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
This commit is contained in:
+15
-2
@@ -1,6 +1,10 @@
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# base.py
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from __future__ import annotations
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import logging
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from abc import ABC, abstractmethod
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from typing import Optional
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import numpy as np
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ArrayLike = np.ndarray
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@@ -8,12 +12,21 @@ ArrayLike = np.ndarray
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class SpectrumComponent(ABC):
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"""
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Base class for multiplicative components of beta-spectrum
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Base class for multiplicative components of beta-spectrum.
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Parameters
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----------
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logger : logging.Logger, optional
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Logger instance for debug/info output. If None, logging is disabled.
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Opt-in design: components are silent by default for library use.
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"""
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def __init__(self, logger: Optional["logging.Logger"] = None) -> None:
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self._logger = logger
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@abstractmethod
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def __call__(self, W: ArrayLike) -> ArrayLike:
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"""
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Evaluate component at total energy W (in m_e units)
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Evaluate component at total energy W (in m_e units).
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"""
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pass
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+252
-3
@@ -13,6 +13,12 @@ Usage examples:
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# With detector response
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bs_pnpi --nuclide Tc99 --detector sigma=1.0 --output convolved.csv
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# Verbose with log file
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bs_pnpi --nuclide Tc99 --output spectrum.csv -vv --log-file calc.log
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# Dry run to inspect resolved configuration
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bs_pnpi --nuclide Tc99 --dry-run
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"""
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from __future__ import annotations
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@@ -21,6 +27,8 @@ import argparse
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import sys
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from typing import Any, Dict
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from beta_spectrum.logging_utils import LoggingConfig, setup_logging
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def _build_parser() -> argparse.ArgumentParser:
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"""Build the argument parser."""
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@@ -35,9 +43,18 @@ def _build_parser() -> argparse.ArgumentParser:
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" bs_pnpi --input custom_input.json --output spectrum.csv\n"
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" bs_pnpi --nuclide Tc99 --plot spectrum.png --output spectrum.csv\n"
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" bs_pnpi --nuclide Tc99 --detector sigma=1.0 --output convolved.csv\n"
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" bs_pnpi --nuclide Tc99 --output spectrum.csv -vv --log-file calc.log\n"
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" bs_pnpi --nuclide Tc99 --dry-run\n"
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),
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)
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# Version
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parser.add_argument(
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"--version",
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action="version",
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version=f"%(prog)s {__import__('beta_spectrum').__version__}",
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)
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# Source selection (mutually exclusive)
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source_group = parser.add_mutually_exclusive_group(required=True)
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source_group.add_argument(
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@@ -129,6 +146,33 @@ def _build_parser() -> argparse.ArgumentParser:
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help="Low-energy tail fraction (0.0–1.0, default: 0.0).",
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)
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# Logging and output control
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log_group = parser.add_argument_group("logging and output")
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log_group.add_argument(
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"-v",
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"--verbose",
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action="count",
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default=0,
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help="Increase verbosity: -v=INFO, -vv=DEBUG (repeatable).",
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)
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log_group.add_argument(
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"-q",
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"--quiet",
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action="store_true",
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help="Suppress all terminal output (only errors shown).",
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)
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log_group.add_argument(
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"--log-file",
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type=str,
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metavar="FILE",
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help="Append log messages to the specified file.",
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)
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log_group.add_argument(
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"--dry-run",
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action="store_true",
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help="Validate input and display resolved configuration without computing spectrum.",
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)
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return parser
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@@ -148,6 +192,9 @@ def _parse_detector_args(args: argparse.Namespace) -> Dict[str, Any]:
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def _run(args: argparse.Namespace) -> None:
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"""Execute the CLI command."""
