bayesian-optimization 1.5.0__tar.gz → 1.5.1__tar.gz

{bayesian_optimization-1.5.0 → bayesian_optimization-1.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bayesian-optimization
-Version: 1.5.0
+Version: 1.5.1
 Summary: Bayesian Optimization package
 License: MIT
 Author: Fernando Nogueira
@@ -12,20 +12,20 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: colorama (>=0.4.6,<0.5.0)
-Requires-Dist: numpy (>=1.9.0,<2.0.0)
+Requires-Dist: numpy (>=1.25)
 Requires-Dist: scikit-learn (>=1.0.0,<2.0.0)
 Requires-Dist: scipy (>=1.0.0,<2.0.0)
 Description-Content-Type: text/markdown
 
 <div align="center">
-  <img src="https://raw.githubusercontent.com/bayesian-optimization/BayesianOptimization/master/static/func.png"><br><br>
+  <img src="https://raw.githubusercontent.com/bayesian-optimization/BayesianOptimization/master/docsrc/static/func.png"><br><br>
 </div>
 
 # Bayesian Optimization
 
 ![tests](https://github.com/bayesian-optimization/BayesianOptimization/actions/workflows/run_tests.yml/badge.svg)
 [![Codecov](https://codecov.io/github/bayesian-optimization/BayesianOptimization/badge.svg?branch=master&service=github)](https://codecov.io/github/bayesian-optimization/BayesianOptimization?branch=master)
-[![Pypi](https://img.shields.io/pypi/v/bayesian-optimization.svg)](https://pypi.python.org/pypi/bayesian-optimization)
+[![Pypi](https://img.shields.io/pypi/v/bayesian-optimization.svg)](https://pypi.python.org/pypi/bayesian-optimization)![PyPI - Python Version](https://img.shields.io/pypi/pyversions/bayesian-optimization)
 
 Pure Python implementation of bayesian global optimization with gaussian
 processes.
@@ -70,11 +70,11 @@ for ideas on how to implement bayesian optimization in a distributed fashion usi
 
 Bayesian optimization works by constructing a posterior distribution of functions (gaussian process) that best describes the function you want to optimize. As the number of observations grows, the posterior distribution improves, and the algorithm becomes more certain of which regions in parameter space are worth exploring and which are not, as seen in the picture below.
 
-![BayesianOptimization in action](./static/bo_example.png)
+![BayesianOptimization in action](docsrc/static/bo_example.png)
 
 As you iterate over and over, the algorithm balances its needs of exploration and exploitation taking into account what it knows about the target function. At each step a Gaussian Process is fitted to the known samples (points previously explored), and the posterior distribution, combined with a exploration strategy (such as UCB (Upper Confidence Bound), or EI (Expected Improvement)), are used to determine the next point that should be explored (see the gif below).
 
-![BayesianOptimization in action](./static/bayesian_optimization.gif)
+![BayesianOptimization in action](docsrc/static/bayesian_optimization.gif)
 
 This process is designed to minimize the number of steps required to find a combination of parameters that are close to the optimal combination. To do so, this method uses a proxy optimization problem (finding the maximum of the acquisition function) that, albeit still a hard problem, is cheaper (in the computational sense) and common tools can be employed. Therefore Bayesian Optimization is most adequate for situations where sampling the function to be optimized is a very expensive endeavor. See the references for a proper discussion of this method.
 
@@ -202,7 +202,7 @@ Sometimes the initial boundaries specified for a problem are too wide, and addin
 
 When it's worthwhile to converge on an optimal point quickly rather than try to find the optimal point, contracting the domain around the current optimal value as the search progresses can speed up the search progress considerably. Using the `SequentialDomainReductionTransformer` the bounds of the problem can be panned and zoomed dynamically in an attempt to improve convergence.
 
-![sequential domain reduction](./static/sdr.png)
+![sequential domain reduction](docsrc/static/sdr.png)
 
 An example of using the `SequentialDomainReductionTransformer` is shown in the [domain reduction notebook](http://bayesian-optimization.github.io/BayesianOptimization/domain_reduction.html). More information about this method can be found in the paper ["On the robustness of a simple domain reduction scheme for simulation‐based optimization"](http://www.truegrid.com/srsm_revised.pdf).
 

