Merge pull request #1111 from glotzerlab/release/2.13.0

Release/2.13.0

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -26,7 +26,7 @@ body:
     attributes:
       label: freud Version
       description: What version of freud are you using?
-      placeholder: v2.12.1
+      placeholder: v2.13.0
     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: 'v3.3.1'
+    rev: 'v3.4.0'
     hooks:
       - id: pyupgrade
         args:
@@ -83,7 +83,7 @@ repos:
     hooks:
       - id: cmake-format
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: 'v16.0.0'
+    rev: 'v16.0.3'
     hooks:
       - id: clang-format
         types_or: [c, c++]

ChangeLog.md

@@ -4,13 +4,18 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.13.0 -- YYYY-MM-DD
+## v2.13.0 -- 2023-05-09
 
 ### Added
 * Filter neighborlists with `freud.locality.FilterSANN` and `freud.locality.FilterRAD`.
 
 ### Fixed
 * Neighborlists generated by certain compute objects now exist after the compute object is garbage collected.
+* All source files have the freud license header at the top.
+* The `compute()` method of each compute object returns self.
+
+### Changed
+* Documentation renders with the furo theme.
 
 ### Removed
 * Support for Python 3.6

contributors.txt

@@ -1,18 +1,18 @@
   2357	Bradley Dice <[email protected]>
-  2146	Vyas Ramasubramani <[email protected]>
+  2148	Vyas Ramasubramani <[email protected]>
   1030	Eric Harper <[email protected]>
-   491	Tommy Waltmann <[email protected]>
+   690	Tommy Waltmann <[email protected]>
    456	Jin Soo Ihm <[email protected]>
-   316	Joshua A. Anderson <[email protected]>
+   318	Joshua A. Anderson <[email protected]>
    240	Matthew Spellings <[email protected]>
-   169	dependabot <dependabot[bot]@users.noreply.github.com>
+   207	dependabot <dependabot[bot]@users.noreply.github.com>
+   168	DomFijan <[email protected]>
    167	Kelly Wang <[email protected]>
-   137	DomFijan <[email protected]>
    110	Erin Teich <[email protected]>
-    97	Brandon Butler <[email protected]>
-    89	Charlotte Shiqi Zhao <[email protected]>
+    98	Brandon Butler <[email protected]>
+    94	Charlotte Shiqi Zhao <[email protected]>
+    72	pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
     66	M. Eric Irrgang <[email protected]>
-    54	pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
     53	Chrisy Du <[email protected]>
     41	Yezhi Jin <[email protected]>
     40	Antonio Osorio <[email protected]>

cpp/box/Box.h

@@ -608,6 +608,6 @@ class Box
     bool m_2d;             //!< Specify whether box is 2D.
 };
 
-}; };  // end namespace freud::box
+}; }; // end namespace freud::box
 
 #endif // BOX_H

cpp/cluster/Cluster.h

@@ -77,6 +77,6 @@ class Cluster
                                                     const std::vector<size_t>& min_ids);
 };
 
-}; };  // end namespace freud::cluster
+}; }; // end namespace freud::cluster
 
 #endif // CLUSTER_H

cpp/cluster/ClusterProperties.h

@@ -88,6 +88,6 @@ class ClusterProperties
     util::ManagedArray<float> m_cluster_masses;                //!< Mass per cluster
 };
 
-}; };  // end namespace freud::cluster
+}; }; // end namespace freud::cluster
 
 #endif // CLUSTER_PROPERTIES_H

cpp/density/CorrelationFunction.h

@@ -78,6 +78,6 @@ template<typename T> class CorrelationFunction : public locality::BondHistogramC
     CFThreadHistogram m_local_correlation_function; //!< Thread local copy of the correlation function
 };
 
-}; };  // end namespace freud::density
+}; }; // end namespace freud::density
 
 #endif // CORRELATION_FUNCTION_H

cpp/density/GaussianDensity.h

@@ -57,15 +57,15 @@ class GaussianDensity
     vec3<unsigned int> getWidth();
 
 private:
-    box::Box m_box;                            //!< Simulation box containing the points.
-    vec3<unsigned int> m_width;                //!< Number of bins in the grid in each dimension.
-    float m_r_max;                             //!< Max distance at which to compute density.
-    float m_sigma;                             //!< Gaussian width sigma.
-    bool m_has_computed;                       //!< Tracks whether a call to compute has been made.
+    box::Box m_box;             //!< Simulation box containing the points.
+    vec3<unsigned int> m_width; //!< Number of bins in the grid in each dimension.
+    float m_r_max;              //!< Max distance at which to compute density.
+    float m_sigma;              //!< Gaussian width sigma.
+    bool m_has_computed;        //!< Tracks whether a call to compute has been made.
 
