Bump peaceiris/actions-gh-pages from 3 to 4

.github/workflows/publish_docs.yml

@@ -30,7 +30,7 @@ jobs:
         poetry run sphinx-build -b html docs/source docs/build/html
 
     - name: Deploy to GitHub Pages
-      uses: peaceiris/actions-gh-pages@v3
+      uses: peaceiris/actions-gh-pages@v4
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./docs/build/html

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -16,33 +16,34 @@ repos:
       - id: detect-private-key
       - id: forbid-new-submodules
       - id: check-docstring-first
-  - repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
-    hooks:
-      - id: reorder-python-imports
+      #- repo: https://github.com/asottile/reorder-python-imports
+      #rev: v3.14.0
+      #hooks:
+      #- id: reorder-python-imports
+      # removed until blank line conflict with ruff-format is resolved
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.15
+    rev: v0.9.2
     hooks:
       - id: ruff
         args: [ --fix ]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.8.0'
+    rev: 'v1.14.1'
     hooks:
     -   id: mypy
         args: [--strict, --ignore-missing-imports, --allow-untyped-decorators, --allow-subclassing-any]
         exclude: "^examples/blueprint_example"
 
   - repo: https://github.com/econchick/interrogate
-    rev: 1.5.0
+    rev: 1.7.0
     hooks:
       - id: interrogate
         args: [--verbose, --ignore-init-method, --ignore-init-module, --fail-under=100]
         # --ignore-init-module seems not to work as intended, so adding __init__.py to excludes as well
         exclude: "^docs|__init__.py"
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    rev: eb1df347edd128b30cd3368dddc3aa65edcfac38 # Don't autoupdate until https://github.com/PyCQA/docformatter/issues/293 is fixed
     hooks:
       - id: docformatter
         args: [--in-place, --black]

CHANGELOG.md

@@ -2,9 +2,11 @@
 
 For more details, refer to the [documentation](https://surfquantum.github.io/yotse/).
 
-## (upcoming)
+## [1.0.1] - 2025-01-16
 * added `dependabot` to update `github-actions`
 * added [zenodo](https://zenodo.org/) DOI
+* fixed for `bayesian-optimization >= 2.0.0`
+* updated dependencies
 
 ## [1.0.0] - 2024-01-31
 * separated optimizations in blackbox and analytical (where the function is known).

examples/blueprint_example/src/example_blueprint_main.py

@@ -7,6 +7,7 @@
 executor class tailored for the NlBlueprint team and utility functions for pre-
 submission setup and post-run cleanup.
 """
+
 import os
 import shutil
 from typing import Any

examples/blueprint_example/src/processing_function.py

@@ -3,6 +3,7 @@
 the cost function defined in total_cost and writes it, together with the optimization
 parameters to a csv file in a format that can be read by smart-stopos and use to
 generate new sets of parameters."""
+
 import os
 import pickle
 from argparse import ArgumentParser

examples/blueprint_example/src/unified_simulation_script_state_with_translation.py

@@ -10,6 +10,7 @@
 saved, how many runs per data point to simulate, the name of the saved file and whether
 the simulation results should be plotted.
 """
+
 import copy
 import os
 import pickle

examples/run_examples.py

@@ -5,6 +5,7 @@
 If the `main`-method takes an argument `no_output` this will be passed as `True`
 to avoid creating plots etc.
 """
+
 import importlib
 import inspect
 import os

examples/wobbly_function/analyse_function_output.py

@@ -3,6 +3,7 @@
 
 csv_output.csv.
 """
+
 import csv
 import os
 from argparse import ArgumentParser

examples/wobbly_function/example_wobbly_bayesian.py

@@ -1,6 +1,7 @@
 """This module demonstrates the process for a blackbox bayesian optimization using the
 Yotse framework."""
-from bayes_opt import UtilityFunction
+
+from bayes_opt.acquisition import UpperConfidenceBound
 
 from examples.wobbly_function.example_wobbly_main import remove_files_after_run
 from examples.wobbly_function.example_wobbly_main import wobbly_pre
@@ -27,7 +28,7 @@ def main() -> None:
         name="bayesopt",
         blackbox_optimization=True,
         opt_parameters={
-            "utility_function": UtilityFunction(kind="ucb", kappa=2.5, xi=0.0),
+            "utility_function": UpperConfidenceBound(kappa=2.5),
             "n_iter": 10,
         },
         is_active=True,

examples/wobbly_function/example_wobbly_main.py

@@ -4,6 +4,7 @@
 It leverages genetic algorithms for the optimization process, handles file management,
 and cleans up after execution, showcasing a very basic use-case.
 """
+
 import os
 import shutil
 from typing import Any

examples/wobbly_function/example_wobbly_param_switching.py

@@ -1,5 +1,6 @@
 """This module demonstrates the process for parameter switching during optimization
 using the Yotse framework."""
+
 from examples.wobbly_function.example_wobbly_main import remove_files_after_run
 from examples.wobbly_function.example_wobbly_main import wobbly_pre
 from yotse.execution import Executor

examples/wobbly_function/example_wobbly_resume.py

@@ -4,6 +4,7 @@
 It initializes the optimization process, runs for a few generations, and then showcases
 how to resume the process from where it left off.
 """
+
 from examples.wobbly_function.example_wobbly_main import remove_files_after_run
 from examples.wobbly_function.example_wobbly_main import wobbly_pre
 from yotse.execution import Executor
@@ -27,9 +28,9 @@ def main() -> None:
 
     # write resume parameter to experiment
     resume_experiment = wobbly_pre()
-    resume_experiment.system_setup.cmdline_arguments[
-        "--resume"
-    ] = stop_resume_example.aux_dir
+    resume_experiment.system_setup.cmdline_arguments["--resume"] = (
+        stop_resume_example.aux_dir
+    )
 
     resume_example = Executor(experiment=resume_experiment)
     for i in range(

examples/wobbly_function/example_wobbly_whitebox.py

@@ -1,5 +1,6 @@
 """This module demonstrates the process for a whitebox optimization using the Yotse
 framework."""
+
 import random
 from typing import Any
 

examples/wobbly_function/wobbly_function.py

@@ -2,6 +2,7 @@
 Usage:
     python3 function.py -filebasename <folder-to-store-output>/<somefilebasename> -x 3 -y 5.5
 """
+
 import csv
 from argparse import ArgumentParser
 from typing import Any