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)

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'}")