bayesian-optimization 3.0.1__tar.gz → 3.2.0__tar.gz

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/PKG-INFO

@@ -1,7 +1,9 @@
 Metadata-Version: 2.3
 Name: bayesian-optimization
-Version: 3.0.1
+Version: 3.2.0
 Summary: Bayesian Optimization package
+Author: Fernando Nogueira
+Author-email: Fernando Nogueira <fmfnogueira@gmail.com>
 License: The MIT License (MIT)
          
          Copyright (c) 2014 Fernando M. F. Nogueira
@@ -11,9 +13,6 @@ License: The MIT License (MIT)
          The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
          
          THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-Author: Fernando Nogueira
-Author-email: fmfnogueira@gmail.com
-Requires-Python: >=3.9,<4.0
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
@@ -22,12 +21,31 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: colorama (>=0.4.6,<1.0.0)
-Requires-Dist: numpy (>=1.25) ; python_version < "3.13"
-Requires-Dist: numpy (>=2.1.3) ; python_version >= "3.13"
-Requires-Dist: scikit-learn (>=1.0.0,<2.0.0)
-Requires-Dist: scipy (>=1.0.0,<2.0.0) ; python_version < "3.13"
-Requires-Dist: scipy (>=1.14.1,<2.0.0) ; python_version >= "3.13"
+Classifier: Programming Language :: Python :: 3.14
+Requires-Dist: colorama>=0.4.6
+Requires-Dist: numpy>=1.25 ; python_full_version < '3.13'
+Requires-Dist: numpy>=2.1.3 ; python_full_version >= '3.13'
+Requires-Dist: packaging>=20.0
+Requires-Dist: scikit-learn>=1.0.0
+Requires-Dist: scipy>=1.0.0 ; python_full_version < '3.13'
+Requires-Dist: scipy>=1.14.1 ; python_full_version >= '3.13'
+Requires-Dist: coverage>=7.4.1 ; extra == 'dev'
+Requires-Dist: jupyter>=1.0.0 ; extra == 'dev'
+Requires-Dist: matplotlib>=3.0 ; extra == 'dev'
+Requires-Dist: nbconvert>=7.14.2 ; extra == 'dev'
+Requires-Dist: nbformat>=5.9.2 ; extra == 'dev'
+Requires-Dist: nbsphinx>=0.9.4 ; extra == 'dev'
+Requires-Dist: pre-commit>=3.7.1 ; extra == 'dev'
+Requires-Dist: pytest>=8.0.0 ; extra == 'dev'
+Requires-Dist: pytest-cov>=4.1.0 ; extra == 'dev'
+Requires-Dist: ruff>=0.12.3 ; extra == 'dev'
+Requires-Dist: sphinx-immaterial>=0.12.0 ; extra == 'dev'
+Requires-Dist: sphinx>=7.0.0 ; python_full_version < '3.10' and extra == 'dev'
+Requires-Dist: sphinx>=8.0.0 ; python_full_version >= '3.10' and extra == 'dev'
+Requires-Dist: sphinx-autodoc-typehints>=2.3.0 ; python_full_version < '3.10' and extra == 'dev'
+Requires-Dist: sphinx-autodoc-typehints>=2.4.0 ; python_full_version >= '3.10' and extra == 'dev'
+Requires-Python: >=3.9
+Provides-Extra: dev
 Description-Content-Type: text/markdown
 
 <div align="center">
@@ -230,4 +248,3 @@ For optimization over non-float parameters:
   publisher={Elsevier}
 }
 ```
-

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/acquisition.py

@@ -452,6 +452,14 @@ class UpperConfidenceBound(AcquisitionFunction):
         if kappa < 0:
             error_msg = "kappa must be greater than or equal to 0."
             raise ValueError(error_msg)
+        if exploration_decay is not None and not (0 < exploration_decay <= 1):
+            error_msg = "exploration_decay must be greater than 0 and less than or equal to 1."
+            raise ValueError(error_msg)
+        if exploration_decay_delay is not None and (
+            not isinstance(exploration_decay_delay, int) or exploration_decay_delay < 0
+        ):
+            error_msg = "exploration_decay_delay must be an integer greater than or equal to 0."
+            raise ValueError(error_msg)
 
         super().__init__(random_state=random_state)
         self.kappa = kappa
@@ -604,6 +612,18 @@ class ProbabilityOfImprovement(AcquisitionFunction):
         exploration_decay_delay: int | None = None,
         random_state: int | RandomState | None = None,
     ) -> None:
+        if xi < 0:
+            error_msg = "xi must be greater than or equal to 0."
