Merge branch 'master' into cmake-updates

.github/workflows/build_wheels.yml

@@ -29,12 +29,12 @@ jobs:
         pyver: ["3.6", "3.7", "3.8", "3.9", "3.10"]
 
     steps:
-      - uses: actions/checkout@v3.0.0
+      - uses: actions/checkout@v3.0.2
         with:
           submodules: "recursive"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.3.1
+        uses: pypa/cibuildwheel@2.5.0
         env:
           # Build for cpython >= 3.6.
           CIBW_PROJECT_REQUIRES_PYTHON: "==${{ matrix.pyver }}.*"
@@ -69,7 +69,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3.0.0
+      - uses: actions/checkout@v3.0.2
         with:
           submodules: "recursive"
 

ChangeLog.md

@@ -4,6 +4,14 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## vX.Y.Z -- YYYY-MM-DD
+
+### Added
+* `include_input_points` argument to `freud.locality.PeriodicBuffer`.
+
+### Changed
+* `freud.data.UnitCell.generate_system` now generates positions in the same order as the basis positions.
+
 ## v2.9.0 -- 2022-04-19
 
 ### Added

cpp/locality/PeriodicBuffer.cc

@@ -12,7 +12,7 @@
 namespace freud { namespace locality {
 
 void PeriodicBuffer::compute(const freud::locality::NeighborQuery* neighbor_query, const vec3<float>& buff,
-                             const bool use_images)
+                             const bool use_images, const bool include_input_points)
 {
     m_box = neighbor_query->getBox();
     if (buff.x < 0)
@@ -68,7 +68,7 @@ void PeriodicBuffer::compute(const freud::locality::NeighborQuery* neighbor_quer
                 for (int k = use_images ? 0 : -images.z; k <= images.z; k++)
                 {
                     // Skip the origin image
-                    if (i == 0 && j == 0 && k == 0)
+                    if (!include_input_points && i == 0 && j == 0 && k == 0)
                     {
                         continue;
                     }

cpp/locality/PeriodicBuffer.h

@@ -36,7 +36,7 @@ class PeriodicBuffer
 
     //! Compute the periodic buffer
     void compute(const freud::locality::NeighborQuery* neighbor_query, const vec3<float>& buff,
-                 const bool use_images);
+                 const bool use_images, const bool include_input_points);
 
     //! Return the buffer points
     std::vector<vec3<float>> getBufferPoints() const

doc/source/gettingstarted/installation.rst

@@ -85,7 +85,7 @@ CMake Options
 
 The scikit-build tool allows setup.py to accept three different sets of options separated by ``--``, where each set is provided directly to scikit-build, to CMake, or to the code generator of choice, respectively.
 For example, the command ``python setup.py build_ext --inplace -- -DCOVERAGE=ON -G Ninja -- -j 4`` tell scikit-build to perform an in-place build, it tells CMake to turn on the ``COVERAGE`` option and use Ninja for compilation, and it tells Ninja to compile with 4 parallel threads.
-For more information on these options, see the `scikit-build docs <scikit-build.readthedocs.io/>`__.
+For more information on these options, see the `scikit-build docs <https://scikit-build.readthedocs.io/>`__.
 
 In addition to standard CMake flags, the following CMake options are available for **freud**:
 

freud/_locality.pxd

@@ -130,6 +130,7 @@ cdef extern from "PeriodicBuffer.h" namespace "freud::locality":
         void compute(
             const NeighborQuery*,
             const vec3[float],
+            const bool,
             const bool) except +
         vector[vec3[float]] getBufferPoints() const
         vector[uint] getBufferIds() const

freud/box.pyx

@@ -855,8 +855,9 @@ cdef class Box:
     def from_matrix(cls, box_matrix, dimensions=None):
         r"""Initialize a Box instance from a box matrix.
 
-        For more information and the source for this code,
-        see: https://hoomd-blue.readthedocs.io/en/stable/box.html
+        For more information and the source for this code, see:
+        `HOOMD-blue's box documentation \
+        <https://hoomd-blue.readthedocs.io/en/stable/package-hoomd.html#hoomd.Box>`_.
 
