        If True, normalize each branch to 1, ignoring intensity.
+    separate_branches : bool
+        If True, emit separate branch spectra, each normalized to
+        integrate to 1 (intensity ignored; no total spectrum column).
 
     Returns
     -------
@@ -535,7 +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,
     )
 
 
@@ -708,7 +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,
@@ -716,7 +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,
@@ -12,7 +12,7 @@ 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.
 """
 
@@ -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:
@@ -189,7 +189,7 @@ class CSVEmitter:
                 "is degenerate (check neutrino_mass vs branch endpoints "
                 "and intensity_cutoff)"
             )
-        if not to_one:
+        if not separate:
             data["total_spectrum"] = total_raw / integral
 
         for i in range(n_branches):
@@ -199,7 +199,7 @@ 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

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 = (
-        False  # If True, normalize each branch to 1, ignoring intensity
+    separate_branches: bool = (
+        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]:

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "beta-spectrum"
-version = "0.4.0"
+version = "0.4.1"
 description = "High-precision beta spectrum calculation for nuclear physics"
 authors = [
     { name = "Evgeniy Unzhakov" }

tests/integration/test_cli_flows.py

@@ -66,12 +66,12 @@ def n_points_of(header: List[str]) -> int:
 class TestCLIJsonFlows:
     """Options must propagate through the JSON config flow (D2)."""
 
-    def test_json_honors_normalize_to_one_and_tab_separator(
+    def test_json_honors_separate_branches_and_tab_separator(
         self, tmp_path: Any
     ) -> None:
         src = write_json(tmp_path)
         out = str(tmp_path / "to_one.csv")
-        main([src, "--output", out, "--normalize-to-one", "--csv-separator", "tab"])
+        main([src, "--output", out, "--separate-branches", "--csv-separator", "tab"])
 
         with open(out) as f:
             body = "".join(ln for ln in f if not ln.startswith("#"))
@@ -136,7 +136,7 @@ class TestCLIDegenerateFlows:
                     out,
                     "--neutrino-mass",
                     "0.35",
-                    "--normalize-to-one",
+                    "--separate-branches",
                 ]
             )
         assert exc.value.code == 1
@@ -147,9 +147,9 @@ class TestCLIDegenerateFlows:
 class TestCLIPaceENSDF:
     """paceENSDF flow honors the same export options."""
 
-    def test_paceensdf_honors_normalize_to_one(self, tmp_path: Any) -> None:
+    def test_paceensdf_honors_separate_branches(self, tmp_path: Any) -> None:
         out = str(tmp_path / "p32.csv")
-        main(["P32", "--output", out, "--normalize-to-one"])
+        main(["P32", "--output", out, "--separate-branches"])
 
         df = read_export(out)
         assert "total_spectrum" not in df.columns

tests/physics/test_core_spectrum.py

@@ -313,8 +313,8 @@ class TestCSVExportCoreSemantics:
         assert "phase_space" in core_line[0]
         assert "fermi" in core_line[0]
 
-    def test_normalize_to_one_per_branch_unit_area(self, tmp_path: Any) -> None:
-        config = make_multi_config(normalize_to_one=True)
+    def test_separate_branches_per_branch_unit_area(self, tmp_path: Any) -> None:
+        config = make_multi_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         _, df = export_and_read(analyzer, tmp_path)
@@ -334,12 +334,12 @@ class TestCSVExportCoreSemantics:
             analyzer.export_to_csv(path)
         assert not (tmp_path / "degenerate.csv").exists()
 
-    def test_degenerate_export_raises_in_normalize_to_one_mode(
+    def test_degenerate_export_raises_in_separate_branches_mode(
         self, tmp_path: Any
     ) -> None:
-        """The positive-integral guard must apply in to_one mode too:
+        """The positive-integral guard must apply in separate-branches mode too:
         no all-zero CSV may be written for a degenerate spectrum."""
-        config = make_degenerate_config(normalize_to_one=True)
+        config = make_degenerate_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         path = str(tmp_path / "degenerate_to_one.csv")
@@ -567,13 +567,13 @@ class TestAnalyzerUniversalFactor:
 
 
 class TestNormalizationModeMatrix:
-    """to_one and intensity modes must behave consistently across CSV
+    """separate_branches and intensity modes must behave consistently across CSV
     verbosity, branch count and the CSV-driven visualizer."""
 