+            raise ValueError(error_msg)
+        if exploration_decay is not None and not (0 < exploration_decay <= 1):
+            error_msg = "exploration_decay must be greater than 0 and less than or equal to 1."
+            raise ValueError(error_msg)
+        if exploration_decay_delay is not None and (
+            not isinstance(exploration_decay_delay, int) or exploration_decay_delay < 0
+        ):
+            error_msg = "exploration_decay_delay must be an integer greater than or equal to 0."
+            raise ValueError(error_msg)
+
         super().__init__(random_state=random_state)
         self.xi = xi
         self.exploration_decay = exploration_decay
@@ -766,6 +786,7 @@ class ExpectedImprovement(AcquisitionFunction):
         Decay rate for xi. If None, no decay is applied.
 
     exploration_decay_delay : int, default None
+        Delay for decay. If None, decay is applied from the start.
 
     random_state : int, RandomState, default None
         Set the random state for reproducibility.
@@ -778,6 +799,18 @@ class ExpectedImprovement(AcquisitionFunction):
         exploration_decay_delay: int | None = None,
         random_state: int | RandomState | None = None,
     ) -> None:
+        if xi < 0:
+            error_msg = "xi must be greater than or equal to 0."
+            raise ValueError(error_msg)
+        if exploration_decay is not None and not (0 < exploration_decay <= 1):
+            error_msg = "exploration_decay must be greater than 0 and less than or equal to 1."
+            raise ValueError(error_msg)
+        if exploration_decay_delay is not None and (
+            not isinstance(exploration_decay_delay, int) or exploration_decay_delay < 0
+        ):
+            error_msg = "exploration_decay_delay must be an integer greater than or equal to 0."
+            raise ValueError(error_msg)
+
         super().__init__(random_state=random_state)
         self.xi = xi
         self.exploration_decay = exploration_decay

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/bayesian_optimization.py

@@ -8,6 +8,7 @@ from __future__ import annotations
 
 import json
 from collections import deque
+from collections.abc import Iterable
 from os import PathLike
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
@@ -55,6 +56,11 @@ class BayesianOptimization:
         Dictionary with parameters names as keys and a tuple with minimum
         and maximum values.
 
+    acquisition_function: AcquisitionFunction, optional(default=None)
+            The acquisition function to use for suggesting new points to evaluate.
+            If None, defaults to UpperConfidenceBound for unconstrained problems
+            and ExpectedImprovement for constrained problems.
+
     constraint: NonlinearConstraint.
         Note that the names of arguments of the constraint function and of
         f need to be the same.
@@ -170,6 +176,92 @@ class BayesianOptimization:
         """
         return self._space.res()
 
+    def predict(
+        self,
+        params: dict[str, Any] | Iterable[dict[str, Any]],
+        return_std=False,
+        return_cov=False,
+        fit_gp=True,
+    ) -> float | NDArray[Float] | tuple[float | NDArray[Float], float | NDArray[Float]]:
+        """Predict the target function value at given parameters.
+
+        Parameters
+        ---------
+        params: dict or iterable of dicts
+            The parameters where the prediction is made.
+
+        return_std: bool, optional(default=False)
+            If True, the standard deviation of the prediction is returned.
+
+        return_cov: bool, optional(default=False)
+            If True, the covariance of the prediction is returned.
+
+        fit_gp: bool, optional(default=True)
+            If True, the internal Gaussian Process model is fitted before
+            making the prediction.
+
+        Returns
+        -------
+        mean: float or np.ndarray
+            The predicted mean of the target function at the given parameters.
+            When params is a dict, returns a scalar. When params is an iterable,
+            returns a 1D array.
+
+        std_or_cov: float or np.ndarray (only if return_std or return_cov is True)
+            The predicted standard deviation or covariance of the target function
+            at the given parameters.
+        """
+        # Validate param types
+        if isinstance(params, dict):
+            params_array = self._space.params_to_array(params).reshape(1, -1)
+            single_param = True
+        elif isinstance(params, Iterable) and not isinstance(params, str):
+            # convert iterable of dicts to 2D array
+            params_array = np.array([self._space.params_to_array(p) for p in params])
+            single_param = False
+        else:
+            msg = f"params must be a dict or iterable of dicts, got {type(params).__name__}"
+            raise TypeError(msg)
+
+        # Validate mutual exclusivity of return_std and return_cov
+        if return_std and return_cov:
+            msg = "return_std and return_cov cannot both be True"
+            raise ValueError(msg)
+
+        if fit_gp:
+            if len(self._space) == 0:
+                msg = (
+                    "The Gaussian Process model cannot be fitted with zero observations. To use predict(), "
+                    "without fitting the GP, set fit_gp=False. The predictions will then be made using the "
+                    "GP prior."