         Args:
             box_matrix (array-like):

freud/data.py

@@ -65,6 +65,12 @@ def generate_system(self, num_replicas=1, scale=1, sigma_noise=0, seed=None):
             tuple (:class:`freud.box.Box`, :class:`np.ndarray`):
                 A system-like object (see
                 :class:`~freud.locality.NeighborQuery.from_system`).
+
+        Note:
+            Positions are generated in the order of the instance's
+            ``basis_positions``. The first :math:`N_{replica}`
+            positions come from the first basis position, the next
+            :math:`N_{replica}` the second, etc.
         """
         try:
             nx, ny, nz = num_replicas
@@ -87,10 +93,13 @@ def generate_system(self, num_replicas=1, scale=1, sigma_noise=0, seed=None):
             pbuff = freud.locality.PeriodicBuffer()
             abs_positions = self.box.make_absolute(self.basis_positions)
             pbuff.compute(
-                (self.box, abs_positions), buffer=(nx - 1, ny - 1, nz - 1), images=True
+                (self.box, abs_positions),
+                buffer=(nx - 1, ny - 1, nz - 1),
+                images=True,
+                include_input_points=True,
             )
             box = pbuff.buffer_box * scale
-            positions = np.concatenate((abs_positions, pbuff.buffer_points))
+            positions = pbuff.buffer_points
         else:
             box = self.box * scale
             positions = self.box.make_absolute(self.basis_positions)

freud/locality.pyx

@@ -1083,7 +1083,7 @@ cdef class PeriodicBuffer(_Compute):
     def __dealloc__(self):
         del self.thisptr
 
-    def compute(self, system, buffer, cbool images=False):
+    def compute(self, system, buffer, cbool images=False, include_input_points=False):
         r"""Compute the periodic buffer.
 
         Args:
@@ -1099,6 +1099,9 @@ cdef class PeriodicBuffer(_Compute):
                 each side, meaning that one image doubles the box side lengths,
                 two images triples the box side lengths, and so on.
                 (Default value = :code:`False`).
+            include_input_points (bool, optional):
+                Whether the original points provided by ``system`` are
+                included in the buffer, (Default value = :code:`False`).
         """
         cdef NeighborQuery nq = _make_default_nq(system)
         cdef vec3[float] buffer_vec
@@ -1110,7 +1113,7 @@ cdef class PeriodicBuffer(_Compute):
         else:
             raise ValueError('buffer must be a scalar or have length 3.')
 
-        self.thisptr.compute(nq.get_ptr(), buffer_vec, images)
+        self.thisptr.compute(nq.get_ptr(), buffer_vec, images, include_input_points)
         return self
 
     @_Compute._computed_property

requirements/requirements-precommit.txt

@@ -1 +1 @@
-pre-commit==2.17.0
+pre-commit==2.18.1

requirements/requirements-test.txt

@@ -1,18 +1,18 @@
 ase==3.22.1
-cmake==3.22.3
+cmake==3.22.4
 codecov==2.1.12
 coverage==6.3.2
 cython==0.29.28
 dynasor==1.1.1; platform_system != "Windows"
 garnett==0.7.1
 GitPython==3.1.27
-gsd==2.5.1
+gsd==2.5.2
 matplotlib>=3.0.0
 numpy==1.22.3
 pillow>=8.0.0 --only-binary=pillow
-pytest==7.1.1
+pytest==7.1.2
 pytest-cov==3.0.0
 rowan==1.3.0.post1
-scikit-build==0.13.1
+scikit-build==0.14.1
 scipy==1.8.0
 sympy==1.10.1

tests/test_locality_PeriodicBuffer.py

@@ -1,5 +1,6 @@
 import numpy as np
 import numpy.testing as npt
+import pytest
 
 import freud
 
@@ -204,6 +205,21 @@ def test_triclinic(self):
         assert len(pbuff.buffer_ids) == 3 * N
         npt.assert_array_equal(pbuff.buffer_box.L, box.L * np.array([2, 1, 2]))
 
+    @pytest.mark.parametrize("is2d, points_fac", [(True, 9), (False, 27)])
+    def test_include_input_points(self, is2d, points_fac):
+        L = 10  # Box length
+        N = 50  # Number of points
+
+        box, positions = freud.data.make_random_system(L, N, is2D=is2d)
+        positions.flags["WRITEABLE"] = False
+
+        pbuff = freud.locality.PeriodicBuffer()
+        pbuff.compute(
+            (box, positions), buffer=2, images=True, include_input_points=True
+        )
+
+        assert len(pbuff.buffer_points) == points_fac * N
+
     def test_repr(self):
         pbuff = freud.locality.PeriodicBuffer()
         assert str(pbuff) == str(eval(repr(pbuff)))