autoemulate 2.1.0__tar.gz → 2.1.2__tar.gz

{autoemulate-2.1.0 → autoemulate-2.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: autoemulate
-Version: 2.1.0
+Version: 2.1.2
 Summary: A python package for semi-automated emulation
 Author: AutoEmulate contributors (see our GitHub page)
 License-Expression: MIT
@@ -20,7 +20,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib>=3.7.2
 Requires-Dist: seaborn>=0.12.2
-Requires-Dist: scikit-learn<1.6.0,>=1.3.0
+Requires-Dist: scikit-learn>=1.3.0
 Requires-Dist: pandas>=2.1
 Requires-Dist: torch>=2.1.0
 Requires-Dist: scipy>=1.11.3
@@ -36,7 +36,7 @@ Requires-Dist: anytree>=2.12.1
 Requires-Dist: torchmetrics>=1.7.1
 Requires-Dist: pyro-ppl>=1.9.1
 Requires-Dist: torchrbf>=0.0.1
-Requires-Dist: arviz>=0.21.0
+Requires-Dist: arviz<1.0,>=0.21.0
 Requires-Dist: getdist>=1.7.2
 Requires-Dist: einops>=0.8.1
 Requires-Dist: harmonic>=1.3.0
@@ -87,7 +87,7 @@ You can find the project documentation [here](https://alan-turing-institute.gith
 
 - The AutoEmulate project is run out of the [Alan Turing Institute](https://www.turing.ac.uk/).
 - Visit [autoemulate.com](https://www.autoemulate.com/) to learn more.
-- Feel free to reach out to us at [ai4physics@turing.ac.uk](mailto:ai4physics@turing.ac.uk) for queries about AutoEmulate or ideas for collaboration
+- Feel free to reach out to us at [aiphys@turing.ac.uk](mailto:aiphys@turing.ac.uk) for queries about AutoEmulate or ideas for collaboration.
 - We have also published a paper in [The Journal of Open Source Software](https://joss.theoj.org/papers/10.21105/joss.07626). 
 
   Please cite this paper if you use the package in your work:
@@ -137,14 +137,15 @@ You can find the project documentation [here](https://alan-turing-institute.gith
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/vchhabra-turing"><img src="https://avatars.githubusercontent.com/u/140401853?v=4?s=100" width="100px;" alt="vchhabra-turing"/><br /><sub><b>vchhabra-turing</b></sub></a><br /><a href="#ideas-vchhabra-turing" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/era-23"><img src="https://avatars.githubusercontent.com/u/115151590?v=4?s=100" width="100px;" alt="Ethan Attwood"/><br /><sub><b>Ethan Attwood</b></sub></a><br /><a href="#bug-era-23" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/TheCSGuy25"><img src="https://avatars.githubusercontent.com/u/87066683?v=4?s=100" width="100px;" alt="__aar0n__.py"/><br /><sub><b>__aar0n__.py</b></sub></a><br /><a href="#code-TheCSGuy25" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/SyedHaider2084"><img src="https://avatars.githubusercontent.com/u/227389830?v=4?s=100" width="100px;" alt="SyedHaider2084"/><br /><sub><b>SyedHaider2084</b></sub></a><br /><a href="#code-SyedHaider2084" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/SyedHaider2084"><img src="https://avatars.githubusercontent.com/u/227389830?v=4?s=100" width="100px;" alt="SyedHaider2084"/><br /><sub><b>SyedHaider2084</b></sub></a><br /><a href="#code-SyedHaider2084" title="Code">💻</a> <a href="#doc-SyedHaider2084" title="Documentation">📖</a></td>
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://www.linkedin.com/in/lcm98/"><img src="https://avatars.githubusercontent.com/u/102757707?v=4?s=100" width="100px;" alt="Loh Chun Mun"/><br /><sub><b>Loh Chun Mun</b></sub></a><br /><a href="#doc-cmsamaaa" title="Documentation">📖</a> <a href="#code-cmsamaaa" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/z7076"><img src="https://avatars.githubusercontent.com/u/69681924?v=4?s=100" width="100px;" alt="Jichen Zhang"/><br /><sub><b>Jichen Zhang</b></sub></a><br /><a href="#code-z7076" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/RemDelaporteMathurin"><img src="https://avatars.githubusercontent.com/u/40028739?v=4?s=100" width="100px;" alt="Rémi Delaporte-Mathurin"/><br /><sub><b>Rémi Delaporte-Mathurin</b></sub></a><br /><a href="#bug-RemDelaporteMathurin" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/z7076"><img src="https://avatars.githubusercontent.com/u/69681924?v=4?s=100" width="100px;" alt="Jichen Zhang"/><br /><sub><b>Jichen Zhang</b></sub></a><br /><a href="#code-z7076" title="Code">💻</a> <a href="#doc-z7076" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/RemDelaporteMathurin"><img src="https://avatars.githubusercontent.com/u/40028739?v=4?s=100" width="100px;" alt="Rémi Delaporte-Mathurin"/><br /><sub><b>Rémi Delaporte-Mathurin</b></sub></a><br /><a href="#bug-RemDelaporteMathurin" title="Bug reports">🐛</a> <a href="#doc-RemDelaporteMathurin" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/pmeier"><img src="https://avatars.githubusercontent.com/u/6849766?v=4?s=100" width="100px;" alt="Philip Meier"/><br /><sub><b>Philip Meier</b></sub></a><br /><a href="#bug-pmeier" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/penelopeysm"><img src="https://avatars.githubusercontent.com/u/122629585?v=4?s=100" width="100px;" alt="Penelope Yong"/><br /><sub><b>Penelope Yong</b></sub></a><br /><a href="#ideas-penelopeysm" title="Ideas, Planning, & Feedback">🤔</a> <a href="#review-penelopeysm" title="Reviewed Pull Requests">👀</a> <a href="#code-penelopeysm" title="Code">💻</a> <a href="#doc-penelopeysm" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/ykd007"><img src="https://avatars.githubusercontent.com/u/79036688?v=4?s=100" width="100px;" alt="Yash Dhawan"/><br /><sub><b>Yash Dhawan</b></sub></a><br /><a href="#doc-ykd007" title="Documentation">📖</a></td>
     </tr>
   </tbody>
 </table>

