Remove gA-extraction notes, nuclear-structure notes, paper-summary
refs, detector-response correction note and the finished test
migration checklist. Rewrite the vault index for the single-package
theory calculator; repoint dangling wiki-links in surviving notes to
inline citations; refresh docs_check.py (drop bs_exp CLI check,
register removed files).
Literature and nuclear-structure research resumes in dedicated
projects; the removed notes are recoverable from history.
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.
The experimental CLI and the PyROOT extra existed only for the
removed analysis packages. Version bump reflects the scope reduction
to theory-only spectrum calculation; calculation logic is unchanged.
Raw Tc99/A-major runs, Am-241 calibration files and the ROOT
histogram macro were measurement inputs for the analysis track that
left the project scope; the canonical copies live on the experiment
storage. Also removes scripts/analyze_raw.py, a rate-stability
analysis utility built on the exp_data reader.
Spectrum model, convolution, chi2 fit engine, C(W) and g_V/g_A
extractors and result containers are analysis code outside the
theory-only scope. Removes the package and its test suites.
Detector data handling, energy calibration, peak fitting and
instrumental corrections leave the project scope (theory-only
spectrum shape calculation). Removes the package, its tests, the
exp pipeline integration test, the calibration notebook, and the
ExpSpectrum fixtures from the shared conftest.
- --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
- DEFAULT_JSON_SCHEMA: drop the 8 detector_* keys left over from the
removed detector_response module; CLI dry-run drops the dead
'Detector: not configured (Phase 4)' line
- CSV export: single-mode no longer writes branch_1_PhaseSpace /
branch_1_Radiative duplicates next to the bare PhaseSpace/Radiative
columns; per-branch core factors only in multi-branch mode
- Visualizer: debug panels fall back to the unprefixed core-factor
columns for single-mode CSVs instead of skipping them
- Spectrum ylabel now states the actual units: normalized spectrum
[MeV^-1], not 'Normalized Counts / keV'
- tests: defaults assert detector keys gone; column layout pinned for
single vs multi; panel and ylabel assertions
paceENSDF stores the measured beta endpoint energy of each transition
(ENSDF column 7). The parser instead derived branch endpoints as
base-endpoint minus level energy with the base taken from an arbitrary
first-listed branch, so Co60 produced negative branch endpoints and a
hard ValueError (bs_pnpi Co60 exited 1 regardless of cutoff).
- BranchInfo carries the measured endpoint_MeV
- overall endpoint = max measured endpoint over all branches
- decay_info_to_config prefers measured endpoints; the subtraction is
retained only as a legacy fallback for hand-built DecayInfo objects
- Co60/Tc99/Cs137 endpoint tests + CLI dry-run/export tests (D3)
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
CSVEmitter.export_to_csv raised ValueError only in intensity mode;
degenerate exports with --normalize-to-one silently wrote all-zero
CSV files. The guard now runs before the mode split and no file is
written in either mode.
When config.branches carries exactly one branch (e.g. after
--intensity-cutoff filtering), the branch endpoint/transition define
the spectrum, energy grid, analyzer unified branch view and CSV
header. The stale top-level endpoint inherited from the parent decay
no longer leaks into physics (proven wrong on Cs137: spectrum
extended to 1176 keV while the lone survivor ends at 514 keV).
- 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
- Use find_peaks width=(5,50) to reject noise bumps
- Simplify peak matching: find two strongest peaks with largest
channel separation, assign min/max known energies
- Require absolute threshold of 400 counts to avoid noise peaks
- Calibration now correctly maps: ch 97→13.0 keV, ch 537→59.54 keV
- Tc-99 endpoint at ch 2750 → 293.6 keV (expected ~294)
- Add .rpiv/ to .gitignore
- Search full spectrum (exclude pulser region) instead of just low-energy
- Include 59.54 keV line in known Am-241 energies
- Brute-force peak-to-energy matching with physical gain constraint
(3-40 ch/keV) to reject spurious fits
- Fixed find_peaks parameters: height=100, distance=5 for accurate
peak detection
- Calibration now correctly maps: ch 97→13 keV, ch 134→17.4 keV,
ch 537→59.6 keV, giving Tc-99 endpoint at ch 2750→291.6 keV
- Add .rpiv/ to .gitignore
- 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
- Document current test suite state (230 tests, 79 CQT + 151 PT)
- Propose new directory structure: tests/{common,physics,quality,integration}
- Identify 18 duplicate test patterns across correction components
- Define pytest markers for test categorization
- Create implementation plan with 5 phases
- 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
unzhakov