hybrax 0.1.0__py3-none-any.whl

hybrax/__init__.py

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+"""Hybrax: bioprocess hybrid models and data management in JAX."""
+
+from importlib.metadata import version
+
+__version__ = version("hybrax")

hybrax/format/__init__.py

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+"""Bioprocess data structures, validation, serialization, and mechanistic modeling."""
+
+import importlib
+import os
+import sys
+from typing import TYPE_CHECKING, Any
+
+# hybrax.format requires float64 throughout. Configure future JAX imports without
+# importing JAX just to initialize this package.
+os.environ["JAX_ENABLE_X64"] = "true"
+if "jax" in sys.modules:
+    importlib.import_module("jax").config.update("jax_enable_x64", True)
+
+from hybrax import __version__
+
+if TYPE_CHECKING:
+    from . import mechanistic, serialization, splines, validate  # noqa: F401
+    from .dataclasses import (  # noqa: F401
+        AugmentedBioProcess,
+        BioProcess,
+        BioProcessCollection,
+        BioProcessMetadata,
+        Bounds,
+        DiscreteEvents,
+        FeedMedium,
+        FeedMediumComponent,
+        Inflow,
+        Outflow,
+        ProcessOrdering,
+        ProcessVariable,
+        PseudobatchTransform,
+        ReactionOde,
+        ReactorMedium,
+        ReactorMediumComponent,
+        StaticVariable,
+        TimeAxis,
+        TimeSeries,
+        Volume,
+        VolumeChange,
+        silence_assumptions,
+    )
+    from .inspect import (  # noqa: F401
+        plot_collection,
+        plot_process,
+        print_collection_structure,
+        print_process_structure,
+        print_rhs_ode,
+    )
+    from .simulation import Simulation, SimulationEvent, SimulationResult  # noqa: F401
+    from .validate import (  # noqa: F401
+        validate_augmented_parent_refs,
+        validate_biomass_in_reactor_medium,
+        validate_bounds,
+        validate_bounds_against_data,
+        validate_cross_process_consistency,
+        validate_discrete_events,
+        validate_for_publication,
+        validate_initial_state_alignment,
+        validate_measurement_sampling_alignment,
+        validate_outflow_retention,
+        validate_process,
+        validate_reaction_ode,
+        validate_reaction_ode_equivalence,
+        validate_time_axis,
+        validate_timeseries_shape,
+        validate_timestamp_bounds,
+        validate_volume_change_sign,
+        validate_volume_change_states,
+        validate_volume_consistency,
+        validate_volume_units,
+    )
+
+_EXPORT_MODULES = {
+    ".dataclasses": (
+        "TimeAxis",
+        "DiscreteEvents",
+        "TimeSeries",
+        "StaticVariable",
+        "BioProcessMetadata",
+        "ProcessVariable",
+        "FeedMediumComponent",
+        "ReactorMediumComponent",
+        "VolumeChange",
+        "Inflow",
+        "Outflow",
+        "Volume",
+        "FeedMedium",
+        "ReactorMedium",
+        "Bounds",
+        "ReactionOde",
+        "ProcessOrdering",
+        "PseudobatchTransform",
+        "BioProcess",
+        "AugmentedBioProcess",
+        "BioProcessCollection",
+        "silence_assumptions",
+    ),
+    ".simulation": ("Simulation", "SimulationEvent", "SimulationResult"),
+    ".inspect": (
+        "print_process_structure",
+        "print_collection_structure",
+        "print_rhs_ode",
+        "plot_process",
+        "plot_collection",
+    ),
+    ".validate": (
+        "validate_time_axis",
+        "validate_timeseries_shape",
+        "validate_discrete_events",
+        "validate_timestamp_bounds",
+        "validate_volume_change_sign",
+        "validate_volume_change_states",
+        "validate_volume_units",
+        "validate_outflow_retention",
+        "validate_biomass_in_reactor_medium",
+        "validate_initial_state_alignment",
+        "validate_measurement_sampling_alignment",
+        "validate_process",
+        "validate_volume_consistency",
+        "validate_for_publication",
+        "validate_augmented_parent_refs",
+        "validate_reaction_ode",
+        "validate_reaction_ode_equivalence",
+        "validate_bounds",
+        "validate_bounds_against_data",
+        "validate_cross_process_consistency",
+    ),
+}
+_EXPORTS = {
+    name: module_name
+    for module_name, names in _EXPORT_MODULES.items()
+    for name in names
+}
+_EXPORTS.update(
+    {
+        "serialization": ".serialization",
+        "validate": ".validate",
+        "mechanistic": ".mechanistic",
+        "splines": ".splines",
+    }
+)
+
+# Ruff cannot infer that unpacking _EXPORTS yields only string keys.
+__all__ = ["__version__", *_EXPORTS]  # noqa: PLE0604
+
+
+def __getattr__(name: str) -> Any:
+    """Load public objects only when accessed."""
+    module_name = _EXPORTS.get(name)
+    if module_name is None:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    module = importlib.import_module(module_name, __name__)
+    value = module if name == module_name.removeprefix(".") else getattr(module, name)
+    globals()[name] = value
+    return value
+
+
+def __dir__() -> list[str]:
+    """Include lazy exports in interactive discovery."""
+    return sorted(set(globals()) | set(__all__))

hybrax/format/_logging.py

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+"""Shared logging setup for hybrax.format."""
+
+import logging
+
+
+def get_logger(name: str) -> logging.Logger:
+    """Return a logger under the ``hybrax.format`` namespace.
+
+    Library code must never call ``logging.basicConfig()`` or set a shared
+    logger's level — that decision belongs solely to the hosting application.
+    A ``NullHandler`` is attached once so that, absent app-level logging
+    configuration, records are silently discarded instead of falling through
+    to ``logging.lastResort``.
+    """
+    top = logging.getLogger("hybrax.format")
+    if not top.handlers:
+        top.addHandler(logging.NullHandler())
+    return logging.getLogger(name)