{autoemulate-2.1.0 → autoemulate-2.1.2}/README.md

@@ -19,7 +19,7 @@ You can find the project documentation [here](https://alan-turing-institute.gith
 
 - The AutoEmulate project is run out of the [Alan Turing Institute](https://www.turing.ac.uk/).
 - Visit [autoemulate.com](https://www.autoemulate.com/) to learn more.
-- Feel free to reach out to us at [ai4physics@turing.ac.uk](mailto:ai4physics@turing.ac.uk) for queries about AutoEmulate or ideas for collaboration
+- Feel free to reach out to us at [aiphys@turing.ac.uk](mailto:aiphys@turing.ac.uk) for queries about AutoEmulate or ideas for collaboration.
 - We have also published a paper in [The Journal of Open Source Software](https://joss.theoj.org/papers/10.21105/joss.07626). 
 
   Please cite this paper if you use the package in your work:
@@ -69,14 +69,15 @@ You can find the project documentation [here](https://alan-turing-institute.gith
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/vchhabra-turing"><img src="https://avatars.githubusercontent.com/u/140401853?v=4?s=100" width="100px;" alt="vchhabra-turing"/><br /><sub><b>vchhabra-turing</b></sub></a><br /><a href="#ideas-vchhabra-turing" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/era-23"><img src="https://avatars.githubusercontent.com/u/115151590?v=4?s=100" width="100px;" alt="Ethan Attwood"/><br /><sub><b>Ethan Attwood</b></sub></a><br /><a href="#bug-era-23" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/TheCSGuy25"><img src="https://avatars.githubusercontent.com/u/87066683?v=4?s=100" width="100px;" alt="__aar0n__.py"/><br /><sub><b>__aar0n__.py</b></sub></a><br /><a href="#code-TheCSGuy25" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/SyedHaider2084"><img src="https://avatars.githubusercontent.com/u/227389830?v=4?s=100" width="100px;" alt="SyedHaider2084"/><br /><sub><b>SyedHaider2084</b></sub></a><br /><a href="#code-SyedHaider2084" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/SyedHaider2084"><img src="https://avatars.githubusercontent.com/u/227389830?v=4?s=100" width="100px;" alt="SyedHaider2084"/><br /><sub><b>SyedHaider2084</b></sub></a><br /><a href="#code-SyedHaider2084" title="Code">💻</a> <a href="#doc-SyedHaider2084" title="Documentation">📖</a></td>
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://www.linkedin.com/in/lcm98/"><img src="https://avatars.githubusercontent.com/u/102757707?v=4?s=100" width="100px;" alt="Loh Chun Mun"/><br /><sub><b>Loh Chun Mun</b></sub></a><br /><a href="#doc-cmsamaaa" title="Documentation">📖</a> <a href="#code-cmsamaaa" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/z7076"><img src="https://avatars.githubusercontent.com/u/69681924?v=4?s=100" width="100px;" alt="Jichen Zhang"/><br /><sub><b>Jichen Zhang</b></sub></a><br /><a href="#code-z7076" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/RemDelaporteMathurin"><img src="https://avatars.githubusercontent.com/u/40028739?v=4?s=100" width="100px;" alt="Rémi Delaporte-Mathurin"/><br /><sub><b>Rémi Delaporte-Mathurin</b></sub></a><br /><a href="#bug-RemDelaporteMathurin" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/z7076"><img src="https://avatars.githubusercontent.com/u/69681924?v=4?s=100" width="100px;" alt="Jichen Zhang"/><br /><sub><b>Jichen Zhang</b></sub></a><br /><a href="#code-z7076" title="Code">💻</a> <a href="#doc-z7076" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/RemDelaporteMathurin"><img src="https://avatars.githubusercontent.com/u/40028739?v=4?s=100" width="100px;" alt="Rémi Delaporte-Mathurin"/><br /><sub><b>Rémi Delaporte-Mathurin</b></sub></a><br /><a href="#bug-RemDelaporteMathurin" title="Bug reports">🐛</a> <a href="#doc-RemDelaporteMathurin" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/pmeier"><img