diff --git a/autofit/non_linear/checkpoint.py b/autofit/non_linear/checkpoint.py new file mode 100644 index 000000000..6e5d2fed8 --- /dev/null +++ b/autofit/non_linear/checkpoint.py @@ -0,0 +1,378 @@ +""" +Where a non-linear search keeps its internal state on disk, and for how long. + +A search has two kinds of internal state (decision D5 of the search-extensibility +epic, ``docs/design/checkpointing.md``): + +- ``result_internal``, the **archive**: the backend's final state, written when a + fit completes and read back by ``Result.search_internal`` and by + ``samples_via_internal_from`` on a completed output folder (the emcee HDF file, + the NUTS and SMC dicts, the dill of every other search); +- ``resume_state``: the file an *interrupted* run resumes from (dynesty's + ``savestate.save``, nautilus's ``checkpoint.hdf5``, NSS's ``nss_checkpoint.pkl``, + MultiStart's dill). Only searches that genuinely resume have one. + +Each search chooses its strategies with two class attributes, +``NonLinearSearch.checkpointer`` (the archive, ``DillCheckpointer()`` by default) and +``NonLinearSearch.resume_state`` (``None`` by default). Three strategies cover every +search: + +- ``DillCheckpointer``: ``search_internal.dill`` (the default); +- ``PickleCheckpointer``: ``search_internal.pickle``, plain ``pickle`` of NumPy data + (BlackJAX NUTS and SMC); +- ``NativeFileCheckpointer(filename, loader)``: a file the backend writes itself and + only autofit reads (emcee's HDF backend, dynesty's savestate, nautilus's hdf5 + checkpoint, NSS's pickle). + +Every strategy offers ``save``, ``load``, ``exists`` and ``finalize`` and declares +``retain_after_completion``: whether its file survives the end of a fit when the +``output.search_internal`` config is off. Strategies are stateless: they take the +search's ``paths`` on every call, so one class-level instance serves every copy of a +search (``copy_with_paths``) and is never serialised with it. + +Only ``DirectoryPaths`` stores anything. ``NullPaths`` (no output) and +``DatabasePaths`` (results live in the database) make ``save`` a no-op and ``load`` +return ``None``, as their ``save_search_internal`` / ``load_search_internal`` always +have. +""" +import logging +import os +import pickle +from pathlib import Path +from typing import Any, Callable, Optional + +logger = logging.getLogger(__name__) + +DILL_FILENAME = "search_internal.dill" +PICKLE_FILENAME = "search_internal.pickle" +EMCEE_FILENAME = "search_internal.hdf" + + +def _directory(paths) -> Optional[Path]: + """ + The ``search_internal`` folder of ``paths``, or ``None`` when ``paths`` stores no + internal state (``NullPaths``, ``DatabasePaths``). + """ + if paths is None or not getattr(paths, "stores_search_internal", True): + return None + try: + directory = paths.search_internal_path + except TypeError: + return None + if directory is None: + return None + return Path(directory) + + +def _atomic_dump(path: Path, obj, dump: Callable): + from autofit.tools.util import open_atomic + + with open_atomic(path, "wb") as f: + dump(obj, f) + + +def load_emcee_backend(path: Path): + """ + Open an emcee ``HDFBackend`` file (the emcee archive and resume state). + """ + import emcee + + return emcee.backends.HDFBackend(filename=str(path)) + + +def _load_dill(path: Path): + import dill + + with open(path, "rb") as f: + return dill.load(f) + + +def _load_pickle(path: Path): + with open(path, "rb") as f: + return pickle.load(f) + + +def load_legacy_search_internal(directory) -> Any: + """ + Load whatever internal state a ``search_internal`` folder holds, detecting its + format from the files present. + + This is the format-aware detection ``DirectoryPaths.load_search_internal`` used + to do inline (it probed for emcee's ``search_internal.hdf`` first), kept for + callers that do not know which search wrote the folder and as the fallback for + a folder written before its search chose a strategy. In order: + + - ``search_internal.hdf``, opened as an emcee ``HDFBackend`` (when emcee is + installed); + - ``search_internal.pickle`` (BlackJAX NUTS / SMC); + - ``search_internal.dill`` (every other search). + + Raises + ------ + FileNotFoundError + If the folder holds none of them. + """ + directory = Path(directory) + + hdf = directory / EMCEE_FILENAME + if hdf.is_file(): + try: + return load_emcee_backend(hdf) + except ImportError: + pass + + pickled = directory / PICKLE_FILENAME + if pickled.is_file(): + return _load_pickle(pickled) + + return _load_dill(directory / DILL_FILENAME) + + +class Checkpointer: + """ + A strategy for one internal-state file of a search (see the module docstring). + + Parameters + ---------- + filename + The file's name inside the search's ``search_internal`` folder. + retain_after_completion + Whether the file is kept when a fit completes even though the + ``output.search_internal`` config is off. For an archive this replaces the + old practice of a search forcing that config on in its ``__init__``; for a + resume state it says the file is also the archive. + """ + + kind = "abstract" + + def __init__(self, filename: str, retain_after_completion: bool = False): + self.filename = filename + self.retain_after_completion = retain_after_completion + + def path(self, paths) -> Optional[Path]: + """ + The file's full path, or ``None`` when ``paths`` stores no internal state. + """ + directory = _directory(paths) + if directory is None: + return None + return directory / self.filename + + def exists(self, paths) -> bool: + path = self.path(paths) + return path is not None and path.is_file() + + def save(self, paths, obj): + """ + Write ``obj`` atomically (a sibling temporary file renamed into place), so an + interrupted write leaves the previous file whole. A no-op when ``paths`` + stores nothing. + """ + raise NotImplementedError + + def _load(self, path: Path): + raise NotImplementedError + + def load(self, paths): + """ + Read the file back. + + Returns ``None`` when ``paths`` stores nothing. When this strategy's own file + is absent the folder is probed by ``load_legacy_search_internal``, so an + output written before the search chose this strategy still loads. + + Raises + ------ + FileNotFoundError + If the folder holds no internal state at all. + """ + path = self.path(paths) + if path is None: + return None + if path.is_file(): + return self._load(path) + return load_legacy_search_internal(path.parent) + + def finalize(self, paths, obj=None): + """ + Write the final state when a fit completes. For an archive strategy that is + ``save(obj)``; a strategy whose file the backend writes itself has nothing + to add. + """ + if obj is not None: + self.save(paths, obj) + + def discard(self, paths): + """ + Delete the file (a resume state, once the fit it would resume has completed). + """ + path = self.path(paths) + if path is None: + return + try: + os.remove(path) + except FileNotFoundError: + pass + + def __repr__(self): + return ( + f"{type(self).__name__}({self.filename!r}, " + f"retain_after_completion={self.retain_after_completion})" + ) + + def __eq__(self, other): + return ( + type(self) is type(other) + and self.filename == other.filename + and self.retain_after_completion == other.retain_after_completion + ) + + def __hash__(self): + return hash((type(self), self.filename, self.retain_after_completion)) + + +class DillCheckpointer(Checkpointer): + """ + ``search_internal.dill``: the backend object serialised with ``dill`` (the + default for every search). + + Parameters + ---------- + strip_attributes + Attributes set to ``None`` for the duration of the dump and restored + afterwards, for members that cannot be serialised (nautilus's + multiprocessing pools ``pool_l`` / ``pool_s``). + """ + + kind = "dill" + + def __init__( + self, + filename: str = DILL_FILENAME, + retain_after_completion: bool = False, + strip_attributes=(), + ): + super().__init__( + filename=filename, retain_after_completion=retain_after_completion + ) + self.strip_attributes = tuple(strip_attributes) + + def save(self, paths, obj): + path = self.path(paths) + if path is None: + return + + import dill + + stripped = {} + for name in self.strip_attributes: + if hasattr(obj, name): + stripped[name] = getattr(obj, name) + setattr(obj, name, None) + try: + _atomic_dump(path, obj, dill.dump) + finally: + for name, value in stripped.items(): + setattr(obj, name, value) + + def _load(self, path: Path): + return _load_dill(path) + + +class PickleCheckpointer(Checkpointer): + """ + ``search_internal.pickle``: plain ``pickle`` of already-NumPy data (BlackJAX NUTS + and SMC, whose dicts ``dill`` does not need and which then load without it). + """ + + kind = "pickle" + + def __init__( + self, filename: str = PICKLE_FILENAME, retain_after_completion: bool = True + ): + super().__init__( + filename=filename, retain_after_completion=retain_after_completion + ) + + def save(self, paths, obj): + path = self.path(paths) + if path is None: + return + _atomic_dump(path, obj, pickle.dump) + + def _load(self, path: Path): + return _load_pickle(path) + + +class NativeFileCheckpointer(Checkpointer): + """ + A file in the backend's own format, which the backend writes itself (emcee's HDF + backend, dynesty's ``savestate.save``, nautilus's ``checkpoint.hdf5``, NSS's + ``nss_checkpoint.pkl``): autofit only locates, loads and (for a resume state) + deletes it. + + Parameters + ---------- + filename + The file's name inside ``search_internal``. + loader + ``loader(path)`` opens the file (for example ``load_emcee_backend``). + retain_after_completion + See ``Checkpointer``. + """ + + kind = "native" + + def __init__( + self, + filename: str, + loader: Callable[[Path], Any], + retain_after_completion: bool = False, + ): + super().__init__( + filename=filename, retain_after_completion=retain_after_completion + ) + self.loader = loader + + def save(self, paths, obj): + """ + A no-op: the backend writes this file itself, during the run. + """ + + def finalize(self, paths, obj=None): + """ + A no-op: the backend has already written the final state. + """ + + def load(self, paths): + """ + Open the file with ``loader``. A native file is the backend's own format, so + there is no format probing; ``FileNotFoundError`` if it is absent, except + that an absent archive falls back to the legacy probe like every strategy. + """ + path = self.path(paths) + if path is None: + return None + if path.is_file(): + return self.loader(path) + if self.retain_after_completion: + return load_legacy_search_internal(path.parent) + raise FileNotFoundError(f"No {self.filename} exists at {path.parent}") + + def __eq__(self, other): + return super().__eq__(other) and self.loader is other.loader + + def __hash__(self): + return super().__hash__() + + +def checkpointer_kind(checkpointer: Optional[Checkpointer]) -> Optional[str]: + """ + The manifest spelling of a strategy: ``"dill"``, ``"pickle"``, + ``"native:"``, or ``None``. + """ + if checkpointer is None: + return None + if checkpointer.kind == "native": + return f"native:{checkpointer.filename}" + return checkpointer.kind diff --git a/autofit/non_linear/paths/abstract.py b/autofit/non_linear/paths/abstract.py index 6fb6e2713..df08ca88b 100644 --- a/autofit/non_linear/paths/abstract.py +++ b/autofit/non_linear/paths/abstract.py @@ -104,6 +104,13 @@ def _replace_zip_member(zip_path, arcname: str, file_path): class AbstractPaths(ABC): + stores_search_internal = True + """ + Whether the search's internal state (``autofit.non_linear.checkpoint``) is + stored on disk under ``search_internal/``. ``NullPaths`` (no output) and + ``DatabasePaths`` (results live in the database) store none. + """ + def __init__( self, name: Optional[str] = None, diff --git a/autofit/non_linear/paths/database.py b/autofit/non_linear/paths/database.py index 6f7d03092..bbe548d8e 100644 --- a/autofit/non_linear/paths/database.py +++ b/autofit/non_linear/paths/database.py @@ -15,6 +15,8 @@ class DatabasePaths(AbstractPaths): + stores_search_internal = False + def __init__( self, session, diff --git a/autofit/non_linear/paths/directory.py b/autofit/non_linear/paths/directory.py index 78110cb37..a1a8bb792 100644 --- a/autofit/non_linear/paths/directory.py +++ b/autofit/non_linear/paths/directory.py @@ -20,6 +20,7 @@ from autofit.non_linear.test_mode import skip_visualization from .abstract import AbstractPaths, _test_mode_segment +from ..checkpoint import load_legacy_search_internal from ..samples import load_from_table from autofit.non_linear.samples.pdf import SamplesPDF @@ -224,31 +225,33 @@ def save_search_internal(self, obj): def load_search_internal(self): """ - Load the internal representation of a non-linear search from a pickle or dill file. + Load the internal representation of a non-linear search (its archive). - The results in this representation are required to use a search's in-built tools for visualization, - analysing samples and other tasks. + Loading is injected: the search that owns these paths (``self.search``) + loads through its ``checkpointer`` (emcee's HDF backend, the NUTS / SMC + pickle, or the dill of every other search), so ``paths`` knows no backend + format. A folder opened without its search falls back to format-aware + detection (``autofit.non_linear.checkpoint.load_legacy_search_internal``: + ``search_internal.hdf``, then ``.pickle``, then ``.dill``), which is also what + a checkpointer falls back to when its own file is absent, so outputs written + before A3 still load. Returns ------- The results of the non-linear search in its internal representation. - """ - - # This is a nasty hack to load emcee backends. It will be removed once the source code is more stable. - - try: - import emcee - backend_filename = self.search_internal_path / "search_internal.hdf" - if backend_filename.is_file(): - return emcee.backends.HDFBackend(filename=str(backend_filename)) - except ImportError: - pass + Raises + ------ + FileNotFoundError + If no internal state is stored (for example a summary-only output, or + ``output.search_internal: false``). + """ + checkpointer = getattr(getattr(self, "search", None), "checkpointer", None) - filename = self.search_internal_path / "search_internal.dill" + if checkpointer is not None: + return checkpointer.load(self) - with open_(filename, "rb") as f: - return dill.load(f) + return load_legacy_search_internal(self.search_internal_path) def remove_search_internal(self): """ diff --git a/autofit/non_linear/paths/null.py b/autofit/non_linear/paths/null.py index 7b7f76bc1..e3686eba5 100644 --- a/autofit/non_linear/paths/null.py +++ b/autofit/non_linear/paths/null.py @@ -9,6 +9,8 @@ class NullPaths(AbstractPaths): Null version of paths object for avoiding writing of files to disk """ + stores_search_internal = False + @property def samples(self): return None diff --git a/autofit/non_linear/samples/adapter.py b/autofit/non_linear/samples/adapter.py new file mode 100644 index 000000000..28f0eb1ea --- /dev/null +++ b/autofit/non_linear/samples/adapter.py @@ -0,0 +1,358 @@ +""" +The one conversion from a backend's raw samples to a ``Samples`` object. + +Every search turns its backend's internal state into the same five things: the +parameter vectors, a log likelihood or a log posterior per vector, a weight per +vector, and the backend-specific ``samples_info`` entries. A search expresses that +as a ``RawSamples`` (``NonLinearSearch.raw_samples_from``) and ``samples_from_raw`` +does everything else, once, for every search: + +- the log prior of every vector, through one helper (``log_prior_list_from``); +- the log likelihood from a log posterior (``log_likelihood = log_posterior - + log_prior``) when the backend reports a posterior; +- the length checks that keep parameters, log values and weights in correspondence + (PyAutoFit#1628); +- recognition of the backends' invalid-model sentinels (``-1e99``, ``-1e30``, + ``-inf``) through one predicate (``is_invalid``); +- the injection of ``samples_info["time"]`` and, through the ``Samples`` class, + ``samples_info["class_path"]``. + +Representations are preserved (decision D13 of the search-extensibility epic). +Parameter vectors, log likelihoods and weights reach ``Sample.from_lists`` exactly +as the backend produced them, in the backend's order: equally weighted draws keep +weight 1, weighted samples keep the weights their search computed (normalised or +not), nothing is renormalised and no sentinel value is rewritten. The ordering of +the vectors is the search's to specify (for example ``ChainPosterior`` flattens +draw-major for emcee and zeus and chain-major for BlackJAX NUTS), and diagnostics +belong to the search's ``info`` entries, which are passed through untouched. +""" +import logging +import math +from dataclasses import dataclass, field +from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple, Type + +import numpy as np + +from autofit import exc + +logger = logging.getLogger(__name__) + +INVALID_SENTINELS = (-1.0e99, -1.0e30, -float("inf")) +""" +The values backends use for a model whose likelihood is invalid: ``-1e99`` +(dynesty and the post-fit ``Fitness`` resample value), ``-1e30`` (NSS sampling) and +``-inf`` (emcee, zeus, BlackJAX, the MLE searches). +""" + +INVALID_THRESHOLD = -1.0e30 +""" +Every log likelihood at or below this value is one of ``INVALID_SENTINELS`` (or a +value derived from one, such as ``-1e99 - log_prior``), never a likelihood a real +model evaluates to. +""" + + +def is_invalid(value) -> bool: + """ + Whether a log likelihood or log posterior is a backend's invalid-model sentinel. + + This is the single recognition rule for all three sentinels; the value itself is + never rewritten, so stored samples keep the representation their backend gave + them. NaN (the MultiStart diagnostic lanes, which carry no likelihood) is not a + sentinel. + """ + try: + value = float(value) + except (TypeError, ValueError): + return False + if math.isnan(value): + return False + return value <= INVALID_THRESHOLD + + +def invalid_count(values: Sequence) -> int: + """ + The number of entries of ``values`` that are invalid-model sentinels. + """ + return sum(1 for value in values if is_invalid(value)) + + +def log_prior_list_from(model, parameter_lists: Sequence[Sequence[float]]) -> List: + """ + The log prior of every parameter vector: the one log-prior helper of sample + conversion (``model.log_prior_list_from``, the sum of each vector's per-prior log + densities). + """ + return model.log_prior_list_from(parameter_lists=parameter_lists) + + +def _as_list(values): + """ + ``values`` as a list, without changing the type of its elements unless it is a + NumPy array (whose ``tolist`` gives plain Python scalars, as every search did + before the adapter). + """ + if values is None: + return None + if isinstance(values, np.ndarray): + return values.tolist() + return list(values) + + +@dataclass(frozen=True) +class RawSamples: + """ + What a backend produced, before any conversion. + + Parameters + ---------- + parameters + The parameter vectors, ``(N, D)``, in physical coordinates and in the + search's sample order. + log_likelihood + The log likelihood of every vector, ``(N,)``. Give either this or + ``log_posterior``. + log_posterior + The log posterior of every vector, ``(N,)``; the log likelihood is then + ``log_posterior - log_prior``. + weights + The weight of every vector, ``(N,)``, exactly as