{bayesian_optimization-1.5.0 → bayesian_optimization-1.5.1}/README.md

@@ -1,12 +1,12 @@
 <div align="center">
-  <img src="https://raw.githubusercontent.com/bayesian-optimization/BayesianOptimization/master/static/func.png"><br><br>
+  <img src="https://raw.githubusercontent.com/bayesian-optimization/BayesianOptimization/master/docsrc/static/func.png"><br><br>
 </div>
 
 # Bayesian Optimization
 
 ![tests](https://github.com/bayesian-optimization/BayesianOptimization/actions/workflows/run_tests.yml/badge.svg)
 [![Codecov](https://codecov.io/github/bayesian-optimization/BayesianOptimization/badge.svg?branch=master&service=github)](https://codecov.io/github/bayesian-optimization/BayesianOptimization?branch=master)
-[![Pypi](https://img.shields.io/pypi/v/bayesian-optimization.svg)](https://pypi.python.org/pypi/bayesian-optimization)
+[![Pypi](https://img.shields.io/pypi/v/bayesian-optimization.svg)](https://pypi.python.org/pypi/bayesian-optimization)![PyPI - Python Version](https://img.shields.io/pypi/pyversions/bayesian-optimization)
 
 Pure Python implementation of bayesian global optimization with gaussian
 processes.
@@ -51,11 +51,11 @@ for ideas on how to implement bayesian optimization in a distributed fashion usi
 
 Bayesian optimization works by constructing a posterior distribution of functions (gaussian process) that best describes the function you want to optimize. As the number of observations grows, the posterior distribution improves, and the algorithm becomes more certain of which regions in parameter space are worth exploring and which are not, as seen in the picture below.
 
-![BayesianOptimization in action](./static/bo_example.png)
+![BayesianOptimization in action](docsrc/static/bo_example.png)
 
 As you iterate over and over, the algorithm balances its needs of exploration and exploitation taking into account what it knows about the target function. At each step a Gaussian Process is fitted to the known samples (points previously explored), and the posterior distribution, combined with a exploration strategy (such as UCB (Upper Confidence Bound), or EI (Expected Improvement)), are used to determine the next point that should be explored (see the gif below).
 
-![BayesianOptimization in action](./static/bayesian_optimization.gif)
+![BayesianOptimization in action](docsrc/static/bayesian_optimization.gif)
 
 This process is designed to minimize the number of steps required to find a combination of parameters that are close to the optimal combination. To do so, this method uses a proxy optimization problem (finding the maximum of the acquisition function) that, albeit still a hard problem, is cheaper (in the computational sense) and common tools can be employed. Therefore Bayesian Optimization is most adequate for situations where sampling the function to be optimized is a very expensive endeavor. See the references for a proper discussion of this method.
 
@@ -183,7 +183,7 @@ Sometimes the initial boundaries specified for a problem are too wide, and addin
 
 When it's worthwhile to converge on an optimal point quickly rather than try to find the optimal point, contracting the domain around the current optimal value as the search progresses can speed up the search progress considerably. Using the `SequentialDomainReductionTransformer` the bounds of the problem can be panned and zoomed dynamically in an attempt to improve convergence.
 
-![sequential domain reduction](./static/sdr.png)
+![sequential domain reduction](docsrc/static/sdr.png)
 
 An example of using the `SequentialDomainReductionTransformer` is shown in the [domain reduction notebook](http://bayesian-optimization.github.io/BayesianOptimization/domain_reduction.html). More information about this method can be found in the paper ["On the robustness of a simple domain reduction scheme for simulation‐based optimization"](http://www.truegrid.com/srsm_revised.pdf).
 

{bayesian_optimization-1.5.0 → bayesian_optimization-1.5.1}/bayes_opt/logger.py

@@ -2,6 +2,7 @@
 from __future__ import print_function
 import os
 import json
+import numpy as np
 from .observer import _Tracker
 from .event import Events
 from colorama import Fore, just_fix_windows_console
@@ -45,7 +46,10 @@ class ScreenLogger(_Tracker):
 
     _default_cell_size = 9
     _default_precision = 4
-
+    _colour_new_max = Fore.MAGENTA
+    _colour_regular_message = Fore.RESET
+    _colour_reset = Fore.RESET
+    
     def __init__(self, verbose=2, is_constrained=False):
         self._verbose = verbose
         self._is_constrained = is_constrained
@@ -135,7 +139,7 @@ class ScreenLogger(_Tracker):
             return s[:self._default_cell_size - 3] + "..."
         return s
 
-    def _step(self, instance, colour=Fore.BLACK):
+    def _step(self, instance, colour=_colour_regular_message):
         """Log a step.
 
