Merge pull request #1153 from glotzerlab/release/v2.13.1

Release/v2.13.1

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -26,7 +26,7 @@ body:
     attributes:
       label: freud Version
       description: What version of freud are you using?
-      placeholder: v2.13.0
+      placeholder: v2.13.1
     validations:
       required: true
   - type: input

.pre-commit-config.yaml

@@ -56,7 +56,7 @@ repos:
           - --add=This file is from the freud project, released under the BSD 3-Clause License.
           - --comment-prefix=//
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v3.8.0'
+    rev: 'v3.10.1'
     hooks:
       - id: pyupgrade
         args:
@@ -66,11 +66,11 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: '23.3.0'
+    rev: '23.9.1'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
-    rev: '6.0.0'
+    rev: '6.1.0'
     hooks:
       - id: flake8
         types: ["file"]

ChangeLog.md

@@ -4,7 +4,7 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.13.1 -- YYYY-MM-DD
+## v2.13.1 -- 2023-09-14
 
 ### Added
 * The `gsd.hoomd.Frame` class is supported as a system-like input.

contributors.txt

@@ -1,17 +1,17 @@
   2357	Bradley Dice <bdice@bradleydice.com>
   2148	Vyas Ramasubramani <vramasub@umich.edu>
   1030	Eric Harper <harperic@umich.edu>
-   690	Tommy Waltmann <tomwalt@umich.edu>
+   786	Tommy Waltmann <tomwalt@umich.edu>
    456	Jin Soo Ihm <jinihm@umich.edu>
    318	Joshua A. Anderson <joaander@umich.edu>
    240	Matthew Spellings <mspells@umich.edu>
-   207	dependabot <dependabot[bot]@users.noreply.github.com>
-   168	DomFijan <domagoj.fijan@gmail.com>
+   235	dependabot <dependabot[bot]@users.noreply.github.com>
+   173	DomFijan <domagoj.fijan@gmail.com>
    167	Kelly Wang <kelwang@umich.edu>
    110	Erin Teich <erteich@umich.edu>
     98	Brandon Butler <butlerbr@umich.edu>
     94	Charlotte Shiqi Zhao <zshiqi@umich.edu>
-    72	pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
+    76	pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
     66	M. Eric Irrgang <eirrgang@umich.edu>
     53	Chrisy Du <xiyudu@umich.edu>
     41	Yezhi Jin <jinyezhi@umich.edu>

doc/source/conf.py

@@ -72,8 +72,8 @@
 # built documents.
 #
 # version and release are set the same for this package.
-version = "2.13.0"
-release = "2.13.0"
+version = "2.13.1"
+release = "2.13.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/gettingstarted/installation.rst

@@ -36,7 +36,7 @@ The following are **required** for building and installing **freud** from source
 - `Python <https://www.python.org/>`__ (>=3.7)
 - `NumPy <https://www.numpy.org/>`__ (>=1.14)
 - `Intel Threading Building Blocks <https://www.threadingbuildingblocks.org/>`__ (>=2019.7)
-- `Cython <https://cython.org/>`__ (>=0.29.14)
+- `Cython <https://cython.org/>`__ (>=3.0.2)
 - `scikit-build <https://scikit-build.readthedocs.io/>`__ (>=0.10.0)
 - `CMake <https://cmake.org/>`__ (>=3.13.0)
 

freud/__init__.py

@@ -23,7 +23,7 @@
 # automatic selection runs, the user cannot change it.
 set_num_threads(0)
 
-__version__ = "2.13.0"
+__version__ = "2.13.1"
 
 __all__ = [
     "__version__",

freud/density.pyx

@@ -611,7 +611,7 @@ cdef class RDF(_SpatialHistogram1D):
 
     def __cinit__(self, unsigned int bins, float r_max, float r_min=0,
                   normalize=False):
-        if type(self) == RDF:
+        if type(self) is RDF:
             self.thisptr = self.histptr = new freud._density.RDF(
                 bins, r_max, r_min, normalize)
 
@@ -621,7 +621,7 @@ cdef class RDF(_SpatialHistogram1D):
             self.r_max = r_max
 
     def __dealloc__(self):
-        if type(self) == RDF:
+        if type(self) is RDF:
             del self.thisptr
 
     def compute(self, system, query_points=None, neighbors=None,

freud/diffraction.pyx

@@ -144,14 +144,14 @@ cdef class StaticStructureFactorDebye(_StaticStructureFactor):
     cdef freud._diffraction.StaticStructureFactorDebye * thisptr
 
     def __cinit__(self, unsigned int num_k_values, float k_max, float k_min=0):
-        if type(self) == StaticStructureFactorDebye:
+        if type(self) is StaticStructureFactorDebye:
             self.thisptr = self.ssfptr = new \
                 freud._diffraction.StaticStructureFactorDebye(num_k_values,
                                                               k_max,
                                                               k_min)
 
     def __dealloc__(self):
-        if type(self) == StaticStructureFactorDebye:
+        if type(self) is StaticStructureFactorDebye:
             del self.thisptr
 