stored. ``None`` means + equally weighted draws (weight 1 each). Never renormalised here. + info + The search-specific ``samples_info`` entries (diagnostics, settings, + counters). ``time`` is injected by ``samples_from_raw`` when absent. + log_prior + The log prior of every vector when the backend already has it; ``None`` + (the usual case) computes it with ``log_prior_list_from``. + samples_kwargs + Extra keyword arguments of the ``Samples`` class (for example + ``SamplesMCMC``'s ``auto_correlations``). + label + The backend's name, used in error messages. + """ + + parameters: Any + log_likelihood: Optional[Any] = None + log_posterior: Optional[Any] = None + weights: Optional[Any] = None + info: Dict[str, Any] = field(default_factory=dict) + log_prior: Optional[Any] = None + samples_kwargs: Dict[str, Any] = field(default_factory=dict) + label: str = "search" + + def __post_init__(self): + if (self.log_likelihood is None) == (self.log_posterior is None): + raise exc.SamplesException( + f"The raw samples of {self.label} must give exactly one of " + "log_likelihood and log_posterior." + ) + + +def _check_length(label: str, n_parameters: int, values, name: str): + """ + Raise when a per-sample column does not have one entry per parameter vector. + """ + if values is not None and len(values) != n_parameters: + raise exc.SamplesException( + f"The number of {label} parameter samples does not match the number of " + f"{name} values returned by the sampler: " + f"{n_parameters} parameter samples versus " + f"{len(values)} {name} values. " + f"The parameters and {name}s are therefore not in correspondence " + "and the samples cannot be built." + ) + + +def samples_from_raw( + model, + raw: RawSamples, + samples_cls: Type, + time: Optional[float] = None, + **samples_kwargs, +): + """ + Build the ``Samples`` object of ``raw`` (see the module docstring for what is + done here, once, for every search). + + Parameters + ---------- + model + The model the parameter vectors belong to. + raw + The backend's raw samples. + samples_cls + The ``Samples`` class to build (``Samples``, ``SamplesMCMC``, + ``SamplesNest``, ``SamplesSMC``, ``NSSamples``, ...). Its constructor stamps + ``samples_info["class_path"]``, which the aggregator and + ``DirectoryPaths.samples`` use to rebuild it. + time + The search's run time, injected as ``samples_info["time"]`` unless the + search's own ``info`` already gives one. + samples_kwargs + Extra keyword arguments of ``samples_cls``, merged over + ``raw.samples_kwargs``. + """ + from autofit.non_linear.samples.sample import Sample + + parameter_lists = _as_list(raw.parameters) + n = len(parameter_lists) + + if raw.log_posterior is not None: + log_posterior_list = _as_list(raw.log_posterior) + _check_length(raw.label, n, log_posterior_list, "log posterior") + else: + log_posterior_list = None + + log_likelihood_list = _as_list(raw.log_likelihood) + _check_length(raw.label, n, log_likelihood_list, "log likelihood") + + if raw.log_prior is not None: + log_prior_list = _as_list(raw.log_prior) + _check_length(raw.label, n, log_prior_list, "log prior") + else: + log_prior_list = log_prior_list_from( + model=model, parameter_lists=parameter_lists + ) + + if log_likelihood_list is None: + log_likelihood_list = [ + log_posterior - log_prior + for log_posterior, log_prior in zip(log_posterior_list, log_prior_list) + ] + + if raw.weights is None: + weight_list = n * [1.0] + else: + weight_list = _as_list(raw.weights) + _check_length(raw.label, n, weight_list, "weight") + + invalid = invalid_count(log_likelihood_list) + if invalid: + logger.debug( + f"{invalid} of the {n} {raw.label} samples carry an invalid-model " + "sentinel log likelihood; they are kept as stored." + ) + + sample_list = Sample.from_lists( + model=model, + parameter_lists=parameter_lists, + log_likelihood_list=log_likelihood_list, + log_prior_list=log_prior_list, + weight_list=weight_list, + ) + + info = dict(raw.info) + if "time" not in info: + info["time"] = time + + return samples_cls( + model=model, + sample_list=sample_list, + samples_info=info, + **{**raw.samples_kwargs, **samples_kwargs}, + ) + + +class ChainPosterior: + """ + The equally weighted draws of an ensemble or multi-chain MCMC backend, thinned and + with burn-in removed: the one implementation shared by Emcee, Zeus and + BlackJAX NUTS. + + ``get_chain(discard, thin)`` and ``get_log_prob(discard, thin)`` return the flat + ``(N, D)`` draws and ``(N,)`` log values for a burn-in and thinning, so emcee's and + zeus's own ``get_chain(discard=..., thin=..., flat=True)`` slicing is used + unchanged. ``from_arrays`` builds the getters for a backend that only stores + arrays. + """ + + def __init__( + self, + get_chain: Callable[[int, int], np.ndarray], + get_log_prob: Callable[[int, int], np.ndarray], + label: str = "MCMC", + ): + self.get_chain = get_chain + self.get_log_prob = get_log_prob + self.label = label + + @classmethod + def from_sampler(cls, sampler, label: str = "MCMC") -> "ChainPosterior": + """ + For an emcee or zeus sampler (or backend), via their ``get_chain`` and + ``get_log_prob`` with ``flat=True``. + """ + return cls( + get_chain=lambda discard, thin: sampler.get_chain( + discard=discard, thin=thin, flat=True + ), + get_log_prob=lambda discard, thin: sampler.get_log_prob( + discard=discard, thin=thin, flat=True + ), + label=label, + ) + + @classmethod + def from_arrays( + cls, + chain: np.ndarray, + log_prob: np.ndarray, + chain_major: bool = False, + label: str = "MCMC", + ) -> "ChainPosterior": + """ + For draws stored as arrays of shape ``(n_steps, n_chains, n_dim)`` and + ``(n_steps, n_chains)``. + + Burn-in and thinning slice the step axis as emcee does + (``[discard + thin - 1 :: thin]``, the whole chain for ``discard=0, + thin=1``). ``chain_major=True`` flattens chain by chain (all of chain 0's + draws in order, then chain 1's, ...); otherwise draw by draw, as emcee's + ``flat=True`` does. + """ + chain = np.asarray(chain) + log_prob = np.asarray(log_prob) + + def _flat(values, discard, thin): + values = values[discard + thin - 1 :: thin] + if chain_major: + values = np.moveaxis(values, 0, 1) + return values.reshape((-1,) + values.shape[2:]) + + return cls( + get_chain=lambda discard, thin: _flat(chain, discard, thin), + get_log_prob=lambda discard, thin: _flat(log_prob, discard, thin), + label=label, + ) + + def thin(self, discard: int, thin: int) -> Tuple[np.ndarray, np.ndarray]: + """ + The draws and log values after removing ``discard`` burn-in steps and keeping + every ``thin``-th step. + + When that leaves no draws (an unconverged chain whose auto-correlation time + is comparable to its length), the whole chain is used instead, with a log + message, so the samples can still be built and inspected. The log values are + always requested with the same ``discard`` and ``thin`` as the draws, so the + two stay in correspondence (PyAutoFit#1628). + """ + draws = self.get_chain(discard, thin) + + if len(draws) == 0: + logger.info( + f""" + After thinning the {self.label} samples in order to remove burn-in, no samples were left. + + To create a samples object containing samples, so that the code can continue and results + can be inspected, the full list of samples before removing burn-in has been used. This may + indicate that the sampler has not converged and therefore your results may not be reliable. + + To fix this, run {self.label} with more steps to ensure convergence is achieved or change the + auto correlation settings to be less aggressive in thinning samples. + """ + ) + discard = 0 + thin = 1 + draws = self.get_chain(discard, thin) + + return draws, self.get_log_prob(discard, thin) diff --git a/autofit/non_linear/search/abstract_search.py b/autofit/non_linear/search/abstract_search.py index b0d7715ac..1bcebb7dc 100644 --- a/autofit/non_linear/search/abstract_search.py +++ b/autofit/non_linear/search/abstract_search.py @@ -50,6 +50,7 @@ from autofit.non_linear.paths.sub_directory_paths import SubDirectoryPaths from autofit.non_linear.samples.samples import Samples from autofit.non_linear.samples.summary import SamplesSummary +from autofit.non_linear.checkpoint import Checkpointer, DillCheckpointer from autofit.non_linear.timer import Timer from autofit.non_linear.analysis import Analysis from autofit.non_linear.paths.null import NullPaths @@ -1194,7 +1195,7 @@ def post_fit_output(self, search_internal): search_internal The internal search. """ - if not conf.instance["output"]["search_internal"]: + if not self.retains_search_internal: self.logger.info("Removing search internal folder.") self.paths.remove_search_internal() elif search_internal is not None: @@ -1439,9 +1440,6 @@ def _build_fake_samples(model, parameter_vector, log_likelihood): # result through the initializer, so it has no starting point to plot. _plots_start_point = True - # The `Samples` class `samples_from_raw` builds for a `run(ctx)` search. - samples_cls = Samples - @abstractmethod def _fit(self, model: AbstractPriorModel, analysis: Analysis): """ @@ -1493,18 +1491,13 @@ def run(self, ctx) -> Any: run._is_bridge_default = True - def raw_samples_from(self, model: AbstractPriorModel, internal): - """ - Map a ``run(ctx)`` search's internal state onto a ``RawSamples`` - (``autofit.non_linear.search.fit_context``). - """ - raise NotImplementedError - - def info_from(self, internal) -> Optional[dict]: + def info_from(self, internal) -> dict: """ - The ``samples_info`` entries of a ``run(ctx)`` search's internal state. + The ``samples_info`` entries of a ``run(ctx)`` search's internal state, the + ``info`` its ``raw_samples_from`` puts on the ``RawSamples`` + (``autofit.non_linear.samples.adapter``). """ - return None + return {} def fitness_overrides(self, analysis: Analysis) -> dict: """ @@ -1589,11 +1582,55 @@ def apply_test_mode(self): """ pass - def output_search_internal(self, search_internal): - self.paths.save_search_internal( - obj=search_internal, + # --- internal state: archive and resume state (search-extensibility A3, D5) ---- + # + # See ``autofit.non_linear.checkpoint`` and ``docs/design/checkpointing.md``. + + checkpointer: Checkpointer = DillCheckpointer() + """ + The archive strategy: where the backend's final state is stored when a fit + completes, for ``Result.search_internal`` and ``samples_via_internal_from``. + """ + + resume_state: Optional[Checkpointer] = None + """ + The file an interrupted run resumes from, for searches that genuinely resume + (``None`` otherwise). Deleted when the fit completes unless it is the archive's + own file or declares ``retain_after_completion``. + """ + + @property + def retains_search_internal(self) -> bool: + """ + Whether ``search_internal/`` survives the end of a fit: always when the + archive declares ``retain_after_completion`` (its results cannot be rebuilt + without it), otherwise when the ``output.search_internal`` config is on. + Constructing or running a search never changes that config. + """ + return bool( + self.checkpointer.retain_after_completion + or conf.instance["output"]["search_internal"] ) + def output_search_internal(self, search_internal): + """ + Archive ``search_internal`` through the search's ``checkpointer`` and, once a + fit has completed, discard its resume state (there is nothing left to + resume). + + ``_fit`` of the searches that archive mid-run (BlackJAX NUTS, SMC) also + calls this after every chunk; their resume state is ``None``. + """ + self.checkpointer.finalize(self.paths, search_internal) + + resume_state = self.resume_state + if ( + resume_state is not None + and not resume_state.retain_after_completion + and resume_state.filename != self.checkpointer.filename + ): + resume_state.discard(self.paths) + def _steps_until_full_update(self, iterations_remaining: int) -> int: """ How many iterations to run before the next ``perform_update`` @@ -1857,6 +1894,19 @@ def start_points( return unit_parameter_lists, parameter_lists, figure_of_merit_list + # --- samples conversion (search-extensibility phase A3) ------------------------- + # + # A search maps its backend's internal state onto a ``RawSamples`` in + # ``raw_samples_from``; ``samples_via_internal_from`` below is implemented once, + # here, on top of it (``autofit.non_linear.samples.adapter``). + + samples_cls = Samples + """ + The ``Samples`` class ``samples_via_internal_from`` builds (``SamplesMCMC`` and + ``SamplesNest`` on the family bases, ``SamplesSMC`` / ``NSSamples`` on those + searches). + """ + def samples_from(self, model: AbstractPriorModel, search_internal=None) -> Samples: """ Loads the samples of a non-linear search from its output files. @@ -1888,25 +1938,54 @@ def samples_from(self, model: AbstractPriorModel, search_internal=None) -> Sampl def samples_via_internal_from( self, model: AbstractPriorModel, search_internal=None - ): - """ - The samples of the internal state. A ``run(ctx)`` search gets them from its - ``raw_samples_from``; any other search overrides this. + ) -> Samples: """ - if type(self).raw_samples_from is NonLinearSearch.raw_samples_from: - raise NotImplementedError + The samples of the search, converted from its internal state. - from autofit.non_linear.search.fit_context import samples_from_raw + ``search_internal`` is the backend's in-memory state when given; otherwise + it is loaded from the output folder (``load_search_internal``). The search's + ``raw_samples_from`` maps it onto a ``RawSamples`` and ``samples_from_raw`` + builds the ``samples_cls`` object (log priors, the log likelihood from a log + posterior, length checks, ``time`` / ``class_path``), the same way for every + search. + + Raises + ------ + NotImplementedError + When the search does not implement ``raw_samples_from``. + FileNotFoundError + When no internal state is stored. + """ + from autofit.non_linear.samples.adapter import samples_from_raw if search_internal is None: - search_internal = self.paths.load_search_internal() + search_internal = self.load_search_internal() + + raw = self.raw_samples_from(model, search_internal) return samples_from_raw( model=model, - raw=self.raw_samples_from(model, search_internal), + raw=raw, samples_cls=self.samples_cls, + time=self.timer.time if self.timer else None, ) + def raw_samples_from(self, model: AbstractPriorModel, search_internal): + """ + Map the backend's internal state onto a + ``autofit.non_linear.samples.adapter.RawSamples``: its parameter vectors, + log likelihoods (or log posteriors), weights and ``samples_info`` entries, + exactly as the backend stores them. Every concrete search implements it. + """ + raise NotImplementedError + + def load_search_internal(self): + """ + The search's internal state as stored in its output folder, or ``None`` when + its paths store nothing (``NullPaths``, ``DatabasePaths``). + """ + return self.paths.load_search_internal() + def _pools(self) -> PoolFactory: """ The current fit's `PoolFactory` (the JAX fork rule applied to its analysis), or, @@ -1915,6 +1994,7 @@ def _pools(self) -> PoolFactory: pools = self.__dict__.get("_fit_pools") return pools if pools is not None else PoolFactory(self) + @check_cores def make_pool(self): """Make the pool instance used to parallelize a `NonLinearSearch` alongside a set of unique ids for every process in the pool. If the specified number of cores is 1, a pool instance is not made and None is returned. diff --git a/autofit/non_linear/search/capabilities.py b/autofit/non_linear/search/capabilities.py index a9b891950..283835461 100644 --- a/autofit/non_linear/search/capabilities.py +++ b/autofit/non_linear/search/capabilities.py @@ -29,6 +29,9 @@ ``test_mode_budget`` The reduced budget ``PYAUTO_TEST_MODE=1`` applies. ``objective_target`` What the backend's objective returns and in which coordinates. ``invalid_value`` The sentinel the objective returns for an invalid model. +``checkpointer`` Where the search archives its internal state when a fit + completes (``autofit.non_linear.checkpoint``): ``dill``, + ``pickle`` or ``native:``. ======================== ============================================================== ``invalid_value`` records what the backend actually sees and is not yet normalised. For @@ -172,6 +175,7 @@ def to_dict(self) -> Dict[str, str]: "test_mode_budget", "objective_target", "invalid_value", + "checkpointer", ) """ The names of the static capability attributes, in manifest order. @@ -196,6 +200,10 @@ def capability_value(name: str, value: Any) -> Any: return value.to_dict() if value is not None else None if name == "invalid_value": return invalid_value_to_str(value) + if name == "checkpointer": + from autofit.non_linear.checkpoint import checkpointer_kind + + return checkpointer_kind(value) if name == "citation_keys": return list(value) if name == "test_mode_budget": diff --git a/autofit/non_linear/search/fit_context.py b/autofit/non_linear/search/fit_context.py index 7d7677918..9f2c29dd6 100644 --- a/autofit/non_linear/search/fit_context.py +++ b/autofit/non_linear/search/fit_context.py @@ -7,79 +7,24 @@ a search that overrides ``_fit`` keeps working unchanged. ``Drawer`` and ``Nautilus`` are the first two searches on the bridge. -Members filled by later phases are present with their A2 value: +Members filled by later phases: -- ``ctx.resume`` is ``None`` and ``ctx.checkpointer`` is ``None`` (phase A3 fills both; - until then a backend resumes from its own native checkpoint, as ``Nautilus`` does); +- ``ctx.checkpointer`` is the search's archive strategy (``NonLinearSearch.checkpointer``) + and ``ctx.resume`` its resume state (``NonLinearSearch.resume_state``) when the + interrupted run's file exists, else ``None`` (phase A3, ``autofit.non_linear.checkpoint``); + ``ctx.resume`` is the ``Checkpointer`` handle, not the loaded state, because some + backends reopen their own native file (``Nautilus``); - ``ctx.rng`` is a ``numpy.random.SeedSequence`` from the search's ``seed`` attribute when it has one (phase A4 adds one search-level seed and feeds the initializer). -``RawSamples`` and ``samples_from_raw`` are a provisional, minimal stand-in for phase -A3's samples adapter (``autofit/non_linear/samples/adapter.py``), so a ``run(ctx)`` search -has the right shape now; A3's adapter replaces them. +``RawSamples`` and ``samples_from_raw`` are phase A3's samples adapter +(``autofit/non_linear/samples/adapter.py``), re-exported here for ``run(ctx)`` searches. """ -from typing import Any, Iterator, List, NamedTuple, Optional +from typing import Any, Iterator import numpy as np - -class RawSamples(NamedTuple): - """ - A backend's samples, before conversion to ``Samples``: parameter vectors, their log - likelihoods **or** log posteriors, their weights and the ``samples_info`` entries. - - Provisional: phase A3's ``samples/adapter.py`` owns the final type. - """ - - parameters: List[List[float]] - log_likelihood: Optional[List[float]] = None - log_posterior: Optional[List[float]] = None - weights: Optional[List[float]] = None - info: Optional[dict] = None - - -def samples_from_raw(model, raw: RawSamples, samples_cls): - """ - Convert ``raw`` into a ``samples_cls`` instance: the log prior of every vector, the log - likelihood from the log posterior when only that was given, and unit weights when none - were. Weights are never renormalised. - - Provisional: phase A3's adapter replaces it. - """ - from autofit.non_linear.samples.sample