refactor of group 5 (configuration and parsing) started (8214dc7d) · Commits · Gaetano Scandariato / PyAETNA

PyAETNA/sampling/config/parser/init.py

+15 −0

Changes for PyAETNA/sampling/config/parser/__init__.py: 15 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		"""
		parser/__init__.py \u2014 Top-level configuration parsing for PyAETNA.

		This package exposes :func:`parse_config`, the single entry point for
		converting a raw YAML configuration dictionary into the structured parameter
		dictionaries used by the sampling engine. Individual subsections are
		delegated to the sibling modules:

		* :mod:`.detrending` \u2014 normalisation, polynomial, Fourier, EIV
		* :mod:`.gp` \u2014 Gaussian Process detrending
		* :mod:`.planets` \u2014 transit, RV, and TTV parameters
		* :mod:`.star` \u2014 stellar properties and RM effect
		* :mod:`.scoping` \u2014 scope keyword parsing and parameter expansion
		* :mod:`.prior_refs` \u2014 ``@name`` reference resolution
		"""
		import warnings

		import jax.numpy as jnp

+11 −2

Changes for PyAETNA/sampling/config/parser/detrending.py: 11 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		"""
		detrending.py — Detrending configuration parsers for PyAETNA.

		This module provides functions to parse detrending-related subsections of the
		YAML configuration: baseline normalisation, polynomial and Fourier series
		corrections, and Errors-in-Variables (EIV) linear detrending.
		"""
		import numpy as np
		from ...utils import _safe_eval_math
		from .prior_refs import is_resolved_prior_reference, resolve_config_value
		@@ -205,6 +212,7 @@ def parse_fourier(detrending, plModel, n_instruments, visit_ids, instrument_ids,
		n_instruments, f'{fourier_name}.c{harmonic}'
		)
		coeff_scopes_dict[harmonic] = coeff_scope
		hybrid_all = frozenset() # accumulate across sin and cos coefficients
		for sc in ['s', 'c']:
		base_name = f'{fourier_name}_c{harmonic}_{sc}'
		hybrid = _expand_detrend_coeff(
		@@ -214,8 +222,9 @@ def parse_fourier(detrending, plModel, n_instruments, visit_ids, instrument_ids,
		plModel.instrument_names,
		global_name_override=tied_name
		)
		if hybrid:
		coeff_hybrid_insts_dict[harmonic] = hybrid
		hybrid_all = hybrid_all \| hybrid
		if hybrid_all:
		coeff_hybrid_insts_dict[harmonic] = hybrid_all

		fourier_config = {
		'name': fourier_name,

+7 −0

Changes for PyAETNA/sampling/config/parser/gp.py: 7 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		"""
		gp.py — Gaussian Process detrending configuration parser for PyAETNA.

		This module provides :func:`parse_gp`, which reads the ``detrending.GP``
		subsection of the YAML configuration and builds per-instrument kernel
		specifications consumed by the sampling engine.
		"""
		from ...utils import _get_default_param_order
		from .prior_refs import is_resolved_prior_reference, resolve_config_value
		from .scoping import _SCOPE_KEYWORDS, _parse_scoped_param

+8 −0

Changes for PyAETNA/sampling/config/parser/planets.py: 8 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		"""
		planets.py — Planet parameter configuration parser for PyAETNA.

		This module provides :func:`parse_planets`, which reads all ``planet_*``
		sections of the YAML configuration and registers transit, RV, and TTV
		parameters in ``free_params`` / ``fixed_params``. It also performs TTV
		coverage analysis and emits warnings when transit epochs lack data coverage.
		"""
		import math as _math
		import numpy as np
		import warnings

+11 −0

Changes for PyAETNA/sampling/config/parser/prior_refs.py: 11 added lines, 0 removed lines.
Original line number	Diff line number	Diff line
		"""
		prior_refs.py — Named prior reference resolution for PyAETNA configuration.

		This module handles the ``@name`` reference syntax that allows the same prior
		specification to be shared across multiple configuration fields. The public
		entry points are :func:`load_named_priors` (reads the top-level ``priors:``
		block) and :func:`resolve_config_value` (substitutes ``@name`` tokens in any
		configuration value).
		"""
		import re

		from .. import priors


		_PRIOR_REF_RE = re.compile(r'^@([A-Za-z_][A-Za-z0-9_]*)$')
		# NOTE: _SCOPE_KEYWORDS is intentionally duplicated from scoping.py to avoid
		# a circular import (scoping.py already imports from this module).
		_SCOPE_KEYWORDS = frozenset(('global', 'per_instrument', 'per_visit'))