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

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- --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)
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unzhakov
2026-10-03 01:08:51 +03:00
parent 7f47a876ae
commit 2788ea0683
12 changed files with 210 additions and 53 deletions
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README.md
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@@ -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)