+                )
+                raise RuntimeError(msg)
+            self.acquisition_function._fit_gp(self._gp, self._space)
+
+        res = self._gp.predict(params_array, return_std=return_std, return_cov=return_cov)
+
+        if return_std or return_cov:
+            mean, std_or_cov = res
+        else:
+            mean = res
+
+        # Shape semantics: dict input returns scalars, list input returns arrays
+        # Ensure list input always returns arrays (convert scalar to 1D if needed)
+        if not single_param and mean.ndim == 0:
+            mean = np.atleast_1d(mean)
+        # ruff complains when nesting conditionals, so this three-way split is necessary
+        if not single_param and (return_std or return_cov) and std_or_cov.ndim == 0:
+            std_or_cov = np.atleast_1d(std_or_cov)
+
+        if single_param and mean.ndim > 0:
+            mean = mean[0]
+        if single_param and return_std and std_or_cov.ndim > 0:
+            std_or_cov = std_or_cov[0]
+
+        if return_std or return_cov:
+            return mean, std_or_cov
+        return mean
+
     def register(
         self, params: ParamsType, target: float, constraint_value: float | NDArray[Float] | None = None
     ) -> None:
@@ -298,8 +390,8 @@ class BayesianOptimization:
             probe based on the acquisition function. This means that the GP may
             not be fitted on all points registered to the target space when the
             method completes. If you intend to use the GP model after the
-            optimization routine, make sure to fit it manually, e.g. by calling
-            ``optimizer._gp.fit(optimizer.space.params, optimizer.space.target)``.
+            optimization routine, make sure to call predict() with fit_gp=True.
+
         """
         # Log optimization start
         self.logger.log_optimization_start(self._space.keys)
@@ -347,19 +439,7 @@ class BayesianOptimization:
         ----------
         path : str or PathLike
             Path to save the optimization state
-
-        Raises
-        ------
-        ValueError
-            If attempting to save state before collecting any samples.
         """
-        if len(self._space) == 0:
-            msg = (
-                "Cannot save optimizer state before collecting any samples. "
-                "Please probe or register at least one point before saving."
-            )
-            raise ValueError(msg)
-
         random_state = None
         if self._random_state is not None:
             state_tuple = self._random_state.get_state()
@@ -438,7 +518,8 @@ class BayesianOptimization:
         # Set the GP parameters
         self.set_gp_params(**gp_params)
 
-        self._gp.fit(self._space.params, self._space.target)
+        if len(self._space):
+            self._gp.fit(self._space.params, self._space.target)
 
         if state["random_state"] is not None:
             random_state_tuple = (

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/constraint.py

@@ -240,7 +240,7 @@ class ConstraintModel:
             return self._model[0].predict(X).reshape(X_shape[:-1])
 
         result = np.column_stack([gp.predict(X) for gp in self._model])
-        return result.reshape(X_shape[:-1] + (len(self._lb),))
+        return result.reshape(*X_shape[:-1], len(self._lb))
 
     def allowed(self, constraint_values: NDArray[Float]) -> NDArray[np.bool_]:
         """Check whether `constraint_values` fulfills the specified limits.

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/logger.py

@@ -82,7 +82,7 @@ class ScreenLogger:
             result = ""
             width = self._default_cell_size
             # Keep negative sign, exponent, and as many decimal places as possible
-            if "-" in s:
+            if x < 0:
                 result += "-"
                 width -= 1
                 s = s[1:]
@@ -96,8 +96,6 @@ class ScreenLogger:
                 width -= dot_pos
                 if width > 0:
                     result += s[dot_pos : dot_pos + width]
-            else:
-                result += s[:width]
             if "e" in s:
                 result += end
             result = result.ljust(self._default_cell_size)

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/parameter.py