src="https://avatars.githubusercontent.com/u/6849766?v=4?s=100" width="100px;" alt="Philip Meier"/><br /><sub><b>Philip Meier</b></sub></a><br /><a href="#bug-pmeier" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/penelopeysm"><img src="https://avatars.githubusercontent.com/u/122629585?v=4?s=100" width="100px;" alt="Penelope Yong"/><br /><sub><b>Penelope Yong</b></sub></a><br /><a href="#ideas-penelopeysm" title="Ideas, Planning, & Feedback">🤔</a> <a href="#review-penelopeysm" title="Reviewed Pull Requests">👀</a> <a href="#code-penelopeysm" title="Code">💻</a> <a href="#doc-penelopeysm" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/ykd007"><img src="https://avatars.githubusercontent.com/u/79036688?v=4?s=100" width="100px;" alt="Yash Dhawan"/><br /><sub><b>Yash Dhawan</b></sub></a><br /><a href="#doc-ykd007" title="Documentation">📖</a></td>
     </tr>
   </tbody>
 </table>

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate/core/compare.py

@@ -84,18 +84,18 @@ class AutoEmulate(ConversionMixin, TorchDeviceMixin, Results):
         ----------
         x: InputLike
             Input features.
-        y: InputLike or None
-            Target values (not needed if x is a Dataset).
+        y: InputLike
+            Target values.
         test_data: tuple[InputLike, InputLike] | None
             Optional test data as a tuple (x_test, y_test). If None, a random split
             from the provided data is used. Defaults to None.
-        models: list[type[Emulator]] | None
-            List of emulator classes to compare. If None, all available emulators
-            are used.
-        x_transforms_list: list[list[Transform]] | None
+        models: list[type[Emulator] | str] | None
+            List of emulator classes or registered emulator names to compare. If None,
+            all available emulators are used.
+        x_transforms_list: list[list[Transform | dict]] | None
             An optional list of sequences of transforms to apply to the input data.
             Defaults to None, in which case the data is standardized.
-        y_transforms_list: list[list[Transform]] | None
+        y_transforms_list: list[list[Transform | dict]] | None
             An optional list of sequences of transforms to apply to the output data.
             Defaults to None, in which case the data is standardized.
         model_params: ModelParams | None
@@ -125,13 +125,13 @@ class AutoEmulate(ConversionMixin, TorchDeviceMixin, Results):
             Random seed for reproducibility. If None, no seed is set. Defaults to None.
         log_level: str | None
             Deprecated. Configure logging in the calling application instead.
-        tuning_metric: str | TorchMetrics
+        tuning_metric: str | Metric
             Metric to use for hyperparameter tuning. Can be a string shortcut
-            ("r2", "rmse", "mse", "mae") or a MetricConfig object. Defaults to "r2".
-        evaluation_metrics: list[str | TorchMetrics] | None
+            ("r2", "rmse", "mse", "mae") or a Metric object. Defaults to "r2".
+        evaluation_metrics: list[str | Metric] | None
             Metrics to compute during evaluation.
             If None, then defaults to ["r2", "rmse"].
-            Each entry can be a string shortcut or a MetricConfig object.
+            Each entry can be a string shortcut or a Metric object.
             IMPORTANT: The first metric in the list is used to
             determine the best model.
         show_progress_bar: bool
@@ -245,7 +245,7 @@ class AutoEmulate(ConversionMixin, TorchDeviceMixin, Results):
 
         Parameters
         ----------
-        subset: bool
+        default_only: bool
             Whether to display only default or all available emulators. Defaults to
             True (default emulators only).
 