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import time
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from beta_spectrum.logging_utils import get_logger
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from beta_spectrum.nuclear_data import (
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create_config_from_source,
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json_to_config,
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@@ -155,10 +202,33 @@ def _run(args: argparse.Namespace) -> None:
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)
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from beta_spectrum.spectrum import BetaSpectrum, BetaSpectrumAnalyzer
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# Determine logging level
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if args.quiet:
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log_level = "WARNING"
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elif args.verbose >= 2:
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log_level = "DEBUG"
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elif args.verbose >= 1:
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log_level = "INFO"
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else:
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log_level = "WARNING"
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# Setup logging
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log_config = LoggingConfig(
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level=log_level,
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log_file=args.log_file,
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)
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logger = setup_logging(log_config)
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logger = get_logger("cli")
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logger.info("bs_pnpi starting...")
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logger.debug("Verbosity: %s | Log file: %s", log_level, args.log_file or "none")
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# Build config
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detector_kwargs = _parse_detector_args(args)
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source_type: str
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if args.nuclide:
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logger.info("Source: paceENSDF nuclide=%s mode=%s", args.nuclide, args.mode)
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config = create_config_from_source(
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"paceENSDF",
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nuclide=args.nuclide,
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@@ -171,32 +241,208 @@ def _run(args: argparse.Namespace) -> None:
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detector_tau_keV=detector_kwargs.get("detector_tau_keV", 5.0),
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detector_tail_fraction=detector_kwargs.get("detector_tail_fraction", 0.0),
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)
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source_type = "paceENSDF"
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elif args.input:
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logger.info("Source: JSON file=%s", args.input)
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data = load_json_input(args.input)
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if args.transition_type:
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data["transition_type"] = args.transition_type
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config = json_to_config(data)
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source_type = "json"
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else:
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logger.error("No source specified (use --nuclide or --input)")
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sys.exit(1)
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# Override transition type if explicitly provided
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if args.transition_type:
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config.transition_type = args.transition_type
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logger.info("Override transition_type=%s", args.transition_type)
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# Dry run: display resolved config and exit
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if args.dry_run:
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_print_dry_run_output(config, source_type)
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return
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# Create and calculate spectrum
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start_time = time.time()
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logger.info(
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"Creating BetaSpectrum for %s -> Z=%d,%d, A=%d, endpoint=%.3f MeV",
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_element_symbol(config.Z_parent),
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config.Z_parent,
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config.Z_daughter,
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config.A_number,
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config.endpoint_MeV,
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)
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spectrum = BetaSpectrum.from_config(config)
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_W, _kinetic_MeV = spectrum.get_energy_grid(config)
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_ = spectrum(_W)
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elapsed = time.time() - start_time
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logger.info(
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"Spectrum calculation done in %.3fs (%d points)", elapsed, len(_kinetic_MeV)
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)
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# Export to CSV
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if args.output:
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analyzer = BetaSpectrumAnalyzer(spectrum, config)
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analyzer.export_to_csv(args.output)
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print(f"Spectrum exported to {args.output}")
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analyzer.export_to_csv(args.output, source_type=source_type)
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logger.info("Spectrum exported to %s", args.output)
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# Generate plot
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if args.plot:
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analyzer = BetaSpectrumAnalyzer(spectrum, config)
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analyzer.plot_analysis(save_path=args.plot)
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print(f"Analysis plot saved to {args.plot}")
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logger.info("Analysis plot saved to %s", args.plot)
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logger.info("Done.")
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def _print_dry_run_output(config, source_type: str) -> None:
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"""Print resolved configuration for dry-run mode."""
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from beta_spectrum.logging_utils import get_git_short_hash
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enabled = []
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if config.use_phase_space:
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enabled.append("phase_space")
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if config.use_fermi:
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enabled.append("fermi")
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if config.use_screening:
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enabled.append("screening")
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if config.use_finite_size:
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enabled.append("finite_size")
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if config.use_charge_dist:
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enabled.append("charge_dist")
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if config.use_radiative:
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enabled.append("radiative")
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if config.use_exchange:
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enabled.append("exchange")
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print("=== Dry Run: Resolved Configuration ===")
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print(f"Package: beta-spectrum v{__import__('beta_spectrum').__version__}")
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print(f"Git commit: {get_git_short_hash()}")
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print(f"Source: {source_type}")
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print(f"Nuclide: {config.Z_parent} -> {config.Z_daughter}, A={config.A_number}")
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print(f"Endpoint: {config.endpoint_MeV * 1000:.1f} keV")
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print(f"Transition: {config.transition_type}")
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print(f"e_step: {config.e_step_MeV:.4f} MeV")
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print(f"Corrections: {', '.join(enabled) if enabled else 'none'}")
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if config.use_detector_response:
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print(
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f"Detector: {config.detector_model} (sigma={config.detector_sigma_a_keV} keV, "
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f"tail={config.detector_tail_fraction})"
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)
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else:
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print("Detector: disabled")
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print("========================================")
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def _element_symbol(Z: int) -> str:
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"""Get element symbol from atomic number."""
