Merge pull request #1305 from glotzerlab/nanobind-misc

Bump CI dependencies to the latest versions.
glotzerlab · Feb 5, 2025 · 299af7c · 299af7c
2 parents af99cc9 + 667480a
commit 299af7c
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diff --git a/.github/workflows/environments/py310-conda-lock.yml b/.github/workflows/environments/py310-conda-lock.yml
diff --git a/.github/workflows/environments/py311-conda-lock.yml b/.github/workflows/environments/py311-conda-lock.yml
diff --git a/.github/workflows/environments/py312-conda-lock.yml b/.github/workflows/environments/py312-conda-lock.yml
diff --git a/.github/workflows/environments/py313-conda-lock.yml b/.github/workflows/environments/py313-conda-lock.yml
diff --git a/.github/workflows/environments/py39-conda-lock.yml b/.github/workflows/environments/py39-conda-lock.yml
diff --git a/.github/workflows/environments/requirements-build-sdist.txt b/.github/workflows/environments/requirements-build-sdist.txt
@@ -2,7 +2,7 @@
 #    uv pip compile --python-version 3.13 --python-platform linux requirements-build-sdist.in
 build==1.2.2.post1
     # via -r requirements-build-sdist.in
-packaging==24.1
+packaging==24.2
     # via build
 pyproject-hooks==1.2.0
     # via build
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,7 +6,7 @@ exclude: (?:^extern/)
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.6.0'
+    rev: 'v5.0.0'
     hooks:
       - id: end-of-file-fixer
         exclude: |
@@ -30,7 +30,7 @@ repos:
       - id: debug-statements
       - id: requirements-txt-fixer
   - repo: https://github.com/glotzerlab/fix-license-header
-    rev: v0.4.0
+    rev: v0.4.1
     hooks:
       - id: fix-license-header
         name: Fix License Headers (Python)
@@ -48,13 +48,13 @@ repos:
           - --add=This file is from the freud project, released under the BSD 3-Clause License.
           - --keep-before=#!
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v3.16.0'
+    rev: 'v3.19.1'
     hooks:
       - id: pyupgrade
         args:
           - --py39-plus
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.6.3'
+    rev: 'v0.9.4'
     hooks:
     - id: ruff-format
     - id: ruff
@@ -63,7 +63,7 @@ repos:
     hooks:
       - id: cmake-format
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: 'v18.1.6'
+    rev: 'v19.1.7'
     hooks:
       - id: clang-format
         types_or: [c, c++]
@@ -82,9 +82,7 @@ repos:
       exclude: |
         (?x)^(
           ^extern/|
-          ^freud/density/|
-          ^freud/diffraction/|
-          ^freud/order/
+          ^freud/density/
         )
       args:
       - --warnings-as-errors=*
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 BSD 3-Clause License for freud
 
-Copyright (c) 2010-2024 The Regents of the University of Michigan
+Copyright (c) 2010-2025 The Regents of the University of Michigan
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/benchmarks/benchmark.py b/benchmarks/benchmark.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import cProfile

diff --git a/benchmarks/benchmark_cluster_Cluster.py b/benchmarks/benchmark_cluster_Cluster.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_density_CorrelationFunction.py b/benchmarks/benchmark_density_CorrelationFunction.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_density_GaussianDensity.py b/benchmarks/benchmark_density_GaussianDensity.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_density_LocalDensity.py b/benchmarks/benchmark_density_LocalDensity.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import math

