Merge remote-tracking branch 'upstream/dev' into feat-hypothesis-test

Author: vpratz

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,36 @@
+---
+name: Bug report
+about: Create a bug report to help us improve BayesFlow
+title: "[BUG]"
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Minimal steps to reproduce the behavior:
+1. Import '...'
+2. Create network '....'
+3. Call '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Traceback**
+If you encounter an error, please provide a complete traceback to help explain your problem.
+
+**Environment**
+- OS: [e.g. Ubuntu]
+- Python Version: [e.g. 3.11]
+- Backend: [e.g. jax, tensorflow, pytorch]
+- BayesFlow Version: [e.g. 2.0.2]
+
+**Additional context**
+Add any other context about the problem here.
+
+**Minimality**
+- [ ] I verify that my example is minimal, does not rely on third-party packages, and is most likely an issue in BayesFlow.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest a new feature to be implemented in BayesFlow
+title: "[FEATURE]"
+labels: feature
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/style.yaml

@@ -6,12 +6,10 @@ on:
     branches:
       - main
       - dev
-      - update-workflows
   push:
     branches:
       - main
       - dev
-      - update-workflows
 
 jobs:
   check-code-style:

.github/workflows/tests.yaml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10"]  # we usually only need to test the oldest python version
         backend: ["jax", "tensorflow", "torch"]
 
     runs-on: ${{ matrix.os }}
@@ -73,8 +73,11 @@ jobs:
           pytest -x -m "not slow"
 
       - name: Run Slow Tests
-        # run all slow tests only on manual trigger
-        if: github.event_name == 'workflow_dispatch'
+        # Run slow tests on manual trigger and pushes/PRs to main.
+        # Limit to one OS and Python version to save compute.
+        # Multiline if statements are weird, https://github.com/orgs/community/discussions/25641,
+        # but feel free to convert it.
+        if: ${{ ((github.event_name == 'workflow_dispatch') || (github.event_name == 'push' && github.ref_name == 'main') || (github.event_name == 'pull_request' && github.base_ref == 'main')) && ((matrix.os == 'windows-latest') && (matrix.python-version == '3.10')) }}
         run: |
           pytest -m "slow"
 

README.md

@@ -3,6 +3,7 @@
 ![Codecov](https://img.shields.io/codecov/c/github/bayesflow-org/bayesflow?style=for-the-badge&link=https%3A%2F%2Fapp.codecov.io%2Fgh%2Fbayesflow-org%2Fbayesflow%2Ftree%2Fmain)
 [![DOI](https://img.shields.io/badge/DOI-10.21105%2Fjoss.05702-blue?style=for-the-badge)](https://doi.org/10.21105/joss.05702)
 ![PyPI - License](https://img.shields.io/pypi/l/bayesflow?style=for-the-badge)
+![NumFOCUS Affiliated Project](https://img.shields.io/badge/NumFOCUS-Affiliated%20Project-orange?style=for-the-badge)
 
 BayesFlow is a Python library for simulation-based **Amortized Bayesian Inference** with neural networks.
 It provides users and researchers with:
@@ -225,8 +226,10 @@ You can find and install the old Bayesflow version via the `stable-legacy` branc
 
 ## Awesome Amortized Inference
 
-If you are interested in a curated list of resources, including reviews, software, papers, and other resources related to amortized inference, feel free to explore our [community-driven list](https://github.com/bayesflow-org/awesome-amortized-inference).
+If you are interested in a curated list of resources, including reviews, software, papers, and other resources related to amortized inference, feel free to explore our [community-driven list](https://github.com/bayesflow-org/awesome-amortized-inference). If you'd like a paper (by yourself or someone else) featured, please add it to the list with a pull request, an issue, or a message to the maintainers.
 
 ## Acknowledgments
 
 This project is currently managed by researchers from Rensselaer Polytechnic Institute, TU Dortmund University, and Heidelberg University. It is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Projects 528702768 and 508399956. The project is further supported by Germany's Excellence Strategy -- EXC-2075 - 390740016 (Stuttgart Cluster of Excellence SimTech) and EXC-2181 - 390900948 (Heidelberg Cluster of Excellence STRUCTURES), the collaborative research cluster TRR 391 – 520388526, as well as the Informatics for Life initiative funded by the Klaus Tschira Foundation.
+
+BayesFlow is a [NumFOCUS Affiliated Project](https://numfocus.org/sponsored-projects/affiliated-projects).

bayesflow/__init__.py

@@ -33,7 +33,7 @@ def setup():
 
     from bayesflow.utils import logging
 
-    logging.debug(f"Using backend {keras.backend.backend()!r}")
+    logging.info(f"Using backend {keras.backend.backend()!r}")
 
     if keras.backend.backend() == "torch":
         import torch

bayesflow/approximators/approximator.py

@@ -23,7 +23,7 @@ def build_adapter(cls, **kwargs) -> Adapter:
         raise NotImplementedError
 
     def build_from_data(self, data: Mapping[str, any]) -> None:
-        self.compute_metrics(**data, stage="training")
+        self.compute_metrics(**filter_kwargs(data, self.compute_metrics), stage="training")
         self.built = True
 
     @classmethod

bayesflow/approximators/continuous_approximator.py

@@ -32,6 +32,8 @@ class ContinuousApproximator(Approximator):
         Additional arguments passed to the :py:class:`bayesflow.approximators.Approximator` class.
     """
 