import Sample - - parameter_lists = raw.parameters - - log_prior_list = [ - sum(model.log_prior_list_from_vector(vector=vector)) - for vector in parameter_lists - ] - - if raw.log_likelihood is not None: - log_likelihood_list = raw.log_likelihood - else: - log_likelihood_list = [ - log_posterior - log_prior - for log_posterior, log_prior in zip(raw.log_posterior, log_prior_list) - ] - - weight_list = ( - raw.weights if raw.weights is not None else len(log_likelihood_list) * [1.0] - ) - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - - return samples_cls( - model=model, - sample_list=sample_list, - samples_info=raw.info, - ) +from autofit.non_linear.samples.adapter import RawSamples, samples_from_raw class UpdateSchedule: @@ -136,8 +81,13 @@ def __init__( self.test_mode_level = test_mode_level self.pool = pool self.rng = np.random.SeedSequence(getattr(search, "seed", None)) - self.resume = None - self.checkpointer = None + self.checkpointer = search.checkpointer + resume_state = search.resume_state + self.resume = ( + resume_state + if resume_state is not None and resume_state.exists(search.paths) + else None + ) self.schedule = UpdateSchedule(search) def objective(self, kind: str): diff --git a/autofit/non_linear/search/mcmc/abstract_mcmc.py b/autofit/non_linear/search/mcmc/abstract_mcmc.py index 77ff4489b..49de061ec 100644 --- a/autofit/non_linear/search/mcmc/abstract_mcmc.py +++ b/autofit/non_linear/search/mcmc/abstract_mcmc.py @@ -7,12 +7,15 @@ from autofit.non_linear.initializer import Initializer, InitializerBall from autofit.non_linear.search.mcmc.auto_correlations import AutoCorrelationsSettings from autofit.non_linear.plot import corner_cornerpy +from autofit.non_linear.samples.mcmc import SamplesMCMC if TYPE_CHECKING: from autofit.database.sqlalchemy_ import sa class AbstractMCMC(NonLinearSearch): + samples_cls = SamplesMCMC + def __init__( self, name: Optional[str] = None, diff --git a/autofit/non_linear/search/mcmc/blackjax/nuts/search.py b/autofit/non_linear/search/mcmc/blackjax/nuts/search.py index a0876de53..af1d43837 100644 --- a/autofit/non_linear/search/mcmc/blackjax/nuts/search.py +++ b/autofit/non_linear/search/mcmc/blackjax/nuts/search.py @@ -2,15 +2,13 @@ import logging import os -import pickle from pathlib import Path from typing import Optional, TYPE_CHECKING import numpy as np -from autonerves import conf - from autofit.mapper.prior_model.abstract import AbstractPriorModel +from autofit.non_linear.checkpoint import PICKLE_FILENAME, PickleCheckpointer from autofit.non_linear.fitness import Fitness from autofit.non_linear.initializer import Initializer from autofit.non_linear.search.mcmc.abstract_mcmc import AbstractMCMC @@ -25,8 +23,7 @@ stack_initial_positions, ) from autofit.non_linear.test_mode import is_test_mode -from autofit.non_linear.samples.mcmc import SamplesMCMC -from autofit.non_linear.samples.sample import Sample +from autofit.non_linear.samples.adapter import ChainPosterior, RawSamples from autofit.non_linear.search import capabilities as cap if TYPE_CHECKING: @@ -53,6 +50,10 @@ class BlackJAXNUTS(AbstractMCMC): test_mode_budget = {"num_warmup": 20, "num_samples": 20, "num_chains": 2} objective_target = cap.ObjectiveTarget(cap.ObjectiveQuantity.LOG_POSTERIOR, cap.CoordinateSpace.PHYSICAL) invalid_value = -float("inf") + # The chain dict is plain NumPy, pickled (atomically) after every chunk and kept + # after completion: the samples cannot be rebuilt without it. Not a resume state: + # every ``_fit`` starts afresh (``resumable = False``). + checkpointer = PickleCheckpointer() __identifier_fields__ = ( "num_warmup", @@ -262,8 +263,6 @@ def __init__( self.logger.debug("Creating BlackJAXNUTS Search") - conf.instance["output"]["search_internal"] = True - def apply_test_mode(self): logger.warning( "TEST MODE 1 (reduced iterations): BlackJAXNUTS will run with " @@ -497,38 +496,16 @@ def run_chunk(rng_key, initial_state, n_steps): @property def backend_filename(self): - return self.paths.search_internal_path / "search_internal.pickle" + return self.paths.search_internal_path / PICKLE_FILENAME @property def backend(self) -> dict: - """Load the pickled search-internal dict written by ``_fit``.""" - if not Path(self.backend_filename).is_file(): + """The search-internal dict archived by ``_fit`` (``search_internal.pickle``).""" + if not self.checkpointer.exists(self.paths): raise FileNotFoundError( - f"search_internal.pickle does not exist at " - f"{self.paths.search_internal_path}" + f"{PICKLE_FILENAME} does not exist at {self.paths.search_internal_path}" ) - with open(self.backend_filename, "rb") as f: - return pickle.load(f) - - def output_search_internal(self, search_internal): - """ - Pickle the search-internal dict. - - BlackJAX has no native on-disk format (cf. emcee's HDFBackend), so we - round-trip the chain + diagnostics via pickle. We bypass - ``self.paths.save_search_internal`` because the autofit dill path - chokes on a few numpy/jax-backed members; a direct pickle of - already-numpy data is robust. - - ``NullPaths`` (no ``name``/``path_prefix``) sets - ``search_internal_path`` to ``None`` to suppress disk output — - skip silently in that case. - """ - if self.paths.search_internal_path is None: - return - os.makedirs(self.paths.search_internal_path, exist_ok=True) - with open(self.backend_filename, "wb") as f: - pickle.dump(search_internal, f) + return self.checkpointer.load(self.paths) def _test_mode_samples_info(self) -> dict: return { @@ -613,48 +590,32 @@ def samples_info_from(self, search_internal=None): "time": self.timer.time if self.timer else None, } - def samples_via_internal_from(self, model, search_internal=None): + def raw_samples_from(self, model, search_internal): """ - Convert the BlackJAX chain pickled under ``search_internal/`` into a - standard ``SamplesMCMC``. NUTS samples are unweighted draws from the - posterior, so weights are 1.0. + The BlackJAX chains pickled under ``search_internal/`` as raw samples. NUTS + samples are unweighted draws from the posterior, so every weight is 1. """ - search_internal = search_internal if search_internal is not None else self.backend - - positions = search_internal["positions"] # (n_samples, n_chains, n_dim) - log_likelihood_array = search_internal["log_likelihood_history"] # (n_samples, n_chains) - # Chain-major flatten: all of chain 0's samples (in draw order), then - # chain 1's, etc. -- matches `total_walkers = num_chains` below. - n_samples, n_chains, n_dim = positions.shape - positions_chain_major = np.moveaxis(positions, 0, 1).reshape( - n_chains * n_samples, n_dim - ) - log_likelihood_chain_major = np.moveaxis(log_likelihood_array, 0, 1).reshape( - n_chains * n_samples - ) - - parameter_lists = positions_chain_major.tolist() - log_likelihood_list = [float(x) for x in log_likelihood_chain_major] - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) - weight_list = [1.0] * len(parameter_lists) - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - - return SamplesMCMC( - model=model, - sample_list=sample_list, - samples_info=self.samples_info_from(search_internal=search_internal), - auto_correlation_settings=self.auto_correlation_settings, - auto_correlations=self.auto_correlations_from( - search_internal=search_internal + # chain 1's, etc. -- matches `total_walkers = num_chains` below. NUTS keeps + # every post-warmup draw (no burn-in removal or thinning). + parameters, log_likelihood = ChainPosterior.from_arrays( + chain=search_internal["positions"], # (n_samples, n_chains, n_dim) + log_prob=search_internal["log_likelihood_history"], # (n_samples, n_chains) + chain_major=True, + label="BlackJAXNUTS", + ).thin(discard=0, thin=1) + + return RawSamples( + parameters=parameters, + log_likelihood=[float(x) for x in log_likelihood], + info=self.samples_info_from(search_internal=search_internal), + samples_kwargs=dict( + auto_correlation_settings=self.auto_correlation_settings, + auto_correlations=self.auto_correlations_from( + search_internal=search_internal + ), ), + label="BlackJAXNUTS", ) def auto_correlations_from(self, search_internal=None): diff --git a/autofit/non_linear/search/mcmc/blackjax/smc/search.py b/autofit/non_linear/search/mcmc/blackjax/smc/search.py index 0b3f5c48e..33e17dbf4 100644 --- a/autofit/non_linear/search/mcmc/blackjax/smc/search.py +++ b/autofit/non_linear/search/mcmc/blackjax/smc/search.py @@ -3,15 +3,13 @@ import logging import math import os -import pickle from pathlib import Path from typing import List, Optional, Tuple, TYPE_CHECKING import numpy as np -from autonerves import conf - from autofit.mapper.prior_model.abstract import AbstractPriorModel +from autofit.non_linear.checkpoint import PICKLE_FILENAME, PickleCheckpointer from autofit.non_linear.objective import jax_objective from autofit.non_linear.initializer import Initializer, InitializerPrior from autofit.non_linear.search.mcmc.abstract_mcmc import AbstractMCMC @@ -26,7 +24,7 @@ ) from autofit.non_linear.search.mcmc.blackjax.smc.samples import SamplesSMC from autofit.non_linear.test_mode import is_test_mode -from autofit.non_linear.samples.sample import Sample +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.search import capabilities as cap if TYPE_CHECKING: @@ -52,6 +50,8 @@ class SMC(AbstractMCMC): + samples_cls = SamplesSMC + # Static capabilities (see ``autofit.non_linear.search.capabilities``); mirrored # by ``search/registry.py``. Never identifier fields. jax_use = cap.JaxUse.REQUIRED @@ -69,6 +69,10 @@ class SMC(AbstractMCMC): test_mode_budget = {"num_particles": 16, "num_mcmc_steps": 2, "max_smc_steps": 5} objective_target = cap.ObjectiveTarget(cap.ObjectiveQuantity.LOG_LIKELIHOOD, cap.CoordinateSpace.PHYSICAL) invalid_value = -1.0e99 + # The chain dict is plain NumPy, pickled (atomically) after every chunk and kept + # after completion: the samples cannot be rebuilt without it. Not a resume state: + # every ``_fit`` starts afresh (``resumable = False``). + checkpointer = PickleCheckpointer() __identifier_fields__ = ( "num_particles", @@ -312,8 +316,6 @@ def __init__( self.logger.debug("Creating SMC Search") - conf.instance["output"]["search_internal"] = True - def apply_test_mode(self): logger.warning( "TEST MODE 1 (reduced iterations): SMC will run with num_particles<=16, num_mcmc_steps=2, " @@ -661,35 +663,16 @@ def effective_step_size(self, n_dim: int) -> float: @property def backend_filename(self): - return self.paths.search_internal_path / "search_internal.pickle" + return self.paths.search_internal_path / PICKLE_FILENAME @property def backend(self) -> dict: - """Load the pickled search-internal dict written by ``_fit``.""" - if not Path(self.backend_filename).is_file(): + """The search-internal dict archived by ``_fit`` (``search_internal.pickle``).""" + if not self.checkpointer.exists(self.paths): raise FileNotFoundError( - f"search_internal.pickle does not exist at {self.paths.search_internal_path}" + f"{PICKLE_FILENAME} does not exist at {self.paths.search_internal_path}" ) - with open(self.backend_filename, "rb") as f: - return pickle.load(f) - - def output_search_internal(self, search_internal): - """ - Pickle the search-internal dict. - - BlackJAX has no native on-disk format (cf. emcee's HDFBackend), so we round-trip the particle cloud + - tempering diagnostics via pickle, bypassing ``self.paths.save_search_internal`` for the same reason - `BlackJAXNUTS` does: the autofit dill path chokes on a few numpy/jax-backed members, and a direct pickle - of already-numpy data is robust. - - ``NullPaths`` (no ``name``/``path_prefix``) sets ``search_internal_path`` to ``None`` to suppress disk - output -- skip silently in that case. - """ - if self.paths.search_internal_path is None: - return - os.makedirs(self.paths.search_internal_path, exist_ok=True) - with open(self.backend_filename, "wb") as f: - pickle.dump(search_internal, f) + return self.checkpointer.load(self.paths) def _test_mode_samples_info(self) -> dict: return { @@ -746,23 +729,19 @@ def samples_info_from(self, search_internal=None): "time": self.timer.time if self.timer else None, } - def samples_via_internal_from(self, model, search_internal=None): + def raw_samples_from(self, model, search_internal): """ - Convert the particle cloud pickled under ``search_internal/`` into a `SamplesSMC`. + The particle cloud pickled under ``search_internal/`` as raw samples. SMC particles are **weighted** samples: each carries the normalised importance weight blackjax assigns it at the current temperature, so the weights (not a uniform 1.0) are what the PDF, medians - and errors are computed from. + and errors are computed from. They are normalised here, by the search, as they always were; the + samples adapter never renormalises. """ - search_internal = ( - search_internal if search_internal is not None else self.backend - ) - parameter_lists = np.asarray(search_internal["particles"]).tolist() log_likelihood_list = [ float(x) for x in np.asarray(search_internal["log_likelihood_list"]) ] - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) weights = np.asarray(search_internal["weights"], dtype=float) weight_sum = weights.sum() @@ -771,18 +750,12 @@ def samples_via_internal_from(self, model, search_internal=None): else: weights = weights / weight_sum - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weights.tolist(), - ) - - return SamplesSMC( - model=model, - sample_list=sample_list, - samples_info=self.samples_info_from(search_internal=search_internal), + return RawSamples( + parameters=parameter_lists, + log_likelihood=log_likelihood_list, + weights=weights.tolist(), + info=self.samples_info_from(search_internal=search_internal), + label="SMC", ) diff --git a/autofit/non_linear/search/mcmc/emcee/search.py b/autofit/non_linear/search/mcmc/emcee/search.py index 3b158e375..5f0dcc1cc 100644 --- a/autofit/non_linear/search/mcmc/emcee/search.py +++ b/autofit/non_linear/search/mcmc/emcee/search.py @@ -7,18 +7,20 @@ import numpy as np -from autonerves import conf - from autofit import exc from autofit.mapper.model_mapper import ModelMapper from autofit.mapper.prior_model.abstract import AbstractPriorModel +from autofit.non_linear.checkpoint import ( + EMCEE_FILENAME, + NativeFileCheckpointer, + load_emcee_backend, +) from autofit.non_linear.initializer import Initializer from autofit.non_linear.search.mcmc.abstract_mcmc import AbstractMCMC from autofit.non_linear.search.mcmc.auto_correlations import AutoCorrelationsSettings from autofit.non_linear.search.mcmc.auto_correlations import AutoCorrelations from autofit.non_linear.test_mode import is_test_mode -from autofit.non_linear.samples.sample import Sample -from autofit.non_linear.samples.mcmc import SamplesMCMC +from autofit.non_linear.samples.adapter import ChainPosterior, RawSamples from autofit.non_linear.search import capabilities as cap if TYPE_CHECKING: @@ -49,6 +51,12 @@ class Emcee(AbstractMCMC): test_mode_budget = {"nwalkers": 20, "nsteps": 10} objective_target = cap.ObjectiveTarget(cap.ObjectiveQuantity.LOG_POSTERIOR, cap.CoordinateSpace.PHYSICAL) invalid_value = -float("inf") + # emcee's own HDF backend is both the archive and the resume state; it is kept + # after completion because the samples cannot be rebuilt without it. + checkpointer = NativeFileCheckpointer( + EMCEE_FILENAME, loader=load_emcee_backend, retain_after_completion=True + ) + resume_state = checkpointer __identifier_fields__ = ("nwalkers",) @@ -127,8 +135,6 @@ def __init__( self.logger.debug("Creating Emcee Search") - conf.instance["output"]["search_internal"] = True - def apply_test_mode(self): logger.warning( "TEST MODE 1 (reduced iterations): Sampler will run with " @@ -252,20 +258,6 @@ def _fit(self, model: AbstractPriorModel, analysis): return search_internal, fitness - def output_search_internal(self, search_internal): - """ - Output the sampler results to hard-disk in their internal format. - - Emcee uses a backend to store and load results, therefore the outputting of the search internal to a - dill file is disabled. - - Parameters - ---------- - sampler - The nautilus sampler object containing the results of the model-fit. - """ - pass - def samples_info_from(self, search_internal=None, auto_correlations=None): search_internal = search_internal or self.backend @@ -283,24 +275,23 @@ def samples_info_from(self, search_internal=None, auto_correlations=None): "time": self.timer.time if self.timer else None, } - def samples_via_internal_from(self, model, search_internal=None): + def raw_samples_from(self, model, search_internal): """ - Returns a `Samples` object from the emcee internal results. + The emcee chain after burn-in and thinning, as raw samples. - The samples contain all information on the parameter space sampling (e.g. the parameters, - log likelihoods, etc.). - - The internal search results are converted from the native format used by the search to lists of values - (e.g. `parameter_lists`, `log_likelihood_list`). + The parameters and log posteriors come out of emcee under the *same* + ``discard`` / ``thin`` (PyAutoFit#1628), through ``ChainPosterior.thin``, + which falls back to the whole chain when burn-in removal leaves no draws; the log likelihood is the log + posterior minus the log prior (``samples_from_raw``), and every draw has + weight 1. Parameters ---------- model Maps input vectors of unit parameter values to physical values and model instances via priors. + search_internal + The ``emcee.EnsembleSampler`` or its ``HDFBackend``. """ - - search_internal = search_internal or self.backend - # Computed once per conversion and shared by the burn-in, `samples_info` and # `SamplesMCMC`; each computation integrates the whole chain twice. auto_correlations = self.auto_correlations_from( @@ -315,55 +306,22 @@ def samples_via_internal_from(self, model, search_internal=None): discard = int(3.0 * np.max(auto_correlations.times)) thin = int(np.max(auto_correlations.times) / 2.0) - samples_after_burn_in = search_internal.get_chain( - discard=discard, thin=thin, flat=True - ) - - parameter_lists = samples_after_burn_in.tolist() - - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) - - # The log posteriors must be requested with the *same* `discard` and `thin` - # as the chain above, otherwise sample `i`'s parameters are paired with a - # different sample's log posterior (PyAutoFit#1628). - log_posterior_list = search_internal.get_log_prob( - discard=discard, thin=thin, flat=True - ).tolist() - - if len(parameter_lists) != len(log_posterior_list): - raise exc.SamplesException( - "The number of Emcee parameter samples does not match the number of log " - "posterior values returned by the sampler: " - f"{len(parameter_lists)} parameter samples versus " - f"{len(log_posterior_list)} log posterior values. " - "The parameters and log posteriors are therefore not in correspondence " - "and the samples cannot be built." - ) - - log_likelihood_list = [ - log_posterior - log_prior - for log_posterior, log_prior in zip(log_posterior_list, log_prior_list) - ] + parameters, log_posterior = ChainPosterior.from_sampler( + search_internal, label="Emcee" + ).thin(discard=discard, thin=thin) - weight_list = len(log_likelihood_list) * [1.0] - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - - return SamplesMCMC( - model=model, - sample_list=sample_list, - samples_info=self.samples_info_from( + return