         Parameters
@@ -144,7 +148,7 @@ class ScreenLogger(_Tracker):
             The instance associated with the event.
             
         colour :
-            (Default value = Fore.BLACK)
+            (Default value = _colour_regular_message, equivalent to Fore.RESET)
 
         Returns
         -------
@@ -162,7 +166,7 @@ class ScreenLogger(_Tracker):
         for key in instance.space.keys:
             cells.append(self._format_number(res["params"][key]))
 
-        return "| " + " | ".join([colour + cells[i] for i in range(len(cells))]) + " |"
+        return "| " + " | ".join([colour + cells[i] + self._colour_reset for i in range(len(cells))]) + " |"
 
     def _header(self, instance):
         """Print the header of the log.
@@ -230,7 +234,7 @@ class ScreenLogger(_Tracker):
             if self._verbose == 1 and not is_new_max:
                 line = ""
             else:
-                colour = Fore.MAGENTA if is_new_max else Fore.BLACK
+                colour = self._colour_new_max if is_new_max else self._colour_regular_message
                 line = self._step(instance, colour=colour) + "\n"
         elif event == Events.OPTIMIZATION_END:
             line = "=" * self._header_length + "\n"
@@ -291,6 +295,9 @@ class JSONLogger(_Tracker):
 
             if "allowed" in data: # fix: github.com/fmfn/BayesianOptimization/issues/361
                 data["allowed"] = bool(data["allowed"])
+            
+            if "constraint" in data and isinstance(data["constraint"], np.ndarray):
+                data["constraint"] = data["constraint"].tolist()
 
             with open(self._path, "a") as f:
                 f.write(json.dumps(data) + "\n")

{bayesian_optimization-1.5.0 → bayesian_optimization-1.5.1}/bayes_opt/target_space.py

@@ -302,7 +302,7 @@ class TargetSpace():
                 self.n_duplicate_points = self.n_duplicate_points + 1
 
                 print(Fore.RED + f'Data point {x} is not unique. {self.n_duplicate_points}'
-                              ' duplicates registered. Continuing ...')
+                              ' duplicates registered. Continuing ...' + Fore.RESET)
             else:
                 raise NotUniqueError(f'Data point {x} is not unique. You can set'
                                      ' "allow_duplicate_points=True" to avoid this error')
@@ -312,21 +312,30 @@ class TargetSpace():
             if not np.all((self._bounds[:, 0] <= x) & (x <= self._bounds[:, 1])):
                 warn(f'\nData point {x} is outside the bounds of the parameter space. ', stacklevel=2)
 
-        self._params = np.concatenate([self._params, x.reshape(1, -1)])
-        self._target = np.concatenate([self._target, [target]])
+        # Make copies of the data, so as not to modify the originals incase something fails
+        # during the registration process. This prevents out-of-sync data.
+        params_copy = np.concatenate([self._params, x.reshape(1, -1)])
+        target_copy = np.concatenate([self._target, [target]])
+        cache_copy = self._cache.copy() # shallow copy suffices
 
         if self._constraint is None:
             # Insert data into unique dictionary
-            self._cache[_hashable(x.ravel())] = target
+            cache_copy[_hashable(x.ravel())] = target
         else:
             if constraint_value is None:
                 msg = ("When registering a point to a constrained TargetSpace" +
                        " a constraint value needs to be present.")
                 raise ValueError(msg)
             # Insert data into unique dictionary
-            self._cache[_hashable(x.ravel())] = (target, constraint_value)
-            self._constraint_values = np.concatenate([self._constraint_values,
-                                                      [constraint_value]])
+            cache_copy[_hashable(x.ravel())] = (target, constraint_value)
+            constraint_values_copy = np.concatenate([self._constraint_values,
+                                                     [constraint_value]])
+            self._constraint_values = constraint_values_copy
+
+        # Operations passed, update the variables
+        self._params = params_copy
+        self._target = target_copy
+        self._cache = cache_copy
 
     def probe(self, params):
         """Evaluate the target function on a point and register the result.

{bayesian_optimization-1.5.0 → bayesian_optimization-1.5.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bayesian-optimization"
-version = "1.5.0"
+version = "1.5.1"
 description = "Bayesian Optimization package"
 authors = ["Fernando Nogueira"]
 license = "MIT"
@@ -10,7 +10,7 @@ packages = [{include = "bayes_opt"}]
 [tool.poetry.dependencies]
 python = "^3.9"
 scikit-learn = "^1.0.0"
-numpy = "^1.9.0"
+numpy = ">=1.25"
 scipy = "^1.0.0"
 colorama = "^0.4.6"
 
@@ -31,6 +31,10 @@ nbformat = "^5.9.2"
 nbconvert = "^7.14.2"
 jupyter = "^1.0.0"
 matplotlib = "^3.0"
+sphinx = "^7.3.7"
+nbsphinx = "^0.9.4"
+sphinx-rtd-theme = "^2.0.0"
+myst-parser = "^3.0.1"
 
 
 [build-system]