Merge pull request #992 from glotzerlab/fix/cpp17-support

Fully Support C++17

.github/workflows/build_wheels.yml

@@ -5,11 +5,14 @@ on:
   # twice when the pull request source branch is in the same repository.
   push:
     branches:
-      - "maint"
       - "master"
+      - "next"
     tags:
       - "v*"
 
+  pull_request:
+      types: [opened, labeled, reopened, synchronize]
+
   # Trigger on request.
   workflow_dispatch:
 
@@ -20,9 +23,10 @@ jobs:
   build_wheels:
     name: Build wheel for ${{ matrix.os }}, Python ${{ matrix.pyver }}
     runs-on: ${{ matrix.os }}
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'build_wheels') || github.event_name != 'pull_request' }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-10.15] #, windows-2019]
+        os: [ubuntu-20.04, macos-12] #, windows-2019]
         pyver: ["3.6", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
@@ -45,6 +49,7 @@ jobs:
           # Configure environment variables.
           CIBW_ENVIRONMENT_LINUX: "CMAKE_PREFIX_PATH=/project/tbb LD_LIBRARY_PATH=/project/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH"
           CIBW_ENVIRONMENT_MACOS: "CMAKE_PREFIX_PATH=/Users/runner/work/freud/freud/tbb LD_LIBRARY_PATH=/Users/runner/work/freud/freud/tbb/lib/intel64/gcc4.8:$LD_LIBRARY_PATH"
+          MACOSX_DEPLOYMENT_TARGET: "10.14"
 
           # Set up TBB.
           CIBW_BEFORE_BUILD_LINUX: "source .github/workflows/cibuildwheel-before-build.sh {package} linux"
@@ -65,6 +70,7 @@ jobs:
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'build_wheels') || github.event_name != 'pull_request' }}
     steps:
       - uses: actions/[email protected]
         with:
@@ -90,6 +96,7 @@ jobs:
     name: Publish [PyPI]
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
+    if: ${{ contains(github.event.pull_request.labels.*.name, 'build_wheels') || github.event_name != 'pull_request' }}
 
     steps:
       - name: Download artifacts

.github/workflows/run_tests.yml

@@ -12,6 +12,7 @@ on:
   push:
     branches:
       - "master"
+      - "next"
 
   # trigger on request
   workflow_dispatch:

ChangeLog.md

@@ -8,6 +8,7 @@ and this project adheres to
 
 ### Added
 * Support for 2D systems in `freud.diffraction.StaticStructureFactorDebye`.
+* Compilation uses the C++17 standard.
 
 ### Fixed
 * `EnvironmentMotifMatch` correctly handles `NeighborList`s with more neighbors per particle than the motif.

cpp/diffraction/StaticStructureFactorDebye.cc

@@ -4,6 +4,7 @@
 #ifdef __clang__
 #include <bessel-library.hpp>
 #endif
+#include <algorithm>
 #include <cmath>
 #include <limits>
 #include <stdexcept>
@@ -86,17 +87,17 @@ void StaticStructureFactorDebye::accumulate(const freud::locality::NeighborQuery
                     // floating point precision errors can cause k to be
                     // slightly negative, and make evaluating the cylindrical
                     // bessel function impossible.
-                    auto abs_k = std::abs(k);
+                    auto nonnegative_k = std::max(float(0.0), k);
 
 #ifdef __clang__
                     // clang doesn't support the special math functions in
                     // C++17, so we use another library instead. The cast is
                     // needed because the other library's implementation is
                     // unique only for complex numbers, otherwise it just tries
                     // to call std::cyl_bessel_j.
-                    S_k += std::real(bessel::cyl_j0(std::complex<double>(abs_k * distance)));
+                    S_k += std::real(bessel::cyl_j0(std::complex<double>(nonnegative_k * distance)));
 #else
-                    S_k += std::cyl_bessel_j(0, abs_k * distance);
+                    S_k += std::cyl_bessel_j(0, nonnegative_k * distance);
 #endif
                 }
                 else

doc/source/reference/credits.rst

@@ -331,6 +331,7 @@ Tommy Waltmann
 * Reformat static structure factor tests.
 * ``DiffractionPattern`` now raises an error when used with non-cubic boxes.
 * Implement ``StaticStructureFactorDebye`` for 2D systems.
+* Add support for compilation with the C++17 standard.
 
 Maya Martirossyan
 

doc/source/reference/freud.bib

@@ -258,3 +258,16 @@ @article{Teich2019
   title = {Identity crisis in alchemical space drives the entropic colloidal glass transition},
   url = {https://doi.org/10.1038/s41467-018-07977-2}
 }
+
+@article{Wieder2012,
+  author = {Thomas Wieder},
+  issn = {1927-5307},
+  issue = {4},
+  journal = {Journal of Mathematical and Computational Sciences},
+  year = {2012},
+  volume = {2},
+  pages = {1086-1090},
+  publisher = {SCIK Publishing Corporation},
+  title = {The Debye Scattering Formula in n Dimensions},
+  url = {https://www.scik.org/index.php/jmcs/article/viewFile/263/120}
+}

extern/bessel-library.hpp

@@ -1,5 +1,5 @@
 /*
- * Taken from https://gtihub.com/jodesarro/bessel-library.git, distributed under
+ * Taken from https://github.com/jodesarro/bessel-library.git, distributed under
  * the MIT license.
  *
  * */

freud/diffraction.pyx

@@ -98,15 +98,14 @@ cdef class StaticStructureFactorDebye(_StaticStructureFactor):
 
     .. note::
 
-        For 2D systems freud uses the bessel function :math:`J_0` instead of the
-        :math:`\text{sinc}` function in the equation above. See this `link
-        <http://www.scik.org/index.php/jmcs/article/viewFile/263/120>`__
-        for more information. For users wishing to calculate the structure
-        factor of quasi 2D systems (i.e. a 2D simulation is used to model a real
-        system such as particles on a 2D interface or similar) the 3D
-        formula should be used. In these cases users should use a 3D box with
-        its longest dimension being in the z-direction and particle positions of
-        the form :math:`(x, y, 0)`.
+        For 2D systems freud uses the Bessel function :math:`J_0` instead of the
+        :math:`\text{sinc}` function in the equation above. See
+        :cite:`Wieder2012` for more information. For users wishing to calculate
+        the structure factor of quasi 2D systems (i.e. a 2D simulation is used
+        to model a real system such as particles on a 2D interface or similar)
+        the 3D formula should be used. In these cases users should use a 3D box
+        with its longest dimension being in the z-direction and particle
+        positions of the form :math:`(x, y, 0)`.
 
     This implementation uses an evenly spaced number of :math:`k` points between
     `k_min`` and ``k_max``. If ``k_min`` is set to 0 (the default behavior), the