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symbols = [
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"",
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"H",
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"He",
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"Li",
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"Be",
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"B",
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"C",
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"N",
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"O",
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"F",
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"Ne",
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"Na",
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"Mg",
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"Al",
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"Si",
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"P",
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"S",
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"Cl",
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"Ar",
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"K",
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"Ca",
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"Sc",
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"Ti",
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"V",
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"Cr",
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"Mn",
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"Fe",
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"Co",
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"Ni",
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"Cu",
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"Zn",
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"Ga",
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"Ge",
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"As",
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"Se",
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"Br",
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"Kr",
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"Rb",
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"Sr",
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"Y",
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"Zr",
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"Nb",
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"Mo",
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"Tc",
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"Ru",
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"Rh",
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"Pd",
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"Ag",
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"Cd",
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"In",
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"Sn",
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"Sb",
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"Te",
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"I",
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"Xe",
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"Cs",
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"Ba",
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"La",
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"Ce",
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"Pr",
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"Nd",
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"Pm",
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"Sm",
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"Eu",
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"Gd",
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"Tb",
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"Dy",
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"Ho",
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"Er",
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"Tm",
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"Yb",
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"Lu",
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"Hf",
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"Ta",
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"W",
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"Re",
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"Os",
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"Ir",
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"Pt",
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"Au",
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"Hg",
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"Tl",
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"Pb",
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"Bi",
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"Po",
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"At",
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"Rn",
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"Fr",
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"Ra",
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"Ac",
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"Th",
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"Pa",
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"U",
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"Np",
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"Pu",
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"Am",
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"Cm",
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"Bk",
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"Cf",
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"Es",
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"Fm",
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]
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return symbols[Z] if Z < len(symbols) else f"Z{Z}"
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def main() -> None:
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@@ -206,6 +452,9 @@ def main() -> None:
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try:
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_run(args)
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except KeyboardInterrupt:
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print("\nInterrupted by user.", file=sys.stderr)
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sys.exit(130)
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except Exception as e:
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print(f"Error: {e}", file=sys.stderr)
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sys.exit(1)
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@@ -0,0 +1,164 @@
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"""
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Logging infrastructure for beta-spectrum package.
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Provides a centralized logging setup with:
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- Configurable verbosity levels (WARNING, INFO, DEBUG)
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- Optional file output
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- Consistent formatting across all modules
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- Opt-in design: logging is disabled by default for library use,
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enabled via setup_logging() for CLI/workflow use
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Usage (library):
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# No logging by default — silent, zero overhead
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Usage (CLI):
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from beta_spectrum.logging_utils import setup_logging, get_logger
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setup_logging(level="INFO", log_file="calc.log")
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logger = get_logger("spectrum")
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logger.info("Starting calculation...")
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"""
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from __future__ import annotations
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import logging
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import sys
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from dataclasses import dataclass, field
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from typing import Optional
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@dataclass
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class LoggingConfig:
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"""Configuration for logging setup."""
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level: str = "WARNING"
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"""Logging level: 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'."""
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log_file: Optional[str] = None
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"""Path to log file. If None, only stdout is used."""
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log_format: str = "[%(asctime)s] [%(levelname)-8s] [%(name)s] %(message)s"
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"""Log message format string."""
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date_format: str = "%H:%M:%S"
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"""Date/time format for timestamps."""
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_handlers_configured: bool = field(default=False, repr=False)
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"""Internal flag to prevent double configuration."""