@@ -298,9 +298,7 @@ class AutoEmulate(ConversionMixin, TorchDeviceMixin, Results):
         ----------
         models: list[type[Emulator] | str] | None
             List of model classes or names to use for comparison. If None, all available
-            emulators are used (or subset based on only_pytorch and only_probabilistic).
-        only_pytorch: bool
-            If True, only PyTorch emulators are returned. Defaults to False.
+            emulators are used, or probabilistic defaults when only_probabilistic=True.
         only_probabilistic: bool
             If True, only probabilistic emulators are returned. Defaults to False.
         """

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate/core/model_selection.py

@@ -73,18 +73,23 @@ def cross_validate(
         specified cross-validation strategy (e.g., KFold, LeaveOneOut).
     dataset: Dataset
         The data to use for model training and validation.
-    model: Emulator
-        An instance of an Emulator subclass.
+    model: type[Emulator]
+        An Emulator subclass to fit during validation.
     model_params: ModelParams
         Model parameters to be used to construct model upon initialization. Passing an
         empty dictionary `{}` will use default parameters.
     transformed_emulator_params: None | TransformedEmulatorParams
         Parameters for the transformed emulator. Defaults to None.
+    x_transforms: list[Transform] | None
+        Transforms to apply to input data before fitting the emulator. Defaults to None.
+    y_transforms: list[Transform] | None
+        Transforms to apply to output data before fitting the emulator.
+        Defaults to None.
     device: DeviceLike
         The device to use for model training and evaluation.
     random_seed: int | None
         Optional random seed for reproducibility.
-    metrics: list[TorchMetrics] | None
+    metrics: list[Metric] | None
         List of metrics to compute. If None, uses r2 and rmse.
     deterministic: bool
         Whether to use deterministic algorithms in PyTorch. Defaults to False.
@@ -173,14 +178,11 @@ def bootstrap(
         Target values corresponding to the input features.
     n_bootstraps: int | None
         Number of bootstrap samples to generate. When None the evaluation uses all
-        all given data and returns a single value with no measure of the uncertainty.
+        given data and returns a single value with no measure of the uncertainty.
         Defaults to 100.
-    n_samples: int
-        Number of samples to generate to predict mean when emulator does not have a
-        mean directly available. Defaults to 1000.
     device: str | torch.device
         The device to use for computations. Default is "cpu".
-    metrics: list[MetricConfig] | None
+    metrics: list[Metric] | None
         List of metrics to compute. If None, uses r2 and rmse.
     metric_params: MetricParams | None
         Additional parameters to pass to the metrics. Defaults to None.

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate/core/plotting.py

@@ -1,5 +1,6 @@
 from typing import Literal
 
+import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 import torch
@@ -10,6 +11,8 @@ from matplotlib.figure import Figure
 from autoemulate.core.types import DistributionLike, GaussianLike, NumpyLike, TensorLike
 from autoemulate.emulators.base import Emulator, PyTorchBackend
 
+_NON_INTERACTIVE_BACKENDS = {"agg", "cairo", "pdf", "pgf", "ps", "svg", "template"}
+
 
 def display_figure(fig: Figure):
     """
@@ -38,9 +41,18 @@ def display_figure(fig: Figure):
         # we don't show otherwise it will double plot
         plt.close(fig)
         return fig
-    # in terminal, show the plot
+
+    backend = mpl.get_backend().lower()
+    if any(
+        backend.endswith(non_interactive)
+        for non_interactive in _NON_INTERACTIVE_BACKENDS
+    ):
+        plt.close(fig)
+        return fig
+
+    # in terminal with an interactive backend, show the plot
+    fig.show()
     plt.close(fig)
-    plt.show()
     return fig
 
 