RawSamples( + parameters=parameters, + log_posterior=log_posterior, + info=self.samples_info_from( search_internal=search_internal, auto_correlations=auto_correlations, ), - auto_correlation_settings=self.auto_correlation_settings, - auto_correlations=auto_correlations, + samples_kwargs=dict( + auto_correlation_settings=self.auto_correlation_settings, + auto_correlations=auto_correlations, + ), + label="Emcee", ) def auto_correlations_from(self, search_internal=None): @@ -390,7 +348,7 @@ def auto_correlations_from(self, search_internal=None): @property def backend_filename(self): - return self.paths.search_internal_path / "search_internal.hdf" + return self.paths.search_internal_path / EMCEE_FILENAME @property def backend(self) -> "emcee.backends.HDFBackend": diff --git a/autofit/non_linear/search/mcmc/zeus/search.py b/autofit/non_linear/search/mcmc/zeus/search.py index 9fbd0a62b..e0ac628f2 100644 --- a/autofit/non_linear/search/mcmc/zeus/search.py +++ b/autofit/non_linear/search/mcmc/zeus/search.py @@ -13,9 +13,8 @@ from autofit.non_linear.search.mcmc.abstract_mcmc import AbstractMCMC from autofit.non_linear.search.mcmc.auto_correlations import AutoCorrelationsSettings from autofit.non_linear.search.mcmc.auto_correlations import AutoCorrelations -from autofit.non_linear.samples.sample import Sample from autofit.non_linear.test_mode import is_test_mode -from autofit.non_linear.samples.mcmc import SamplesMCMC +from autofit.non_linear.samples.adapter import ChainPosterior, RawSamples from autofit.non_linear.search import capabilities as cap if TYPE_CHECKING: @@ -297,10 +296,13 @@ def _fit(self, model: AbstractPriorModel, analysis): return search_internal, fitness - def samples_info_from(self, search_internal=None): + def samples_info_from(self, search_internal=None, auto_correlations=None): search_internal = search_internal or self.paths.load_search_internal() - auto_correlations = self.auto_correlations_from(search_internal=search_internal) + if auto_correlations is None: + auto_correlations = self.auto_correlations_from( + search_internal=search_internal + ) return { "check_size": auto_correlations.check_size, @@ -311,108 +313,53 @@ def samples_info_from(self, search_internal=None): "time": self.timer.time if self.timer else None, } - def samples_via_internal_from(self, model, search_internal=None): + def raw_samples_from(self, model, search_internal): """ - Returns a `Samples` object from the zeus internal results. - - The samples contain all information on the parameter space sampling (e.g. the parameters, - log likelihoods, etc.). + The zeus chain after burn-in and thinning, as raw samples. - The internal search results are converted from the native format used by the search to lists of values - (e.g. `parameter_lists`, `log_likelihood_list`). + The parameters and log posteriors come out of zeus under the *same* + ``discard`` / ``thin`` (PyAutoFit#1628), through ``ChainPosterior.thin``, + which falls back to the whole chain when burn-in removal leaves no draws; the log likelihood is the log + posterior minus the log prior (``samples_from_raw``), and every draw has + weight 1. Parameters ---------- model Maps input vectors of unit parameter values to physical values and model instances via priors. + search_internal + The ``zeus.EnsembleSampler``. """ + # Computed once per conversion and shared by the burn-in, `samples_info` and + # `SamplesMCMC`. + auto_correlations = self.auto_correlations_from( + search_internal=search_internal + ) - search_internal = search_internal or self.paths.load_search_internal() - - test_mode = is_test_mode() - - if test_mode: - + if is_test_mode(): discard = 5 thin = 5 else: - auto_correlations = self.auto_correlations_from( - search_internal=search_internal - ) - discard = int(3.0 * np.max(auto_correlations.times)) thin = int(np.max(auto_correlations.times) / 2.0) - samples_after_burn_in = search_internal.get_chain( - discard=discard, thin=thin, flat=True - ) - - if not test_mode and len(samples_after_burn_in) == 0: - - logging.info( - """ - After thinnng the Zeus samples in order to remove burn-in, no samples were left. - - To create a samples object containing samples, so that the code can continue and results - can be inspected, the full list of samples before removing burn-in has been used. This may - indicate that the sampler has not converged and therefore your results may not be reliable. - - To fix this, run Zeus with more steps to ensure convergence is achieved or change the auto - correlation settings to be less aggressive in thinning samples. - """ - ) - - discard = 0 - thin = 1 - - samples_after_burn_in = search_internal.get_chain(flat=True) - - parameter_lists = samples_after_burn_in.tolist() - - # The log posteriors must be requested with the *same* `discard` and `thin` - # as whichever branch above produced the chain, otherwise sample `i`'s - # parameters are paired with a different sample's log posterior, and the - # `zip` below silently truncates to the shorter list (PyAutoFit#1628). - log_posterior_list = search_internal.get_log_prob( - discard=discard, thin=thin, flat=True - ).tolist() - - if len(parameter_lists) != len(log_posterior_list): - raise exc.SamplesException( - "The number of Zeus parameter samples does not match the number of log " - "posterior values returned by the sampler: " - f"{len(parameter_lists)} parameter samples versus " - f"{len(log_posterior_list)} log posterior values. " - "The parameters and log posteriors are therefore not in correspondence " - "and the samples cannot be built." - ) - - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) + parameters, log_posterior = ChainPosterior.from_sampler( + search_internal, label="Zeus" + ).thin(discard=discard, thin=thin) - log_likelihood_list = [ - log_posterior - log_prior - for log_posterior, log_prior in zip(log_posterior_list, log_prior_list) - ] - - weight_list = len(log_likelihood_list) * [1.0] - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - - return SamplesMCMC( - model=model, - sample_list=sample_list, - samples_info=self.samples_info_from(search_internal=search_internal), - auto_correlation_settings=self.auto_correlation_settings, - auto_correlations=self.auto_correlations_from( - search_internal=search_internal + return RawSamples( + parameters=parameters, + log_posterior=log_posterior, + info=self.samples_info_from( + search_internal=search_internal, + auto_correlations=auto_correlations, + ), + samples_kwargs=dict( + auto_correlation_settings=self.auto_correlation_settings, + auto_correlations=auto_correlations, ), + label="Zeus", ) def auto_correlations_from(self, search_internal=None): diff --git a/autofit/non_linear/search/mle/bfgs/search.py b/autofit/non_linear/search/mle/bfgs/search.py index 6dfa30563..ba8665bc1 100644 --- a/autofit/non_linear/search/mle/bfgs/search.py +++ b/autofit/non_linear/search/mle/bfgs/search.py @@ -13,8 +13,7 @@ ClipperPriorBoxJoint, ) from autofit.non_linear.initializer import AbstractInitializer -from autofit.non_linear.samples.sample import Sample -from autofit.non_linear.samples.samples import Samples +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.search import capabilities as cap import numpy as np @@ -361,55 +360,21 @@ def _fit( return search_internal, fitness - def samples_via_internal_from( - self, model: AbstractPriorModel, search_internal=None - ): + def raw_samples_from(self, model: AbstractPriorModel, search_internal): """ - Returns a `Samples` object from the LBFGS internal results. - - The samples contain all information on the parameter space sampling (e.g. the parameters, - log likelihoods, etc.). - - The internal search results are converted from the native format used by the search to lists of values - (e.g. `parameter_lists`, `log_likelihood_list`). + The LBFGS internal results as raw samples: the full history when the start + point is plotted, otherwise the single optimum ``x``. Parameters ---------- model Maps input vectors of unit parameter values to physical values and model instances via priors. + search_internal + The scipy ``OptimizeResult``-like object the search stores. """ - - if search_internal is None: - search_internal = self.paths.load_search_internal() - x0 = search_internal.x total_iterations = search_internal.nit - if self.should_plot_start_point: - - parameter_lists = search_internal.parameters_history_list - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) - log_likelihood_list = search_internal.log_likelihood_history_list - - else: - - parameter_lists = [list(x0)] - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) - log_posterior_list = np.array([search_internal.log_posterior_list]) - log_likelihood_list = [ - lp - prior for lp, prior in zip(log_posterior_list, log_prior_list) - ] - - weight_list = len(log_likelihood_list) * [1.0] - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - samples_info = { "total_iterations": total_iterations, # Prior-support enforcement (PyAutoFit#1477). The name only, with @@ -424,10 +389,26 @@ def samples_via_internal_from( "time": self.timer.time if self.timer else None, } - return Samples( - model=model, - sample_list=sample_list, - samples_info=samples_info, + if self.should_plot_start_point: + return RawSamples( + parameters=search_internal.parameters_history_list, + log_likelihood=search_internal.log_likelihood_history_list, + info=samples_info, + label="LBFGS", + ) + + parameter_lists = [list(x0)] + log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) + log_posterior_list = np.array([search_internal.log_posterior_list]) + + return RawSamples( + parameters=parameter_lists, + log_likelihood=[ + lp - prior for lp, prior in zip(log_posterior_list, log_prior_list) + ], + log_prior=log_prior_list, + info=samples_info, + label="LBFGS", ) diff --git a/autofit/non_linear/search/mle/drawer/search.py b/autofit/non_linear/search/mle/drawer/search.py index 3491776bb..741edb52b 100644 --- a/autofit/non_linear/search/mle/drawer/search.py +++ b/autofit/non_linear/search/mle/drawer/search.py @@ -7,7 +7,7 @@ from autofit.mapper.prior_model.abstract import AbstractPriorModel from autofit.non_linear.search.mle.abstract_mle import AbstractMLE from autofit.non_linear.initializer import AbstractInitializer -from autofit.non_linear.samples import Samples, Sample +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.search import capabilities as cap if TYPE_CHECKING: @@ -150,18 +150,32 @@ def run(self, ctx): return search_internal - def raw_samples_from(self, model, internal): + def raw_samples_from(self, model, search_internal): """ - The drawn points as ``RawSamples``: log posteriors, unit weights, and the internal - dictionary itself as ``samples_info``. - """ - from autofit.non_linear.search.fit_context import RawSamples + The Drawer's draws as raw samples: the parameter lists and log posteriors + ``run`` stores, each with weight 1. The stored dictionary (including the run + ``time`` recorded by ``run``) is the ``samples_info``. + + The ``search_internal`` dictionary returned by `run` is used when passed, so a fit with `NullPaths` + (which writes nothing to disk) can still build its samples; otherwise it is loaded from the output folder. + Parameters + ---------- + model + Maps input vectors of unit parameter values to physical values and model instances via priors. + search_internal + The dictionary of parameter lists, log posteriors and run time that `run` returns. + """ return RawSamples( - parameters=internal["parameter_lists"], - log_posterior=internal["log_posterior_list"], - info=self.info_from(internal), + parameters=search_internal["parameter_lists"], + log_posterior=search_internal["log_posterior_list"], + info=self.info_from(search_internal), + label="Drawer", ) def info_from(self, internal): + """ + The stored dictionary itself (including the run ``time`` recorded by ``run``) + is the ``samples_info``. + """ return internal diff --git a/autofit/non_linear/search/mle/multi_start_gradient/search.py b/autofit/non_linear/search/mle/multi_start_gradient/search.py index 9103e176b..490036fb9 100644 --- a/autofit/non_linear/search/mle/multi_start_gradient/search.py +++ b/autofit/non_linear/search/mle/multi_start_gradient/search.py @@ -26,8 +26,8 @@ ) from autofit.non_linear.scaler import AbstractScaler, ScalerNone from autofit.non_linear.initializer import AbstractInitializer -from autofit.non_linear.samples.sample import Sample -from autofit.non_linear.samples.samples import Samples +from autofit.non_linear.checkpoint import DillCheckpointer +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.search import capabilities as cap from autofit.non_linear.search.mle.multi_start_gradient.convergence import ( MultiStartGradientConvergence, @@ -67,6 +67,9 @@ class AbstractMultiStartGradient(AbstractMLE): # ``FitException`` early return (numpy) and a failed traced assertion still return # ``-inf``. Normalising it is the A3 objective adapter's job, not A1's. invalid_value = float("inf") + # The dill written after every step is both the archive and the resume state. + checkpointer = DillCheckpointer() + resume_state = checkpointer __identifier_fields__ = ("clipper",) @@ -1997,19 +2000,14 @@ def _broad_starts(self, model, value_and_grad_single, jnp): return jnp.stack(starts) - def samples_via_internal_from( - self, model: AbstractPriorModel, search_internal=None - ): + def raw_samples_from(self, model: AbstractPriorModel, search_internal): """ - Returns a `Samples` object from the MultiStartGradient internal results. + The MultiStartGradient internal results as raw samples. - The best-basin (maximum-log-posterior) start is the first sample; every - start's final point is retained as a diagnostic sample so per-start basin - spread can be inspected downstream. + The best-basin (maximum-log-posterior) start is the first sample (weight 1); + every start's final point is retained as a diagnostic sample (weight 0, log + likelihood NaN) so per-start basin spread can be inspected downstream. """ - if search_internal is None: - search_internal = self.paths.load_search_internal() - best_params = np.asarray(search_internal["best_params"]) per_start_params = np.asarray(search_internal["params"]) total_steps = int(search_internal["total_steps"]) @@ -2030,14 +2028,6 @@ def samples_via_internal_from( weight_list = [1.0] + [0.0] * (len(parameter_lists) - 1) - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - samples_info = { "n_starts": self.n_starts, "n_steps": self.n_steps, @@ -2128,10 +2118,13 @@ def samples_via_internal_from( "time": self.timer.time if self.timer else None, } - return Samples( - model=model, - sample_list=sample_list, - samples_info=samples_info, + return RawSamples( + parameters=parameter_lists, + log_likelihood=log_likelihood_list, + log_prior=log_prior_list, + weights=weight_list, + info=samples_info, + label=type(self).__name__, ) diff --git a/autofit/non_linear/search/nest/abstract_nest.py b/autofit/non_linear/search/nest/abstract_nest.py index 32bfae58d..acefeb3b2 100644 --- a/autofit/non_linear/search/nest/abstract_nest.py +++ b/autofit/non_linear/search/nest/abstract_nest.py @@ -12,12 +12,15 @@ InitializerParamBounds, ) from autofit.non_linear.plot import corner_anesthetic +from autofit.non_linear.samples.nest import SamplesNest if TYPE_CHECKING: from autofit.database.sqlalchemy_ import sa class AbstractNest(NonLinearSearch, ABC): + samples_cls = SamplesNest + def __init__( self, name: Optional[str] = None, diff --git a/autofit/non_linear/search/nest/dynesty/search/abstract.py b/autofit/non_linear/search/nest/dynesty/search/abstract.py index d22bc8d29..e6328ec51 100644 --- a/autofit/non_linear/search/nest/dynesty/search/abstract.py +++ b/autofit/non_linear/search/nest/dynesty/search/abstract.py @@ -14,8 +14,7 @@ from autofit.mapper.prior_model.abstract import AbstractPriorModel from autofit.non_linear.paths.null import NullPaths from autofit.non_linear.search.nest.abstract_nest import AbstractNest -from autofit.non_linear.samples.sample import Sample -from autofit.non_linear.samples.nest import SamplesNest +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.test_mode import is_test_mode from autofit.non_linear.search import capabilities as cap @@ -56,6 +55,12 @@ def __enter__(self): return ForkPool +DYNESTY_FILENAME = "savestate.save" +""" +dynesty's checkpoint file, the search's resume state. +""" + + def prior_transform(cube, model): phys_cube = model.vector_from_unit_vector( unit_vector=cube, @@ -358,51 +363,49 @@ def samples_info_from(self, search_internal=None): "number_live_points": self.number_live_points, } - def samples_via_internal_from(self, model, search_internal=None): + def load_search_internal(self): """ - Returns a `Samples` object from the dynesty internal results. - - The samples contain all information on the parameter space sampling (e.g. the parameters, - log likelihoods, etc.). + The archive (``search_internal.dill``, written when the fit completed) or, + for a run that has not completed, the sampler restored from its resume state + (``savestate.save``). + """ + try: + return super().load_search_internal() + except FileNotFoundError: + return self.search_internal - The internal search results are converted from the native format used by the search to lists of values - (e.g. `parameter_lists`, `log_likelihood_list`). + def raw_samples_from(self, model, search_internal): + """ + The dynesty run's samples, log likelihoods and nested-sampling weights + (``exp(logwt - logz[-1])``) as raw samples. Parameters ---------- model Maps input vectors of unit parameter values to physical values and model instances via priors. + search_internal + The dynesty sampler. """ - search_internal = search_internal or self.search_internal - - parameter_lists = search_internal.results.samples.tolist() - log_prior_list = model.log_prior_list_from(parameter_lists=parameter_lists) - log_likelihood_list = list(search_internal.results.logl) - - weight_list = list( - np.exp( - np.asarray(search_internal.results.logwt) - - search_internal.results.logz[-1] - ) - ) - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - - return SamplesNest( - model=model, - sample_list=sample_list, - samples_info=self.samples_info_from(search_internal=search_internal), + return RawSamples( + parameters=search_internal.results.samples.tolist(), + log_likelihood=list(search_internal.results.logl), + weights=list( + np.exp( + np.asarray(search_internal.results.logwt) + - search_internal.results.logz[-1] + ) + ), + info=self.samples_info_from(search_internal=search_internal), + label="Dynesty", ) @property def search_internal(self): - raise NotImplementedError + """ + The sampler restored from the resume state (``savestate.save``) of a run that + has not completed. + """ + return self.resume_state.load(self.paths) def iterations_from( self, search_internal: "Union[NestedSampler, DynamicNestedSampler]" @@ -547,7 +550,7 @@ def checkpoint_file(self) -> str: If autofit is not outputting results to hard-disk (e.g. paths is `NullPaths`), this function is bypassed. """ try: - return str(self.paths.search_internal_path / "savestate.save") + return str(self.paths.search_internal_path / DYNESTY_FILENAME) except TypeError: pass @@ -619,17 +622,6 @@ def search_internal_from( ): raise NotImplementedError() - def output_search_internal(self, search_internal): - - self.paths.save_search_internal( - obj=search_internal, - ) - - try: - os.remove(self.checkpoint_file) - except (TypeError, FileNotFoundError): - pass - def check_pool(self, uses_pool: bool, pool): if (uses_pool and pool is None) or (not uses_pool and pool is not None): raise exc.SearchException( diff --git a/autofit/non_linear/search/nest/dynesty/search/dynamic.py b/autofit/non_linear/search/nest/dynesty/search/dynamic.py index 705bb8a98..6478fb125 100644 --- a/autofit/non_linear/search/nest/dynesty/search/dynamic.py +++ b/autofit/non_linear/search/nest/dynesty/search/dynamic.py @@ -3,10 +3,25 @@ from autofit.mapper.prior_model.abstract import AbstractPriorModel -from .abstract import AbstractDynesty, prior_transform +from autofit.non_linear.checkpoint import NativeFileCheckpointer + +from .abstract import DYNESTY_FILENAME, AbstractDynesty, prior_transform + + +def _restore_dynamic(path): + """ + Restore a dynesty sampler from its ``savestate.save`` resume state. + """ + from dynesty.dynesty import DynamicNestedSampler as Sampler + + return Sampler.restore(str(path)) class DynestyDynamic(AbstractDynesty): + # dynesty's own checkpoint, deleted once the fit completes (the archive is + # ``search_internal.dill``). + resume_state = NativeFileCheckpointer(DYNESTY_FILENAME, loader=_restore_dynamic) + __identifier_fields__ = ( "bound", "sample", @@ -98,11 +113,6 @@ def run_kwargs(self) -> Dict: "nlive_init": self.nlive_init, } - @property - def search_internal(self): - from dynesty.dynesty import DynamicNestedSampler - return DynamicNestedSampler.restore(self.checkpoint_file) - def search_internal_from( self, model: AbstractPriorModel, diff --git a/autofit/non_linear/search/nest/dynesty/search/static.py b/autofit/non_linear/search/nest/dynesty/search/static.py index b2bb2cf44..75b616529 100644 --- a/autofit/non_linear/search/nest/dynesty/search/static.py +++ b/autofit/non_linear/search/nest/dynesty/search/static.py @@ -7,12 +7,27 @@ from autofit.mapper.prior_model.abstract import AbstractPriorModel -from .abstract import AbstractDynesty, prior_transform +from autofit.non_linear.checkpoint import NativeFileCheckpointer + +from .abstract import DYNESTY_FILENAME, AbstractDynesty, prior_transform if TYPE_CHECKING: from autofit.database.sqlalchemy_ import sa +def _restore_static(path): + """ + Restore a dynesty sampler from its ``savestate.save`` resume state. + """ + from dynesty import NestedSampler as Sampler + + return Sampler.restore(str(path)) + + class DynestyStatic(AbstractDynesty): + # dynesty's own checkpoint, deleted once the fit completes (the archive is + # ``search_internal.dill``). + resume_state = NativeFileCheckpointer(DYNESTY_FILENAME, loader=_restore_static) + __identifier_fields__ = ( "nlive", "bound", @@ -105,11 +120,6 @@ def run_kwargs(self) -> Dict: "logl_max": self.logl_max, } - @property - def search_internal(self): - from dynesty import NestedSampler as StaticSampler - return StaticSampler.restore(self.checkpoint_file) - def search_internal_from( self, model: AbstractPriorModel, diff --git a/autofit/non_linear/search/nest/nautilus/search.py b/autofit/non_linear/search/nest/nautilus/search.py index c5802bfa3..9e57c9afc 100644 --- a/autofit/non_linear/search/nest/nautilus/search.py +++ b/autofit/non_linear/search/nest/nautilus/search.py @@ -13,11 +13,11 @@ from autofit import exc from autofit.mapper.prior_model.abstract import AbstractPriorModel from autofit.mapper.prior.vectorized import PriorVectorized +from autofit.non_linear.checkpoint import DillCheckpointer, NativeFileCheckpointer from autofit.non_linear.parallel import fork_context from autofit.non_linear.paths.null import NullPaths from autofit.non_linear.search.nest import abstract_nest -from autofit.non_linear.samples.sample import Sample -from autofit.non_linear.samples.nest import SamplesNest +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.test_mode import is_test_mode from autofit.non_linear.search import capabilities as cap @@ -27,6 +27,23 @@ logger = logging.getLogger(__name__) +NAUTILUS_FILENAME = "checkpoint.hdf5" +""" +nautilus's checkpoint file, the search's resume state. +""" + + +def _resumed_by_nautilus(path): + """ + A nautilus checkpoint cannot be opened on its own: nautilus reopens it inside a + ``Sampler`` built with the run's prior and likelihood, which ``run`` does. + """ + raise NotImplementedError( + f"The nautilus checkpoint {path} is resumed by nautilus.Sampler(filepath=...) " + "inside the search's run(ctx); it holds no samples until the fit completes." + ) + + # How often `_LikelihoodWorkerPool.map` wakes up to check that the pool's # workers are the ones it was built with. Read at call time (not bound at @@ -172,6 +189,14 @@ class Nautilus(abstract_nest.AbstractNest): test_mode_budget = {"n_like_max": 1} objective_target = cap.ObjectiveTarget(cap.ObjectiveQuantity.LOG_LIKELIHOOD, cap.CoordinateSpace.UNIT_CUBE) invalid_value = -1.0e99 + # The archive is the sampler dill-dumped without its multiprocessing pools (which + # cannot be pickled); the resume state is nautilus's own ``checkpoint.hdf5``, + # which nautilus itself reopens (``Sampler(filepath=...)``) and which is deleted + # once the fit completes. + checkpointer = DillCheckpointer(strip_attributes=("pool_l", "pool_s")) + resume_state = NativeFileCheckpointer( + NAUTILUS_FILENAME, loader=_resumed_by_nautilus + ) __identifier_fields__ = ( "n_live", @@ -405,7 +430,7 @@ def checkpoint_file(self): If autofit is not outputting results to hard-disk (e.g. paths is `NullPaths`), this function is bypassed. """ try: - return self.paths.search_internal_path / "checkpoint.hdf5" + return self.paths.search_internal_path / NAUTILUS_FILENAME except TypeError: pass @@ -706,37 +731,6 @@ def iterations_from( return iterations, total_iterations - def output_search_internal(self, search_internal): - """ - Output the sampler results to hard-disk in their internal format. - - The multiprocessing `Pool` object cannot be pickled and thus the sampler cannot be saved to hard-disk. This - function therefore extracts the necessary information from the sampler and saves it to hard-disk. - - Parameters - ---------- - sampler - The nautilus sampler object containing the results of the model-fit. - """ - - pool_l = search_internal.pool_l - pool_s = search_internal.pool_s - - search_internal.pool_l = None - search_internal.pool_s = None - - self.paths.save_search_internal( - obj=search_internal, - ) - - search_internal.pool_l = pool_l - search_internal.pool_s = pool_s - - try: - os.remove(self.checkpoint_file) - except (TypeError, FileNotFoundError): - pass - def samples_info_from(self, search_internal=None): return { "log_evidence": search_internal.log_z, @@ -746,22 +740,26 @@ def samples_info_from(self, search_internal=None): "number_live_points": int(search_internal.n_live), } - samples_cls = SamplesNest - - def raw_samples_from(self, model, internal): - """ - Nautilus's posterior as ``RawSamples``: parameters, log likelihoods and the - exponentiated log weights. + def raw_samples_from(self, model, search_internal): """ - from autofit.non_linear.search.fit_context import RawSamples + The nautilus posterior (``Sampler.posterior()``: points, log weights, log + likelihoods) as raw samples, with weights ``exp(log_w)``. - parameters, log_weights, log_likelihoods = internal.posterior() + Parameters + ---------- + model + Maps input vectors of unit parameter values to physical values and model instances via priors. + search_internal + The nautilus sampler. + """ + parameters, log_weights, log_likelihoods = search_internal.posterior() return RawSamples( - parameters=parameters.tolist(), - log_likelihood=log_likelihoods.tolist(), - weights=np.exp(log_weights).tolist(), - info=self.info_from(internal), + parameters=parameters, + log_likelihood=log_likelihoods, + weights=np.exp(log_weights), + info=self.info_from(search_internal), + label="Nautilus", ) def info_from(self, internal): diff --git a/autofit/non_linear/search/nest/nss/search.py b/autofit/non_linear/search/nest/nss/search.py index d90ff2261..2856e34fb 100644 --- a/autofit/non_linear/search/nest/nss/search.py +++ b/autofit/non_linear/search/nest/nss/search.py @@ -9,11 +9,12 @@ import numpy as np from autofit.mapper.prior_model.abstract import AbstractPriorModel +from autofit.non_linear.checkpoint import NativeFileCheckpointer from autofit.non_linear.fitness import Fitness, get_log_likelihood_ceiling from autofit.non_linear.paths.null import NullPaths from autofit.non_linear.search.nest import abstract_nest from .samples import NSSamples -from autofit.non_linear.samples.sample import Sample +from autofit.non_linear.samples.adapter import RawSamples from autofit.non_linear.test_mode import is_test_mode from autofit.non_linear.search import capabilities as cap @@ -193,6 +194,8 @@ def __init__( class NSS(abstract_nest.AbstractNest): + samples_cls = NSSamples + # Static capabilities (see ``autofit.non_linear.search.capabilities``); mirrored # by ``search/registry.py``. Never identifier fields. jax_use = cap.JaxUse.REQUIRED @@ -213,6 +216,9 @@ class NSS(abstract_nest.AbstractNest): # physical-space prior density. objective_target = cap.ObjectiveTarget(cap.ObjectiveQuantity.LOG_LIKELIHOOD, cap.CoordinateSpace.PHYSICAL) invalid_value = NSS_INVALID_LOG_LIKELIHOOD + # The resume state is NSS's own atomic ``nss_checkpoint.pkl`` (``_fit`` writes, + # reads and deletes it); the archive is the default ``search_internal.dill``. + resume_state = NativeFileCheckpointer(_CHECKPOINT_FILENAME, loader=_load_checkpoint) __identifier_fields__ = ( "n_live", @@ -657,18 +663,9 @@ def samples_info_from(self, search_internal: Optional[_NSSInternal] = None): "ess": int(search_internal.ess), } - def samples_via_internal_from( - self, - model: AbstractPriorModel, - search_internal: Optional[_NSSInternal] = None, - ): - """Convert the stored ``_NSSInternal`` holder into an ``NSSamples``.""" - - if search_internal is None: - search_internal = self.paths.load_search_internal() - - parameter_lists = np.asarray(search_internal.positions).tolist() - log_likelihood_list = np.asarray(search_internal.loglikelihoods).tolist() + def raw_samples_from(self, model, search_internal: _NSSInternal): + """The stored ``_NSSInternal`` holder as raw samples, with its log weights + exponentiated and normalised by the search (as they always were).""" log_w = np.asarray(search_internal.log_weights) log_w_norm = log_w - log_w.max() @@ -676,23 +673,11 @@ def samples_via_internal_from( weight_total = weights.sum() if weight_total > 0: weights = weights / weight_total - weight_list = weights.tolist() - - log_prior_list = [ - sum(model.log_prior_list_from_vector(vector=vector)) - for vector in parameter_lists - ] - - sample_list = Sample.from_lists( - model=model, - parameter_lists=parameter_lists, - log_likelihood_list=log_likelihood_list, - log_prior_list=log_prior_list, - weight_list=weight_list, - ) - return NSSamples( - model=model, - sample_list=sample_list, - samples_info=self.samples_info_from(search_internal=search_internal), + return RawSamples( + parameters=np.asarray(search_internal.positions), + log_likelihood=np.asarray(search_internal.loglikelihoods), + weights=weights, + info=self.samples_info_from(search_internal=search_internal), + label="NSS", ) diff --git a/autofit/non_linear/search/registry.py b/autofit/non_linear/search/registry.py index 18bcf0dca..2b95f21ad 100644 --- a/autofit/non_linear/search/registry.py +++ b/autofit/non_linear/search/registry.py @@ -149,6 +149,7 @@ def _capabilities( test_mode_budget: Dict[str, Any], objective_target: Tuple[str, str], invalid_value: str, + checkpointer: str = "dill", ) -> Dict[str, Any]: quantity, space = objective_target values = dict( @@ -167,6 +168,7 @@ def _capabilities( test_mode_budget=dict(test_mode_budget), objective_target={"quantity": quantity, "space": space}, invalid_value=invalid_value, + checkpointer=checkpointer, ) return {name: values[name] for name in CAPABILITY_ATTRIBUTES} @@ -299,6 +301,7 @@ def _multi_start( test_mode_budget=_EMCEE_ZEUS_BUDGET, objective_target=("log_posterior", "physical"), invalid_value="-inf", + checkpointer="native:search_internal.hdf", ), example=f"{_WORKSPACE}/mcmc.py#Search: Emcee", integration_test=f"{_WORKSPACE_TEST}/Emcee.py", @@ -351,6 +354,7 @@ def _multi_start( test_mode_budget={"num_warmup": 20, "num_samples": 20, "num_chains": 2}, objective_target=("log_posterior", "physical"), invalid_value="-inf", + checkpointer="pickle", ), example=f"{_WORKSPACE}/mcmc.py#Search: BlackJAXNUTS", integration_test=f"{_WORKSPACE_TEST}/BlackJAXNUTS.py", @@ -381,6 +385,7 @@ def _multi_start( }, objective_target=("log_likelihood", "physical"), invalid_value="-1e+99", + checkpointer="pickle", ), example=None, integration_test=f"{_WORKSPACE_TEST}/SMC.py", diff --git a/docs/_generate_searches.py b/docs/_generate_searches.py index 2daef4e9e..0747cc32b 100644 --- a/docs/_generate_searches.py +++ b/docs/_generate_searches.py @@ -246,26 +246,40 @@ def searches_index_rst(manifest: dict) -> str: "What each search's objective returns, the coordinates its backend proposes " "points in (``unit_cube`` backends map through the prior transform; the " "likelihood always receives physical parameters), the value it returns for an " - "invalid model, and the reduced budget ``PYAUTO_TEST_MODE=1`` applies.\n\n", + "invalid model, where it archives its internal state when a fit completes, " + "and the reduced budget ``PYAUTO_TEST_MODE=1`` applies.\n\n", + ] + header = [ + "Search", + "Objective", + "Coordinates", + "Invalid value", + "Archive", + "Test-mode budget", ] - header = ["Search", "Objective", "Coordinates", "Invalid value", "Test-mode budget"] rows = [ [ _link(search), f"``{search['capabilities']['objective_target']['quantity']}``", f"``{search['capabilities']['objective_target']['space']}``", f"``{search['capabilities']['invalid_value']}``", + f"``{search['capabilities']['checkpointer']}``", _budget(search["capabilities"]["test_mode_budget"]), ] for search in manifest["searches"] ] - lines += _list_table(header, rows, "16 18 12 12 42") + lines += _list_table(header, rows, "14 16 11 11 16 32") lines += [ "The invalid value is what the backend actually sees, not yet normalised. For " "the ``neg2_log_posterior`` minimizers it is conditional: a NaN or infinite " "likelihood is replaced by ``-inf`` and then multiplied by -2 into ``inf`` " "(the value listed), while a model rejected by a ``FitException`` or a failed " "assertion returns ``-inf``.\n\n", + "The archive is ``dill`` (``search_internal.dill``), ``pickle`` " + "(``search_internal.pickle``, plain NumPy data) or ``native:`` (a file " + "the backend writes itself). Emcee, BlackJAXNUTS and SMC keep their archive " + "after a fit completes whatever the ``output.search_internal`` config says, " + "because their samples cannot be rebuilt without it.\n\n", ] lines += [ "Column meanings\n", diff --git a/docs/design/checkpointing.md b/docs/design/checkpointing.md new file mode 100644 index 000000000..31e766c0f --- /dev/null +++ b/docs/design/checkpointing.md @@ -0,0 +1,122 @@ +# Design note: archives, resume states and checkpointing + +Status: search-extensibility phase A3 (decision D5). Implemented in +`autofit/non_linear/checkpoint.py`; the samples conversion that reads the archive is +`autofit/non_linear/samples/adapter.py`. This note fixes the meaning of the two kinds +of internal state, how they are written, what happens when they are corrupt, and which +files survive the end of a fit. + +## Two kinds of internal state + +A search's `search_internal/` folder used to hold one thing that meant two things: a +checkpoint an interrupted run resumes from, and the post-hoc archive of the backend's +results. The config key `output.search_internal: false` deletes the folder at the end +of a fit, so searches whose results could not be rebuilt without it (Emcee, +BlackJAX NUTS, SMC) forced the key on in their `__init__`, which leaked to every later +search in the process. A3 separates the two: + +| Role | Class attribute | Default | Written | Read by | +|---|---|---|---|---| +| **archive** (`result_internal`) | `NonLinearSearch.checkpointer` | `DillCheckpointer()` | at the end of the fit (`output_search_internal` -> `checkpointer.finalize`), and by searches that also save it mid-run | `Result.search_internal`, `samples_via_internal_from` on a completed folder | +| **resume state** | `NonLinearSearch.resume_state` | `None` | by the backend during the run | the search's own resume path; `samples_via_internal_from` falls back to it when no archive exists yet | + +Only searches that genuinely resume an interrupted run declare a resume state, and +`resumable = True` is declared only for them: Dynesty and Nautilus (native backend +checkpoints), NSS (its own pickle), MultiStart (whose archive dill is also its resume +state) and Emcee (whose HDF backend is both). BlackJAX NUTS and SMC start every `_fit` +afresh, so they are not resumable and have no resume state. + +| Search | Archive | Resume state | +|---|---|---| +| Emcee | `NativeFileCheckpointer("search_internal.hdf", load_emcee_backend, retain_after_completion=True)` | the same file | +| Zeus, BFGS, LBFGS, Drawer | `DillCheckpointer()` | none | +| BlackJAX NUTS, SMC | `PickleCheckpointer()` (`search_internal.pickle`, retained) | none | +| DynestyStatic, DynestyDynamic | `DillCheckpointer()` | `NativeFileCheckpointer("savestate.save", .restore)` | +| Nautilus | `DillCheckpointer(strip_attributes=("pool_l", "pool_s"))` | `NativeFileCheckpointer("checkpoint.hdf5", ...)`; only nautilus can reopen it (inside a `Sampler` built with the run's prior and likelihood), so its loader raises `NotImplementedError` | +| NSS | `DillCheckpointer()` | `NativeFileCheckpointer("nss_checkpoint.pkl", _load_checkpoint)` (written, read and deleted by NSS's own `_fit`) | +| MultiStart* | `DillCheckpointer()` | the same file | + +Every existing filename is kept, so output folders written before A3 still load. + +## Atomic writes + +Every file autofit writes itself is written atomically: `Checkpointer.save` dumps to a +sibling temporary file (`..tmp`) and `os.replace`s it into place +(`autofit.tools.util.open_atomic`). A write interrupted by an exception, a +`KeyboardInterrupt`, a full disk or a killed process therefore leaves the previous +file whole, and the temporary file is removed on the exception paths. + +Native files are written by their backend, with the backend's own guarantees: +dynesty's `save_sampler` writes `savestate.save.tmp` and renames it; NSS's +`_save_checkpoint` uses the same tmp-and-rename; emcee's `HDFBackend` and nautilus's +`checkpoint.hdf5` are HDF5 files appended in place by `h5py`, so an interrupted write +can leave them unreadable. `NativeFileCheckpointer.save` and `finalize` are no-ops: +autofit never writes or rewrites a native file. + +## Corruption + +A corrupt file is never silently replaced by a different source of samples: + +- `Checkpointer.load` raises whatever its deserialiser raises (`EOFError`, + `pickle.UnpicklingError`, `OSError` from `h5py`, ...). It never converts a corrupt + file into `FileNotFoundError`. +- `NonLinearSearch.samples_from` falls back to `samples.csv` (with a WARNING) only for + `FileNotFoundError` and `NotImplementedError` (A0b's narrowed fallback), so a + corrupt archive surfaces as an error rather than as silently older samples. +- On the resume path a search decides. MultiStart treats a corrupt dill as absent and + starts a fresh run with a warning (the state is only a resume aid). Dynesty, Nautilus + and NSS let their backend's error propagate, because resuming from a damaged + checkpoint is not safe and starting over silently would discard the run; deleting + the named file restarts the fit. + +## Retention precedence + +When a fit completes, `NonLinearSearch.post_fit_output` decides which files survive, +in this order: + +1. **`checkpointer.retain_after_completion`.