-    def test_to_one_concise_multi_unit_area_no_total_no_components(
+    def test_separate_branches_concise_multi_unit_area_no_total_no_components(
         self, tmp_path: Any
     ) -> None:
-        config = make_multi_config(normalize_to_one=True)
+        config = make_multi_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         path, df = export_and_read(
@@ -587,14 +587,14 @@ class TestNormalizationModeMatrix:
             "branch_3",
         }
         header = header_lines_of(path)
-        assert any("branch normalization: to_one" in h for h in header)
+        assert any("branch normalization: separate" in h for h in header)
         energies = df["energy_MeV"].to_numpy()
         for col in ("branch_1", "branch_2", "branch_3"):
             area = np.trapezoid(df[col].to_numpy(), energies)
             assert np.isclose(area, 1.0, rtol=5e-4)
 
-    def test_to_one_single_mode_unit_area(self, tmp_path: Any) -> None:
-        config = make_single_config(normalize_to_one=True)
+    def test_separate_branches_single_mode_unit_area(self, tmp_path: Any) -> None:
+        config = make_single_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         _path, df = export_and_read(analyzer, tmp_path, "to_one_single.csv")
@@ -622,10 +622,10 @@ class TestNormalizationModeMatrix:
         nonzero = total > 1e-12
         assert np.all(np.abs(summed[nonzero] - total[nonzero]) <= total[nonzero] * 5e-4)
 
-    def test_plot_from_csv_to_one_plots_branches_without_total(
+    def test_plot_from_csv_separate_branches_plots_branches_without_total(
         self, tmp_path: Any
     ) -> None:
-        config = make_multi_config(normalize_to_one=True)
+        config = make_multi_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         path, df = export_and_read(analyzer, tmp_path, "to_one_plot.csv")
@@ -633,7 +633,7 @@ class TestNormalizationModeMatrix:
         fig = Visualizer.plot_from_csv(path, save_path=None, show_components=True)
         assert len(fig.axes) == 4
         # Panel 1 has exactly the 3 branch curves — no total spectrum
-        # exists in to_one mode.
+        # exists in separate-branches mode.
         panel = fig.axes[0]
         curves = [np.asarray(ln.get_xydata()) for ln in panel.lines]
         assert len(curves) == 3
@@ -641,8 +641,10 @@ class TestNormalizationModeMatrix:
         assert np.allclose(curves[0][:, 0], energies)
         assert np.allclose(curves[0][:, 1], df["branch_1_spectrum"].to_numpy())
 
-    def test_plot_analysis_to_one_returns_figure(self, tmp_path: Any) -> None:
-        config = make_multi_config(normalize_to_one=True)
+    def test_plot_analysis_separate_branches_returns_figure(
+        self, tmp_path: Any
+    ) -> None:
+        config = make_multi_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         save = str(tmp_path / "analysis.png")
@@ -650,10 +652,10 @@ class TestNormalizationModeMatrix:
         assert len(fig.axes) == 4
         assert (tmp_path / "analysis.png").exists()
 
-    def test_plot_from_csv_to_one_concise_warns_and_falls_back(
+    def test_plot_from_csv_separate_branches_concise_warns_and_falls_back(
         self, tmp_path: Any, capsys: Any
     ) -> None:
-        config = make_multi_config(normalize_to_one=True)
+        config = make_multi_config(separate_branches=True)
         spectrum = BetaSpectrum.from_config(config)
         analyzer = BetaSpectrumAnalyzer(spectrum, config)
         path, df = export_and_read(