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate/core/tuner.py

@@ -28,7 +28,7 @@ class Tuner(ConversionMixin, TorchDeviceMixin):
     ----------
     x: InputLike
         Input features.
-    y: OutputLike or None
+    y: InputLike | None
         Target values (not needed if x is a Dataset).
     n_iter: int
         Number of parameter settings to randomly sample and test.
@@ -37,6 +37,8 @@ class Tuner(ConversionMixin, TorchDeviceMixin):
         device (usually CPU or GPU).
     random_seed: int | None
         Random seed for reproducibility. If None, no seed is set.
+    tuning_metric: str | Metric
+        Metric to use for hyperparameter tuning. Defaults to "r2".
     deterministic: bool
         Whether to use deterministic algorithms in PyTorch. Defaults to False.
     """
@@ -85,12 +87,10 @@ class Tuner(ConversionMixin, TorchDeviceMixin):
         ----------
         model_class: type[Emulator]
             A concrete Emulator subclass.
-        x_transforms_list: list[list[AutoEmulateTransform]] | None
-            An optional list of sequences of transforms to apply to the input data.
-            Defaults to None, in which case the data is standardized.
-        y_transforms_list: list[list[AutoEmulateTransform]] | None
-            An optional list of sequences of transforms to apply to the output data.
-            Defaults to None, in which case the data is standardized.
+        x_transforms: list[Transform] | None
+            Optional sequence of transforms to apply to the input data.
+        y_transforms: list[Transform] | None
+            Optional sequence of transforms to apply to the output data.
         transformed_emulator_params: None | TransformedEmulatorParams
             Parameters for the transformed emulator. Defaults to None.
         n_splits: int

autoemulate-2.1.2/autoemulate/learners/__init__.py

@@ -0,0 +1,8 @@
+from autoemulate.learners.base import Emulator
+
+from . import stream
+
+# from .base import Emulator, Simulator
+from .base import Simulator
+
+__all__ = ["Emulator", "Simulator", "stream"]

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate/transforms/base.py

@@ -613,16 +613,3 @@ def _is_affine_empirical(transform: Transform, x: TensorLike) -> bool:
     for _ in range(AFFINE_TRIALS):
         errs.append(_measure_affine_err(transform, test_input))  # type: ignore as Tensor input will transform to Tensor output
     return (sum(errs) / len(errs)) < AFFINE_TOL
-
-
-# TODO (#536): complete implementation
-# class AutoEmulateTransformModule(TransformModule):
-#     @abstractmethod
-#     def fit(self, x): ...
-#     def _inverse_gaussian(self, y: GaussianLike) -> GaussianLike:
-#         msg = "This method should be implemented in subclasses."
-#         raise NotImplementedError(msg)
-
-#     def _inverse_sample(self, y: GaussianLike, n_samples: int = 100) -> GaussianLike:
-#         msg = "This method should be implemented in subclasses."
-#         raise NotImplementedError(msg)

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: autoemulate
-Version: 2.1.0
+Version: 2.1.2
 Summary: A python package for semi-automated emulation
 Author: AutoEmulate contributors (see our GitHub page)
 License-Expression: MIT
@@ -20,7 +20,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib>=3.7.2
 Requires-Dist: seaborn>=0.12.2
-Requires-Dist: scikit-learn<1.6.0,>=1.3.0
+Requires-Dist: scikit-learn>=1.3.0
 Requires-Dist: pandas>=2.1
 Requires-Dist: torch>=2.1.0
 Requires-Dist: scipy>=1.11.3
@@ -36,7 +36,7 @@ Requires-Dist: anytree>=2.12.1
 Requires-Dist: torchmetrics>=1.7.1
 Requires-Dist: pyro-ppl>=1.9.1
 Requires-Dist: torchrbf>=0.0.1
-Requires-Dist: arviz>=0.21.0
+Requires-Dist: arviz<1.0,>=0.21.0
 Requires-Dist: getdist>=1.7.2
 Requires-Dist: einops>=0.8.1
 Requires-Dist: harmonic>=1.3.0
@@ -87,7 +87,7 @@ You can find the project documentation [here](https://alan-turing-institute.gith
 
 - The AutoEmulate project is run out of the [Alan Turing Institute](https://www.turing.ac.uk/).
 - Visit [autoemulate.com](https://www.autoemulate.com/) to learn more.
-- Feel free to reach out to us at [ai4physics@turing.ac.uk](mailto:ai4physics@turing.ac.uk) for queries about AutoEmulate or ideas for collaboration
+- Feel free to reach out to us at [aiphys@turing.ac.uk](mailto:aiphys@turing.ac.uk) for queries about AutoEmulate or ideas for collaboration.
 - We have also published a paper in [The Journal of Open Source Software](https://joss.theoj.org/papers/10.21105/joss.07626). 
 