** When true (Emcee, BlackJAX NUTS, SMC), + the archive is always kept: their results cannot be rebuilt without it. This + replaces the three `conf.instance["output"]["search_internal"] = True` mutations + those searches made in `__init__`; constructing a search never changes the + configuration. +2. **`output.search_internal`** (`config/output.yaml`). Otherwise, `true` keeps the + archive and `false` removes the whole `search_internal/` folder (archive, resume + state and timer files). +3. **The resume state** is deleted once the fit completes, because there is nothing + left to resume, unless it is the archive's own file (Emcee, MultiStart) or declares + `retain_after_completion`. +4. **Zipping.** Whatever survives is archived in `.zip` and restored by + `paths.restore()`, so a completed folder unzipped later loads its archive again. + +A retained archive is therefore always readable after completion: a completed Dynesty +folder keeps `search_internal.dill`, which is what `samples_via_internal_from` reads +(`savestate.save` is the resume state and is removed). + +## Loading, and outputs written before A3 + +Loading is injected rather than hard-coded in `paths`: `DirectoryPaths` knows its +search (`paths.search`), and `DirectoryPaths.load_search_internal()` asks that +search's `checkpointer`. `Result.search_internal` and every `samples_via_internal_from` +go through it. + +Format-aware legacy detection is kept, not replaced by a dill-only fallback. The emcee +probe that used to live inline in `DirectoryPaths.load_search_internal` ("a nasty +hack") moved to `checkpoint.load_legacy_search_internal(directory)`, which tries, in +order, `search_internal.hdf` (an emcee `HDFBackend`), `search_internal.pickle` (NUTS, +SMC) and `search_internal.dill`. It is used when the paths has no search (a folder +opened on its own) and when a checkpointer's own archive file is absent, so an output +folder written before its search chose a strategy still loads. + +Per output kind: + +| Paths | Archive save | Archive load | +|---|---|---| +| `DirectoryPaths` (and `SubDirectoryPaths`) | the strategy's file under `files/search_internal/` | the strategy, then the legacy probe | +| zipped output | restored from the `.zip` by `paths.restore()` | as `DirectoryPaths` | +| `DatabasePaths` | no-op (results live in the database) | `None` | +| `NullPaths` | no-op | `None` | +| summary-only output (no `search_internal/`, e.g. `output.search_internal: false`) | n/a | `FileNotFoundError`, so `samples_from` and `Result.samples` use `samples.csv` | + +The aggregator never reads the archive: it rebuilds samples from `samples.csv` and +`samples_info.json["class_path"]`, which A3 leaves unchanged (the golden fixtures in +`test_autofit/non_linear/samples/golden/` pin `samples.csv` byte for byte). diff --git a/docs/design/run_ctx.md b/docs/design/run_ctx.md index 91c4cb18d..1f088d04b 100644 --- a/docs/design/run_ctx.md +++ b/docs/design/run_ctx.md @@ -129,7 +129,12 @@ pins the following details the table left open; each is flagged for review in th - **`ctx.update(internal)`** is synchronous: the backend is paused while it runs, so the internal state is read as it stands (no copy). The snapshot hand-off arrives with A3's samples adapter, which converts the samples once. -- **`ctx.resume`, `ctx.checkpointer`** are `None` until A3 fills them; **`ctx.rng`** is a +- **`ctx.checkpointer`** is the search's archive strategy, the class attribute + `NonLinearSearch.checkpointer` (A3, `autofit/non_linear/checkpoint.py`, + `docs/design/checkpointing.md`). **`ctx.resume`** is the search's + `NonLinearSearch.resume_state` when the interrupted run's file exists, else `None`: the + `Checkpointer` handle, not the loaded state, because a backend may reopen its own native + file (`Nautilus` resumes through `Sampler(filepath=...)`). **`ctx.rng`** is a `SeedSequence` of the search's `seed` attribute, if any, until A4's search-level seed. - **`ctx.close(failed)`** is the cleanup the lifecycle rules require; on failure it closes the pools the context built, shuts the quick-update threads down and releases the @@ -141,5 +146,6 @@ pins the following details the table left open; each is flagged for review in th - **Search-side hooks** (not context members): `fitness_overrides(analysis)` lets a search add `Fitness` arguments (`Nautilus`: `batched`, `batch_size`), and `samples_cls` names the `Samples` class `raw_samples_from`'s result is converted into. `RawSamples` and - `samples_from_raw` live provisionally in `autofit/non_linear/search/fit_context.py` until - A3's `samples/adapter.py` replaces them. + `samples_from_raw` are A3's `autofit/non_linear/samples/adapter.py` (re-exported from + `autofit/non_linear/search/fit_context.py`), and `samples_via_internal_from` is + implemented once on `NonLinearSearch` over `raw_samples_from` for every search. diff --git a/docs/index.md b/docs/index.md index 723aa00fb..bf8b68910 100644 --- a/docs/index.md +++ b/docs/index.md @@ -105,6 +105,7 @@ cookbooks/multi_level_model searches/index searches/citations design/run_ctx +design/checkpointing ``` ```{toctree} diff --git a/docs/searches/index.rst b/docs/searches/index.rst index a8288e623..8bea2811b 100644 --- a/docs/searches/index.rst +++ b/docs/searches/index.rst @@ -220,95 +220,113 @@ Capabilities Objectives ---------- -What each search's objective returns, the coordinates its backend proposes points in (``unit_cube`` backends map through the prior transform; the likelihood always receives physical parameters), the value it returns for an invalid model, and the reduced budget ``PYAUTO_TEST_MODE=1`` applies. +What each search's objective returns, the coordinates its backend proposes points in (``unit_cube`` backends map through the prior transform; the likelihood always receives physical parameters), the value it returns for an invalid model, where it archives its internal state when a fit completes, and the reduced budget ``PYAUTO_TEST_MODE=1`` applies. .. list-table:: :header-rows: 1 - :widths: 16 18 12 12 42 + :widths: 14 16 11 11 16 32 * - Search - Objective - Coordinates - Invalid value + - Archive - Test-mode budget * - :class:`~autofit.Emcee` - ``log_posterior`` - ``physical`` - ``-inf`` + - ``native:search_internal.hdf`` - ``nwalkers=20``, ``nsteps=10`` * - :class:`~autofit.Zeus` - ``log_posterior`` - ``physical`` - ``-inf`` + - ``dill`` - ``nwalkers=20``, ``nsteps=10`` * - :class:`~autofit.BlackJAXNUTS` - ``log_posterior`` - ``physical`` - ``-inf`` + - ``pickle`` - ``num_warmup=20``, ``num_samples=20``, ``num_chains=2`` * - :class:`~autofit.SMC` - ``log_likelihood`` - ``physical`` - ``-1e+99`` + - ``pickle`` - ``num_particles=16``, ``num_mcmc_steps=2``, ``max_smc_steps=5`` * - :class:`~autofit.DynestyStatic` - ``log_likelihood`` - ``unit_cube`` - ``-1e+99`` + - ``dill`` - ``maxcall=1`` * - :class:`~autofit.DynestyDynamic` - ``log_likelihood`` - ``unit_cube`` - ``-1e+99`` + - ``dill`` - ``maxcall=1`` * - :class:`~autofit.Nautilus` - ``log_likelihood`` - ``unit_cube`` - ``-1e+99`` + - ``dill`` - ``n_like_max=1`` * - :class:`~autofit.NSS` - ``log_likelihood`` - ``physical`` - ``-1e+30`` + - ``dill`` - ``termination=-1.0`` * - :class:`~autofit.Drawer` - ``log_posterior`` - ``physical`` - ``-inf`` + - ``dill`` - -- * - :class:`~autofit.BFGS` - ``neg2_log_posterior`` - ``physical`` - ``inf`` + - ``dill`` - -- * - :class:`~autofit.LBFGS` - ``neg2_log_posterior`` - ``physical`` - ``inf`` + - ``dill`` - -- * - :class:`~autofit.MultiStartAdam` - ``neg2_log_posterior`` - ``physical`` - ``inf`` + - ``dill`` - ``convergence.window=1``, ``convergence.min_steps=1`` * - :class:`~autofit.MultiStartADABelief` - ``neg2_log_posterior`` - ``physical`` - ``inf`` + - ``dill`` - ``convergence.window=1``, ``convergence.min_steps=1`` * - :class:`~autofit.MultiStartLion` - ``neg2_log_posterior`` - ``physical`` - ``inf`` + - ``dill`` - ``convergence.window=1``, ``convergence.min_steps=1`` * - :class:`~autofit.MultiStartProdigy` - ``neg2_log_posterior`` - ``physical`` - ``inf`` + - ``dill`` - ``convergence.window=1``, ``convergence.min_steps=1`` The invalid value is what the backend actually sees, not yet normalised. For the ``neg2_log_posterior`` minimizers it is conditional: a NaN or infinite likelihood is replaced by ``-inf`` and then multiplied by -2 into ``inf`` (the value listed), while a model rejected by a ``FitException`` or a failed assertion returns ``-inf``. +The archive is ``dill`` (``search_internal.dill``), ``pickle`` (``search_internal.pickle``, plain NumPy data) or ``native:`` (a file the backend writes itself). Emcee, BlackJAXNUTS and SMC keep their archive after a fit completes whatever the ``output.search_internal`` config says, because their samples cannot be rebuilt without it. + Column meanings --------------- diff --git a/test_autofit/non_linear/paths/test_search_internal_loading.py b/test_autofit/non_linear/paths/test_search_internal_loading.py new file mode 100644 index 000000000..c8d463624 --- /dev/null +++ b/test_autofit/non_linear/paths/test_search_internal_loading.py @@ -0,0 +1,154 @@ +""" +Loading a search's internal state per output kind (search-extensibility phase A3, D5): +directory (through the search's injected ``checkpointer`` or, without a search, the +format-aware legacy probe), zipped, database, null and summary-only outputs. +""" +import logging +from pathlib import Path + +import dill +import numpy as np +import pytest + +import autofit as af +from autofit.non_linear.checkpoint import load_legacy_search_internal +from autofit.non_linear.paths.directory import DirectoryPaths +from autofit.non_linear.paths.null import NullPaths +from autofit.non_linear.result import Result +from autonerves import conf + +CONFIG = Path(__file__).parents[2] / "config" + + +@pytest.fixture(name="output", autouse=True) +def make_output(tmp_path): + conf.instance.push(new_path=str(CONFIG), output_path=str(tmp_path)) + return tmp_path + + +def _write_dill(paths, obj): + with open(paths.search_internal_path / "search_internal.dill", "wb") as f: + dill.dump(obj, f) + + +def test_directory_without_a_search_uses_the_legacy_probe(): + paths = DirectoryPaths(name="loading_legacy") + _write_dill(paths, {"state": 1}) + + assert paths.search is None + assert paths.load_search_internal() == {"state": 1} + + +def test_directory_with_a_search_loads_through_its_checkpointer(): + search = af.Drawer(name="loading_injected") + _write_dill(search.paths, {"state": 2}) + + assert search.paths.search is search + assert search.paths.load_search_internal() == {"state": 2} + assert search.load_search_internal() == {"state": 2} + + +def _emcee_hdf(paths): + emcee = pytest.importorskip("emcee") + pytest.importorskip("h5py") + + backend = emcee.backends.HDFBackend( + str(paths.search_internal_path / "search_internal.hdf") + ) + sampler = emcee.EnsembleSampler( + nwalkers=4, + ndim=1, + log_prob_fn=lambda x: -0.5 * float(np.sum(x**2)), + backend=backend, + ) + sampler.run_mcmc(np.random.default_rng(1).normal(size=(4, 1)), 3) + return emcee + + +def test_emcee_hdf_loads_with_and_without_the_search(): + """ + The emcee HDF detection that used to live inline in + ``DirectoryPaths.load_search_internal`` is the Emcee checkpointer's loader, and is + kept as the first format of the legacy probe for a folder opened on its own. + """ + search = af.Emcee(name="loading_emcee") + emcee = _emcee_hdf(search.paths) + + via_search = search.paths.load_search_internal() + assert isinstance(via_search, emcee.backends.HDFBackend) + assert via_search.iteration == 3 + + legacy = load_legacy_search_internal(search.paths.search_internal_path) + assert isinstance(legacy, emcee.backends.HDFBackend) + + +def test_zipped_output_loads_after_restore(): + search = af.Drawer(name="loading_zipped") + paths = search.paths + _write_dill(paths, {"state": 3}) + + paths.zip_remove() + assert Path(paths._zip_path).exists() + + paths.restore() + + assert paths.load_search_internal() == {"state": 3} + + +def test_database_paths_load_nothing(session): + paths = af.DatabasePaths(session=session, name="loading_database") + + assert paths.load_search_internal() is None + assert Result(samples_summary=None, paths=paths).search_internal is None + + +def test_null_paths_load_nothing(): + paths = NullPaths() + + assert paths.load_search_internal() is None + assert Result(samples_summary=None, paths=paths).search_internal is None + + +@pytest.fixture(name="search_internal_off") +def make_search_internal_off(tmp_path): + original_configs = list(conf.instance.configs) + config = tmp_path / "config_off" + config.mkdir() + (config / "output.yaml").write_text("search_internal: false\n") + conf.instance.push(new_path=str(config)) + conf.instance["general"]["output"]["samples_to_csv"] = True + yield + conf.instance.configs = original_configs + + +def test_summary_only_output_falls_back_to_samples_csv( + search_internal_off, monkeypatch, caplog +): + """ + A completed output without ``search_internal/`` (``output.search_internal: + false``) has no archive: loading raises ``FileNotFoundError``, + ``Result.search_internal`` is ``None`` and the samples come from ``samples.csv``. + """ + monkeypatch.setenv("PYAUTO_TEST_MODE", "1") + + analysis = af.ex.Analysis(data=np.full(10, 5.0), noise_map=np.ones(10)) + search = af.Drawer(name="loading_summary_only", total_draws=5) + search.fit(model=af.Model(af.ex.Gaussian), analysis=analysis) + + resumed = af.Drawer(name="loading_summary_only", total_draws=5) + result = resumed.fit(model=af.Model(af.ex.Gaussian), analysis=analysis) + resumed.paths.restore() + + with pytest.raises(FileNotFoundError): + resumed.paths.load_search_internal() + + assert Result(samples_summary=None, paths=resumed.paths).search_internal is None + + with caplog.at_level(logging.WARNING): + samples = resumed.samples_from(resumed.paths.model) + + assert len(samples.sample_list) == len(result.samples.sample_list) + assert any( + "could not be loaded from its internal results" in record.getMessage() + for record in caplog.records + ) diff --git a/test_autofit/non_linear/samples/golden/.gitattributes b/test_autofit/non_linear/samples/golden/.gitattributes new file mode 100644 index 000000000..0c6cf9492 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/.gitattributes @@ -0,0 +1,3 @@ +# Byte-exact golden fixtures: samples.csv is written with CRLF line endings by the csv +# module and is compared byte for byte, so git must not normalise it. +* -text diff --git a/test_autofit/non_linear/samples/golden/__init__.py b/test_autofit/non_linear/samples/golden/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/test_autofit/non_linear/samples/golden/cases.py b/test_autofit/non_linear/samples/golden/cases.py new file mode 100644 index 000000000..11b0c6299 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/cases.py @@ -0,0 +1,129 @@ +""" +The golden samples cases: how each stored backend internal is loaded and converted. + +Shared by ``generate.py`` (which writes the fixtures on the reference checkout) and +``test_golden_samples.py`` (which replays the conversion and compares the tables), so the +two can never drift apart. +""" +import json +import pickle +from pathlib import Path + + +HERE = Path(__file__).parent + +#: name -> (search class path inside ``autofit``, constructor kwargs, internal file, +#: modules the conversion needs). +CASES = { + "emcee": ("Emcee", dict(nwalkers=12, nsteps=400), "emcee.pickle", ("emcee",)), + "dynesty": ("DynestyStatic", dict(nlive=40, maxcall=4000), "dynesty.pickle", ()), + "nautilus": ("Nautilus", dict(n_live=100, n_like_max=4000), "nautilus.pickle", ()), + "nuts": ( + "BlackJAXNUTS", + dict(num_warmup=50, num_samples=60, num_chains=2), + "nuts.pickle", + ("jax", "blackjax"), + ), + "smc": ("SMC", dict(num_particles=200), "smc.pickle", ()), +} + + +def model_from(name): + from autonerves.dictable import from_dict + + with open(HERE / name / "model.json") as f: + return from_dict(json.load(f)) + + +class DynestyResults: + """ + The fields of a ``dynesty`` ``Results`` that sample conversion reads. + """ + + def __init__(self, samples, logl, logwt, logz, ncall): + self.samples = samples + self.logl = logl + self.logwt = logwt + self.logz = logz + self.ncall = ncall + + +class DynestyInternal: + """ + A stored ``dynesty`` sampler reduced to its ``results``: everything + ``samples_via_internal_from`` reads, without the sampler's likelihood, prior + transform, pool or bounds (which tie a pickled sampler to one dynesty version). + """ + + def __init__(self, results: dict): + self.results = DynestyResults(**results) + + +class NautilusInternal: + """ + A stored ``nautilus.Sampler`` reduced to what sample conversion reads: the + output of ``posterior()`` and the ``log_z`` / ``n_like`` / ``n_live`` + attributes (the sampler's neural-network bounds make the real object ~15 MB). + """ + + def __init__(self, state: dict): + self._posterior = ( + state["parameters"], + state["log_weights"], + state["log_likelihoods"], + ) + self.log_z = state["log_z"] + self.n_like = state["n_like"] + self.n_live = state["n_live"] + + def posterior(self): + return self._posterior + + +def internal_from(name): + """ + The stored internal of case ``name`` in the form the search converts: emcee's own + in-memory ``Backend`` (the same ``get_chain`` / ``get_log_prob`` slicing as its + ``HDFBackend``), the reduced dynesty and nautilus samplers above, and the plain + NumPy dicts NUTS and SMC pickle. + """ + _, _, filename, _ = CASES[name] + + with open(HERE / name / filename, "rb") as f: + state = pickle.load(f) + + if name == "dynesty": + return DynestyInternal(state) + if name == "nautilus": + return NautilusInternal(state) + return state + + +def search_from(name): + import autofit as af + + class_name, kwargs, _, _ = CASES[name] + return getattr(af, class_name)(**kwargs) + + +def samples_from(name): + """ + Convert the stored internal of case ``name`` to a ``Samples`` object through the + search's public ``samples_via_internal_from``, under ``NullPaths`` (no timer). + """ + search = search_from(name) + model = model_from(name) + return search.samples_via_internal_from( + model=model, search_internal=internal_from(name) + ) + + +def samples_info_for_comparison(samples): + """ + ``samples_info`` without the run-dependent ``time`` key, JSON round-tripped so + NumPy scalars compare as the plain values ``samples_info.json`` stores. + """ + from autofit.tools.util import NumpyEncoder + + info = {k: v for k, v in samples.samples_info.items() if k != "time"} + return json.loads(json.dumps(info, cls=NumpyEncoder)) diff --git a/test_autofit/non_linear/samples/golden/dynesty/dynesty.pickle b/test_autofit/non_linear/samples/golden/dynesty/dynesty.pickle new file mode 100644 index 000000000..5803d74d0 Binary files /dev/null and b/test_autofit/non_linear/samples/golden/dynesty/dynesty.pickle differ diff --git