@@ -489,7 +489,10 @@ def wrap_kernel(kernel: kernels.Kernel, transform: Callable[[Any], Any]) -> kern
         def __reduce__(self) -> str | tuple[Any, ...]:
             return (wrap_kernel, (kernel, transform))
 
-    return WrappedKernel(**kernel.get_params())
+    wrapped_instance = WrappedKernel.__new__(WrappedKernel)
+    wrapped_instance.__dict__.update(kernel.__dict__)
+    wrapped_instance._transform = transform
+    return wrapped_instance
 
 
 def _copy_signature(source_fct: Callable[..., Any]) -> Callable[[Callable[..., Any]], Callable[..., Any]]:

bayesian_optimization-3.2.0/pyproject.toml

@@ -0,0 +1,61 @@
+[project]
+name = "bayesian-optimization"
+version = "3.2.0"
+description = "Bayesian Optimization package"
+authors = [{ name = "Fernando Nogueira", email = "fmfnogueira@gmail.com" }]
+license = { file = "LICENSE" }
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+]
+dependencies = [
+    "colorama>=0.4.6",
+    "numpy>=1.25; python_version<'3.13'",
+    "numpy>=2.1.3; python_version>='3.13'",
+    "packaging>=20.0",
+    "scikit-learn>=1.0.0",
+    "scipy>=1.0.0; python_version<'3.13'",
+    "scipy>=1.14.1; python_version>='3.13'",
+]
+
+[project.optional-dependencies]
+dev = [
+    "coverage>=7.4.1",
+    "jupyter>=1.0.0",
+    "matplotlib>=3.0",
+    "nbconvert>=7.14.2",
+    "nbformat>=5.9.2",
+    "nbsphinx>=0.9.4",
+    "pre-commit>=3.7.1",
+    "pytest>=8.0.0",
+    "pytest-cov>=4.1.0",
+    "ruff>=0.12.3",
+    "sphinx-immaterial>=0.12.0",
+    "sphinx>=7.0.0; python_version<'3.10'",
+    "sphinx>=8.0.0; python_version>='3.10'",
+    "sphinx-autodoc-typehints>=2.3.0; python_version<'3.10'",
+    "sphinx-autodoc-typehints>=2.4.0; python_version>='3.10'",
+]
+
+[build-system]
+requires = ["uv_build>=0.7.21,<0.8.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "bayes_opt"
+module-root = ""
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+]

bayesian_optimization-3.0.1/pyproject.toml

@@ -1,70 +0,0 @@
-[project]
-name = "bayesian-optimization"
-version = "3.0.1"
-description = "Bayesian Optimization package"
-authors = [{ name = "Fernando Nogueira", email = "fmfnogueira@gmail.com" }]
-license = { file = "LICENSE" }
-readme = "README.md"
-requires-python = ">=3.9,<4.0"
-classifiers = [
-    "License :: OSI Approved :: MIT License",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
-]
-dependencies = [
-    "scikit-learn>=1.0.0,<2.0.0",
-    "numpy>=1.25; python_version<'3.13'",
-    "numpy>=2.1.3; python_version>='3.13'",
-    "scipy>=1.0.0,<2.0.0; python_version<'3.13'",
-    "scipy>=1.14.1,<2.0.0; python_version>='3.13'",
-    "colorama>=0.4.6,<1.0.0",
-]
-
-[tool.poetry]
-requires-poetry = ">=2.0"
-packages = [{ include = "bayes_opt" }]
-
-
-[tool.poetry.group.dev] # for testing/developing
-optional = true
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.0.0"
-pytest-cov = "^4.1.0"
-coverage = "^7.4.1"
-ruff = "0.6.6"
-pre-commit = "^3.7.1"
-
-
-[tool.poetry.group.nbtools] # for running/converting notebooks
-optional = true
-[tool.poetry.group.nbtools.dependencies]
-nbformat = "^5.9.2"
-nbconvert = "^7.14.2"
-jupyter = "^1.0.0"
-matplotlib = "^3.0"
-nbsphinx = "^0.9.4"
-sphinx-immaterial = "^0.12.0"
-sphinx = [
-    { version = "^7.0.0", python = "<3.10" },
-    { version = "^8.0.0", python = ">=3.10" },
-]
-sphinx-autodoc-typehints = [
-    { version = "^2.3.0", python = "<3.10" },
-    { version = "^2.4.0", python = ">=3.10" },
-]
-
-
-[build-system]
-requires = ["poetry-core>=2.0"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.coverage.report]
-exclude_lines = [
-    "pragma: no cover",
-    "if TYPE_CHECKING:",
-]

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/__init__.py

@@ -15,10 +15,10 @@ __version__ = importlib.metadata.version("bayesian-optimization")
 
 
 __all__ = [
-    "acquisition",
     "BayesianOptimization",
-    "TargetSpace",
     "ConstraintModel",
     "ScreenLogger",
     "SequentialDomainReductionTransformer",
+    "TargetSpace",
+    "acquisition",
 ]

{bayesian_optimization-3.0.1 → bayesian_optimization-3.2.0}/bayes_opt/exception.py

@@ -4,9 +4,9 @@ from __future__ import annotations
 
 __all__ = [
     "BayesianOptimizationError",
-    "NotUniqueError",
     "ConstraintNotSupportedError",
     "NoValidPointRegisteredError",
+    "NotUniqueError",
     "TargetSpaceEmptyError",
 ]