[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -31,18 +31,18 @@ repos:
         exclude: '(\.Rd|python/doc/source/reference/.*|test-doctest-.*)'
 
   - repo: https://github.com/tox-dev/tox-ini-fmt
-    rev: 1.7.2
+    rev: 1.10.0
     hooks:
       - id: tox-ini-fmt
 
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.25.2
+    rev: v2.30.3
     hooks:
       - id: pyproject-fmt
         additional_dependencies: ["tox>=4.12.1"]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.21
+    rev: v0.17.2
     hooks:
       # Run the formatter.
       - id: ruff-format
@@ -54,7 +54,7 @@ repos:
         require_serial: true
 
   - repo: https://github.com/astral-sh/ty-pre-commit
-    rev: v0.0.89
+    rev: v0.0.92
     hooks:
       - id: ty
         args: [--project=python, --isolated]
@@ -65,7 +65,7 @@ repos:
       - id: sphinx-lint
 
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9030
+    rev: v0.4.3.9032
     hooks:
       - id: parsable-R
       - id: no-browser-statement

c/update_readme.py

@@ -1,5 +1,5 @@
-from pathlib import Path
 import subprocess
+from pathlib import Path
 
 
 def replace_between_markers(

python/benchmarks/bench.py

@@ -1,14 +1,16 @@
+import importlib
 import pathlib
-import numpy as np
-import pandas as pd
+import shutil
+import subprocess
+import timeit
+
+import cpuinfo
 import matplotlib.pyplot as plt
 import matplotlib.ticker as mticker
+import numpy as np
+import pandas as pd
+
 import moocore
-import timeit
-import cpuinfo
-import shutil
-import subprocess
-import importlib
 
 timeit_template_return_1_value = """
 def inner(_it, _timer{init}):

python/benchmarks/bench_epsilon.py

@@ -5,15 +5,15 @@
 
 """
 
-from bench import Bench, read_data, check_float_values
-
-import numpy as np
-import moocore
 import pathlib
-import matplotlib.pyplot as plt
 
+import matplotlib.pyplot as plt
+import numpy as np
+from bench import Bench, check_float_values, read_data
 from jmetal.core.quality_indicator import EpsilonIndicator as jmetal_EPS
 
+import moocore
+
 path_to_data = "../../testsuite/data/"
 if not pathlib.Path(path_to_data).expanduser().exists():
     path_to_data = (

python/benchmarks/bench_hv.py

@@ -5,23 +5,19 @@
 
 """
 
+import pathlib
+
+import matplotlib.pyplot as plt
+import numpy as np
+import torch
 from bench import (
     Bench,
-    read_datasets_and_filter_dominated,
-    get_geomrange,
     check_float_values,
+    get_geomrange,
+    read_datasets_and_filter_dominated,
 )
-
-import numpy as np
-import moocore
-import pathlib
-import matplotlib.pyplot as plt
-
 from botorch.utils.multi_objective.hypervolume import Hypervolume as botorch_HV
-import torch
-from nevergrad.optimization.multiobjective import HypervolumeIndicator as ng_HV
 from fast_pareto import hypervolume as fp_hv
-from optuna._hypervolume import compute_hypervolume as optuna_hv
 
 ## paretobench is 2x slower than botorch, so too slow for benchmarking.
 ## https://github.com/electronsandstuff/ParetoBench/issues/57
@@ -31,8 +27,11 @@
 ## https://github.com/secondmind-labs/trieste/issues/917
 # from trieste.acquisition.multi_objective import Pareto as trieste_Pareto
 # import tensorflow as tf
-
 from moarchiving import get_mo_archive as moarch_get_mo_archive
+from nevergrad.optimization.multiobjective import HypervolumeIndicator as ng_HV
+from optuna._hypervolume import compute_hypervolume as optuna_hv
+
+import moocore
 
 # FIXME: How to test both float and Fractions?
 moarch_get_mo_archive.hypervolume_computation_float_type = float

python/benchmarks/bench_hvapprox.py

@@ -6,19 +6,20 @@
 
 """
 