a/test_autofit/non_linear/samples/golden/dynesty/model.json b/test_autofit/non_linear/samples/golden/dynesty/model.json new file mode 100644 index 000000000..2fa3226b2 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/dynesty/model.json @@ -0,0 +1,24 @@ +{ + "class_path": "autofit.example.model.Gaussian", + "type": "model", + "arguments": { + "centre": { + "type": "Gaussian", + "id": 3, + "mean": 25.0, + "sigma": 10.0 + }, + "normalization": { + "type": "Uniform", + "id": 4, + "lower_limit": 0.0, + "upper_limit": 50.0 + }, + "sigma": { + "type": "LogUniform", + "id": 5, + "lower_limit": 0.1, + "upper_limit": 20.0 + } + } +} \ No newline at end of file diff --git a/test_autofit/non_linear/samples/golden/dynesty/samples.csv b/test_autofit/non_linear/samples/golden/dynesty/samples.csv new file mode 100644 index 000000000..b0ec6630d --- /dev/null +++ b/test_autofit/non_linear/samples/golden/dynesty/samples.csv @@ -0,0 +1,730 @@ + centre, normalization, sigma, log_likelihood, log_prior, log_posterior, weight +21.090624895240904,45.07935892249056, 0.1485816977809966, -5986.966442202521, 1.8302042500623512, -5985.136237952458, 0.0 + 42.72498840488177,49.61799895865763,0.15246589730451826, -3082.860094866696, 0.3099382624089986,-3082.5501566042867, 0.0 + 2.223655039478732,46.54207452940832, 1.5176729039877959, -2929.390953741875, -3.0109876262890642, -2932.401941368164, 0.0 + 25.11677757585025,30.15800352133338,0.19168508579618299,-2888.2041029650877, 1.6518332466529075,-2886.5522697184347, 0.0 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000000000..bde3c5f73 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/dynesty/samples_info.json @@ -0,0 +1,7 @@ +{ + "class_path": "autofit.non_linear.samples.nest.SamplesNest", + "log_evidence": -1794.7419342233939, + "number_live_points": 40, + "total_accepted_samples": 729, + "total_samples": 3777 +} \ No newline at end of file diff --git a/test_autofit/non_linear/samples/golden/emcee/emcee.pickle b/test_autofit/non_linear/samples/golden/emcee/emcee.pickle new file mode 100644 index 000000000..5a8ed767b Binary files /dev/null and b/test_autofit/non_linear/samples/golden/emcee/emcee.pickle differ diff --git a/test_autofit/non_linear/samples/golden/emcee/model.json b/test_autofit/non_linear/samples/golden/emcee/model.json new file mode 100644 index 000000000..2fa3226b2 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/emcee/model.json @@ -0,0 +1,24 @@ +{ + "class_path": "autofit.example.model.Gaussian", + "type": "model", + "arguments": { + "centre": { + "type": 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b/test_autofit/non_linear/samples/golden/emcee/samples_info.json @@ -0,0 +1,8 @@ +{ + "change_threshold": 0.01, + "check_size": 100, + "class_path": "autofit.non_linear.samples.mcmc.SamplesMCMC", + "required_length": 50, + "total_steps": 400, + "total_walkers": 12 +} \ No newline at end of file diff --git a/test_autofit/non_linear/samples/golden/generate.py b/test_autofit/non_linear/samples/golden/generate.py new file mode 100644 index 000000000..8223f176a --- /dev/null +++ b/test_autofit/non_linear/samples/golden/generate.py @@ -0,0 +1,175 @@ +""" +Regenerate the golden ``samples.csv`` fixtures (search-extensibility phase A3). + +Run ONLY on a checkout whose sample conversion is the reference: ``origin/main`` +before the A3 samples adapter landed (generated at 0dbf258c4). It runs a small real +fit with each of Emcee, DynestyStatic, Nautilus, BlackJAXNUTS and SMC and stores +the backend's own internal state; then, in a fresh process, it converts that stored +state back through ``samples_via_internal_from`` (``cases.samples_from``) and writes +the ``samples.csv`` and ``samples_info.json`` the conversion produces. +``test_golden_samples.py`` replays the same conversion and requires ``samples.csv`` +to match: same header and row order, values equal to floating-point roundoff. + + python test_autofit/non_linear/samples/golden/generate.py [case ...] + +The internals are stored so that they load without the fit that produced them: + +- ``emcee.hdf``: emcee's own ``HDFBackend`` file; +- ``dynesty.dill`` / ``nautilus.dill``: the sampler with its likelihood, prior + transform and pools removed (conversion reads only the stored points, weights + and bounds); +- ``nuts.pickle`` / ``smc.pickle``: the plain NumPy dicts those searches pickle. + +``model.json`` is the fitted model, so the fixtures do not depend on the prior +configuration of the config directory the tests run under. +""" +import json +import os +import pickle +import shutil +import subprocess +import sys +import tempfile +from pathlib import Path + +HERE = Path(__file__).parent +ROOT = HERE.parents[3] + + +def fit(name): + import numpy as np + + import autofit as af + from autonerves import conf + from autonerves.dictable import to_dict + + from test_autofit.non_linear.samples.golden.cases import CASES + + class_name, kwargs, filename, _ = CASES[name] + + rng = np.random.default_rng(1) + xvalues = np.arange(50) + data = 25.0 * np.exp(-0.5 * ((xvalues - 25.0) / 5.0) ** 2) + rng.normal(size=50) + noise_map = np.ones(50) + + model = af.Model(af.ex.Gaussian) + # Non-uniform priors so the log prior column, and the log-likelihood derived from + # a log posterior (Emcee), are not trivially zero. + model.centre = af.GaussianPrior(mean=25.0, sigma=10.0) + model.normalization = af.UniformPrior(lower_limit=0.0, upper_limit=50.0) + model.sigma = af.LogUniformPrior(lower_limit=0.1, upper_limit=20.0) + + output = Path(tempfile.mkdtemp()) + conf.instance.push( + new_path=str(Path(af.__file__).parent / "config"), output_path=str(output) + ) + + np.random.seed(1) + use_jax = name in ("nuts", "smc") + analysis = af.ex.Analysis(data=data, noise_map=noise_map, use_jax=use_jax) + search = getattr(af, class_name)(name=f"golden_{name}", **kwargs) + result = search.fit(model=model, analysis=analysis) + + directory = HERE / name + shutil.rmtree(directory, ignore_errors=True) + directory.mkdir() + + if name == "emcee": + import emcee + + search.paths.restore() + internal = emcee.backends.HDFBackend( + filename=str(search.paths.search_internal_path / "search_internal.hdf"), + read_only=True, + ) + state = emcee.backends.Backend() + state.reset(internal.shape[0], internal.shape[1]) + state.chain = internal.get_chain() + state.log_prob = internal.get_log_prob() + state.accepted = np.asarray(internal.accepted) + state.iteration = internal.iteration + state.random_state = internal.random_state + state.blobs = None + else: + internal = result.search_internal + if name == "dynesty": + results = internal.results + state = { + key: np.asarray(getattr(results, key)) + for key in ("samples", "logl", "logwt", "logz", "ncall") + } + elif name == "nautilus": + parameters, log_weights, log_likelihoods = internal.posterior() + state = { + "parameters": parameters, + "log_weights": log_weights, + "log_likelihoods": log_likelihoods, + "log_z": internal.log_z, + "n_like": internal.n_like, + "n_live": internal.n_live, + } + else: + state = internal + + with open(directory / filename, "wb") as f: + pickle.dump(state, f) + + # The stored form must convert exactly as the live internal does. + from test_autofit.non_linear.samples.golden.cases import internal_from, search_from + + def table(search_internal): + samples = search_from(name).samples_via_internal_from( + model=model, search_internal=search_internal + ) + path = output / "check.csv" + samples.write_table(filename=path) + return path.read_bytes() + + assert table(internal) == table(internal_from(name)), name + + with open(directory / "model.json", "w") as f: + json.dump(to_dict(model), f, indent=4) + + shutil.rmtree(output, ignore_errors=True) + + +def convert(name): + from autofit.non_linear.paths.null import NullPaths # noqa: F401 + + from test_autofit.non_linear.samples.golden.cases import ( + HERE as CASES_HERE, + samples_from, + samples_info_for_comparison, + ) + + samples = samples_from(name) + samples.write_table(filename=CASES_HERE / name / "samples.csv") + with open(CASES_HERE / name / "samples_info.json", "w") as f: + json.dump(samples_info_for_comparison(samples), f, indent=4, sort_keys=True) + + +def main(): + from test_autofit.non_linear.samples.golden.cases import CASES + + names = sys.argv[2:] if len(sys.argv) > 2 else list(CASES) + + if len(sys.argv) > 1 and sys.argv[1] in ("fit", "convert"): + action = sys.argv[1] + for name in names: + (fit if action == "fit" else convert)(name) + return + + env = {**os.environ, "PYAUTO_SKIP_VISUALIZATION": "1"} + env.pop("PYAUTO_TEST_MODE", None) + names = sys.argv[1:] or list(CASES) + for action in ("fit", "convert"): + for name in names: + # One fresh process per step: conversion must not see the fit's state. + subprocess.run( + [sys.executable, __file__, action, name], check=True, cwd=ROOT, env=env + ) + + +if __name__ == "__main__": + sys.path.insert(0, str(ROOT)) + main() diff --git a/test_autofit/non_linear/samples/golden/nautilus/model.json b/test_autofit/non_linear/samples/golden/nautilus/model.json new file mode 100644 index 000000000..2fa3226b2 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/nautilus/model.json @@ -0,0 +1,24 @@ +{ + "class_path": "autofit.example.model.Gaussian", + "type": "model", + "arguments": { + "centre": { + "type": "Gaussian", + "id": 3, + "mean": 25.0, + "sigma": 10.0 + }, + "normalization": { + "type": "Uniform", + "id": 4, + "lower_limit": 0.0, + "upper_limit": 50.0 + }, + "sigma": { + "type": "LogUniform", + "id": 5, + "lower_limit": 0.1, + "upper_limit": 20.0 + } + } +} \ No newline at end of file diff --git a/test_autofit/non_linear/samples/golden/nautilus/nautilus.pickle b/test_autofit/non_linear/samples/golden/nautilus/nautilus.pickle new file mode 100644 index 000000000..43ed61522 Binary files /dev/null and b/test_autofit/non_linear/samples/golden/nautilus/nautilus.pickle differ diff --git a/test_autofit/non_linear/samples/golden/nautilus/samples.csv b/test_autofit/non_linear/samples/golden/nautilus/samples.csv new file mode 100644 index 000000000..d1c96f5cf --- /dev/null +++ b/test_autofit/non_linear/samples/golden/nautilus/samples.csv @@ -0,0 +1,3201 @@ + centre, normalization, sigma, log_likelihood, log_prior, log_posterior, weight + 37.01836263934637, 48.86600736804591, 3.7291577471492054,-2678.5600263210076, 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b/test_autofit/non_linear/samples/golden/nautilus/samples_info.json new file mode 100644 index 000000000..d579ef3d1 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/nautilus/samples_info.json @@ -0,0 +1,7 @@ +{ + "class_path": "autofit.non_linear.samples.nest.SamplesNest", + "log_evidence": -1795.2976164340837, + "number_live_points": 100, + "total_accepted_samples": 3200, + "total_samples": 3200 +} \ No newline at end of file diff --git a/test_autofit/non_linear/samples/golden/nuts/model.json b/test_autofit/non_linear/samples/golden/nuts/model.json new file mode 100644 index 000000000..2fa3226b2 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/nuts/model.json @@ -0,0 +1,24 @@ +{ + "class_path": "autofit.example.model.Gaussian", + "type": "model", + "arguments": { + "centre": { + "type": "Gaussian", + "id": 3, + "mean": 25.0, + "sigma": 10.0 + }, + "normalization": { + "type": "Uniform", + "id": 4, + "lower_limit": 0.0, + "upper_limit": 50.0 + }, + "sigma": { + 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a/test_autofit/non_linear/samples/golden/smc/samples_info.json b/test_autofit/non_linear/samples/golden/smc/samples_info.json new file mode 100644 index 000000000..2961f8b25 --- /dev/null +++ b/test_autofit/non_linear/samples/golden/smc/samples_info.json @@ -0,0 +1,88 @@ +{ + "acceptance_rate_list": [ + 0.594318138504432, + 0.6984474105671555, + 0.7216489429246097, + 0.6694394122572644, + 0.5334982798088242, + 0.27065273110976906, + 0.09714782101215369, + 0.007352785219150317, + 1.920843432515693e-06, + 0.0, + 0.0, + 0.0 + ], + "class_path": "autofit.non_linear.search.mcmc.blackjax.smc.samples.SamplesSMC", + "converged": true, + "ess_list": [ + 95.2335672865771, + 121.91889275285874, + 133.56520457671039, + 147.42617187297083, + 133.4192498983835, + 135.61538475822888, + 136.7748449668647, + 146.64429651963684, + 142.12996563535467, + 143.14139574224683, + 113.39243050406584, + 164.27984953287873 + ], + "inverse_mass_matrix_kind": "none", + "is_warm_start": false, + "kernel": "mala", + "lambda_list": [ + 0.0030570030212402344, + 0.00600304841424304, + 0.009704790677982035, + 0.015362805546764278, + 0.026141852897770494, + 0.04267162975908095, + 0.06963191377589456, + 0.11707591621975688, + 0.21558575662199592, + 0.4311512553286282, + 0.7701724691557529, + 1.0 + ], + "log_evidence": -1794.8893451211445, + "log_jacobian": 6.574563816281148, + "log_likelihood_increment_list": [ + -7.5876058205195935, + -6.696719349492044, + -7.751762385802995, + -11.083755261248019, + -20.26590152387964, + -30.430854721131045, + -48.95808070598031, + -85.36781286735801, + -176.44181828051043, + -385.20307699568895, + -605.1767735462062, + -409.92518366332735 + ], + "max_log_likelihood_list": [ + -1873.081612092529, + -1810.1515248986411, + -1816.5956630869034, + -1798.373343170037, + -1785.5740233574256, + -1785.5740233574256, + -1781.9668969251127, + -1781.9668969251127, + -1781.9668969251127, + -1781.9668969251127, + -1781.9668969251127, + -1781.9668969251127 + ], + "n_smc_steps": 12, + "num_integration_steps": 8, + "num_mcmc_steps": 5, + "num_particles": 200, + "step_size": 0.019637378012158674, + "target_ess": 0.5, + "total_samples": 200, + "warm_start_source": "InitializerPrior", + "whitening_kind": "prior-scale diagonal (cold)" +} \ No newline at end of file diff --git a/test_autofit/non_linear/samples/golden/smc/smc.pickle b/test_autofit/non_linear/samples/golden/smc/smc.pickle new file mode 100644 index 000000000..71b7ecd99 Binary files /dev/null and b/test_autofit/non_linear/samples/golden/smc/smc.pickle differ diff --git a/test_autofit/non_linear/samples/test_adapter.py b/test_autofit/non_linear/samples/test_adapter.py new file mode 100644 index 000000000..e4914ee63 --- /dev/null +++ b/test_autofit/non_linear/samples/test_adapter.py @@ -0,0 +1,222 @@ +import numpy as np +import pytest + +import autofit as af +from autofit import exc +from autofit.non_linear.samples.adapter import ( + ChainPosterior, + RawSamples, + invalid_count, + is_invalid, + log_prior_list_from, + samples_from_raw, +) +from autofit.non_linear.search.mcmc.auto_correlations import AutoCorrelations + + +@pytest.fixture(name="model") +def make_model(): + model = af.Model(af.ex.Gaussian) + model.centre = af.GaussianPrior(mean=1.0, sigma=2.0) + model.normalization = af.UniformPrior(lower_limit=0.0, upper_limit=10.0) + model.sigma = af.UniformPrior(lower_limit=0.0, upper_limit=10.0) + return model + + +PARAMETERS = [[1.0, 2.0, 3.0], [1.5, 2.5, 3.5]] + + +def test_log_likelihood_from_log_posterior(model): + log_prior = log_prior_list_from(model, PARAMETERS) + + samples = samples_from_raw( + model, + RawSamples(parameters=PARAMETERS, log_posterior=[-1.0, -2.0]), + af.SamplesMCMC, + ) + + assert samples.log_prior_list == log_prior + assert samples.log_likelihood_list == [ + -1.0 - log_prior[0], + -2.0 - log_prior[1], + ] + assert samples.weight_list == [1.0, 1.0] + + +def test_weights_are_never_renormalised(model): + samples = samples_from_raw( + model, + RawSamples( + parameters=PARAMETERS, log_likelihood=[-1.0, -2.0], weights=[3.0, 5.0] + ), + af.SamplesNest, + ) + + assert samples.weight_list == [3.0, 5.0] + + +def test_time_and_class_path_are_injected(model): + samples = samples_from_raw( + model, + RawSamples(parameters=PARAMETERS, log_likelihood=[-1.0, -2.0], info={"a": 1}), + af.Samples, + time=12.5, + ) + + assert samples.samples_info["a"] == 1 + assert samples.samples_info["time"] == 12.5 + assert samples.samples_info["class_path"].endswith(".Samples") + + +def test_a_search_time_wins_over_the_injected_one(model): + samples = samples_from_raw( + model, + RawSamples( + parameters=PARAMETERS, log_likelihood=[-1.0, -2.0], info={"time": 3.0} + ), + af.Samples, + time=12.5, + ) + + assert samples.samples_info["time"] == 3.0 + + +@pytest.mark.parametrize( + "field, name", + [ + ("log_posterior", "log posterior"), + ("log_likelihood", "log likelihood"), + ], +) +def test_length_mismatch_raises(model, field, name): + with pytest.raises(exc.SamplesException, match=f"number of {name} values"): + samples_from_raw( + model, + RawSamples(parameters=PARAMETERS, label="Test", **{field: [-1.0]}), + af.Samples, + ) + + +def test_weight_length_mismatch_raises(model): + with pytest.raises(exc.SamplesException, match="weight"): + samples_from_raw( + model, + RawSamples( + parameters=PARAMETERS, log_likelihood=[-1.0, -2.0], weights=[1.0] + ), + af.Samples, + ) + + +def test_exactly_one_of_log_likelihood_and_log_posterior(): + with pytest.raises(exc.SamplesException): + RawSamples(parameters=PARAMETERS) + with pytest.raises(exc.SamplesException): + RawSamples(parameters=PARAMETERS, log_likelihood=[1.0], log_posterior=[1.0]) + + +@pytest.mark.parametrize("value", [-1.0e99, -1.0e30, -np.inf, -1.0e99 - 3.0]) +def test_sentinels_are_recognised(value): + assert is_invalid(value) + + +@pytest.mark.parametrize("value", [0.0, -1.0e10, np.nan, "x"]) +def test_ordinary_values_are_not_sentinels(value): + assert not is_invalid(value) + + +def test_sentinels_are_kept_as_stored(model): + samples = samples_from_raw( + model, + RawSamples(parameters=PARAMETERS, log_likelihood=[-1.0e99, -np.inf]), + af.Samples, + ) + + assert invalid_count(samples.log_likelihood_list) == 2 + assert samples.log_likelihood_list[0] == -1.0e99 + assert samples.log_likelihood_list[1] == -np.inf + + +def _chain(n_steps=6, n_chains=2, n_dim=3): + chain = np.arange(n_steps * n_chains * n_dim, dtype=float).reshape( + n_steps, n_chains, n_dim + ) + log_prob = chain[:, :, 0] * 10.0 + return chain, log_prob + + +def _emcee_backend(chain, log_prob): + emcee = pytest.importorskip("emcee") + + backend = emcee.backends.Backend() + backend.reset(chain.shape[1], chain.shape[2]) + backend.chain = chain + backend.log_prob = log_prob + backend.iteration = chain.shape[0] + backend.accepted = np.ones(chain.shape[1]) + return backend + + +def test_from_arrays_thins_like_emcee(): + chain, log_prob = _chain() + backend = _emcee_backend(chain, log_prob) + + for discard, thin in [(0, 1), (1, 2), (2, 3)]: + expected = ChainPosterior.from_sampler(backend).thin(discard, thin) + result = ChainPosterior.from_arrays(chain, log_prob).thin(discard, thin) + + assert np.array_equal(result[0], expected[0]) + assert np.array_equal(result[1], expected[1]) + + +def test_from_arrays_chain_major(): + chain, log_prob = _chain() + + parameters, log_values = ChainPosterior.from_arrays( + chain, log_prob, chain_major=True + ).thin(0, 1) + + assert np.array_equal(parameters, np.moveaxis(chain, 0, 1).reshape(-1, 3)) + assert np.array_equal(log_values, np.moveaxis(log_prob, 0, 1).reshape(-1)) + + +def test_empty_chain_falls_back_to_the_whole_chain(): + chain, log_prob = _chain() + + parameters, log_values = ChainPosterior.from_arrays(chain, log_prob).thin( + discard=100, thin=5 + ) + + assert len(parameters) == chain.shape[0] * chain.shape[1] + assert len(log_values) == len(parameters) + + +def test_emcee_gets_the_empty_chain_fallback(model, monkeypatch): + """ + Emcee shares Zeus's fallback: burn-in