   Please cite this paper if you use the package in your work:
@@ -137,14 +137,15 @@ You can find the project documentation [here](https://alan-turing-institute.gith
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/vchhabra-turing"><img src="https://avatars.githubusercontent.com/u/140401853?v=4?s=100" width="100px;" alt="vchhabra-turing"/><br /><sub><b>vchhabra-turing</b></sub></a><br /><a href="#ideas-vchhabra-turing" title="Ideas, Planning, & Feedback">🤔</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/era-23"><img src="https://avatars.githubusercontent.com/u/115151590?v=4?s=100" width="100px;" alt="Ethan Attwood"/><br /><sub><b>Ethan Attwood</b></sub></a><br /><a href="#bug-era-23" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/TheCSGuy25"><img src="https://avatars.githubusercontent.com/u/87066683?v=4?s=100" width="100px;" alt="__aar0n__.py"/><br /><sub><b>__aar0n__.py</b></sub></a><br /><a href="#code-TheCSGuy25" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/SyedHaider2084"><img src="https://avatars.githubusercontent.com/u/227389830?v=4?s=100" width="100px;" alt="SyedHaider2084"/><br /><sub><b>SyedHaider2084</b></sub></a><br /><a href="#code-SyedHaider2084" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/SyedHaider2084"><img src="https://avatars.githubusercontent.com/u/227389830?v=4?s=100" width="100px;" alt="SyedHaider2084"/><br /><sub><b>SyedHaider2084</b></sub></a><br /><a href="#code-SyedHaider2084" title="Code">💻</a> <a href="#doc-SyedHaider2084" title="Documentation">📖</a></td>
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://www.linkedin.com/in/lcm98/"><img src="https://avatars.githubusercontent.com/u/102757707?v=4?s=100" width="100px;" alt="Loh Chun Mun"/><br /><sub><b>Loh Chun Mun</b></sub></a><br /><a href="#doc-cmsamaaa" title="Documentation">📖</a> <a href="#code-cmsamaaa" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/z7076"><img src="https://avatars.githubusercontent.com/u/69681924?v=4?s=100" width="100px;" alt="Jichen Zhang"/><br /><sub><b>Jichen Zhang</b></sub></a><br /><a href="#code-z7076" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/RemDelaporteMathurin"><img src="https://avatars.githubusercontent.com/u/40028739?v=4?s=100" width="100px;" alt="Rémi Delaporte-Mathurin"/><br /><sub><b>Rémi Delaporte-Mathurin</b></sub></a><br /><a href="#bug-RemDelaporteMathurin" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/z7076"><img src="https://avatars.githubusercontent.com/u/69681924?v=4?s=100" width="100px;" alt="Jichen Zhang"/><br /><sub><b>Jichen Zhang</b></sub></a><br /><a href="#code-z7076" title="Code">💻</a> <a href="#doc-z7076" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/RemDelaporteMathurin"><img src="https://avatars.githubusercontent.com/u/40028739?v=4?s=100" width="100px;" alt="Rémi Delaporte-Mathurin"/><br /><sub><b>Rémi Delaporte-Mathurin</b></sub></a><br /><a href="#bug-RemDelaporteMathurin" title="Bug reports">🐛</a> <a href="#doc-RemDelaporteMathurin" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/pmeier"><img src="https://avatars.githubusercontent.com/u/6849766?v=4?s=100" width="100px;" alt="Philip Meier"/><br /><sub><b>Philip Meier</b></sub></a><br /><a href="#bug-pmeier" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/penelopeysm"><img src="https://avatars.githubusercontent.com/u/122629585?v=4?s=100" width="100px;" alt="Penelope Yong"/><br /><sub><b>Penelope Yong</b></sub></a><br /><a href="#ideas-penelopeysm" title="Ideas, Planning, & Feedback">🤔</a> <a href="#review-penelopeysm" title="Reviewed Pull Requests">👀</a> <a href="#code-penelopeysm" title="Code">💻</a> <a href="#doc-penelopeysm" title="Documentation">📖</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/ykd007"><img src="https://avatars.githubusercontent.com/u/79036688?v=4?s=100" width="100px;" alt="Yash Dhawan"/><br /><sub><b>Yash Dhawan</b></sub></a><br /><a href="#doc-ykd007" title="Documentation">📖</a></td>
     </tr>
   </tbody>
 </table>

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate.egg-info/SOURCES.txt

@@ -95,12 +95,8 @@ autoemulate/emulators/transformed/__init__.py
 autoemulate/emulators/transformed/base.py
 autoemulate/emulators/transformed/delta_method.py
 autoemulate/experimental/data/gaussian.py
-autoemulate/experimental/data/spatiotemporal_dataset.py
-autoemulate/experimental/emulators/fno.py
-autoemulate/experimental/emulators/spatiotemporal.py
 autoemulate/experimental/emulators/nn/gaussian_mlp.py
 autoemulate/experimental/emulators/nn/zoib.py
-autoemulate/experimental/neural_processes/conditional_neural_process.py
 autoemulate/feature_generation/polynomial_features.py
 autoemulate/learners/__init__.py
 autoemulate/learners/base.py

