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
unzhakov