Merge pull request #1294 from glotzerlab/nanobind-diffraction

Refactor Diffraction Module for Nanobind Integration
glotzerlab · Nov 12, 2024 · 6565306 · 6565306
2 parents 2157905 + 69d1354
commit 6565306
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Showing 15 changed files with 281 additions and 225 deletions.
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -125,7 +125,7 @@ jobs:
             gsd==${{ matrix.python.oldest_gsd }}
             matplotlib==${{ matrix.python.oldest_matplotlib }}
           # Test only the currently ported modules
-          CIBW_TEST_COMMAND: "cd {package}/tests && pytest test_box_box.py test_parallel.py test_locality_*.py test_data.py test_pmft.py test_util.py test_msd_msd.py test_interface.py test_order_*.py test_cluster.py -v --log-level=DEBUG"
+          CIBW_TEST_COMMAND: "cd {package}/tests && pytest test_box_box.py test_parallel.py test_locality_*.py test_data.py test_pmft.py test_util.py test_msd_msd.py test_interface.py test_order_*.py test_cluster.py test_diffraction_*.py -v --log-level=DEBUG"
 
           # CIBW_TEST_COMMAND: "cd {package}/tests && pytest . -v --log-level=DEBUG"
 

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_diffraction*.py -v
           pytest tests/test_interface.py -v
           pytest tests/test_msd_msd.py -v
           pytest tests/test_cluster.py -v

diff --git a/.ruff.toml b/.ruff.toml
@@ -1,5 +1,7 @@
 target-version = "py39"
 
+extend-exclude = [ 'extern', 'doc/source/gettingstarted/examples' ]
+
 lint.extend-select = [
     "A",
     "B",

diff --git a/freud/CMakeLists.txt b/freud/CMakeLists.txt
@@ -35,13 +35,12 @@ add_library(
   # density/RDF.cc
   # density/SphereVoxelization.h
   # density/SphereVoxelization.cc
-  # diffraction
-  # diffraction/StaticStructureFactor.h
-  # diffraction/StaticStructureFactor.cc
-  # diffraction/StaticStructureFactorDebye.h
-  # diffraction/StaticStructureFactorDebye.cc
-  # diffraction/StaticStructureFactorDirect.h
-  # diffraction/StaticStructureFactorDirect.cc
+  diffraction/StaticStructureFactor.h
+  diffraction/StaticStructureFactor.cc
+  diffraction/StaticStructureFactorDebye.h
+  diffraction/StaticStructureFactorDebye.cc
+  diffraction/StaticStructureFactorDirect.h
+  diffraction/StaticStructureFactorDirect.cc
   # environment
   # environment/AngularSeparation.h
   # environment/AngularSeparation.cc
@@ -144,9 +143,14 @@ target_set_install_rpath(_cluster)
 # target_link_libraries(_density PUBLIC freud TBB::tbb)
 # target_set_install_rpath(_density)
 
-# diffraction nanobind_add_module(_diffraction diffraction/...)
-# target_link_libraries(_diffraction PUBLIC freud TBB::tbb)
-# target_set_install_rpath(_diffraction)
+nanobind_add_module(
+  _diffraction
+  diffraction/module-diffraction.cc
+  diffraction/export-StaticStructureFactor.cc
+  diffraction/export-StaticStructureFactorDebye.cc
+  diffraction/export-StaticStructureFactorDirect.cc)
+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)
@@ -170,9 +174,6 @@ nanobind_add_module(
 target_link_libraries(_locality PUBLIC freud TBB::tbb)
 target_set_install_rpath(_locality)
 
-# order nanobind_add_module(_order order/...) target_link_libraries(_order
-# PUBLIC freud TBB::tbb) target_set_install_rpath(_order)
-
 # order
 nanobind_add_module(
   _order
@@ -212,6 +213,7 @@ set(python_files
     box.py
     cluster.py
     data.py
+    diffraction.py
     errors.py
     locality.py
     msd.py
@@ -230,8 +232,9 @@ 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 _diffraction
-  # 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)

diff --git a/freud/__init__.py b/freud/__init__.py
@@ -1,8 +1,18 @@
 # 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.
 
-# cluster,; density,; diffraction,; environment,; interface,; msd,;
-from . import box, cluster, data, interface, locality, msd, order, parallel, pmft
+from . import (
+    box,
+    cluster,
+    data,
+    diffraction,
+    interface,
+    locality,
+    msd,
+    order,
+    parallel,
+    pmft,
+)
 from .box import Box
 from .locality import AABBQuery, LinkCell, NeighborList
 from .parallel import NumThreads, get_num_threads, set_num_threads
@@ -19,7 +29,7 @@
     "cluster",
     "data",
     # "density",
-    # "diffraction",
+    "diffraction",
     # "environment",
     "interface",
     "locality",