{autoemulate-2.1.0 → autoemulate-2.1.2}/autoemulate.egg-info/requires.txt

@@ -1,6 +1,6 @@
 matplotlib>=3.7.2
 seaborn>=0.12.2
-scikit-learn<1.6.0,>=1.3.0
+scikit-learn>=1.3.0
 pandas>=2.1
 torch>=2.1.0
 scipy>=1.11.3
@@ -16,7 +16,7 @@ anytree>=2.12.1
 torchmetrics>=1.7.1
 pyro-ppl>=1.9.1
 torchrbf>=0.0.1
-arviz>=0.21.0
+arviz<1.0,>=0.21.0
 getdist>=1.7.2
 einops>=0.8.1
 harmonic>=1.3.0

{autoemulate-2.1.0 → autoemulate-2.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "autoemulate"
-version = "2.1.0"
+version = "2.1.2"
 description = "A python package for semi-automated emulation"
 license = "MIT"
 authors = [{ name = "AutoEmulate contributors (see our GitHub page)" }]
@@ -18,7 +18,7 @@ classifiers = [
 dependencies = [
     "matplotlib>=3.7.2",
     "seaborn>=0.12.2",
-    "scikit-learn>=1.3.0,<1.6.0",
+    "scikit-learn>=1.3.0",
     "pandas>=2.1",
     "torch>=2.1.0",
     "scipy>=1.11.3",
@@ -34,7 +34,7 @@ dependencies = [
     "torchmetrics>=1.7.1",
     "pyro-ppl>=1.9.1",
     "torchrbf>=0.0.1",
-    "arviz>=0.21.0",
+    "arviz>=0.21.0,<1.0",
     "getdist>=1.7.2",
     "einops>=0.8.1",
     "harmonic>=1.3.0",
@@ -119,8 +119,16 @@ filterwarnings = [
     # Raised by PyTorch (via gpytorch) - not actionable here.
     # Remove if dependencies no longer calling `torch.jit.script`.
     "ignore:`torch\\.jit\\.script` is deprecated\\..*:DeprecationWarning",
+    # Raised by Pyro on Python 3.10 when parsing a dependency docstring.
+    "ignore:invalid escape sequence.*:DeprecationWarning:pyro\\.ops\\.stats",
+    # Raised when harmonic imports TensorFlow Probability's JAX backend.
+    "ignore:jax\\.interpreters\\.xla\\.pytype_aval_mappings is deprecated\\..*:DeprecationWarning:tensorflow_probability\\.python\\.internal\\.backend\\.jax\\.ops",
     # PyTorch MPS backend capability fallbacks are backend noise in tests.
     "ignore:The operator .* is not currently supported on the MPS backend.*:UserWarning",
+    # LightGBM automatically adds feature names to training data, which causes warnings when
+    # making predictions with unnamed data
+    # https://github.com/lightgbm-org/LightGBM/issues/6798
+    "ignore:X does not have valid feature names, but LGBMRegressor was fitted with feature names:UserWarning",
 ]
 
 [tool.pyright]

