diff --git a/.github/workflows/docs-link-check.yml b/.github/workflows/docs-link-check.yml new file mode 100644 index 000000000..bf454f17c --- /dev/null +++ b/.github/workflows/docs-link-check.yml @@ -0,0 +1,38 @@ +name: Docs Link Check + +# Validates the hard-coded URLs in llms.txt and AGENTS.md, which are not covered by +# any other CI. Runs monthly rather than per-PR so transient or rate-limited external +# responses don't block contributors. + +on: + schedule: + - cron: '0 6 1 * *' # 06:00 UTC on the 1st of each month + workflow_dispatch: + +permissions: + contents: read + +defaults: + run: + shell: bash + +jobs: + link-check: + name: Check documentation links + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + with: + lfs: false + persist-credentials: false + + - name: Check links with lychee + uses: lycheeverse/lychee-action@e7477775783ea5526144ba13e8db5eec57747ce8 # v2.9.0 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # authenticate github.com links (avoid 60/hr rate limit) + with: + args: >- + --no-progress --verbose + docs/llms.txt AGENTS.md + fail: true diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 000000000..089a9a98a --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,55 @@ +# AGENTS.md — sbi + +Shared guidance for coding agents working in this repository. + +## Setup + +```bash +uv venv --python 3.12 +uv pip install -e ".[dev]" +``` + +Run validation commands through `uv run`; activating the virtual environment is +optional. See `docs/contributing.md` for the full development workflow and +`pyproject.toml` for the authoritative tool configuration. + +## Validation + +Start with checks targeted to the files and behavior you changed, then broaden as +appropriate: + +```bash +uv run pytest tests/path_to_relevant_test.py +uv run pytest -n auto -m "not slow and not gpu" +uv run ruff check +uv run ruff format --check +uv run pyright sbi +uv run pre-commit run --files +``` + +Tests live in `*_test.py` files. Available markers include `slow`, `gpu`, `mcmc`, and +`benchmark`; their definitions are in `pyproject.toml`. + +## Code conventions + +- Use Google-style docstrings. +- Put shared public type aliases in `sbi/sbi_types.py`. +- Keep string identifiers for estimators lowercase (for example, `"maf"`, `"nsf"`, + and `"mdn"`). +- Add or update tests when behavior changes. +- Preserve unrelated local changes. If a checkout is already in use, work in a + separate Git worktree. + +## Code map + +Inspect the current code rather than relying on a duplicated class inventory: + +- `sbi/inference/__init__.py` — public inference methods +- `sbi/inference/trainers/` — training workflows +- `sbi/inference/posteriors/` — posterior implementations +- `sbi/inference/potentials/` — estimator-to-sampler bridges +- `sbi/neural_nets/estimators/` — estimator contracts and implementations +- `sbi/samplers/` — sampling backends + +The documentation is built from `docs/`. Its curated `docs/llms.txt` index is served +at `https://sbi.readthedocs.io/en/latest/llms.txt` for tools that support it. diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 000000000..248e45d22 --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1,6 @@ +# CLAUDE.md + +This repository's instructions for AI coding agents live in `AGENTS.md` (shared across +all tools). Claude Code imports them here: + +@AGENTS.md diff --git a/docs/conf.py b/docs/conf.py index 8ca740457..11166247a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -55,6 +55,9 @@ # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] +# Serve llms.txt at the docs URL root for AI agent discoverability. +html_extra_path = ['llms.txt'] + # Myst-NB myst_enable_extensions = [ "dollarmath", diff --git a/docs/contributor_guide.rst b/docs/contributor_guide.rst index 3939d86bd..c90d438cd 100644 --- a/docs/contributor_guide.rst +++ b/docs/contributor_guide.rst @@ -5,7 +5,8 @@ Developer notes `sbi` welcomes contributions from the community. These are guides to get set up as a developer, as well as -developer-focused resources. +developer-focused resources. For a list of current and former project +maintainers, see the :doc:`credits page `. .. toctree:: diff --git a/docs/credits.md b/docs/credits.md index 4cd52d163..fea10cd09 100644 --- a/docs/credits.md +++ b/docs/credits.md @@ -6,6 +6,22 @@ played a significant role in shaping `sbi`. Their valuable input, suggestions, and direct contributions to the codebase have been instrumental in the development of `sbi`. +## Maintainers + +`sbi` is maintained by the following people. Current maintainers are + +- [Jan Teusen (né Boelts)](https://github.com/janfb) +- [Manuel Gloeckler](https://github.com/manuelgloeckler) +- [Daniel Gedon](https://github.com/dgedon) +- [Stefan Wahl](https://github.com/StefanWahl) + +Former maintainers are + +- [Michael Deistler](https://github.com/michaeldeistler) +- [Guy