-import numpy as np
-import moocore
 import pathlib
-import matplotlib.pyplot as plt
 import timeit  # time_hv_exact
 
+import matplotlib.pyplot as plt
+import numpy as np
 from bench import (
     Bench,
-    read_datasets_and_filter_dominated,
     get_range,
+    read_datasets_and_filter_dominated,
     timeit_template_return_1_value,  # time_hv_exact
 )
 
+import moocore
+
 # See https://github.com/multi-objective/testsuite/tree/main/data
 path_to_data = "../../testsuite/data/"
 assert pathlib.Path(path_to_data).expanduser().exists()

python/benchmarks/bench_igdplus.py

@@ -5,22 +5,21 @@
 
 """
 
+import matplotlib.pyplot as plt
+import numpy as np
 from bench import (
     Bench,
     check_float_values,
     get_geomrange,
     read_datasets_and_filter_dominated,
 )
-
-import numpy as np
-import moocore
-import matplotlib.pyplot as plt
-
 from desdeo.tools.indicators_unary import igd_plus_indicator as desdeo_igd_plus
 from jmetal.core.quality_indicator import (
     InvertedGenerationalDistancePlus as jmetal_IGDplus,
 )
 
+import moocore
+
 files = {
     "ran.1000pts.3d": "ran.1000pts.3d.10",
 }

python/benchmarks/bench_ndom.py

@@ -6,28 +6,27 @@
 """
 
 import gc
-import numpy as np
-import moocore
-import matplotlib.pyplot as plt
-
-from bench import Bench, get_geomrange, check_float_vector
 
+import matplotlib.pyplot as plt
+import numpy as np
 import torch
+from bench import Bench, check_float_vector, get_geomrange
 from botorch.utils.multi_objective.pareto import (
     is_non_dominated as botorch_is_nondominated,
 )
-
 from desdeo.tools.non_dominated_sorting import (
     non_dominated as desdeo_is_nondominated,
 )
+from fast_pareto import is_pareto_front as fast_pareto_is_pf
+from optuna.study._multi_objective import _is_pareto_front as optuna_is_pf
 
 ## paretobench is always slower than botorch, too slower for benchmarking.
 # import paretobench
 from paretoset import paretoset
-from fast_pareto import is_pareto_front as fast_pareto_is_pf
-from optuna.study._multi_objective import _is_pareto_front as optuna_is_pf
 from patatune.util import get_dominated as patatune_get_dominated
 
+import moocore
+
 # See https://github.com/multi-objective/testsuite/tree/main/data
 files = {
     # range are the (start, stop, num) parameters for np.geomspace()

python/benchmarks/bench_ndsort.py

@@ -5,19 +5,19 @@
 
 """
 
-from bench import Bench, get_geomrange, check_array_equal
-
-import numpy as np
 import matplotlib.pyplot as plt
-import moocore
-
-from pymoo.util.nds.non_dominated_sorting import (
-    NonDominatedSorting as pymoo_NDS,
-)
+import numpy as np
+from bench import Bench, check_array_equal, get_geomrange
 from desdeo.tools.non_dominated_sorting import (
     fast_non_dominated_sort as desdeo_nds,
 )
 from paretoset import paretorank as paretoset_paretorank
+from pymoo.util.nds.non_dominated_sorting import (
+    NonDominatedSorting as pymoo_NDS,
+)
+
+import moocore
+
 ## It cannot be installed: https://github.com/esa/pygmo2/issues/152
 # from pygmo import pareto_dominance as pg_pareto_dominance
 

python/conftest.py

@@ -1,5 +1,6 @@
 # ruff: noqa: D100, D103
 import pytest
+
 import moocore
 
 

python/doc/conftest.py

@@ -1,5 +1,6 @@
 # ruff: noqa: D100, D103
 import pytest
+
 import moocore
 
 

python/doc/source/conf.py

@@ -8,11 +8,11 @@
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-from datetime import date
-import sphinx
-
 import os
 import sys
+from datetime import date
+
+import sphinx
 