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def setup_logging(config: Optional[LoggingConfig] = None) -> logging.Logger:
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"""
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Configure the root logger for the beta_spectrum package.
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This is a one-shot setup — calling it multiple times with different
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configs will not reconfigure existing handlers. Call setup_logging()
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once at the start of your application.
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Parameters
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----------
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config : LoggingConfig, optional
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Logging configuration. Uses defaults if None.
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Returns
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-------
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logging.Logger
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The root logger for the beta_spectrum package.
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"""
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if config is None:
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config = LoggingConfig()
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logger = logging.getLogger("beta_spectrum")
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# Prevent double configuration
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if config._handlers_configured:
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return logger
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logger.setLevel(getattr(logging, config.level.upper(), logging.WARNING))
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# Remove any existing handlers to avoid duplicates on re-init
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for handler in logger.handlers[:]:
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logger.removeHandler(handler)
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handler.close()
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# Console handler
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console_handler = logging.StreamHandler(sys.stdout)
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console_handler.setLevel(getattr(logging, config.level.upper(), logging.WARNING))
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console_handler.setFormatter(
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logging.Formatter(config.log_format, config.date_format)
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)
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logger.addHandler(console_handler)
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# File handler (optional)
|
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if config.log_file:
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file_handler = logging.FileHandler(config.log_file, mode="a")
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file_handler.setLevel(logging.DEBUG) # Always log everything to file
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file_handler.setFormatter(
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logging.Formatter(config.log_format, config.date_format)
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)
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logger.addHandler(file_handler)
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|
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config._handlers_configured = True
|
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return logger
|
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|
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|
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def get_logger(name: str) -> logging.Logger:
|
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"""
|
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Get a named logger for the beta_spectrum package.
|
||||
|
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Parameters
|
||||
----------
|
||||
name : str
|
||||
Logger name (e.g., "spectrum", "fitter", "nuclear_data").
|
||||
|
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Returns
|
||||
-------
|
||||
logging.Logger
|
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A logger named "beta_spectrum.{name}".
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> logger = get_logger("spectrum")
|
||||
>>> logger.info("Creating spectrum components")
|
||||
"""
|
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return logging.getLogger(f"beta_spectrum.{name}")
|
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|
||||
|
||||
def get_git_short_hash(length: int = 7) -> str:
|
||||
"""
|
||||
Get the short git commit hash.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
length : int
|
||||
Number of characters to return (default: 7).
|
||||
|
||||
Returns
|
||||
-------
|
||||
str
|
||||
Short git hash, or "unknown" if not in a git repo.
|
||||
"""
|
||||
try:
|
||||
import subprocess
|
||||
|
||||
result = subprocess.run(
|
||||
["git", "rev-parse", f"--short={length}", "HEAD"],
|
||||
capture_output=True,
|
||||
text=True,
|
||||
check=True,
|
||||
cwd=_find_git_root(),
|
||||
)
|
||||
return result.stdout.strip()
|
||||
except (subprocess.CalledProcessError, FileNotFoundError):
|
||||
return "unknown"
|
||||
|
||||
|
||||
def _find_git_root() -> str:
|
||||
"""Find the root directory of the git repository."""
|
||||
from pathlib import Path
|
||||
|
||||
current = Path(__file__).resolve()
|
||||
while current != current.parent:
|
||||
if (current / ".git").exists():
|
||||
return str(current)
|
||||
current = current.parent
|
||||
return str(current)
|
||||
+117
-10
@@ -1,6 +1,8 @@
|
||||
# spectrum.py
|
||||
from __future__ import annotations
|
||||
|
||||
import logging
|
||||
|
||||
import numpy as np
|
||||
import matplotlib.pyplot as plt
|
||||
from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
|
||||
@@ -14,6 +16,7 @@ from beta_spectrum.components.screening import ScreeningCorrection
|
||||
from beta_spectrum.components.exchange import ExchangeCorrection
|
||||
from beta_spectrum.components.radiative import RadiativeCorrection
|
||||
|
||||
from beta_spectrum.logging_utils import get_git_short_hash
|
||||
from beta_spectrum.utils import T_to_W
|
||||
from beta_spectrum.constants import ME_MEV
|
||||
|
||||
@@ -67,11 +70,23 @@ class BetaSpectrum:
|
||||
Precise beta spectrum calculator.