Moss](https://github.com/gmoss13) +- [Jan-Matthis Lückmann](https://github.com/jan-matthis) +- [Alvaro Tejero-Cantero](https://github.com/alvorithm) + ## License `sbi` is licensed under the [Apache License diff --git a/docs/llms.txt b/docs/llms.txt new file mode 100644 index 000000000..2405f2a5c --- /dev/null +++ b/docs/llms.txt @@ -0,0 +1,72 @@ +# sbi: Simulation-Based Inference + +> sbi is a PyTorch-based Python package for simulation-based inference (SBI). +> It estimates full Bayesian posterior distributions over simulator parameters +> from observed data, without requiring access to the simulator's likelihood +> function. Methods include Neural Posterior Estimation (NPE), Neural Likelihood +> Estimation (NLE), Neural Ratio Estimation (NRE), and flow/score matching (FMPE, NPSE). + +sbi provides both a simple one-line interface (`sbi.inference.infer`) and a +flexible class-based interface (`NPE`, `NLE`, `NRE`, `FMPE`). The typical +workflow is: define a prior and simulator, generate simulations, train a neural +density estimator, build a posterior, and validate with diagnostics (SBC, +expected coverage, TARP, L-C2ST). + +## Tutorials + +- [Getting Started](https://sbi.readthedocs.io/en/latest/tutorials/00_getting_started.html): Minimal NPE example from prior to posterior +- [Bayesian Workflow](https://sbi.readthedocs.io/en/latest/tutorials/01_Bayesian_workflow.html): Full workflow with diagnostics and analysis +- [Implemented Methods](https://sbi.readthedocs.io/en/latest/tutorials/16_implemented_methods.html): All NPE, NLE, NRE, FMPE variants with code +- [Vector Field Methods](https://sbi.readthedocs.io/en/latest/advanced_tutorials/19_vector_field_methods.html): FMPE and NPSE — flow matching and score matching for SBI + +## How-To Guides + +- [Custom Priors](https://sbi.readthedocs.io/en/latest/how_to_guide/00_custom_prior.html): MultipleIndependent, process_prior, non-torch priors +- [Summary Statistics](https://sbi.readthedocs.io/en/latest/how_to_guide/01_crafting_summary_statistics.html): Hand-crafted features for high-dim data +- [Multi-Round Inference](https://sbi.readthedocs.io/en/latest/how_to_guide/02_multiround_inference.html): Sequential methods (SNPE, SNLE, SNRE) +- [Density Estimators](https://sbi.readthedocs.io/en/latest/how_to_guide/03_density_estimators.html): Choosing and configuring neural networks +- [Embedding Networks](https://sbi.readthedocs.io/en/latest/how_to_guide/04_embedding_networks.html): FCEmbedding, CNNEmbedding, custom nn.Module +- [Choosing Inference Method](https://sbi.readthedocs.io/en/latest/how_to_guide/06_choosing_inference_method.html): NPE vs NLE vs NRE decision guide +- [Sampler Interface](https://sbi.readthedocs.io/en/latest/how_to_guide/09_sampler_interface.html): MCMC, VI, rejection for NLE/NRE posteriors +- [i.i.d. Observations](https://sbi.readthedocs.io/en/latest/how_to_guide/11_iid_sampling_with_nle_or_nre.html): Multiple observations with NLE/NRE +- [Hyperparameter Tuning](https://sbi.readthedocs.io/en/latest/how_to_guide/21_hyperparameter_tuning.html): Optuna integration for architecture search +- [Abstraction Levels](https://sbi.readthedocs.io/en/latest/how_to_guide/24_abstraction_levels.html): Four levels of control over the density estimator (Trainer classes to custom `nn.Module`), plus sampling-control levels for NLE +- [FMPE and NPSE Recommendations](https://sbi.readthedocs.io/en/latest/how_to_guide/25_choosing_vector_field_options.html): Practical guide for choosing between vector field methods and configuring them + +## Diagnostics + +- [Choosing a Diagnostic](https://sbi.readthedocs.io/en/latest/how_to_guide/14_choose_diagnostic_tool.html): Which validation tool to use +- [Expected Coverage](https://sbi.readthedocs.io/en/latest/how_to_guide/15_expected_coverage.html): Joint posterior calibration check +- [Simulation-Based Calibration](https://sbi.readthedocs.io/en/latest/how_to_guide/16_sbc.html): Per-parameter marginal calibration +- [TARP](https://sbi.readthedocs.io/en/latest/how_to_guide/17_tarp.html): Calibration without density evaluation +- [L-C2ST](https://sbi.readthedocs.io/en/latest/how_to_guide/13_diagnostics_lc2st.html): Per-observation local coverage test +- [Model Misspecification](https://sbi.readthedocs.io/en/latest/how_to_guide/18_model_misspecification.html): Detecting if x_o is outside simulator range + +## Advanced Topics + +- [Time Series Embeddings](https://sbi.readthedocs.io/en/latest/how_to_guide/20_time_series_embedding.html): CausalCNN, Transformer for temporal data +- [Restriction Estimator](https://sbi.readthedocs.io/en/latest/advanced_tutorials/06_restriction_estimator.html): Handling invalid simulations (NaN/Inf) +- [Sensitivity Analysis](https://sbi.readthedocs.io/en/latest/advanced_tutorials/07_sensitivity_analysis.html): ActiveSubspace for parameter importance +- [Posterior