unzhakov/beta_shape_pnpi
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3216c50943c11cb8ef0d7baba24c33f90d40865e
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15 Commits
Author SHA1 Message Date
unzhakov 3216c50943 feat: per-branch transition types from ENSDF and raw-value plotting 
- 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
 2026-05-08 08:33:12 +03:00
unzhakov 5ac004352b Fix mypy type errors and black formatting 
- spectrum.py: Use Axes from TYPE_CHECKING instead of plt.Axes
- fitter.py: Remove unused type: ignore comment
- phase_space.py: Black formatting
 2026-05-05 14:01:28 +03:00
unzhakov d6328d4b24 Enhance plot output with ID tracking and two display modes 
- 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)
 2026-05-05 13:33:46 +03:00
unzhakov 3749220efc Fix pyright type errors and correct paceENSDF Q-value extraction 
- nuclear_data.py: Extract Q-value from ground state branch state[7] instead of
  halflife_data (was reading half-life seconds as Q-value)
- nuclear_data.py: Use ground state branch for forbiddenness code, with fallback
- nuclear_data.py: Add None guards for beta_data and pairs
- spectrum.py: Pass Z=config.Z_daughter, A=config.A_number to RadiativeCorrection
- phase_space.py: Add __init__ debug logging (W0, transition_type, m_e, m_nu)
- phase_space.py: Add output range logging in __call__
- phase_space.py: Fix possibly unbound forbid_factor variable
- logging_utils.py: Fix broken get_git_short_hash indentation
- cli.py: Add explicit SpectrumConfig annotation to fix pyright type identity
- cw_extractor.py: Fix T_to_W ndarray→float conversions (6 locations)
- cw_extractor.py: Fix FermiFunction() calls — was passing Z as __call__ arg
- fitter.py: Add explicit dict type annotation for least_squares kwargs
 2026-05-05 12:43:43 +03:00
unzhakov 330ebddaef refactor: refine CLI options and enhance debug logging 
- 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
 2026-05-05 09:08:08 +03:00
unzhakov 9050019ddd feat: add structured logging, CSV metadata headers, and CLI improvements 
- New module: beta_spectrum/logging_utils.py
  - LoggingConfig dataclass with level, log_file, format options
  - setup_logging() one-shot configuration (opt-in for library use)
  - get_logger() for named child loggers
  - get_git_short_hash() for commit identification
  - _find_git_root() for repo detection

- CLI enhancements (beta_spectrum/cli.py):
  - --verbose/-v (repeatable): -v=INFO, -vv=DEBUG
  - --quiet/-q: suppress all terminal output
  - --log-file PATH: append log to file
  - --dry-run: validate input, display resolved config, exit
  - --version: show package version
  - Replace print() with structured logging throughout
  - Handle KeyboardInterrupt gracefully

- CSV metadata headers (BetaSpectrumAnalyzer.export_to_csv):
  - YAML-style # comments with version, timestamp, source, nuclide info
  - Corrections enabled, e_step, detector settings, git commit hash

- Base class integration (SpectrumComponent):
  - Optional logger parameter for debug/info output (opt-in)

- BetaSpectrum integration:
  - Optional logger parameter passed through from_config()
  - Detector logging in create_detector_from_config()
  - Convolution logging in convolve_with_detector()

- Tests: tests/test_logging_utils.py (28 tests)
  - LoggingConfig, setup_logging, get_logger, git hash, CSV headers, CLI flags

- Update TODO.md: mark B8 as complete, update Current Status
 2026-05-04 15:11:01 +03:00
unzhakov 66a93d9cac fix: satisfy mypy strict type-checking requirements 
- 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
 2026-05-03 01:00:47 +03:00
unzhakov 33ed4f7e44 fix: satisfy mypy strict type-checking requirements 
- 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
 2026-05-03 00:44:11 +03:00
unzhakov 8b4545fe3e refactor: centralize all physical constants in constants.py, fix unit naming 
- Add EULER_GAMMA, ME_KEV, R0_FM to constants.py
- Replace hardcoded 0.511, 0.5772..., 1.2 with imports from constants
- Fix T_to_W parameter name: T_kev -> T_MeV (it takes MeV, not keV)
- Remove duplicate ME_ME from spectrum.py (import ME_MEV from constants)
- Remove hardcoded r_0 from detector_response.py and radiative.py
- Update CONVENTIONS.md to reference correct constant names
 2026-05-01 22:34:15 +03:00
unzhakov 5f99566a0e feat(detector): add detector response module, convolution, and integration 
- Analytical detector response: gaussian, gaussian_tail, tikhonov models
- Low-energy tail modeling for charge collection effects
- Response matrix convolution via R^T · (Φ·ΔW)
- Declarative API: create_detector_from_config(), convolve_detector()
- BetaSpectrumAnalyzer.convolved_spectrum() for auto-convolution
- Integration tests: TestBetaSpectrumIntegration, TestDeclarativeDetectorResponse
- Documentation: docs/08-detector-response.md
 2026-05-01 19:20:59 +03:00
unzhakov 4c0fe493d8 Fix call parameter typo 2026-04-28 11:32:07 +03:00
unzhakov f04f52b747 Update Phase Space calculation 
Add support for proper calculation of phase space component based on the
transition type (allowed/Nth order forbidden).
 2026-04-27 15:36:36 +03:00
unzhakov 04c6a4b250 Output csv precision fix 
Switched to 4 decimal digits.
 2026-04-17 12:52:19 +03:00
unzhakov 91f716c851 Version 0.1.2 
Implemented all planned corrections:
  - finite-size e/m L0 and U
  - atomic screening and exchange
  - radiative (electron only so far)

Added plotter and csv_export
 2026-04-15 18:05:04 +03:00
unzhakov a5e1962fe2 Initial commit 
Base modular structure (phase space, Fermi function)
Initial .gitignore
 2026-04-02 15:38:37 +03:00