|
||||
|
||||
Combines basic spectrum shape (fermi * phase_space) with mutplicative corrections.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
components : List[SpectrumComponent]
|
||||
List of enabled spectral components.
|
||||
logger : logging.Logger, optional
|
||||
Logger for debug/info output.
|
||||
"""
|
||||
|
||||
def __init__(self, components: List[SpectrumComponent]):
|
||||
def __init__(
|
||||
self,
|
||||
components: List[SpectrumComponent],
|
||||
logger: Optional[logging.Logger] = None,
|
||||
):
|
||||
self.components = components
|
||||
self._component_names = [self._get_component_name(c) for c in components]
|
||||
self._logger = logger
|
||||
|
||||
def __call__(self, W: np.ndarray) -> np.ndarray:
|
||||
"""
|
||||
@@ -99,9 +114,18 @@ class BetaSpectrum:
|
||||
return components_dict
|
||||
|
||||
@classmethod
|
||||
def from_config(cls, config: SpectrumConfig) -> BetaSpectrum:
|
||||
def from_config(
|
||||
cls, config: SpectrumConfig, logger: Optional[logging.Logger] = None
|
||||
) -> BetaSpectrum:
|
||||
"""
|
||||
Create a BetaSpectrum from configuration
|
||||
Create a BetaSpectrum from configuration.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
config : SpectrumConfig
|
||||
Configuration with decay parameters and correction toggles.
|
||||
logger : logging.Logger, optional
|
||||
Logger for progress output.
|
||||
"""
|
||||
components: List[SpectrumComponent] = []
|
||||
W0 = float(T_to_W(config.endpoint_MeV))
|
||||
@@ -131,7 +155,7 @@ class BetaSpectrum:
|
||||
if config.use_radiative:
|
||||
components.append(RadiativeCorrection(W0=W0, use_endpoint_resummation=True))
|
||||
|
||||
return cls(components)
|
||||
return cls(components, logger=logger)
|
||||
|
||||
def get_energy_grid(self, config: SpectrumConfig) -> Tuple[np.ndarray, np.ndarray]:
|
||||
"""
|
||||
@@ -221,6 +245,13 @@ class BetaSpectrum:
|
||||
|
||||
theoretical_spectrum = self(W)
|
||||
|
||||
if self._logger:
|
||||
self._logger.debug(
|
||||
"Convolution: %d channels, %d spectrum points",
|
||||
len(detector_response.channel_energies),
|
||||
len(W),
|
||||
)
|
||||
|
||||
convolved = detector_response.convolve(W, theoretical_spectrum, normalize=True)
|
||||
return convolved
|
||||
|
||||
@@ -270,16 +301,31 @@ class BetaSpectrum:
|
||||
class BetaSpectrumAnalyzer:
|
||||
"""
|
||||
Introspection, analysis and debugging tools for BetaSpectrum.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
spectrum : BetaSpectrum
|
||||
The spectrum to analyze.
|
||||
config : SpectrumConfig
|
||||
Configuration used to create the spectrum.
|
||||
logger : logging.Logger, optional
|
||||
Logger for progress output.
|
||||
"""
|
||||
|
||||
def __init__(self, spectrum: BetaSpectrum, config: SpectrumConfig):
|
||||
def __init__(
|
||||
self,
|
||||
spectrum: BetaSpectrum,
|
||||
config: SpectrumConfig,
|
||||
logger: Optional[logging.Logger] = None,
|
||||
):
|
||||
"""
|
||||
Initialize analyzer with a spectrum and configuration
|
||||
Initialize analyzer with a spectrum and configuration.
