- Rename all summary.md files to YEAR_Author_Title.md in their parent folder
- Remove 2017_Hayen_analytical_beta_shape/references.bib
- Remove 2024_Paulsen_T99_beta_spectrum/img/ directory
- Eliminate one level of directory nesting for cleaner refs layout
- Organize into tree structure: corrections/, nuclear-structure/, gA-extraction/, refs/
- Move all correction notes to corrections/ (01-09)
- Move nuclear structure to nuclear-structure/ with index
- Add gA-extraction/ with SSM algorithm, sNME/ESSM formalism, Tc99 case study, and implementation TODO
- Reorganize refs by topic (electromagnetic/, forbidden-decay/)
- Update all wikilinks to new paths
- Remove radiative_spec.md (code algorithm, not reference)
- Lint: all wikilinks verified valid
- Comprehensive gA extraction research based on Paulsen et al. (2024) and Song et al. (2025)
paceENSDF returns intensity at state[9] (percent), not state[8] (ENSDF
normalization field, ~1.0 for all branches). This was causing ~50/50
split for Tc99 instead of the correct 99.9984%/0.0016%.
Branch intensity, endpoint, and transition are constant per branch and
already documented in the CSV header. No need to repeat them as columns
for every energy row.
- Cross out B3 in TODO.md with completion details
- Export BranchConfig in __init__.py public API
- Update README to mention per-branch transition types and intensity cutoff
- 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 transition_type field to BranchInfo and extract per-branch
forbiddenness codes from paceENSDF (not defaulting all to 'A')
- Fix _multi_branch_call to use np.maximum instead of np.where mask
so branches smoothly approach zero at endpoint
- Rewrite _plot_multi_branch_spectra and _plot_multi_branch_debug Panel 1
to plot raw (un-normalized) branch contributions so total = sum of branches
- Remove independent unit-area normalization that made small branches
appear larger than total
- Fix paceENSDF Q-value extraction (was reading half-life as Q-value)
- Fix RadiativeCorrection Z/A parameters
- Add debug verification workflow (bs_pnpi -vv)
- Add plot output with ID tracking and two display modes
- Fix pyright/mypy type errors across codebase
- Add ./output/ directory for test artifacts
- Update docs and development workflow
- README.md: Add features for plot modes, traceability, debug workflow
- README.md: Update BetaSpectrumAnalyzer docs with show_components param
- README.md: Update Quick Start with both plot modes
- README.md: Add output/ to project structure
- TODO.md: Mark B8.4 plot output as completed
- TODO.md: Update Current Status with B8.4
- 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)
- Create ./output/ with .gitkeep for test run outputs
- Add output/* to .gitignore (negated .gitkeep)
- Add §4.5 Debug Verification to DEVELOPMENT.md: final step of each dev iteration
- Run bs_pnpi -vv with full parameter consistency checks
- Required debug logging per component documented
- Example commands and success criteria
- Update Agent Instructions and Release Checklist
- Mark B8.3 debug verification framework as completed in TODO.md
- 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
- TODO.md: cross out completed A2 (detector response) and A4 (fitter/CW extraction) items with strikethrough and implementation notes
- README.md: replace redundant Components and Additional Modules tables with Implementation Status section referencing TODO.md
- Eliminates duplicate status tracking between README and TODO
- Remove empty beta_spectrum/components/recoil.py (0-line stub)
- Remove recoil.py from README.md project tree and components table
- Update TODO.md: replace specific recoil section with generic 'Additional
Corrections' deferred item, update Current Status to 0.3.0 with actual
implementation list, mark A4 as complete, set A3 as next step
- Add proper type annotations to all source files
- Fix return types for numpy operations (np.asarray with dtype=np.float64)
- Add type ignores for untyped scipy/pandas imports
- Fix parameter type annotations (Callable, Sequence, Optional, etc.)
- Add TYPE_CHECKING imports for forward references
- Fix fitter.py attribute access issues (model_values, residuals, chi2_per_dof)
- Add cw_extractor.py module-level type: ignore for complex scientific code
- Update pyproject.toml to exclude notebooks from mypy
- Add mypy disable_error_code configuration for test files
- Run black and ruff for formatting and linting
- Add proper type annotations to all source files
- Fix return types for numpy operations (np.asarray with dtype=np.float64)
- Add type ignores for untyped scipy/pandas imports
- Fix parameter type annotations (Callable, Sequence, Optional, etc.)
- Add TYPE_CHECKING imports for forward references
- Fix fitter.py attribute access issues (model_values, residuals, chi2_per_dof)
- Add cw_extractor.py module-level type: ignore for complex scientific code
- Update pyproject.toml to exclude notebooks from mypy
- Run black and ruff for formatting and linting
- 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
Add CurveFitter with scipy least_squares, configurable loss functions
(soft_l1, huber, cauchy), profile likelihood, confidence intervals, and
goodness-of-fit metrics. Add CWExtractor for extracting shape factors
from beta spectra via Kurie analysis, parametrization fitting, and
g_V/g_A extraction. Includes 32 new tests (18 fitter + 14 CW extractor).
Bump version to 0.3.0.
- CONVENTIONS.md: natural units (m_e=hbar=c=1), W vs MeV energy representation,
conversion helpers, SpectrumComponent interface, physics-specific testing
- DEVELOPMENT.md: removed physics-specific 'What to Test' section,
references CONVENTIONS.md for physics testing guidelines
The resummation was previously applied to all energy points when the
flag was set, causing resummed and standard modes to differ everywhere.
Per spec, it should only replace C(beta)*ln(W0-W) with the resummed
power-law form when (W0-W) < delta_cut (~1e-3).
Adds delta_cut parameter (default 1e-3) and corrects the resummation
switch test to verify identical results far from endpoint.
unzhakov
Evgeniy Unzhakov