Update pre-commit hooks

Author: timmens

.envs/update_envs.py

@@ -40,7 +40,9 @@ def main():
     docs_env.append("      - -e ../")  # add local installation
 
     # write environments
-    for name, env in zip(["linux", "others"], [test_env_linux, test_env_others]):
+    for name, env in zip(
+        ["linux", "others"], [test_env_linux, test_env_others], strict=False
+    ):
         Path(f".envs/testenv-{name}.yml").write_text("\n".join(env) + "\n")
 
 

.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: 1.19.0
     hooks:
       - id: yamlfix
   - repo: local
@@ -18,7 +18,7 @@ repos:
         always_run: true
         require_serial: true
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args:
@@ -46,21 +46,12 @@ repos:
           - --branch
           - main
       - id: trailing-whitespace
+        exclude: docs/
       - id: check-ast
-      - id: check-docstring-first
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.30.0
+    rev: v1.37.1
     hooks:
       - id: yamllint
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-        language_version: python3.10
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.13.0
-    hooks:
-      - id: blacken-docs
   - repo: https://github.com/PyCQA/docformatter
     rev: v1.7.7
     hooks:
@@ -72,58 +63,44 @@ repos:
           - --wrap-descriptions
           - '88'
           - --blank
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.261
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.0
     hooks:
+      # Run the linter.
       - id: ruff
-      #   args:
-      #     - --verbose
-  # - repo: https://github.com/kynan/nbstripout
-  #   rev: 0.6.1
-  #   hooks:
-  #     - id: nbstripout
-  #       args:
-  #         - --extra-keys
-  #         - metadata.kernelspec metadata.language_info.version metadata.vscode
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.0
-    hooks:
-      - id: nbqa-black
-      - id: nbqa-ruff
+        types_or:
+          - python
+          - pyi
+          - jupyter
+        args:
+          - --fix
+      # Run the formatter.
+      - id: ruff-format
+        types_or:
+          - python
+          - pyi
+          - jupyter
   - repo: https://github.com/executablebooks/mdformat
     rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:
           - mdformat-gfm
-          - mdformat-black
+          - mdformat-ruff
         args:
           - --wrap
           - '88'
         files: (README\.md)
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.22
     hooks:
       - id: mdformat
         additional_dependencies:
           - mdformat-myst
-          - mdformat-black
+          - mdformat-ruff
         args:
           - --wrap
           - '88'
         files: (docs/.)
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.2.0
-    hooks:
-      - id: setup-cfg-fmt
-  - repo: https://github.com/mgedmin/check-manifest
-    rev: '0.49'
-    hooks:
-      - id: check-manifest
-        args:
-          - --no-build-isolation
-        additional_dependencies:
-          - setuptools-scm
-          - toml
 ci:
   autoupdate_schedule: monthly

src/tranquilo/acceptance_decision.py

@@ -4,6 +4,7 @@
 also do own function evaluations and decide to accept a different point.
 
 """
+
 from typing import NamedTuple
 
 import numpy as np

src/tranquilo/config.py

@@ -1,5 +1,5 @@
-from pathlib import Path
 import importlib.util
+from pathlib import Path
 
 DOCS_DIR = Path(__file__).parent.parent / "docs"
 

src/tranquilo/estimate_variance.py

@@ -1,12 +1,11 @@
 """Estimate the variance or covariance matrix of the noise in the objective function."""
 
-
 import numpy as np
 
 from tranquilo.get_component import get_component
 from tranquilo.history import History
-from tranquilo.region import Region
 from tranquilo.options import VarianceEstimatorOptions
+from tranquilo.region import Region
 
 
 def get_variance_estimator(fitter, user_options):
@@ -48,14 +47,14 @@ def _estimate_variance_classic(
     if model_type == "scalar":
         samples = list(history.get_fvals(valid_indices).values())
         out = 0.0
-        for weight, sample in zip(weights, samples):
+        for weight, sample in zip(weights, samples, strict=False):
             out += weight * np.var(sample, ddof=1)
     else:
         samples = list(history.get_fvecs(valid_indices).values())
 
         dim = samples[0].shape[1]
         out = np.zeros((dim, dim))
-        for weight, sample in zip(weights, samples):
+        for weight, sample in zip(weights, samples, strict=False):
             out += weight * np.cov(sample, rowvar=False, ddof=1)
 
     return out

src/tranquilo/exploration_sample.py

@@ -1,5 +1,6 @@
 import numpy as np
 from scipy.stats import qmc, triang
+
 from tranquilo.utilities import get_rng
 
 
@@ -46,7 +47,7 @@ def draw_exploration_sample(
     if sampling_distribution not in valid_distributions:
         raise ValueError(f"Unsupported distribution: {sampling_distribution}")
 
-    for name, bound in zip(["lower", "upper"], [lower, upper]):
+    for name, bound in zip(["lower", "upper"], [lower, upper], strict=False):
         if not np.isfinite(bound).all():
             raise ValueError(
                 f"multistart optimization requires finite {name}_bounds or "

src/tranquilo/filter_points.py

@@ -3,8 +3,8 @@
 
 from tranquilo.clustering import cluster
 from tranquilo.get_component import get_component
-from tranquilo.volume import get_radius_after_volume_scaling
 from tranquilo.options import FilterOptions
+from tranquilo.volume import get_radius_after_volume_scaling
 
 
 def get_sample_filter(sample_filter="keep_all", user_options=None):

src/tranquilo/fit_models.py

@@ -6,13 +6,13 @@
 
 from tranquilo.get_component import get_component
 from tranquilo.handle_infinity import get_infinity_handler
-from tranquilo.options import FitterOptions
 from tranquilo.models import (
     VectorModel,
     add_models,
     move_model,
     n_second_order_terms,
 )
+from tranquilo.options import FitterOptions
 
 
 def get_fitter(

src/tranquilo/get_component.py

@@ -3,8 +3,8 @@
 import warnings
 from functools import partial
 
-from tranquilo.utilities import propose_alternatives
 from tranquilo.options import update_option_bundle
+from tranquilo.utilities import propose_alternatives
 
 
 def get_component(
@@ -213,7 +213,7 @@ def _add_redundant_argument_handling(func, signature, warn):
 
     @functools.wraps(func)
     def _wrapper_add_redundant_argument_handling(*args, **kwargs):
-        _kwargs = {**dict(zip(signature[: len(args)], args)), **kwargs}
+        _kwargs = {**dict(zip(signature[: len(args)], args, strict=False)), **kwargs}
 
         _redundant = {k: v for k, v in _kwargs.items() if k not in signature}
         _valid = {k: v for k, v in _kwargs.items() if k in signature}

src/tranquilo/history.py

@@ -104,7 +104,7 @@ def add_evals(self, x_indices, evals):
 
         f_indices = np.arange(self.n_fun, self.n_fun + n_new_points)
 
-        for x_index, f_index in zip(x_indices, f_indices):
+        for x_index, f_index in zip(x_indices, f_indices, strict=False):
             self.index_mapper[x_index].append(f_index)
 
         self.n_fun += n_new_points