|
||||
"""
|
||||
self.spectrum = spectrum
|
||||
self.config = config
|
||||
self.W, self.energies_MeV = spectrum.get_energy_grid(config)
|
||||
self._components_cache: Optional[Dict[str, np.ndarray]] = None
|
||||
self._logger = logger
|
||||
|
||||
@property
|
||||
def components(self) -> Dict[str, np.ndarray]:
|
||||
@@ -583,10 +629,65 @@ class BetaSpectrumAnalyzer:
|
||||
]
|
||||
return symbols[Z] if Z < len(symbols) else f"Z{Z}"
|
||||
|
||||
def export_to_csv(self, filename: str) -> None:
|
||||
def export_to_csv(self, filename: str, source_type: str = "unknown") -> None:
|
||||
"""
|
||||
Export spectrum data to CSV with metadata header.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
filename : str
|
||||
Output CSV file path.
|
||||
source_type : str
|
||||
Data source type (paceENSDF, json, cli) for the header.
|
||||
"""
|
||||
total = self.total_spectrum(normalize=True)
|
||||
components = self.components
|
||||
|
||||
# Build enabled corrections list
|
||||
enabled = []
|
||||
if self.config.use_phase_space:
|
||||
enabled.append("phase_space")
|
||||
if self.config.use_fermi:
|
||||
enabled.append("fermi")
|
||||
if self.config.use_screening:
|
||||
enabled.append("screening")
|
||||
if self.config.use_finite_size:
|
||||
enabled.append("finite_size")
|
||||
if self.config.use_charge_dist:
|
||||
enabled.append("charge_dist")
|
||||
if self.config.use_radiative:
|
||||
enabled.append("radiative")
|
||||
if self.config.use_exchange:
|
||||
enabled.append("exchange")
|
||||
|
||||
# Build metadata header
|
||||
from datetime import datetime, timezone
|
||||
|
||||
header_lines = [
|
||||
f"# beta-spectrum v{__import__('beta_spectrum').__version__}",
|
||||
f"# timestamp: {datetime.now(timezone.utc).isoformat()}",
|
||||
f"# source: {source_type}",
|
||||
f"# nuclide: {self.config.Z_parent}->{self.config.Z_daughter}, A={self.config.A_number}",
|
||||
f"# endpoint: {self.config.endpoint_MeV * 1000:.1f} keV",
|
||||
f"# transition: {self.config.transition_type}",
|
||||
f"# corrections: {', '.join(enabled)}",
|
||||
f"# e_step: {self.config.e_step_MeV:.4f} MeV",
|
||||
]
|
||||
|
||||
if self.config.use_detector_response:
|
||||
header_lines.append(
|
||||
f"# detector: {self.config.detector_model} "
|
||||
f"(sigma={self.config.detector_sigma_a_keV} keV, "
|
||||
f"tail={self.config.detector_tail_fraction})"
|
||||
)
|
||||
else:
|
||||
header_lines.append("# detector: disabled")
|
||||
|
||||
header_lines.append(f"# git_commit: {get_git_short_hash()}")
|
||||
|
||||
# Write CSV with header
|
||||
import pandas as pd
|
||||
|
||||
data: Dict[str, np.ndarray] = {
|
||||
"energy_MeV": self.energies_MeV,
|
||||
"spectrum": total,
|
||||
@@ -594,11 +695,17 @@ class BetaSpectrumAnalyzer:
|
||||
for name, values in components.items():
|
||||
data[name] = values
|
||||
|
||||
import pandas as pd
|
||||
|
||||
df = pd.DataFrame(data)
|
||||
df.to_csv(filename, index=False, float_format="%.4e")
|
||||
print(f"Spectrum exported to {filename}")
|
||||
|
||||
# Prepend header
|
||||
with open(filename, "r") as f:
|
||||
content = f.read()
|
||||
with open(filename, "w") as f:
|
||||
f.write("\n".join(header_lines) + "\n" + content)
|
||||
|
||||
if self._logger:
|
||||
self._logger.info("CSV exported to %s with metadata header", filename)
|
||||
|
||||
def get_data(self) -> Dict[str, Any]:
|
||||
"""Get all numerical data for custom analysis."""
|
||||
|
||||
Reference in New Issue
Block a user