 # Building the docs requires installing the package.
 import moocore

python/doc/source/my_unsrt_style.py

@@ -1,7 +1,7 @@
 # ruff: noqa: D100, D101, D102
-from pybtex.style.formatting.unsrt import Style as UnsrtStyle
-from pybtex.style.template import sentence, href, join, optional, field
 from pybtex.plugin import register_plugin
+from pybtex.style.formatting.unsrt import Style as UnsrtStyle
+from pybtex.style.template import field, href, join, optional, sentence
 
 
 class MyUnsrtStyle(UnsrtStyle):

python/doc/source/my_unused_images.py

@@ -1,5 +1,6 @@
 # ruff: noqa: D100
 from pathlib import Path
+
 from docutils import nodes
 from sphinx.util import logging
 

python/doc/source/super_with_brackets.py

@@ -1,10 +1,11 @@
 # ruff: noqa: D100, D101
 from dataclasses import dataclass, field
-from sphinxcontrib.bibtex.style.referencing import BracketStyle, PersonStyle
-from sphinxcontrib.bibtex.style.referencing.super_ import SuperReferenceStyle
+
 from sphinxcontrib.bibtex.plugin import (
     register_plugin as sphinxcontrib_register_plugin,
 )
+from sphinxcontrib.bibtex.style.referencing import BracketStyle, PersonStyle
+from sphinxcontrib.bibtex.style.referencing.super_ import SuperReferenceStyle
 
 
 @dataclass

python/examples/_utils.py

@@ -1,11 +1,12 @@
-import numpy as np
-import moocore
 import matplotlib.pyplot as plt
-from matplotlib.patches import Arc
-from matplotlib.colors import to_hex
+import numpy as np
 import plotly.graph_objects as go
+from matplotlib.colors import to_hex
+from matplotlib.patches import Arc
 from plotly.subplots import make_subplots
 
+import moocore
+
 
 def plot_3d(what, x, title, plotly=False, rank=False, show_index=False):
     """Scatter plot of 3D points."""

python/examples/plot_eaf.py

@@ -13,6 +13,7 @@
 
 import numpy as np
 import pandas as pd
+
 import moocore
 
 A = moocore.get_dataset("ALG_1_dat.xz")

python/examples/plot_generate.py

@@ -9,12 +9,12 @@
 """
 
 # sphinx_gallery_multi_image = "single"
-import moocore
-import numpy as np
 import matplotlib.pyplot as plt
-
+import numpy as np
 from _utils import plotly_3d, plotly_3d_side_by_side
 
+import moocore
+
 
 def generate_ndset_plotly_3d(n, method, seed):
     """Generate points with moocore.generate_ndset() and plot them with plotly_3d()."""

python/examples/plot_generate_sequence.py

@@ -8,11 +8,11 @@
 """
 
 # sphinx_gallery_multi_image = "single"
-import moocore
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+from _utils import plot_sequence_2d, plotly_3d, plotly_3d_side_by_side
 
-from _utils import plotly_3d, plotly_3d_side_by_side, plot_sequence_2d
+import moocore
 
 
 def plotly_generate_sequence_3d(what, n, method, seed, show_index=False):

python/examples/plot_hv_approx.py

@@ -17,10 +17,11 @@
 """
 
 # sphinx_gallery_multi_image = "single"
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import matplotlib.pyplot as plt
 import seaborn as sns
+
 import moocore
 
 # %%

python/examples/plot_metrics.py

@@ -7,6 +7,7 @@
 """
 
 import numpy as np
+
 import moocore
 
 # %%
@@ -80,8 +81,8 @@
 # Assuming minimization of both objectives, A is better than B in terms of Pareto optimality.
 #
 
-import pandas as pd
 import matplotlib.pyplot as plt
+import pandas as pd
 import seaborn as sns
 
 sns.set_theme()