Parameters](https://sbi.readthedocs.io/en/latest/how_to_guide/19_posterior_parameters.html): Dataclass-based sampler configuration +- [Experiment Tracking](https://sbi.readthedocs.io/en/latest/how_to_guide/22_experiment_tracking.html): TensorBoard, WandB, MLflow adapters +- [Pyro Integration](https://sbi.readthedocs.io/en/latest/how_to_guide/23_using_pyro_with_sbi.html): Neural likelihoods in Pyro hierarchical models + +## API Reference + +- [Inference API](https://sbi.readthedocs.io/en/latest/api_reference.html): NPE, NLE, NRE, FMPE trainers and posteriors +- [Installation](https://sbi.readthedocs.io/en/latest/installation.html): pip install sbi, optional dependencies +- [Changelog](https://sbi.readthedocs.io/en/latest/changelog.html): Version history and migration notes +- [FAQ](https://sbi.readthedocs.io/en/latest/faq.html): Common issues (leakage, NaNs, pickling, unconstrained space) + +## Optional + +- [Hodgkin-Huxley Example](https://sbi.readthedocs.io/en/latest/tutorials/Example_00_HodgkinHuxleyModel.html): Neuroscience application +- [Decision-Making Model](https://sbi.readthedocs.io/en/latest/tutorials/Example_01_DecisionMakingModel.html): Cognitive science application +- [GPU Training](https://sbi.readthedocs.io/en/latest/how_to_guide/07_gpu_training.html): CUDA and MPS device configuration +- [Save and Load](https://sbi.readthedocs.io/en/latest/how_to_guide/07_save_and_load.html): Pickling posteriors, CPU_Unpickler +- [Resume Training](https://sbi.readthedocs.io/en/latest/how_to_guide/07_resume_training.html): Checkpoint and resume +- [MCMC Diagnostics](https://sbi.readthedocs.io/en/latest/how_to_guide/12_mcmc_diagnostics_with_arviz.html): ArviZ trace plots and R-hat +- [Conditional Distributions](https://sbi.readthedocs.io/en/latest/how_to_guide/05_conditional_distributions.html): Conditional pairplots +- [Importance Sampling](https://sbi.readthedocs.io/en/latest/how_to_guide/10_refine_posterior_with_importance_sampling.html): Refining posteriors +- [Permutation-Invariant Embeddings](https://sbi.readthedocs.io/en/latest/how_to_guide/08_permutation_invariant_embeddings.html): i.i.d. data with NPE +- [Contributing Guide](https://sbi.readthedocs.io/en/latest/contributing.html): How to contribute to sbi diff --git a/sbi/inference/posteriors/base_posterior.py b/sbi/inference/posteriors/base_posterior.py index 599622904..f5111cecb 100644 --- a/sbi/inference/posteriors/base_posterior.py +++ b/sbi/inference/posteriors/base_posterior.py @@ -93,7 +93,7 @@ def potential( This can be helpful for e.g. sensitivity analysis, but increases memory consumption. """ - self.potential_fn.set_x(self._x_else_default_x(x)) + self.potential_fn = self.potential_fn.bind(self._x_else_default_x(x)) theta = ensure_theta_batched(torch.as_tensor(theta)) return self.potential_fn( @@ -294,7 +294,7 @@ def map( ) if self._map is None or force_update: - self.potential_fn.set_x(self.default_x) + self.potential_fn = self.potential_fn.bind(self.default_x) self._map = self._calculate_map( num_iter=num_iter, num_to_optimize=num_to_optimize, diff --git a/sbi/inference/posteriors/ensemble_posterior.py b/sbi/inference/posteriors/ensemble_posterior.py index 755f1cebe..fa4015f92 100644 --- a/sbi/inference/posteriors/ensemble_posterior.py +++ b/sbi/inference/posteriors/ensemble_posterior.py @@ -317,7 +317,7 @@ def potential( This can be helpful for e.g. sensitivity analysis, but increases memory consumption. """ - self.potential_fn.set_x(self._x_else_default_x(x)) + self.potential_fn = self.potential_fn.bind(self._x_else_default_x(x)) theta = ensure_theta_batched(torch.as_tensor(theta)) @@ -398,7 +398,7 @@ def map( return log_weights, maps else: - self.potential_fn.set_x(self._x_else_default_x(x)) + self.potential_fn = self.potential_fn.bind(self._x_else_default_x(x)) if init_method == "posterior": inits = self.sample((num_init_samples,), self._x_else_default_x(x)) @@ -488,6 +488,28 @@ def set_x(self, x_o: Optional[Tensor]): for comp_potential in self.potential_fns: comp_potential.set_x(x_o) + def bind( + self, + x_o: Tensor, + x_is_iid: bool = True, + **kwargs, + ) -> "EnsemblePotential": + """Return a new EnsemblePotential with x_o bound to all component potentials.""" + if x_o is not None: + x_o = process_x(x_o).to(self.device) + + bound_potentials = [ + p.bind(x_o, x_is_iid=x_is_iid, **kwargs) for p in self.potential_fns + ] + + return EnsemblePotential( + potential_fns=bound_potentials, + weights=self._weights, + prior=self.prior, + x_o=x_o, + device=self.device, + ) + def __call__(self, theta: Tensor, track_gradients: bool = True) -> Tensor: r"""Returns the potential for posterior-based methods. diff --git a/sbi/inference/posteriors/importance_posterior.py b/sbi/inference/posteriors/importance_posterior.py index cfbc3d2f8..fdc98a9a1 100644 --- a/sbi/inference/posteriors/importance_posterior.py +++ b/sbi/inference/posteriors/importance_posterior.py @@ -128,7 +128,7 @@ def log_prob( `len($\theta$)`-shaped log-probability. """ x = self._x_else_default_x(x) - self.potential_fn.set_x(x) + self.potential_fn = self.potential_fn.bind(x) theta = ensure_theta_batched(torch.as_tensor(theta)) @@ -212,7 +212,7 @@ def sample( method = self.method if method is None else method - self.potential_fn.set_x(self._x_else_default_x(x)) + self.potential_fn = self.potential_fn.bind(self._x_else_default_x(x)) if method == "sir": return self._sir_sample( diff --git a/sbi/inference/posteriors/mcmc_posterior.py b/sbi/inference/posteriors/mcmc_posterior.py index f90db67d6..fc1d254cf 100644 --- a/sbi/inference/posteriors/mcmc_posterior.py +++ b/sbi/inference/posteriors/mcmc_posterior.py @@ -2,7 +2,6 @@ # under the Apache License Version 2.0, see import inspect import warnings -from copy import deepcopy from functools import partial from math import ceil from typing import Any, Callable, Dict, Literal, Optional, Union @@ -237,7 +236,7 @@ def log_prob( warn("The log-probability is unnormalized!", stacklevel=2) x = self._x_else_default_x(x) - self.potential_fn.set_x(x, x_is_iid=True) + self.potential_fn = self.potential_fn.bind(x, x_is_iid=True) theta = ensure_theta_batched(torch.as_tensor(theta)) return self.potential_fn( @@ -291,7 +290,7 @@ def sample( """ x = self._x_else_default_x(x) - self.potential_fn.set_x(x, x_is_iid=True) + self.potential_fn = self.potential_fn.bind(x, x_is_iid=True) # Replace arguments that were not passed with their default. method = self.method if method is None else method @@ -451,7 +450,7 @@ def sample_batched( # in the order of the observations. x_ = x.repeat_interleave(num_chains, dim=0) - self.potential_fn.set_x(x_, x_is_iid=False) + self.potential_fn = self.potential_fn.bind(x_, x_is_iid=False) self.potential_ = self._prepare_potential(method) # type: ignore # For each observation in the batch, we have num_chains independent chains. @@ -662,25 +661,25 @@ def _get_initial_params_batched( Tensor: initial parameters, one for each chain """ - potential_ = deepcopy(self.potential_fn) + potential_ = self.potential_fn initial_params = [] - init_fn = self._build_mcmc_init_fn( - self.proposal, - potential_fn=potential_, - transform=self.theta_transform, - init_strategy=init_strategy, # type: ignore - **kwargs, - ) for xi in x: - # Build init function - potential_.set_x(xi) + # Build init function with bound potential for this specific xi + potential_bound = potential_.bind(xi) + init_fn = self._build_mcmc_init_fn( + self.proposal, + potential_fn=potential_bound, + transform=self.theta_transform, + init_strategy=init_strategy, # type: ignore + **kwargs, + ) # Parallelize inits for resampling or sir. if num_workers > 1 and ( init_strategy == "resample" or init_strategy == "sir" ): - def seeded_init_fn(seed): + def seeded_init_fn(seed, init_fn=init_fn): torch.manual_seed(seed) return init_fn() diff --git a/sbi/inference/posteriors/rejection_posterior.py b/sbi/inference/posteriors/rejection_posterior.py index 7b05160a2..92e173129 100644 --- a/sbi/inference/posteriors/rejection_posterior.py +++ b/sbi/inference/posteriors/rejection_posterior.py @@ -120,7 +120,7 @@ def log_prob( ) warn("The log-probability is unnormalized!", stacklevel=2) - self.potential_fn.set_x(self._x_else_default_x(x)) + self.potential_fn = self.potential_fn.bind(self._x_else_default_x(x)) theta = ensure_theta_batched(torch.as_tensor(theta)) return self.potential_fn( @@ -174,7 +174,7 @@ def sample( Samples from posterior. """ num_samples = torch.Size(sample_shape).numel() - self.potential_fn.set_x(self._x_else_default_x(x)) + self.potential_fn = self.potential_fn.bind(self._x_else_default_x(x)) potential = partial(self.potential_fn, track_gradients=True) diff --git a/sbi/inference/posteriors/vector_field_posterior.py b/sbi/inference/posteriors/vector_field_posterior.py index 20c1990f0..3832afd75 100644 --- a/sbi/inference/posteriors/vector_field_posterior.py +++ b/sbi/inference/posteriors/vector_field_posterior.py @@ -521,7 +521,7 @@ def sample_batched( condition_dim = len(self.vector_field_estimator.condition_shape) batch_shape = x.shape[:-condition_dim] batch_size = batch_shape.numel() - self.potential_fn.set_x(x) + self.potential_fn.set_x(x, x_is_iid=batch_size > 1) max_sampling_batch_size = ( self.max_sampling_batch_size @@ -661,7 +661,9 @@ def map( if self._map is None or force_update: # rebuild coarse flow fast for MAP optimization. - self.potential_fn.set_x(self.default_x, atol=1e-2, rtol=1e-3, exact=True) + self.potential_fn.set_x( + self.default_x, x_is_iid=False, atol=1e-2, rtol=1e-3, exact=True + ) callable_potential_fn = CallableDifferentiablePotentialFunction( self.potential_fn ) diff --git a/sbi/inference/posteriors/vi_posterior.py b/sbi/inference/posteriors/vi_posterior.py index e070d904f..d10162722 100644 --- a/sbi/inference/posteriors/vi_posterior.py +++ b/sbi/inference/posteriors/vi_posterior.py @@ -1229,7 +1229,7 @@ def _compute_amortized_elbo_loss(self, x_batch: Tensor, n_particles: int) -> Ten x_expanded = x_batch.repeat(n_particles, 1) # Set x_o for batched evaluation (x_is_iid=False: each θ paired with its x) - self.potential_fn.set_x(x_expanded, x_is_iid=False) + self.potential_fn = self.potential_fn.bind(x_expanded, x_is_iid=False) log_potential_flat = self.potential_fn(theta_flat) # Reshape: (n_particles * batch_size,) -> (n_particles, batch_size) diff --git a/sbi/inference/potentials/base_potential.py b/sbi/inference/potentials/base_potential.py index d24b05b94..935d0ba56 100644 --- a/sbi/inference/potentials/base_potential.py +++ b/sbi/inference/potentials/base_potential.py @@ -49,7 +49,7 @@ def x_is_iid(self) -> bool: return self._x_is_iid else: raise ValueError( - "No observed data is available. Use `potential_fn.set_x(x_o)`." + "No observed data is available. Use `potential_fn.bind(x_o)`." ) def set_x(self, x_o: Optional[Tensor], x_is_iid: Optional[bool] = True): @@ -66,7 +66,7 @@ def x_o(self) -> Tensor: return self._x_o else: raise ValueError( - "No observed data is available. Use `potential_fn.set_x(x_o)`." + "No observed data is available. Use `potential_fn.bind(x_o)`." ) @x_o.setter @@ -82,6 +82,20 @@ def return_x_o(self) -> Optional[Tensor]: """ return self._x_o + def bind(self, x_o: Tensor, x_is_iid: bool = True) -> "BasePotential": + """Create new potential with x bound, without mutable state. + + Args: + x_o: Observed data to bind. + x_is_iid: Whether x represents iid observations. + + Returns: + New potential instance with x bound. + + Subclasses must implement this method. + """ + raise NotImplementedError(f"{self.__class__.__name__} must implement bind()") + def to(self, device: Union[str, torch.device]) -> "BasePotential": """Move prior and x_o to the given device. @@ -154,3 +168,12 @@ def __call__(self, theta, track_gradients: bool = True): """ with torch.set_grad_enabled(track_gradients): return self.potential_fn(theta, self.x_o) + + def bind(self, x_o: Tensor, x_is_iid: bool = True) -> "CustomPotentialWrapper": + """Create new potential with x bound, without mutable state.""" + return CustomPotentialWrapper( + potential_fn=self.potential_fn, + prior=self.prior, + x_o=x_o, + device=self.device, + ) diff --git a/sbi/inference/potentials/likelihood_based_potential.py b/sbi/inference/potentials/likelihood_based_potential.py index d2907430c..991254489 100644 --- a/sbi/inference/potentials/likelihood_based_potential.py +++ b/sbi/inference/potentials/likelihood_based_potential.py @@ -94,6 +94,17 @@ def to(self, device: Union[str, torch.device]) -> "LikelihoodBasedPotential": self.likelihood_estimator.to(device) return self + def bind(self, x_o: Tensor, x_is_iid: bool = True) -> "LikelihoodBasedPotential": + """Create new potential with x bound, without mutable state.""" + bound = LikelihoodBasedPotential( + likelihood_estimator=self.likelihood_estimator, + prior=self.prior, + x_o=None, + device=self.device, + ) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + def __call__(self, theta: Tensor, track_gradients: bool = True) -> Tensor: r"""Returns the potential $\log(p(x_o|\theta)p(\theta))$. diff --git a/sbi/inference/potentials/posterior_based_potential.py b/sbi/inference/potentials/posterior_based_potential.py index eda384626..bdaae1d9f 100644 --- a/sbi/inference/potentials/posterior_based_potential.py +++ b/sbi/inference/potentials/posterior_based_potential.py @@ -106,6 +106,17 @@ def set_x(self, x_o: Optional[Tensor], x_is_iid: Optional[bool] = False): """ super().set_x(x_o, x_is_iid=x_is_iid) + def bind(self, x_o: Tensor, x_is_iid: bool = False) -> "PosteriorBasedPotential": + """Create new potential with x bound, without mutable state.""" + bound = PosteriorBasedPotential( + posterior_estimator=self.posterior_estimator, + prior=self.prior, + x_o=None, + device=self.device, + ) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + def __call__(self, theta: Tensor, track_gradients: bool = True) -> Tensor: r"""Returns the potential for posterior-based methods. diff --git a/sbi/inference/potentials/ratio_based_potential.py b/sbi/inference/potentials/ratio_based_potential.py index 844405e75..917fede47 100644 --- a/sbi/inference/potentials/ratio_based_potential.py +++ b/sbi/inference/potentials/ratio_based_potential.py @@ -82,6 +82,17 @@ def to(self, device: Union[str, torch.device]) -> "RatioBasedPotential": self.ratio_estimator.to(device) return self + def bind(self, x_o: Tensor, x_is_iid: bool = True) -> "RatioBasedPotential": + """Create new potential with x bound, without mutable state.""" + bound = RatioBasedPotential( + ratio_estimator=self.ratio_estimator, + prior=self.prior, + x_o=None, + device=self.device, + ) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + def __call__(self, theta: Tensor, track_gradients: bool = True) -> Tensor: r"""Returns the potential for likelihood-ratio-based methods. diff --git a/sbi/inference/potentials/vector_field_potential.py b/sbi/inference/potentials/vector_field_potential.py index b7ac4ba45..fbac610fd 100644 --- a/sbi/inference/potentials/vector_field_potential.py +++ b/sbi/inference/potentials/vector_field_potential.py @@ -61,6 +61,7 @@ def __init__( self.vector_field_estimator.eval() self.iid_method = iid_method self.iid_params = iid_params + self.neural_ode_backend = neural_ode_backend neural_ode_kwargs = neural_ode_kwargs or {} self.neural_ode = build_neural_ode( @@ -128,6 +129,37 @@ def set_x( elif self._x_o is not None: self.flows = self.rebuild_flows_for_batch(**ode_kwargs) + def bind( + self, + x_o: Tensor, + x_is_iid: bool = False, + iid_method: Optional[str] = None, + iid_params: Optional[Dict[str, Any]] = None, + guidance_method: Optional[str] = None, + guidance_params: Optional[Dict[str, Any]] = None, + **ode_kwargs, + ) -> "VectorFieldBasedPotential": + """Create new potential with x bound, without mutable state.""" + bound = VectorFieldBasedPotential( + vector_field_estimator=self.vector_field_estimator, + prior=self.prior, + x_o=None, + device=self.device, + iid_method=self.iid_method, + iid_params=self.iid_params, + neural_ode_backend=self.neural_ode_backend, + ) + bound.set_x( + x_o, + x_is_iid=x_is_iid, + iid_method=iid_method, + iid_params=iid_params, + guidance_method=guidance_method, + guidance_params=guidance_params, + **ode_kwargs, + ) + return bound + def __call__( self, theta: Tensor, diff --git a/sbi/utils/conditional_density_utils.py b/sbi/utils/conditional_density_utils.py index 0d48efedb..a42e6b4ed 100644 --- a/sbi/utils/conditional_density_utils.py +++ b/sbi/utils/conditional_density_utils.py @@ -412,7 +412,7 @@ def x_is_iid(self) -> bool: return self._x_is_iid else: raise ValueError( - "No observed data is available. Use `potential_fn.set_x(x_o)`." + "No observed data is available. Use `potential_fn.bind(x_o)`." ) def set_x(self, x_o: Optional[Tensor], x_is_iid: Optional[bool] = True): @@ -420,7 +420,15 @@ def set_x(self, x_o: Optional[Tensor], x_is_iid: Optional[bool] = True): if x_o is not None: x_o = process_x(x_o).to(self.device) self._x_is_iid = x_is_iid - self.potential_fn.set_x(x_o, x_is_iid=x_is_iid) + self.potential_fn = self.potential_fn.bind(x_o, x_is_iid=x_is_iid) + + def bind(self, x_o: Tensor, x_is_iid: bool = True) -> "ConditionedPotential": + """Create new potential with x bound, without mutable state.""" + return ConditionedPotential( + potential_fn=self.potential_fn.bind(x_o, x_is_iid), + condition=self.condition, + dims_to_sample=self.dims_to_sample, + ) @property def x_o(self) -> Tensor: diff --git a/sbi/utils/torchutils.py b/sbi/utils/torchutils.py index f8ed0f7cd..f0e97d534 100644 --- a/sbi/utils/torchutils.py +++ b/sbi/utils/torchutils.py @@ -659,6 +659,7 @@ def _base_recursor( key: Optional[str] = None, check: Callable[..., bool] = lambda obj: False, action: Callable[..., object] = lambda obj: obj, + _active: Optional[set[int]] = None, ): """Recursive function that traverses objects (e.g. Distributions) and applies an action to any encountered object that passes the check. @@ -673,7 +674,17 @@ def _base_recursor( If the check evaluates to True, then ``action`` is applied. action: A function that specifies an operation on an object and returns a modified version. + _active: Object identities on the active recursion path. Used internally + to avoid infinite recursion in cyclic object graphs. """ + _active_holder: Optional[set[int]] = _active + if _active_holder is None: + _active_holder = set() + obj_id = id(obj) + if obj_id in _active_holder: + return + _active_holder.add(obj_id) + if isinstance(obj, Module) and check(obj): action(obj) elif isinstance(obj, (Dict, OrderedDict)): @@ -681,29 +692,43 @@ def _base_recursor( if check(o): obj[k] = action(o) else: - _base_recursor(o, parent=obj, key=k, check=check, action=action) + _base_recursor( + o, + parent=obj, + key=k, + check=check, + action=action, + _active=_active_holder, + ) elif isinstance(obj, type): # Skip class/type objects to avoid modifying immutable C extension types # (e.g. torch.LongTensor) which fail on Python 3.13+. - return + pass elif hasattr(obj, "__dict__"): for k, o in obj.