Compactify the descriptive markdown: scope statement replaces the
g_V-extraction goal, package architecture describes the single
theory-only distributable, roadmap keeps calculator capabilities
(C1-C8) and drops the analysis tracks, structure trees match the
actual file layout, the bs_exp debug step and detector-parameter
convention wording are dropped.
- --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: remove stale detector_response.py tree entry and the
detector-models highlight (module removed); document per-branch
measured transition endpoints from paceENSDF and JSON-flow CLI
override semantics
- TODO: drop the DEFAULT_JSON_SCHEMA detector-keys clause (removed)
- data/custom_input_example.json: strip dead detector_* keys
- Mark v0.4.0 as complete in TODO.md with all phases checked
- Update Phase 4 items with actual outcomes
- Next step: Track A 99Tc spectrum-shape analysis
- Add AGENTS instruction to update project metadata on significant
structural changes (package additions, version bumps, etc.)
- Fixed bug: decay_info_to_config() was dropping branches, causing
create_config_from_source('paceENSDF') to return single-branch config
- Added BranchConfig import to nuclear_data.py
- Marked B1 (paceENSDF integration) as complete in TODO.md
- Updated README.md with paceENSDF details in Implementation Status
- Updated TODO.md Current Status with v0.3.1 notes
- 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
- 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
- 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
unzhakov