     @property
@@ -371,13 +371,13 @@ cdef class StaticStructureFactorDirect(_StaticStructureFactor):
 
     def __cinit__(self, unsigned int bins, float k_max, float k_min=0,
                   unsigned int num_sampled_k_points=0):
-        if type(self) == StaticStructureFactorDirect:
+        if type(self) is StaticStructureFactorDirect:
             self.thisptr = self.ssfptr = \
                 new freud._diffraction.StaticStructureFactorDirect(
                     bins, k_max, k_min, num_sampled_k_points)
 
     def __dealloc__(self):
-        if type(self) == StaticStructureFactorDirect:
+        if type(self) is StaticStructureFactorDirect:
             del self.thisptr
 
     @property

freud/locality.pyx

@@ -43,7 +43,7 @@ cdef class _QueryArgs:
     def __cinit__(self, mode=None, r_min=None, r_max=None, r_guess=None,
                   num_neighbors=None, exclude_ii=None,
                   scale=None, **kwargs):
-        if type(self) == _QueryArgs:
+        if type(self) is _QueryArgs:
             self.thisptr = new freud._locality.QueryArgs()
             self.mode = mode
             if r_max is not None:
@@ -67,7 +67,7 @@ cdef class _QueryArgs:
                     err_str)
 
     def __dealloc__(self):
-        if type(self) == _QueryArgs:
+        if type(self) is _QueryArgs:
             del self.thisptr
 
     def update(self, qargs):
@@ -854,7 +854,7 @@ def _make_default_nlist(system, neighbors, query_points=None):
         NeighborQuery nq
         NeighborList nlist
 
-    if type(neighbors) == NeighborList:
+    if type(neighbors) is NeighborList:
         return neighbors
     else:
         query_args = neighbors.copy()
@@ -1008,10 +1008,10 @@ cdef class _PairCompute(_Compute):
         return (nq, nlist, qargs, l_query_points, num_query_points)
 
     def _resolve_neighbors(self, neighbors, query_points=None):
-        if type(neighbors) == NeighborList:
+        if type(neighbors) is NeighborList:
             nlist = neighbors
             qargs = _QueryArgs()
-        elif neighbors is None or type(neighbors) == dict:
+        elif neighbors is None or type(neighbors) is dict:
             # The default_query_args property must raise a NotImplementedError
             # if no query arguments were passed in and the class has no
             # reasonable choice of defaults.
@@ -1359,7 +1359,7 @@ cdef class Filter(_PairCompute):
         This class is abstract and should not be instantiated directly.
     """
     def __cinit__(self):
-        if type(self) == Filter:
+        if type(self) is Filter:
             raise RuntimeError(
                 "The Filter class is abstract and should not be instantiated directly."
             )
@@ -1460,7 +1460,7 @@ cdef class FilterSANN(Filter):
             new freud._locality.FilterSANN(allow_incomplete_shell)
 
     def __dealloc__(self):
-        if type(self) == FilterSANN:
+        if type(self) is FilterSANN:
             del self._thisptr
 
 cdef class FilterRAD(Filter):
@@ -1521,5 +1521,5 @@ cdef class FilterRAD(Filter):
         )
 
     def __dealloc__(self):
-        if type(self) == FilterRAD:
+        if type(self) is FilterRAD:
             del self._thisptr

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.13.0
+current_version = 2.13.1
 commit = True
 tag = False
 message = Bump up to version {new_version}.

setup.py

@@ -5,7 +5,7 @@
 
 from skbuild import setup
 
-version = "2.13.0"
+version = "2.13.1"
 
 # Read README for PyPI, fallback to short description if it fails.
 description = "Powerful, efficient trajectory analysis in scientific Python."

tests/test_order_Steinhardt.py

@@ -223,7 +223,7 @@ def test_weighted(self, wt):
 
         # Skip test sets without an explicit neighbor list
         for nq, neighbors in filter(
-            lambda ts: type(ts[1]) == freud.locality.NeighborList, test_set
+            lambda ts: type(ts[1]) is freud.locality.NeighborList, test_set
         ):
             nlist = neighbors