diff --git a/benchmarks/benchmark_density_RDF.py b/benchmarks/benchmark_density_RDF.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_environment_BondOrder.py b/benchmarks/benchmark_environment_BondOrder.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_locality_AABBQuery.py b/benchmarks/benchmark_locality_AABBQuery.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_locality_LinkCell.py b/benchmarks/benchmark_locality_LinkCell.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_locality_PeriodicBuffer.py b/benchmarks/benchmark_locality_PeriodicBuffer.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_msd_MSD.py b/benchmarks/benchmark_msd_MSD.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_Cubatic.py b/benchmarks/benchmark_order_Cubatic.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_Hexatic.py b/benchmarks/benchmark_order_Hexatic.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_Nematic.py b/benchmarks/benchmark_order_Nematic.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_RotationalAutocorrelation.py b/benchmarks/benchmark_order_RotationalAutocorrelation.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_SolidLiquid.py b/benchmarks/benchmark_order_SolidLiquid.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_SteinhardtQl.py b/benchmarks/benchmark_order_SteinhardtQl.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_order_SteinhardtWl.py b/benchmarks/benchmark_order_SteinhardtWl.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_pmft_PMFTR12.py b/benchmarks/benchmark_pmft_PMFTR12.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_pmft_PMFTXY.py b/benchmarks/benchmark_pmft_PMFTXY.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_pmft_PMFTXYT.py b/benchmarks/benchmark_pmft_PMFTXYT.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmark_pmft_PMFTXYZ.py b/benchmarks/benchmark_pmft_PMFTXYZ.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import numpy as np

diff --git a/benchmarks/benchmarker.py b/benchmarks/benchmarker.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 import argparse
@@ -387,8 +387,7 @@ def compare_helper(_this_t, _other_t, _N, _thread):
         "filename",
         default="benchmark.json",
         nargs="?",
-        help="The collection that contains the benchmark data"
-        "default='benchmark.json'.",
+        help="The collection that contains the benchmark datadefault='benchmark.json'.",
     )
     parser_report.set_defaults(func=main_report)
 
@@ -426,8 +425,7 @@ def compare_helper(_this_t, _other_t, _N, _thread):
         "--filename",
         default="benchmark.json",
         nargs="?",
-        help="The collection that contains the benchmark data"
-        "default='benchmark.json'.",
+        help="The collection that contains the benchmark datadefault='benchmark.json'.",
     )
     parser_compare.add_argument(
         "-f",

diff --git a/doc/readthedocs-env.yml b/doc/readthedocs-env.yml
@@ -2,22 +2,21 @@ name: freud-rtd
 channels:
   - conda-forge
 dependencies:
-  - python==3.12
-  - pip==24.0
-  - scikit-build==0.17.6
-  - cmake==3.29.3
-  - cython==3.0.10
-  - tbb==2021.12.0
-  - tbb-devel==2021.12.0
-  - nanobind==2.0.0
-  - numpy==1.26.4
-  - rowan==1.3.0.post1
-  - scipy==1.13.1
-  - sphinx==7.3.7
-  - furo==2024.5.6
-  - nbsphinx==0.9.4
+  - python==3.13
+  - pip==25.0
+  - scikit-build-core==0.10.7
+  - cmake==3.31.5
+  - tbb==2022.0.0
+  - tbb-devel==2022.0.0
+  - nanobind==2.5.0
+  - numpy==2.2.2
+  - rowan==1.3.2
+  - scipy==1.15.1
+  - sphinx==8.1.3
+  - furo==2024.8.6
+  - nbsphinx==0.9.6
   - jupyter_sphinx==0.5.3
-  - sphinxcontrib-bibtex==2.6.2
+  - sphinxcontrib-bibtex==2.6.3
   - sphinx-copybutton==0.5.2
   - pip:
     - sphinxcontrib-googleanalytics==0.4
diff --git a/freud/__init__.py b/freud/__init__.py
@@ -1,4 +1,4 @@
-# Copyright (c) 2010-2024 The Regents of the University of Michigan
+# Copyright (c) 2010-2025 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
 # density,
@@ -26,26 +26,26 @@
 __version__ = "3.1.0"
 
 __all__ = [
+    "AABBQuery",
+    "Box",
+    "LinkCell",
+    "NeighborList",
+    "NumThreads",
     "__version__",
     "box",
     "cluster",
     "data",
     # "density",
     "diffraction",
     "environment",
+    "get_num_threads",
     "interface",
     "locality",
     "msd",
     "order",
     "parallel",
     "pmft",
-    "Box",
-    "AABBQuery",
-    "LinkCell",
-    "NeighborList",
-    "get_num_threads",
     "set_num_threads",
-    "NumThreads",
 ]
 
 __citation__ = """@article{freud2020,

diff --git a/freud/_cluster.pxd b/freud/_cluster.pxd
diff --git a/freud/_diffraction.pxd b/freud/_diffraction.pxd