__dict__.items(): if check(o): setattr(obj, k, action(o)) else: - _base_recursor(o, parent=obj, key=k, check=check, action=action) + _base_recursor( + o, + parent=obj, + key=k, + check=check, + action=action, + _active=_active_holder, + ) elif isinstance(obj, (List, Tuple, Generator)): new_obj = [] for o in obj: if check(o): new_obj.append(action(o)) else: - _base_recursor(o, check=check, action=action) + _base_recursor(o, check=check, action=action, _active=_active_holder) new_obj.append(o) if parent is not None and key is not None: setattr(parent, key, type(obj)(new_obj)) # type: ignore - else: - return + + _active_holder.remove(obj_id) def move_all_tensor_to_device(obj: object, device: Union[str, torch.device]) -> None: diff --git a/sbi/utils/user_input_checks_utils.py b/sbi/utils/user_input_checks_utils.py index dbd8a1d5e..9a1f96124 100644 --- a/sbi/utils/user_input_checks_utils.py +++ b/sbi/utils/user_input_checks_utils.py @@ -2,6 +2,7 @@ # under the Apache License Version 2.0, see import warnings +from copy import deepcopy from typing import Dict, Optional, Sequence, Union import torch @@ -181,18 +182,15 @@ def __init__( event_shape=torch.Size(), validate_args=None, ): + self.prior = prior + self.device = None + self.return_type = return_type super().__init__( batch_shape=batch_shape, event_shape=event_shape, - validate_args=( - prior._validate_args if validate_args is None else validate_args - ), + validate_args=False, ) - self.prior = prior - self.device = None - self.return_type = return_type - def log_prob(self, value) -> Tensor: return torch.as_tensor( self.prior.log_prob(value), @@ -236,6 +234,15 @@ def to(self, device: Union[str, torch.device]) -> None: self.prior = move_distribution_to_device(self.prior, device) self.device = device + def __deepcopy__(self, memo): + """Ensure prior attribute is preserved during deepcopy.""" + cls = self.__class__ + result = cls.__new__(cls) + memo[id(self)] = result + for k, v in self.__dict__.items(): + setattr(result, k, deepcopy(v, memo)) + return result + class MultipleIndependent(Distribution): """Wrap a sequence of PyTorch distributions into a joint PyTorch distribution.""" @@ -434,6 +441,15 @@ def to(self, device: Union[str, torch.device]) -> None: self.dists[i] = move_distribution_to_device(self.dists[i], device) self.device = device + def __deepcopy__(self, memo): + """Ensure dists attribute is preserved during deepcopy.""" + cls = self.__class__ + result = cls.__new__(cls) + memo[id(self)] = result + for k, v in self.__dict__.items(): + setattr(result, k, deepcopy(v, memo)) + return result + def build_support( lower_bound: Optional[Tensor] = None, upper_bound: Optional[Tensor] = None @@ -523,15 +539,13 @@ class OneDimPriorWrapper(Distribution): """ def __init__(self, prior: Distribution, validate_args=None) -> None: + self.prior = prior + self.device = None super().__init__( batch_shape=prior.batch_shape, event_shape=prior.event_shape, - validate_args=( - prior._validate_args if validate_args is None else validate_args - ), + validate_args=False, ) - self.prior = prior - self.device = None def to(self, device: Union[str, torch.device]) -> None: """ @@ -568,3 +582,12 @@ def mean(self) -> Tensor: @property def variance(self) -> Tensor: return self.prior.variance + + def __deepcopy__(self, memo): + """Ensure prior attribute is preserved during deepcopy.""" + cls = self.__class__ + result = cls.__new__(cls) + memo[id(self)] = result + for k, v in self.__dict__.items(): + setattr(result, k, deepcopy(v, memo)) + return result diff --git a/tests/inference_on_device_test.py b/tests/inference_on_device_test.py index 395f09a71..a56f323fa 100644 --- a/tests/inference_on_device_test.py +++ b/tests/inference_on_device_test.py @@ -396,6 +396,12 @@ def __call__(self, theta, **kwargs): def allow_iid_x(self) -> bool: return True + def bind(self, x_o: torch.Tensor, x_is_iid: bool = True) -> "FakePotential": + """Create new potential with x bound, without mutable state.""" + bound = FakePotential(prior=self.prior, device=self.device) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + potential_fn = FakePotential( prior=MultivariateNormal( zeros(num_dim, device=device), eye(num_dim, device=device) @@ -450,6 +456,12 @@ def __call__(self, theta, **kwargs): def allow_iid_x(self) -> bool: return True + def bind(self, x_o: torch.Tensor, x_is_iid: bool = True) -> "FakePotential": + """Create new potential with x bound, without mutable state.""" + bound = FakePotential(prior=self.prior, device=self.device) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + potential_fn = FakePotential(prior=prior, device=device) # Generate mock simulation data on device diff --git a/tests/torchutils_test.py b/tests/torchutils_test.py index b60c36237..5be20b51f 100644 --- a/tests/torchutils_test.py +++ b/tests/torchutils_test.py @@ -5,6 +5,8 @@ from __future__ import annotations +from copy import deepcopy + import numpy as np import pytest import torch @@ -16,6 +18,49 @@ from tests.test_utils import kl_d_via_monte_carlo +def test_base_recursor_handles_cyclic_object_graph(): + class CyclicObject: + pass + + root = CyclicObject() + tensor = torch.tensor(1.0) + root.tensor = tensor + root.self = root + root.mapping = {"root": root, "tensor": tensor} + + processed = [] + + def process(obj): + processed.append(obj) + return obj + + torchutils._base_recursor(root, check=torch.is_tensor, action=process) + + assert len(processed) == 2 + assert all(obj is tensor for obj in