Merge branch 'nanobind' into nanobind_density_changes

glotzerlab · Feb 6, 2025 · c5897c3 · c5897c3
2 parents e780ab1 + 299af7c
commit c5897c3
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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/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -65,6 +65,7 @@ jobs:
           pytest tests/test_data.py -v
           pytest tests/test_pmft.py -v
           pytest tests/test_util.py -v
+          pytest tests/test_environment*.py -v
           pytest tests/test_diffraction*.py -v
           pytest tests/test_interface.py -v
           pytest tests/test_msd_msd.py -v

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++]
@@ -82,10 +82,7 @@ repos:
       exclude: |
         (?x)^(
           ^extern/|
-          ^freud/density/|
-          ^freud/diffraction/|
-          ^freud/environment/|
-          ^freud/order/
+          ^freud/density/
         )
       args:
       - --warnings-as-errors=*
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -12,3 +12,5 @@ python:
 submodules:
     include: all
     recursive: true
+sphinx:
+  configuration: doc/source/conf.py
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/CMakeLists.txt b/freud/CMakeLists.txt
@@ -42,17 +42,17 @@ add_library(
   diffraction/StaticStructureFactorDirect.h
   diffraction/StaticStructureFactorDirect.cc
   # environment
-  # environment/AngularSeparation.h
-  # environment/AngularSeparation.cc
-  # environment/BondOrder.h
-  # environment/BondOrder.cc
-  # environment/LocalBondProjection.h
-  # environment/LocalBondProjection.cc
-  # environment/LocalDescriptors.h
-  # environment/LocalDescriptors.cc
-  # environment/MatchEnv.h
-  # environment/MatchEnv.cc
-  # environment/Registration.h
+  environment/AngularSeparation.h
+  environment/AngularSeparation.cc
+  environment/BondOrder.h
+  environment/BondOrder.cc
+  environment/LocalBondProjection.h
+  environment/LocalBondProjection.cc
+  environment/LocalDescriptors.h
+  environment/LocalDescriptors.cc
+  environment/MatchEnv.h
+  environment/MatchEnv.cc
+  environment/Registration.h
   # locality
   locality/AABB.h
   locality/AABBQuery.cc
@@ -148,15 +148,24 @@ nanobind_add_module(
 target_link_libraries(_diffraction PUBLIC freud TBB::tbb)
 target_set_install_rpath(_diffraction)
 
-# environment nanobind_add_module(_environment environment/...)
-# target_link_libraries(_environment PUBLIC freud TBB::tbb)
-# target_set_install_rpath(_environment)
-
 # box
 nanobind_add_module(_box box/module-box.cc box/export-Box.cc box/export-Box.h)
 target_link_libraries(_box PUBLIC TBB::tbb)
 target_set_install_rpath(_box)
 
+# environment
+nanobind_add_module(
+  _environment
+  environment/module-environment.cc
+  environment/export-AngularSeparationNeighbor.cc
+  environment/export-AngularSeparationGlobal.cc
+  environment/export-LocalBondProjection.cc
+  environment/export-LocalDescriptors.cc
+  environment/export-BondOrder.cc
+  environment/export-MatchEnv.cc)
+target_link_libraries(_environment PUBLIC freud TBB::tbb)
+target_set_install_rpath(_environment)
+
 # locality
 nanobind_add_module(
   _locality
@@ -223,6 +232,7 @@ set(python_files
     data.py
     density.py
     diffraction.py
+    environment.py
     errors.py
     locality.py
     msd.py
@@ -232,18 +242,17 @@ set(python_files
     interface.py
     plot.py
     util.py)
-# cluster.py density.py diffraction.py environment.py interface.py msd.py)
 
 copy_files_to_build("${python_files}" "freud" "*.py")
 
 # install
 if(SKBUILD)
   install(FILES ${python_files} DESTINATION freud)
   install(TARGETS _box DESTINATION freud)
-  install(TARGETS _density DESTINATION freud)
   install(TARGETS _cluster DESTINATION freud)
+  install(TARGETS _density DESTINATION freud)
   install(TARGETS _diffraction DESTINATION freud)
-  # install(TARGETS _environment DESTINATION freud)
+  install(TARGETS _environment DESTINATION freud)
   install(TARGETS _locality DESTINATION freud)
   install(TARGETS _order DESTINATION freud)
   install(TARGETS _parallel DESTINATION freud)

diff --git a/freud/__init__.py b/freud/__init__.py
@@ -1,12 +1,14 @@
-# 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,
 from . import (
     box,
     cluster,
     data,
     density,
     diffraction,
+    environment,
     interface,
     locality,
     msd,
@@ -36,8 +38,8 @@
     "data",
     "density",
     "diffraction",
+    "environment",
     "get_num_threads",
-    # "environment",
     "interface",
     "locality",
     "msd",