Merge branch 'main' into nevergrad_documentation_to_new_format

Author: gauravmanmode

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
       - id: check-useless-excludes
         # - id: identity  # Prints all files passed to pre-commits. Debugging.
   - repo: https://github.com/lyz-code/yamlfix
-    rev: 1.17.0
+    rev: 1.19.1
     hooks:
       - id: yamlfix
         exclude: tests/optimagic/optimizers/_pounders/fixtures
@@ -89,7 +89,7 @@ repos:
           - --blank
         exclude: src/optimagic/optimization/algo_options.py
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.14.10
     hooks:
       # Run the linter.
       - id: ruff
@@ -106,7 +106,7 @@ repos:
           - pyi
           - jupyter
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.22
+    rev: 1.0.0
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -118,7 +118,7 @@ repos:
           - '88'
         files: (README\.md)
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.22
+    rev: 1.0.0
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -130,7 +130,7 @@ repos:
         files: (docs/.)
         exclude: docs/source/how_to/how_to_specify_algorithm_and_algo_options.md
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.1
+    rev: 0.8.2
     hooks:
       - id: nbstripout
         exclude: |
@@ -141,7 +141,7 @@ repos:
         args:
           - --drop-empty-cells
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.19.1
     hooks:
       - id: mypy
         files: src|tests
@@ -153,7 +153,13 @@ repos:
           - types-cffi
           - types-openpyxl
           - types-jinja2
+          - bokeh
 ci:
   autoupdate_schedule: monthly
   skip:
     - update-algo-selection-code
+    # Skip mypy stubtest on pre-commit.ci due to maximum size limitations. This is
+    # unlikely to get better in the future as dependencies keep growing. Local runs
+    # of pre-commit would still execute stubtest. For CI, we have a separate GitHub
+    # Action that runs stubtest.
+    - mypy

.tools/envs/testenv-linux.yml

@@ -20,24 +20,28 @@ dependencies:
   - pandas  # run, tests
   - plotly>=6.2  # run, tests
   - matplotlib  # tests
+  - bokeh  # tests
+  - altair  # tests
   - pybaum>=0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy=1.14.1  # dev, tests
+  - mypy=1.19.1  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - annotated-types  # dev, tests
   - iminuit  # dev, tests
   - cma  # dev, tests
   - pygad  # dev, tests
+  - pytorch-cpu  # dev, tests
   - pip:  # dev, tests, docs
       - bayesian-optimization>=2.0.4  # dev, tests
       - DFO-LS>=1.5.3  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido>=1.0  # dev, tests
       - gradient_free_optimizers  # dev, tests
+      - pyswarms  # dev, tests
       - pandas-stubs  # dev, tests
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests

.tools/envs/testenv-nevergrad.yml

@@ -18,29 +18,33 @@ dependencies:
   - pandas  # run, tests
   - plotly>=6.2  # run, tests
   - matplotlib  # tests
+  - bokeh  # tests
+  - altair  # tests
   - pybaum>=0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy=1.14.1  # dev, tests
+  - mypy=1.19.1  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - annotated-types  # dev, tests
   - iminuit  # dev, tests
   - cma  # dev, tests
   - pygad  # dev, tests
+  - pytorch-cpu  # dev, tests
   - pip:  # dev, tests, docs
       - DFO-LS>=1.5.3  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido>=1.0  # dev, tests
       - gradient_free_optimizers  # dev, tests
+      - pyswarms  # dev, tests
       - pandas-stubs  # dev, tests
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests
       - sqlalchemy-stubs  # dev, tests
-      - sphinxcontrib-mermaid  # dev, tests, docs
-      - -e ../../
       - bayesian_optimization==1.4.0
       - nevergrad
+      - sphinxcontrib-mermaid  # dev, tests, docs
+      - -e ../../

