Remove the duplicated inline paceENSDF config builder in the CLI.
It renormalized branch intensities before filtering, diverging from
the library decay_info_to_config path that library callers use
(audit finding D5). CLI paceENSDF configs now come from
create_config_from_source exactly once per run.
Regression test spies on create_config_from_source during a CLI run.
- main(argv) signature enables in-process CLI invocation and testing
- parser defaults for --e-step/--neutrino-mass/--intensity-cutoff/
--csv-separator/--normalize-to-one now None = 'not provided'
- JSON flow applies file values by default and CLI flags as overrides
(previously these five options were silently discarded)
- paceENSDF flow resolves None flags to literal defaults
- new tests/integration/test_cli_flows.py: JSON propagation,
degenerate-mode non-zero exit with no file (JSON + paceENSDF)
- adapted two neutrino-mass default tests to None-parsing semantics
- Add neutrino mass parameter to SpectrumConfig and CLI interface
- Update PhaseSpace component to handle neutrino mass effects properly
- Update CSV headers to show basic endpoint and all transition types
- Add --csv-verbosity option to CLI with 'full' and 'concise' options
- Fix comparison plots to properly show linear scale variations
- Add comprehensive tests for neutrino mass functionality
- Add --intensity-cutoff CLI option to filter negligible branches
- Fetch DecayInfo from paceENSDF and construct SpectrumConfig with
branches including per-branch transition types
- Normalize branch intensities to sum to 1.0, filter by cutoff
- Display branch info in dry-run output and logging
- Add intensity_cutoff to SpectrumConfig
- Add commit hash (6 chars) and UTC timestamp to all plots via text boxes
- Add nuclear data header (nuclide, endpoint, transition, corrections) to plots
- Two display modes:
- DEBUG (-vv): 4-panel debug view with all correction factors
- Normal (default): single spectrum plot with nuclear data header
- CLI: --plot now passes show_components=(args.verbose >= 2)
- Remove --mode, --transition-type, and --decay-index CLI flags
(parameters now come from ENSDF data or custom JSON input)
- Clarify energy units in all CLI help text (MeV throughout, keV for detector params)
- Enhance logging verbosity:
- -v (INFO): shows source, component initialization, workflow steps
- -vv (DEBUG): shows detailed internals of all spectrum components
(parameters, evaluation counts, input/output ranges)
- Improve CSV headers with element notation (e.g. Tc99 -> Ru99)
- Add CONVENTIONS.md documenting energy unit and logging conventions
- Update TODO.md with completion status
- Add nuclear_data.py module for paceENSDF integration and JSON input
- Add DecayInfo and BranchInfo dataclasses for parsed nuclear data
- Implement get_decay_info_from_paceENSDF() to retrieve decay parameters
- Implement load_json_input() and json_to_config() for custom JSON input
- Add create_config_from_source() unified interface for both sources
- Add bs_pnpi CLI with --nuclide, --input, --output, --plot, and detector options
- Add 23 comprehensive tests for nuclear_data module
- Add sample JSON input file
- Update __init__.py and pyproject.toml with new exports and entry point
- Add paceENSDF as optional dependency
unzhakov