removal that leaves nothing builds the + samples from the whole chain instead of failing. + """ + monkeypatch.delenv("PYAUTO_TEST_MODE", raising=False) + + rng = np.random.default_rng(1) + chain = rng.uniform(1.0, 3.0, size=(4, 6, 3)) + backend = _emcee_backend(chain, -np.sum(chain**2, axis=2)) + + search = af.Emcee() + + times = np.array([10.0, 10.0, 10.0]) + monkeypatch.setattr( + type(search), + "auto_correlations_from", + lambda self, search_internal=None: AutoCorrelations( + check_size=2, + required_length=1, + change_threshold=0.01, + times=times, + previous_times=times, + ), + ) + + samples = search.samples_via_internal_from(model=model, search_internal=backend) + + assert len(samples.sample_list) == 24 diff --git a/test_autofit/non_linear/samples/test_golden_samples.py b/test_autofit/non_linear/samples/test_golden_samples.py new file mode 100644 index 000000000..eb18f270f --- /dev/null +++ b/test_autofit/non_linear/samples/test_golden_samples.py @@ -0,0 +1,108 @@ +""" +Golden ``samples.csv`` fixtures for the search-extensibility phase A3 samples adapter. + +Each case under ``golden/`` holds a backend internal stored from a small real fit +(Emcee, DynestyStatic, Nautilus, BlackJAXNUTS, SMC), the fitted model, and the +``samples.csv`` / ``samples_info.json`` that ``samples_via_internal_from`` produced +from that internal on ``origin/main`` before the adapter landed (``golden/generate.py``). +Converting the same internal today must reproduce ``samples.csv``: the same header, +the same rows in the same order, and every parameter, log likelihood, log prior, log +posterior and weight equal to within floating-point roundoff, with no renormalisation +(decision D13). + +The comparison is to ``CSV_RTOL`` rather than byte for byte because NumPy's +vectorised ``exp`` / ``log`` loops are dispatched per CPU (AVX2 vs AVX-512), so the +same NumPy version on a different runner can land one unit in the last place away: +on CI the dynesty and nautilus weights (and two nautilus log priors) differed from the +AVX2-generated fixtures by at most 1 ULP (relative 2.2e-16). Any renormalisation, +reordering or dropped row changes values by many orders of magnitude more. + +``samples_info`` is compared exactly except for the convergence diagnostics BlackJAX +itself computes (ESS, bulk/tail ESS, rank-normalised R-hat), whose estimators change +between BlackJAX releases; for those only the shape is pinned. +""" +import csv +import importlib.util +import json + +import numpy as np +import pytest + +from test_autofit.non_linear.samples.golden import cases + +pytestmark = pytest.mark.filterwarnings("ignore::FutureWarning") + + +def _skip_missing(name): + missing = [ + module + for module in cases.CASES[name][3] + if importlib.util.find_spec(module) is None + ] + if missing: + pytest.skip(f"golden case {name} needs {missing}") + + +@pytest.fixture(autouse=True) +def reference_mode(monkeypatch): + # The fixtures were converted outside test mode, where the MCMC burn-in and + # thinning come from the auto-correlation times rather than fixed values. + monkeypatch.delenv("PYAUTO_TEST_MODE", raising=False) + + +#: Relative tolerance on every numeric ``samples.csv`` entry: ~4500x the largest drift +#: measured across CI runners (2.2e-16), far below any change the adapter could make. +CSV_RTOL = 1e-12 + +#: ``samples_info`` keys computed by ``blackjax.diagnostics`` rather than by autofit. +BACKEND_DIAGNOSTIC_KEYS = ( + "ess_min", + "ess_per_param", + "ess_bulk_min", + "ess_bulk_per_param", + "ess_tail_min", + "ess_tail_per_param", + "rhat_max", + "rhat_per_param", +) + + +def _read_csv(path): + with open(path, newline="") as f: + rows = list(csv.reader(f)) + header = [column.strip() for column in rows[0]] + values = np.array([[float(value) for value in row] for row in rows[1:]]) + return header, values + + +@pytest.mark.parametrize("name", list(cases.CASES)) +def test_samples_csv_is_unchanged(name, tmp_path): + _skip_missing(name) + + samples = cases.samples_from(name) + samples.write_table(filename=tmp_path / "samples.csv") + + header, values = _read_csv(tmp_path / "samples.csv") + expected_header, expected_values = _read_csv(cases.HERE / name / "samples.csv") + + assert header == expected_header + assert values.shape == expected_values.shape + np.testing.assert_allclose(values, expected_values, rtol=CSV_RTOL, atol=0.0) + + +@pytest.mark.parametrize("name", list(cases.CASES)) +def test_samples_info_is_unchanged(name): + _skip_missing(name) + + samples = cases.samples_from(name) + + with open(cases.HERE / name / "samples_info.json") as f: + expected = json.load(f) + + info = cases.samples_info_for_comparison(samples) + + for key in BACKEND_DIAGNOSTIC_KEYS: + if key in expected: + assert np.shape(info.pop(key)) == np.shape(expected.pop(key)), key + + assert info == expected diff --git a/test_autofit/non_linear/search/test_conformance.py b/test_autofit/non_linear/search/test_conformance.py index b513ced5b..78e186602 100644 --- a/test_autofit/non_linear/search/test_conformance.py +++ b/test_autofit/non_linear/search/test_conformance.py @@ -35,15 +35,6 @@ ROSTER = searches_under_test() -CONFIG_MUTATION_XFAIL = { - name: ( - "__init__ sets conf.instance['output']['search_internal'] = True; " - "removed in search-extensibility phase A3." - ) - for name in ("Emcee", "BlackJAXNUTS", "SMC") -} - - def _params(xfails=None, raises=None): """ The roster as pytest params, with strict xfail marks for the named entries. @@ -163,8 +154,13 @@ def make_search_internal_off(tmp_path): conf.instance.configs = original_configs -@pytest.mark.parametrize("entry", _params(CONFIG_MUTATION_XFAIL, raises=AssertionError)) +@pytest.mark.parametrize("entry", _params()) def test_config_unchanged_by_construction(entry, search_internal_off): + """ + Constructing a search never changes the configuration. Emcee, BlackJAXNUTS and + SMC used to force ``output.search_internal`` on; their archives now declare + ``retain_after_completion`` instead (search-extensibility phase A3). + """ cls = _search_class(entry) assert conf.instance["output"]["search_internal"] is False diff --git a/test_autofit/non_linear/search/test_conformance_backend.py b/test_autofit/non_linear/search/test_conformance_backend.py index 69431769e..33a2679df 100644 --- a/test_autofit/non_linear/search/test_conformance_backend.py +++ b/test_autofit/non_linear/search/test_conformance_backend.py @@ -253,21 +253,6 @@ "NSS": "NSSamples", } -# Dynesty's ``samples_via_internal_from`` reads the in-run checkpoint -# (``search_internal/savestate.save``), which ``output_search_internal`` deletes at the -# end of a fit after dumping ``search_internal.dill``. A completed Dynesty output folder -# therefore always falls back to ``samples.csv``. One checkpoint / internal-state path -# per search is phase A3 (survey 01 §5.3 item 2, §9 phase 3). -DISK_INTERNAL_XFAIL = { - name: ( - "samples_via_internal_from reads the deleted savestate.save checkpoint, not the " - "search_internal.dill a completed fit keeps, so it falls back to samples.csv; " - "unified in search-extensibility phase A3." - ) - for name in ("DynestyStatic", "DynestyDynamic") -} - - # ``Emcee``, ``Zeus``, ``BlackJAXNUTS`` and ``SMC`` take ``auto_correlation_settings= # AutoCorrelationsSettings()`` as a default argument, built once at import time, so the # test-mode ``check_size = 1`` reduction applies only when ``PYAUTO_TEST_MODE`` is set @@ -611,8 +596,14 @@ def raise_error(*args, **kwargs): assert any(_FALLBACK_MESSAGE in record.getMessage() for record in caplog.records) -@pytest.mark.parametrize("entry", _params(DISK_INTERNAL_XFAIL, raises=AssertionError)) +@pytest.mark.parametrize("entry", _params()) def test_restored_output_samples_from_none_loads_the_internal_state(entry, backend_run): + """ + A completed, restored output folder keeps the archive ``samples_via_internal_from`` + reads (for Dynesty ``search_internal.dill``; its ``savestate.save`` resume state is + deleted on completion), so the samples load from it without the ``samples.csv`` + fallback. + """ outcome = backend_run(entry).disk_samples_from assert outcome.error is None diff --git a/test_autofit/non_linear/search/test_fit_context.py b/test_autofit/non_linear/search/test_fit_context.py index 1cbd88c19..85ad6159a 100644 --- a/test_autofit/non_linear/search/test_fit_context.py +++ b/test_autofit/non_linear/search/test_fit_context.py @@ -64,7 +64,9 @@ def spy(self, ctx): for member in FROZEN_MEMBERS: assert hasattr(ctx, member), member assert ctx.test_mode_level == 1 - assert ctx.resume is None and ctx.checkpointer is None + # A3: the archive strategy is the search's; Drawer has no resume state. + assert ctx.checkpointer == search.checkpointer + assert ctx.resume is None # Never stored on the search. assert not any(isinstance(value, FitContext) for value in vars(search).values()) @@ -155,3 +157,33 @@ def test_schedule_chunks_cover_the_budget(): from autofit.non_linear.search.fit_context import UpdateSchedule assert list(UpdateSchedule(search).chunks(10)) == [4, 4, 2] + + +def test_resume_is_the_resume_state_only_when_its_file_exists(tmp_path): + from autofit.non_linear.checkpoint import NativeFileCheckpointer + + class ResumableToy(ToySearch): + resume_state = NativeFileCheckpointer("toy_checkpoint.bin", loader=open) + + search = ResumableToy() + search.paths = af.DirectoryPaths(name="toy", path_prefix=str(tmp_path)) + search.paths.model = af.Model(af.ex.Gaussian) + + def ctx(): + return FitContext( + search=search, + model=search.paths.model, + analysis=None, + fitness=None, + pool=None, + test_mode_level=0, + ) + + assert ctx().resume is None + assert ctx().checkpointer is search.checkpointer + + path = search.resume_state.path(search.paths) + path.parent.mkdir(parents=True, exist_ok=True) + path.write_bytes(b"state") + + assert ctx().resume is search.resume_state diff --git a/test_autofit/non_linear/test_checkpoint.py b/test_autofit/non_linear/test_checkpoint.py new file mode 100644 index 000000000..fe3d207ac --- /dev/null +++ b/test_autofit/non_linear/test_checkpoint.py @@ -0,0 +1,309 @@ +""" +The archive / resume-state strategies of ``autofit.non_linear.checkpoint`` (search- +extensibility phase A3, decision D5; ``docs/design/checkpointing.md``). +""" +import os +import pickle +from pathlib import Path + +import dill +import pytest + +import autofit as af +from autofit.non_linear.checkpoint import ( + DillCheckpointer, + NativeFileCheckpointer, + PickleCheckpointer, + checkpointer_kind, + load_legacy_search_internal, +) +from autofit.non_linear.paths.directory import DirectoryPaths +from autofit.non_linear.paths.null import NullPaths +from autonerves import conf + +from test_autofit.non_linear.search.conformance_roster import searches_under_test + + +class Holder: + def __init__(self): + self.value = 1 + self.pool = lambda: None # a lambda dill can serialise; stripped anyway + + +@pytest.fixture(name="paths") +def make_paths(tmp_path): + conf.instance.push( + new_path=str(Path(__file__).parents[1] / "config"), output_path=str(tmp_path) + ) + return DirectoryPaths(name="checkpoint_test") + + +def test_dill_round_trip(paths): + checkpointer = DillCheckpointer() + + assert not checkpointer.exists(paths) + + checkpointer.save(paths, {"a": 1}) + + assert checkpointer.exists(paths) + assert checkpointer.load(paths) == {"a": 1} + assert checkpointer.path(paths) == paths.search_internal_path / "search_internal.dill" + + +def test_dill_strips_and_restores_attributes(paths): + checkpointer = DillCheckpointer(strip_attributes=("pool",)) + holder = Holder() + pool = holder.pool + + checkpointer.save(paths, holder) + + assert holder.pool is pool + assert checkpointer.load(paths).pool is None + + +def test_pickle_round_trip(paths): + checkpointer = PickleCheckpointer() + + checkpointer.finalize(paths, {"positions": [1, 2]}) + + with open(paths.search_internal_path / "search_internal.pickle", "rb") as f: + assert pickle.load(f) == {"positions": [1, 2]} + assert checkpointer.load(paths) == {"positions": [1, 2]} + assert checkpointer.retain_after_completion + + +def test_writes_are_atomic(paths, monkeypatch): + checkpointer = PickleCheckpointer() + checkpointer.save(paths, {"good": True}) + + def broken_dump(obj, f): + f.write(b"partial") + raise RuntimeError("disk full") + + monkeypatch.setattr(pickle, "dump", broken_dump) + + with pytest.raises(RuntimeError): + checkpointer.save(paths, {"good": False}) + + monkeypatch.undo() + assert checkpointer.load(paths) == {"good": True} + assert not any( + name.endswith(".tmp") for name in os.listdir(paths.search_internal_path) + ) + + +def test_corrupt_archive_raises_rather_than_being_treated_as_absent(paths): + path = DillCheckpointer().path(paths) + path.write_bytes(b"not a dill") + + with pytest.raises(Exception) as error: + DillCheckpointer().load(paths) + + assert not isinstance(error.value, FileNotFoundError) + + +def test_native_file(paths): + checkpointer = NativeFileCheckpointer("state.bin", loader=lambda p: p.read_bytes()) + + checkpointer.save(paths, "ignored") + checkpointer.finalize(paths, "ignored") + assert not checkpointer.exists(paths) + + with pytest.raises(FileNotFoundError): + checkpointer.load(paths) + + (paths.search_internal_path / "state.bin").write_bytes(b"abc") + + assert checkpointer.load(paths) == b"abc" + + checkpointer.discard(paths) + assert not checkpointer.exists(paths) + checkpointer.discard(paths) # discarding an absent file is a no-op + + +@pytest.mark.parametrize( + "checkpointer", + [ + DillCheckpointer(), + PickleCheckpointer(), + NativeFileCheckpointer("x", loader=lambda p: None), + ], +) +def test_null_paths_store_nothing(checkpointer): + paths = NullPaths() + + checkpointer.save(paths, {"a": 1}) + + assert checkpointer.path(paths) is None + assert not checkpointer.exists(paths) + assert checkpointer.load(paths) is None + + +def test_database_paths_store_nothing(session): + paths = af.DatabasePaths(session=session, name="checkpoint_database") + + DillCheckpointer().save(paths, {"a": 1}) + PickleCheckpointer().save(paths, {"a": 1}) + + assert DillCheckpointer().load(paths) is None + assert PickleCheckpointer().load(paths) is None + + +def test_legacy_detection(paths): + directory = paths.search_internal_path + + with pytest.raises(FileNotFoundError): + load_legacy_search_internal(directory) + + with open(directory / "search_internal.dill", "wb") as f: + dill.dump("dill", f) + assert load_legacy_search_internal(directory) == "dill" + + with open(directory / "search_internal.pickle", "wb") as f: + pickle.dump("pickle", f) + assert load_legacy_search_internal(directory) == "pickle" + + +def test_archive_falls_back_to_the_legacy_probe(paths): + """ + An output folder written before its search chose a strategy (here: a pickle + archive where the search now expects a dill) still loads. + """ + with open(paths.search_internal_path / "search_internal.pickle", "wb") as f: + pickle.dump("legacy", f) + + assert DillCheckpointer().load(paths) == "legacy" + + +def test_checkpointer_kind(): + assert checkpointer_kind(DillCheckpointer()) == "dill" + assert checkpointer_kind(PickleCheckpointer()) == "pickle" + assert ( + checkpointer_kind(NativeFileCheckpointer("f.hdf", loader=lambda p: None)) + == "native:f.hdf" + ) + assert checkpointer_kind(None) is None + + +# --- per-search declarations ----------------------------------------------------------- + + +@pytest.mark.parametrize( + "entry", searches_under_test(), ids=lambda entry: entry.name +) +def test_resume_state_implies_resumable(entry): + missing = entry.missing_requirements() + if missing: + pytest.skip(f"{entry.name} needs {missing}") + cls = entry.resolve() + + if cls.resume_state is not None: + assert cls.resumable + assert cls.checkpointer is not None + + +def test_nuts_and_smc_have_no_resume_state(): + from autofit.non_linear.search.mcmc.blackjax.nuts.search import BlackJAXNUTS + from autofit.non_linear.search.mcmc.blackjax.smc.search import SMC + + for cls in (BlackJAXNUTS, SMC): + assert cls.resume_state is None + assert not cls.resumable + assert isinstance(cls.checkpointer, PickleCheckpointer) + assert cls.checkpointer.retain_after_completion + + +def test_emcee_archive_is_its_hdf_backend(): + assert isinstance(af.Emcee.checkpointer, NativeFileCheckpointer) + assert af.Emcee.checkpointer.filename == "search_internal.hdf" + assert af.Emcee.checkpointer.retain_after_completion + assert af.Emcee.resume_state is af.Emcee.checkpointer + + +# --- retention precedence --------------------------------------------------------------- + + +@pytest.fixture(name="search_internal_off") +def make_search_internal_off(tmp_path): + original_configs = list(conf.instance.configs) + (tmp_path / "output.yaml").write_text("search_internal: false\n") + conf.instance.push(new_path=str(tmp_path)) + yield + conf.instance.configs = original_configs + + +def test_retention_precedence(search_internal_off): + """ + ``retain_after_completion`` keeps the archive whatever the config says; otherwise + ``output.search_internal: false`` removes the folder. + """ + assert conf.instance["output"]["search_internal"] is False + + assert not af.DynestyStatic().retains_search_internal + assert not af.Drawer().retains_search_internal + assert af.Emcee().retains_search_internal + # Retained by declaration, not by mutating the configuration. + assert conf.instance["output"]["search_internal"] is False + + +def test_output_search_internal_discards_the_resume_state(paths): + search = af.DynestyStatic() + search.paths = paths + + savestate = paths.search_internal_path / "savestate.save" + savestate.write_bytes(b"resume") + + search.output_search_internal({"archive": True}) + + assert not savestate.exists() + assert DillCheckpointer().load(paths) == {"archive": True} + + +def test_output_search_internal_keeps_a_resume_state_that_is_the_archive(paths): + search = af.MultiStartAdam() if hasattr(af, "MultiStartAdam") else None + if search is None: + pytest.skip("MultiStartAdam is not exported") + search.paths = paths + + search.output_search_internal({"params": [1.0]}) + + assert DillCheckpointer().load(paths) == {"params": [1.0]} + + +def _archived(search): + import zipfile + + with zipfile.ZipFile(search.paths._zip_path) as archive: + return set(archive.namelist()) + + +def test_a_retained_archive_survives_with_search_internal_off( + search_internal_off, monkeypatch +): + """ + With ``output.search_internal: false`` a completed Emcee fit still keeps its HDF + archive (``retain_after_completion``), while a Drawer fit loses its dill, and + the Emcee fit leaves the configuration untouched for the Drawer fit after it. + """ + import numpy as np + + monkeypatch.setenv("PYAUTO_TEST_MODE", "1") + model = af.Model(af.ex.Gaussian) + analysis = af.ex.Analysis(data=np.full(10, 5.0), noise_map=np.ones(10)) + + emcee = af.Emcee( + name="retention_emcee", + unique_tag="checkpoint_retention", + auto_correlation_settings=af.AutoCorrelationsSettings( + check_for_convergence=False, check_size=5, required_length=2 + ), + ) + emcee.fit(model=model, analysis=analysis) + + drawer = af.Drawer( + name="retention_drawer", unique_tag="checkpoint_retention", total_draws=5 + ) + drawer.fit(model=af.Model(af.ex.Gaussian), analysis=analysis) + + assert "files/search_internal/search_internal.hdf" in _archived(emcee) + assert not any("search_internal/" in name for name in _archived(drawer))