Merge pull request #1291 from glotzerlab/nanobind-environment

Port environment to nanobind

.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

.pre-commit-config.yaml

@@ -84,7 +84,6 @@ repos:
           ^extern/|
           ^freud/density/|
           ^freud/diffraction/|
-          ^freud/environment/|
           ^freud/order/
         )
       args:

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
@@ -152,15 +152,24 @@ 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
@@ -213,6 +222,7 @@ set(python_files
     box.py
     cluster.py
     data.py
+    environment.py
     diffraction.py
     errors.py
     locality.py
@@ -223,7 +233,7 @@ set(python_files
     interface.py
     plot.py
     util.py)
-# cluster.py density.py diffraction.py environment.py interface.py msd.py)
+# density.py)
 
 copy_files_to_build("${python_files}" "freud" "*.py")
 
@@ -232,9 +242,9 @@ if(SKBUILD)
   install(FILES ${python_files} DESTINATION freud)
   install(TARGETS _box DESTINATION freud)
   install(TARGETS _cluster DESTINATION freud)
+  # install(TARGETS _density DESTINATION freud)
+  install(TARGETS _environment DESTINATION freud)
   install(TARGETS _diffraction DESTINATION freud)
-  # install(TARGETS _density DESTINATION freud) install(TARGETS _environment
-  # DESTINATION freud)
   install(TARGETS _locality DESTINATION freud)
   install(TARGETS _order DESTINATION freud)
   install(TARGETS _parallel DESTINATION freud)

freud/__init__.py

@@ -1,11 +1,13 @@
 # Copyright (c) 2010-2024 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,
     diffraction,
+    environment,
     interface,
     locality,
     msd,
@@ -30,7 +32,7 @@
     "data",
     # "density",
     "diffraction",
-    # "environment",
+    "environment",
     "interface",
     "locality",
     "msd",

freud/box.py

@@ -63,7 +63,9 @@ def __init__(self, Lx, Ly, Lz=0, xy=0, xz=0, yz=0, is2D=None):
         elif not (Lx and Ly and Lz):
             msg = "Lx, Ly, and Lz must be nonzero for 3D boxes."
             raise ValueError(msg)
-        self._cpp_obj = freud._box.Box(Lx, Ly, Lz, xy, xz, yz, is2D)
+        self._cpp_obj = freud._box.Box(
+            *[float(x) for x in [Lx, Ly, Lz, xy, xz, yz]], bool(is2D)
+        )
 
     @property
     def L(self):