Merge branch 'main' into boilerplate

Author: janosg

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,3 @@
+# Code of Conduct
+
+- [NumFOCUS Code of Conduct](https://numfocus.org/code-of-conduct)

.github/workflows/main.yml

@@ -127,6 +127,54 @@ jobs:
         run: |
           micromamba activate optimagic
           pytest -m "not slow and not jax"
+  run-tests-with-old-plotly:
+    name: Run tests for ubuntu-latest on 3.10 with plotly < 6 and kaleido < 0.3
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - name: create build environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ./.tools/envs/testenv-plotly.yml
+          cache-environment: true
+          create-args: |
+            python=3.10
+      - name: run pytest
+        shell: bash -l {0}
+        run: |
+          micromamba activate optimagic
+          pytest -m "not slow and not jax"
+  run-tests-nevergrad:
+    # This job is for running test related to nevergrad with pinned version of
+    # bayesian_optimization == 1.4.0
+    name: Run tests for ubuntu-latest on ${{ matrix.python-version }} bayes_opt==1.4.0
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+        python-version:
+          - '3.10'
+          - '3.11'
+          - '3.12'
+          - '3.13'
+    steps:
+      - uses: actions/checkout@v4
+      - name: create build environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ./.tools/envs/testenv-nevergrad.yml
+          cache-environment: true
+          create-args: |
+            python=${{ matrix.python-version }}
+      - name: run pytest
+        shell: bash -l {0}
+        run: |
+          micromamba activate optimagic
+          pytest tests/optimagic/optimizers/test_nevergrad.py
   code-in-docs:
     name: Run code snippets in documentation
     runs-on: ubuntu-latest

.gitignore

@@ -1,3 +1,6 @@
+# AI
+CLAUDE.md
+
 # Byte-compiled / optimized / DLL files
 *.py[cod]
 *$py.class

.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
@@ -18,20 +18,29 @@ repos:
         language: python
         always_run: true
         require_serial: true
+  - repo: local
+    hooks:
+      - id: check-mypy-versions
+        name: verify that pre-commits and dev env use the same mypy version
+        entry: python .tools/check_mypy_versions.py
+        language: python
+        always_run: true
+        require_serial: true
+        additional_dependencies:
+          - pyyaml
   - repo: local
     hooks:
       - id: update-algo-selection-code
         name: update algo selection code
-        entry: bash .tools/create_and_format_algo_selection_code.sh
+        entry: python .tools/update_algo_selection_hook.py
         language: python
-        files: (src/optimagic/optimizers/.|src/optimagic/algorithms.py|.tools/.)
-        always_run: false
+        files: ^(src/optimagic/optimizers/|src/optimagic/algorithms\.py|\.tools/)
         require_serial: true
         additional_dependencies:
           - hatchling
           - ruff
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args:
@@ -63,12 +72,12 @@ repos:
         exclude: docs/
       - id: check-ast
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.35.1
+    rev: v1.38.0
     hooks:
       - id: yamllint
         exclude: tests/optimagic/optimizers/_pounders/fixtures
   - repo: https://github.com/PyCQA/docformatter
-    rev: eb1df34
+    rev: v1.7.7
     hooks:
       - id: docformatter
         args:
@@ -80,7 +89,7 @@ repos:
           - --blank
         exclude: src/optimagic/optimization/algo_options.py
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.2
+    rev: v0.14.14
     hooks:
       # Run the linter.
       - id: ruff
@@ -97,7 +106,7 @@ repos:
           - pyi
           - jupyter
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.18
+    rev: 1.0.0
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -109,7 +118,7 @@ repos:
           - '88'
         files: (README\.md)
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.18
+    rev: 1.0.0
     hooks:
       - id: mdformat
         additional_dependencies:
@@ -121,7 +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: 0.8.0
+    rev: 0.9.0
     hooks:
       - id: nbstripout
         exclude: |
@@ -132,21 +141,25 @@ repos:
         args:
           - --drop-empty-cells
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.19.1
     hooks:
       - id: mypy
         files: src|tests
         additional_dependencies:
-          - numpy
+          - numpy >= 2
           - packaging
           - pandas-stubs
           - sqlalchemy-stubs
           - types-cffi
           - types-openpyxl
           - types-jinja2
-        args:
-          - --config=pyproject.toml
+          - 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/check_mypy_versions.py