+    SAMPLE_KEYS = ["summary_variables", "inference_conditions"]
+
     def __init__(
         self,
         *,
@@ -51,6 +53,7 @@ def build_adapter(
         inference_variables: Sequence[str],
         inference_conditions: Sequence[str] = None,
         summary_variables: Sequence[str] = None,
+        standardize: bool = True,
         sample_weight: str = None,
     ) -> Adapter:
         """Create an :py:class:`~bayesflow.adapters.Adapter` suited for the approximator.
@@ -63,9 +66,12 @@ def build_adapter(
             Names of the inference conditions in the data
         summary_variables : Sequence of str, optional
             Names of the summary variables in the data
+        standardize : bool, optional
+            Decide whether to standardize all variables, default is True
         sample_weight : str, optional
             Name of the sample weights
         """
+
         adapter = Adapter()
         adapter.to_array()
         adapter.convert_dtype("float64", "float32")
@@ -82,7 +88,9 @@ def build_adapter(
             adapter = adapter.rename(sample_weight, "sample_weight")
 
         adapter.keep(["inference_variables", "inference_conditions", "summary_variables", "sample_weight"])
-        adapter.standardize(exclude="sample_weight")
+
+        if standardize:
+            adapter.standardize(exclude="sample_weight")
 
         return adapter
 
@@ -104,6 +112,12 @@ def compile(
 
         return super().compile(*args, **kwargs)
 
+    def compile_from_config(self, config):
+        self.compile(**deserialize(config))
+        if hasattr(self, "optimizer") and self.built:
+            # Create optimizer variables.
+            self.optimizer.build(self.trainable_variables)
+
     def compute_metrics(
         self,
         inference_variables: Tensor,
@@ -213,6 +227,16 @@ def get_config(self):
 
         return base_config | serialize(config)
 
+    def get_compile_config(self):
+        base_config = super().get_compile_config() or {}
+
+        config = {
+            "inference_metrics": self.inference_network._metrics,
+            "summary_metrics": self.summary_network._metrics if self.summary_network is not None else None,
+        }
+
+        return base_config | serialize(config)
+
     def estimate(
         self,
         conditions: Mapping[str, np.ndarray],
@@ -318,12 +342,18 @@ def sample(
         dict[str, np.ndarray]
             Dictionary containing generated samples with the same keys as `conditions`.
         """
+
+        # Apply adapter transforms to raw simulated / real quantities
         conditions = self.adapter(conditions, strict=False, stage="inference", **kwargs)
-        # at inference time, inference_variables are estimated by the networks and thus ignored in conditions
-        conditions.pop("inference_variables", None)
+
+        # Ensure only keys relevant for sampling are present in the conditions dictionary
+        conditions = {k: v for k, v in conditions.items() if k in ContinuousApproximator.SAMPLE_KEYS}
+
         conditions = keras.tree.map_structure(keras.ops.convert_to_tensor, conditions)
         conditions = {"inference_variables": self._sample(num_samples=num_samples, **conditions, **kwargs)}
         conditions = keras.tree.map_structure(keras.ops.convert_to_numpy, conditions)
+
+        # Back-transform quantities and samples
         conditions = self.adapter(conditions, inverse=True, strict=False, **kwargs)
 
         if split:

bayesflow/approximators/model_comparison_approximator.py

@@ -30,11 +30,13 @@ class ModelComparisonApproximator(Approximator):
         The network backbone (e.g, an MLP) that is used for model classification.
         The input of the classifier network is created by concatenating `classifier_variables`
         and (optional) output of the summary_network.
-    summary_network: bg.networks.SummaryNetwork, optional
+    summary_network: bf.networks.SummaryNetwork, optional
         The summary network used for data summarization (default is None).
         The input of the summary network is `summary_variables`.
     """
 
+    SAMPLE_KEYS = ["summary_variables", "classifier_conditions"]
+
     def __init__(
         self,
         *,
@@ -118,6 +120,12 @@ def compile(
 
         return super().compile(*args, **kwargs)
 
+    def compile_from_config(self, config):
+        self.compile(**deserialize(config))
+        if hasattr(self, "optimizer") and self.built:
+            # Create optimizer variables.
+            self.optimizer.build(self.trainable_variables)
+
     def compute_metrics(
         self,
         *,
@@ -262,6 +270,16 @@ def get_config(self):
 
         return base_config | serialize(config)
 
+    def get_compile_config(self):
+        base_config = super().get_compile_config() or {}
+
+        config = {
+            "classifier_metrics": self.classifier_network._metrics,
+            "summary_metrics": self.summary_network._metrics if self.summary_network is not None else None,
+        }
+
+        return base_config | serialize(config)
+
     def predict(
         self,
         *,
@@ -288,9 +306,13 @@ def predict(
         np.ndarray
             Predicted posterior model probabilities given `conditions`.
         """
+
+        # Apply adapter transforms to raw simulated / real quantities
         conditions = self.adapter(conditions, strict=False, stage="inference", **kwargs)
-        # at inference time, model_indices are predicted by the networks and thus ignored in conditions
-        conditions.pop("model_indices", None)
+
+        # Ensure only keys relevant for sampling are present in the conditions dictionary
+        conditions = {k: v for k, v in conditions.items() if k in ModelComparisonApproximator.SAMPLE_KEYS}
+
         conditions = keras.tree.map_structure(keras.ops.convert_to_tensor, conditions)
 
         output = self._predict(**conditions, **kwargs)

bayesflow/approximators/point_approximator.py

@@ -156,8 +156,10 @@ def log_prob(
 
     def _prepare_conditions(self, conditions: Mapping[str, np.ndarray], **kwargs) -> dict[str, Tensor]:
         """Adapts and converts the conditions to tensors."""
+
         conditions = self.adapter(conditions, strict=False, stage="inference", **kwargs)
-        conditions.pop("inference_variables", None)
+        conditions = {k: v for k, v in conditions.items() if k in ContinuousApproximator.SAMPLE_KEYS}
+
         return keras.tree.map_structure(keras.ops.convert_to_tensor, conditions)
 
     def _apply_inverse_adapter_to_estimates(