processed) + + +def test_base_recursor_processes_aliased_containers(): + class AliasedObject: + pass + + root = AliasedObject() + tensor = torch.tensor(1.0, requires_grad=True) * 2 + shared = [tensor] + root.first = shared + root.second = shared + + torchutils._base_recursor( + root, + check=lambda obj: torch.is_tensor(obj) and not obj.is_leaf, + action=lambda obj: obj.detach(), + ) + + assert root.first[0].is_leaf + assert root.second[0].is_leaf + deepcopy(root) + + # XXX move to pytest? - investigate how to derive from TorchTestCase class TorchUtilsTest(torchtestcase.TorchTestCase): def test_split_leading_dim(self): diff --git a/tests/vi_test.py b/tests/vi_test.py index e1327e56a..f3f187ce9 100644 --- a/tests/vi_test.py +++ b/tests/vi_test.py @@ -57,6 +57,12 @@ def __call__(self, theta, **kwargs): def allow_iid_x(self) -> bool: return True + def bind(self, x_o: torch.Tensor, x_is_iid: bool = True) -> "FakePotential": + """Create new potential with x bound, without mutable state.""" + bound = FakePotential(prior=self.prior, device=self.device) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + def make_tractable_potential(target_distribution, prior): """Create a potential function from a known target distribution.""" @@ -70,6 +76,14 @@ def __call__(self, theta, **kwargs): def allow_iid_x(self) -> bool: return True + def bind( + self, x_o: torch.Tensor, x_is_iid: bool = True + ) -> "TractablePotential": + """Create new potential with x bound, without mutable state.""" + bound = TractablePotential(prior=self.prior, device=self.device) + bound.set_x(x_o, x_is_iid=x_is_iid) + return bound + return TractablePotential(prior=prior) diff --git a/uv.lock b/uv.lock index 4afc6c03a..9f0cbed83 100644 --- a/uv.lock +++ b/uv.lock @@ -815,45 +815,51 @@ wheels = [ [[package]] name = "cuda-toolkit" -version = "13.0.2" +version = "13.0.3.0" source = { registry = "https://pypi.org/simple" } wheels = [ - { url = "https://files.pythonhosted.org/packages/57/b2/453099f5f3b698d7d0eab38916aac44c7f76229f451709e2eb9db6615dcd/cuda_toolkit-13.0.2-py2.py3-none-any.whl", hash = "sha256:b198824cf2f54003f50d64ada3a0f184b42ca0846c1c94192fa269ecd97a66eb", size = 2364, upload-time = "2025-12-19T23:24:07.328Z" }, + { url = "https://files.pythonhosted.org/packages/d1/c7/a79086a62c98befcdb8349656c6f114e2db3b8b2422f6e25c97a7f2a9a3c/cuda_toolkit-13.0.3.0-py2.py3-none-any.whl", hash = "sha256:d693caaa261214ddd7dbb60d68e71cbed884e68c2be7509778f3051da0b91c3f", size = 2512, upload-time = "2026-04-14T00:50:08.173Z" }, ] [package.optional-dependencies] cublas = [ - { name = "nvidia-cublas", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-cublas", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, + { name = "nvidia-cuda-nvrtc", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] cudart = [ - { name = "nvidia-cuda-runtime", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-cuda-runtime", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] cufft = [ - { name = "nvidia-cufft", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-cufft", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, + { name = "nvidia-nvjitlink", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] cufile = [ - { name = "nvidia-cufile", marker = "sys_platform == 'linux'" }, + { name = "nvidia-cufile", marker = "(platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] cupti = [ - { name = "nvidia-cuda-cupti", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-cuda-cupti", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] curand = [ - { name = "nvidia-curand", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-curand", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] cusolver = [ - { name = "nvidia-cusolver", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-cublas", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, + { name = "nvidia-cusolver", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, + { name = "nvidia-cusparse", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, + { name = "nvidia-nvjitlink", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] cusparse = [ - { name = "nvidia-cusparse", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-cusparse", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, + { name = "nvidia-nvjitlink", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] nvjitlink = [ - { name = "nvidia-nvjitlink", marker = "(python_full_version < '3.11' and sys_platform == 'win32') or sys_platform == 'linux'" }, + { name = "nvidia-nvjitlink", marker = "(python_full_version < '3.11' and platform_machine == 'AMD64' and sys_platform == 'win32') or (platform_machine == 'aarch64' and sys_platform == 'linux') or (platform_machine == 'x86_64' and sys_platform == 'linux')" }, ] nvrtc = [ - { name = "nvidia-cuda-nvrtc", marker = "(python_full_version < 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