@@ -0,0 +1,44 @@
+import re
+import sys
+from pathlib import Path
+
+import yaml
+
+
+def _get_mypy_version_from_precommit_config() -> str:
+    config = yaml.safe_load(Path(".pre-commit-config.yaml").read_text())
+    mypy_config = [
+        hook
+        for hook in config["repos"]
+        if hook["repo"] == "https://github.com/pre-commit/mirrors-mypy"
+    ][0]
+    match = re.search(r"v([\d.]+)", mypy_config["rev"])  # Remove "v" prefix
+    if match:
+        return match.group(1)
+    raise ValueError("Mypy version not found in pre-commit config.")
+
+
+def _get_mypy_version_from_conda_environment() -> str:
+    config = yaml.safe_load(Path("environment.yml").read_text())
+    mypy_line = [dep for dep in config["dependencies"] if "mypy" in dep][0]
+    match = re.search(r"mypy=([\d.]+)", mypy_line)
+    if match:
+        return match.group(1)
+    raise ValueError("Mypy version not found in conda environment.")
+
+
+def main() -> None:
+    v_precommit = _get_mypy_version_from_precommit_config()
+    v_conda = _get_mypy_version_from_conda_environment()
+    if v_precommit != v_conda:
+        print(
+            f"Error: Mypy versions do not match:\n"
+            f"  Pre-commit config: {v_precommit}\n"
+            f"  Conda environment: {v_conda}\n"
+        )
+        sys.exit(1)
+    sys.exit(0)
+
+
+if __name__ == "__main__":
+    main()

.tools/create_and_format_algo_selection_code.sh

@@ -4,10 +4,10 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - petsc4py
+  - petsc4py<=3.23.4
   - jax
   - cyipopt>=1.4.0  # dev, tests
-  - pygmo>=2.19.0  # dev, tests
+  - pygmo>=2.19.0  # dev, tests, docs
   - nlopt  # dev, tests, docs
   - pip  # dev, tests, docs
   - pytest  # dev, tests
@@ -18,20 +18,30 @@ dependencies:
   - joblib  # run, tests
   - numpy >= 2  # run, tests
   - pandas  # run, tests
-  - plotly  # 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=1.13  # 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  # 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-linux.yml

@@ -0,0 +1,50 @@
+---
+name: optimagic
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - cyipopt>=1.4.0  # dev, tests
+  - pygmo>=2.19.0  # dev, tests, docs
+  - nlopt  # dev, tests, docs
+  - pip  # dev, tests, docs
+  - pytest  # dev, tests
+  - pytest-cov  # tests
+  - pytest-xdist  # dev, tests
+  - statsmodels  # dev, tests
+  - cloudpickle  # run, tests
+  - joblib  # run, tests
+  - numpy >= 2  # run, tests
+  - 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=1.19.1  # 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
+      - bayesian_optimization==1.4.0
+      - nevergrad
+      - -e ../../

.tools/envs/testenv-nevergrad.yml

@@ -7,7 +7,7 @@ dependencies:
   - pandas>=2
   - numpy<2
   - cyipopt>=1.4.0  # dev, tests
-  - pygmo>=2.19.0  # dev, tests
+  - pygmo>=2.19.0  # dev, tests, docs
   - nlopt  # dev, tests, docs
   - pip  # dev, tests, docs
   - pytest  # dev, tests
@@ -16,20 +16,30 @@ dependencies:
   - statsmodels  # dev, tests
   - cloudpickle  # run, tests
   - joblib  # run, tests
-  - plotly  # 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=1.13  # 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  # 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