autoemulate-2.1.0/autoemulate/experimental/data/spatiotemporal_dataset.py

@@ -1,160 +0,0 @@
-import h5py
-import torch
-from autoemulate.core.types import TensorLike
-from torch.utils.data import Dataset
-
-
-class AutoEmulateDataset(Dataset):
-    """A class for spatio-temporal datasets."""
-
-    def __init__(
-        self,
-        data_path: str | None,
-        data: dict | None = None,
-        n_steps_input: int = 1,
-        n_steps_output: int = 1,
-        stride: int = 1,
-        # TODO: support for passing data from dict
-        input_channel_idxs: tuple[int, ...] | None = None,
-        output_channel_idxs: tuple[int, ...] | None = None,
-        dtype: torch.dtype = torch.float32,
-    ):
-        """
-        Initialize the dataset.
-
-        Parameters
-        ----------
-        data_path: str
-            Path to the HDF5 file containing the dataset.
-        n_steps_input: int
-            Number of input time steps.
-        n_steps_output: int
-            Number of output time steps.
-        stride: int
-            Stride for sampling the data.
-        data: dict | None
-            Preloaded data. Defaults to None.
-        input_channel_idxs: tuple[int, ...] | None
-            Indices of input channels to use. Defaults to None.
-        output_channel_idxs: tuple[int, ...] | None
-            Indices of output channels to use. Defaults to None.
-        dtype: torch.dtype
-            Data type for tensors. Defaults to torch.float32.
-        """
-        self.dtype = dtype
-        self.n_steps_input = n_steps_input
-        self.n_steps_output = n_steps_output
-        self.stride = stride
-        self.input_channel_idxs = input_channel_idxs
-        self.output_channel_idxs = output_channel_idxs
-
-        # Read or parse data
-        self.read_data(data_path) if data_path is not None else self.parse_data(data)
-
-        # Destructured here
-        (
-            self.n_trajectories,
-            self.n_timesteps,
-            self.width,
-            self.height,
-            self.n_channels,
-        ) = self.data.shape
-
-        # Pre-compute all subtrajectories for efficient indexing
-        self.all_input_fields = []
-        self.all_output_fields = []
-        self.all_constant_scalars = []
-
-        for traj_idx in range(self.n_trajectories):
-            # Create subtrajectories for this trajectory
-            fields = (
-                self.data[traj_idx]
-                .unfold(0, self.n_steps_input + self.n_steps_output, self.stride)
-                .permute(0, -1, 1, 2, 3)  # [num_subtrajectories, T_in + T_out, W, H, C]
-            )
-
-            # Split into input and output
-            input_fields = fields[
-                :, : self.n_steps_input, ...
-            ]  # [num_subtrajectories, T_in, W, H, C]
-            output_fields = fields[
-                :, self.n_steps_input :, ...
-            ]  # [num_subtrajectories, T_out, W, H, C]
-
-            # Store each subtrajectory separately
-            for sub_idx in range(input_fields.shape[0]):
-                self.all_input_fields.append(
-                    input_fields[sub_idx].to(self.dtype)
-                )  # [T_in, W, H, C]
-                self.all_output_fields.append(
-                    output_fields[sub_idx].to(self.dtype)
-                )  # [T_out, W, H, C]
-
-                # Handle constant scalars
-                if self.constant_scalars is not None:
-                    self.all_constant_scalars.append(
-                        self.constant_scalars[traj_idx].to(self.dtype)
-                    )
-                else:
-                    self.all_constant_scalars.append(torch.tensor([]))
-
-        print(f"Created {len(self.all_input_fields)} subtrajectory samples")
-        print(f"Each input sample shape: {self.all_input_fields[0].shape}")
-        print(f"Each output sample shape: {self.all_output_fields[0].shape}")
-        print(f"Data type: {self.all_input_fields[0].dtype}")
-
-    def read_data(self, data_path: str):
-        """Read data.
-
-        By default assumes HDF5 format in `data_path` with correct shape and fields.
-        """
-        # TODO: support passing as dict
-        # Load data
-        self.data_path = data_path
-        with h5py.File(self.data_path, "r") as f:
-            assert "data" in f, "HDF5 file must contain 'data' dataset"
-            self.data: TensorLike = torch.Tensor(f["data"][:]).to(self.dtype)  # type: ignore # [N, T, W, H, C]  # noqa: PGH003
-        print(f"Loaded data shape: {self.data.shape}")
-        # TODO: add the constant scalars
-        self.constant_scalars = (
-            torch.Tensor(f["constant_scalars"][:]).to(self.dtype)  # type: ignore  # noqa: PGH003
-            if "constant_scalars" in f
-            else None
-        )  # [N, C]
-        # TODO: add the constant fields
-        # self.constant_fields = torch.Tensor(f['data'][:])  # [N, W, H, C]
-
-    def parse_data(self, data: dict | None):
-        """Parse data from a dictionary."""
-        if data is not None:
-            self.data = (
-                data["data"].to(self.dtype)
-                if torch.is_tensor(data["data"])
-                else torch.tensor(data["data"], dtype=self.dtype)
-            )
-            self.constant_scalars = data.get("constant_scalars", None)
-            self.constant_fields = data.get("constant_fields", None)
-            return
-        msg = "No data provided to parse."
-        raise ValueError(msg)
-
-    def __len__(self):  # noqa: D105
-        return len(self.all_input_fields)
-
-    def __getitem__(self, idx):  # noqa: D105
-        return {
-            "input_fields": self.all_input_fields[idx],
-            "output_fields": self.all_output_fields[idx],
-            "constant_scalars": self.all_constant_scalars[idx],
-            # TODO: add this
-            # "constant_fields": self.all_constant_fields[idx],
-        }
-
-
-class MHDDataset(AutoEmulateDataset):
-    """PyTorch Dataset for MHD data."""
-
-    def __init__(self, data_path: str, t_in: int = 5, t_out: int = 10, stride: int = 1):
-        super().__init__(
-            data_path, n_steps_input=t_in, n_steps_output=t_out, stride=stride
-        )