.tools/envs/testenv-numpy.yml

@@ -18,24 +18,28 @@ dependencies:
   - joblib  # run, tests
   - plotly>=6.2  # run, tests
   - matplotlib  # tests
+  - bokeh  # tests
+  - altair  # tests
   - pybaum>=0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy=1.14.1  # dev, tests
+  - mypy=1.19.1  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - annotated-types  # dev, tests
   - iminuit  # dev, tests
   - cma  # dev, tests
   - pygad  # dev, tests
+  - pytorch-cpu  # dev, tests
   - pip:  # dev, tests, docs
       - bayesian-optimization>=2.0.4  # dev, tests
       - DFO-LS>=1.5.3  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido>=1.0  # dev, tests
       - gradient_free_optimizers  # dev, tests
+      - pyswarms  # dev, tests
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests

.tools/envs/testenv-others.yml

@@ -18,24 +18,28 @@ dependencies:
   - pandas  # run, tests
   - plotly>=6.2  # run, tests
   - matplotlib  # tests
+  - bokeh  # tests
+  - altair  # tests
   - pybaum>=0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy=1.14.1  # dev, tests
+  - mypy=1.19.1  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - annotated-types  # dev, tests
   - iminuit  # dev, tests
   - cma  # dev, tests
   - pygad  # dev, tests
+  - pytorch-cpu  # dev, tests
   - pip:  # dev, tests, docs
       - bayesian-optimization>=2.0.4  # dev, tests
       - DFO-LS>=1.5.3  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido>=1.0  # dev, tests
       - gradient_free_optimizers  # dev, tests
+      - pyswarms  # dev, tests
       - pandas-stubs  # dev, tests
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests

.tools/envs/testenv-pandas.yml

@@ -18,24 +18,28 @@ dependencies:
   - joblib  # run, tests
   - plotly>=6.2  # run, tests
   - matplotlib  # tests
+  - bokeh  # tests
+  - altair  # tests
   - pybaum>=0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy=1.14.1  # dev, tests
+  - mypy=1.19.1  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - annotated-types  # dev, tests
   - iminuit  # dev, tests
   - cma  # dev, tests
   - pygad  # dev, tests
+  - pytorch-cpu  # dev, tests
   - pip:  # dev, tests, docs
       - bayesian-optimization>=2.0.4  # dev, tests
       - DFO-LS>=1.5.3  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
       - kaleido>=1.0  # dev, tests
       - gradient_free_optimizers  # dev, tests
+      - pyswarms  # dev, tests
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests

.tools/envs/testenv-plotly.yml

@@ -18,28 +18,33 @@ dependencies:
   - numpy >= 2  # run, tests
   - pandas  # run, tests
   - matplotlib  # tests
+  - bokeh  # tests
+  - altair  # tests
   - pybaum>=0.1.2  # run, tests
   - scipy>=1.2.1  # run, tests
   - sqlalchemy  # run, tests
   - seaborn  # dev, tests
-  - mypy=1.14.1  # dev, tests
+  - mypy=1.19.1  # dev, tests
   - pyyaml  # dev, tests
   - jinja2  # dev, tests
   - annotated-types  # dev, tests
   - iminuit  # dev, tests
   - cma  # dev, tests
   - pygad  # dev, tests
+  - pytorch-cpu  # dev, tests
   - pip:  # dev, tests, docs
       - bayesian-optimization>=2.0.4  # dev, tests
       - DFO-LS>=1.5.3  # dev, tests
       - Py-BOBYQA  # dev, tests
       - fides==0.7.4  # dev, tests
+      - bayes_optim  # dev, tests
       - gradient_free_optimizers  # dev, tests
+      - pyswarms  # dev, tests
       - pandas-stubs  # dev, tests
       - types-cffi  # dev, tests
       - types-openpyxl  # dev, tests
       - types-jinja2  # dev, tests
       - sqlalchemy-stubs  # dev, tests
-      - sphinxcontrib-mermaid  # dev, tests, docs
-      - -e ../../
       - kaleido<0.3
+      - sphinxcontrib-mermaid  # dev, tests, docs
+      - -e ../../

docs/rtd_environment.yml

@@ -13,12 +13,17 @@ dependencies:
   - sphinxcontrib-bibtex
   - sphinx-copybutton
   - sphinx-design
+  - sphinx-llm
+  - sphinx-llms-txt
   - ipython
   - ipython_genutils
   - myst-nb
   - furo
   - pybaum
   - matplotlib
+  - bokeh
+  - altair
+  - anywidget
   - seaborn
   - numpy
   - pandas