tests/quality/test_cli_options.py

@@ -0,0 +1,137 @@
+"""CLI option surface tests: renamed branch-separation flag, short
+aliases for every long option, and dry-run output shape (audit follow-up
+by the maintainer: rename --normalize-to-one, add short options, drop the
+redundant top-level Transition line)."""
+
+from __future__ import annotations
+
+import dataclasses
+from typing import Any, Optional
+
+import pytest
+
+from beta_spectrum import BranchConfig, SpectrumConfig
+from beta_spectrum.cli import _build_parser, _print_dry_run_output
+
+pytestmark = pytest.mark.quality
+
+
+def make_config() -> SpectrumConfig:
+    return SpectrumConfig(
+        Z_parent=59,
+        Z_daughter=60,
+        A_number=144,
+        endpoint_MeV=2.98,
+        transition_type="F1",
+        e_step_MeV=0.001,
+        branches=[
+            BranchConfig(endpoint_MeV=2.98, transition_type="F1", intensity=0.9),
+            BranchConfig(endpoint_MeV=2.1, transition_type="A", intensity=0.1),
+        ],
+    )
+
+
+class TestSeparateBranchesRename:
+    """--normalize-to-one was renamed to --separate-branches (no alias)."""
+
+    def test_flag_parses_true(self) -> None:
+        parser = _build_parser()
+        args = parser.parse_args(["input.json", "--separate-branches"])
+        assert args.separate_branches is True
+
+    def test_flag_default_is_none(self) -> None:
+        parser = _build_parser()
+        args = parser.parse_args(["input.json"])
+        assert args.separate_branches is None
+
+    def test_old_flag_is_rejected(self) -> None:
+        parser = _build_parser()
+        with pytest.raises(SystemExit):
+            parser.parse_args(["input.json", "--normalize-to-one"])
+
+    def test_config_field_renamed(self) -> None:
+        names = {f.name for f in dataclasses.fields(SpectrumConfig)}
+        assert "separate_branches" in names
+        assert "normalize_to_one" not in names
+
+    def test_config_old_kwarg_rejected(self) -> None:
+        kwargs: dict[str, Any] = {
+            "Z_parent": 15,
+            "Z_daughter": 16,
+            "A_number": 32,
+            "endpoint_MeV": 1.7103,
+            "transition_type": "A",
+            "normalize_to_one": True,
+        }
+        with pytest.raises(TypeError):
+            SpectrumConfig(**kwargs)
+
+
+# (short, long, value-or-None-for-store_true)
+_SHORT_EQUIV = [
+    ("-N", "--nuclide", "Cs137"),
+    ("-i", "--input", "in.json"),
+    ("-s", "--e-step", "0.01"),
+    ("-m", "--neutrino-mass", "0.15"),
+    ("-o", "--output", "out.csv"),
+    ("-p", "--plot", "plot.png"),
+    ("-L", "--log-file", "calc.log"),
+    ("-d", "--dry-run", None),
+    ("-c", "--intensity-cutoff", "0.5"),
+    ("-V", "--csv-verbosity", "concise"),
+    ("-S", "--csv-separator", "tab"),
+    ("-b", "--separate-branches", None),
+]
+
+
+class TestShortOptions:
+    """Every long option gains a single-letter alias (only -v/-q existed)."""
+
+    @pytest.mark.parametrize(
+        "short,long,value",
+        _SHORT_EQUIV,
+        ids=[s.lstrip("-") for s, _, _ in _SHORT_EQUIV],
+    )
+    def test_short_matches_long(
+        self, short: str, long: str, value: Optional[str]
+    ) -> None:
+        parser = _build_parser()
+        argv_long = [long] if value is None else [long, value]
+        argv_short = [short] if value is None else [short, value]
+        args_long = parser.parse_args(["Tc99"] + argv_long)
+        args_short = parser.parse_args(["Tc99"] + argv_short)
+        dest = long.lstrip("-").replace("-", "_")
+        assert getattr(args_short, dest) == getattr(args_long, dest)
+        assert getattr(args_long, dest) is not None or value is None
+
+    def test_existing_shorts_unchanged(self) -> None:
+        parser = _build_parser()
+        args = parser.parse_args(["Tc99", "-v", "-q"])
+        assert args.verbose == 1
+        assert args.quiet is True
+
+
+class TestDryRunOutputShape:
+    """The top-level Transition line is redundant with the per-branch
+    list (for multi-branch runs) and was removed."""
+
+    def test_multi_branch_dry_run_no_top_level_transition(self, capsys: Any) -> None:
+        _print_dry_run_output(make_config(), "paceENSDF")
+        out = capsys.readouterr().out
+        assert "Transition:" not in out
+        assert "transition=F1" in out
+        assert "transition=A" in out
+        assert "Multi-branch mode: 2 branches" in out
+
+    def test_single_branch_dry_run_reports_endpoint(self, capsys: Any) -> None:
+        config = SpectrumConfig(
+            Z_parent=15,
+            Z_daughter=16,
+            A_number=32,
+            endpoint_MeV=1.7103,
+            transition_type="A",
+        )
+        _print_dry_run_output(config, "json")
+        out = capsys.readouterr().out
+        assert "Transition:" not in out
+        assert "Mode: single-branch" in out

tests/quality/test_logging_utils.py

@@ -154,7 +154,7 @@ class TestCSVMetadataHeader:
             lines = f.readlines()
 
         assert any("# beta-spectrum v" in line for line in lines)
-        assert any("0.4.0" in line for line in lines)
+        assert any("0.4.1" in line for line in lines)
         os.unlink(filename)
 
     def test_header_contains_timestamp(self):