     util::ManagedArray<float> m_density_array; //! Computed density array.
 };
 
-}; };  // end namespace freud::density
+}; }; // end namespace freud::density
 
 #endif // GAUSSIAN_DENSITY_H

cpp/density/LocalDensity.h

@@ -64,14 +64,14 @@ class LocalDensity
     }
 
 private:
-    box::Box m_box;                                  //!< Simulation box where the particles belong
-    float m_r_max;                                   //!< Maximum neighbor distance
-    float m_diameter;                                //!< Diameter of the particles
+    box::Box m_box;   //!< Simulation box where the particles belong
+    float m_r_max;    //!< Maximum neighbor distance
+    float m_diameter; //!< Diameter of the particles
 
     util::ManagedArray<float> m_density_array;       //!< density array computed
     util::ManagedArray<float> m_num_neighbors_array; //!< number of neighbors array computed
 };
 
-}; };  // end namespace freud::density
+}; }; // end namespace freud::density
 
 #endif // LOCAL_DENSITY_H

cpp/density/RDF.h

@@ -55,13 +55,13 @@ class RDF : public locality::BondHistogramCompute
                                      //!< num_query_points/num_points).
     util::ManagedArray<float> m_pcf; //!< The computed pair correlation function.
     util::ManagedArray<float>
-        m_N_r;         //!< Cumulative bin sum N(r) (the average number of points in a ball of radius r).
+        m_N_r; //!< Cumulative bin sum N(r) (the average number of points in a ball of radius r).
     util::ManagedArray<float>
         m_vol_array2D; //!< Areas of concentric rings corresponding to the histogram bins in 2D.
     util::ManagedArray<float>
         m_vol_array3D; //!< Areas of concentric spherical shells corresponding to the histogram bins in 3D.
 };
 
-}; };  // end namespace freud::density
+}; }; // end namespace freud::density
 
 #endif // RDF_H

cpp/density/SphereVoxelization.h

@@ -53,14 +53,14 @@ class SphereVoxelization
     vec3<unsigned int> getWidth() const;
 
 private:
-    box::Box m_box;                                  //!< Simulation box containing the points.
-    vec3<unsigned int> m_width;                      //!< Number of bins in the grid in each dimension.
-    float m_r_max;                                   //!< Sphere radius used for voxelization.
-    bool m_has_computed;                             //!< Tracks whether a call to compute has been made.
+    box::Box m_box;             //!< Simulation box containing the points.
+    vec3<unsigned int> m_width; //!< Number of bins in the grid in each dimension.
+    float m_r_max;              //!< Sphere radius used for voxelization.
+    bool m_has_computed;        //!< Tracks whether a call to compute has been made.
 
     util::ManagedArray<unsigned int> m_voxels_array; //! Computed voxels array.
 };
 
-}; };  // end namespace freud::density
+}; }; // end namespace freud::density
 
 #endif // SPHERE_VOXELIZATION_H

cpp/diffraction/StaticStructureFactor.h

@@ -74,12 +74,12 @@ class StaticStructureFactor
 
     StructureFactorHistogram m_structure_factor; //!< Histogram to hold computed structure factor
     StructureFactorHistogram::ThreadLocalHistogram
-        m_local_structure_factor;                //!< Thread local histograms for TBB parallelism
+        m_local_structure_factor; //!< Thread local histograms for TBB parallelism
 
-    bool m_reduce {true};                        //! Whether to reduce local histograms
+    bool m_reduce {true};                                         //! Whether to reduce local histograms
     float m_min_valid_k {std::numeric_limits<float>::infinity()}; //! Minimum valid k-vector magnitude
 };
 
-}; };  // namespace freud::diffraction
+}; }; // namespace freud::diffraction
 
 #endif // STATIC_STRUCTURE_FACTOR_H

cpp/diffraction/StaticStructureFactorDebye.h

@@ -45,6 +45,6 @@ class StaticStructureFactorDebye : public StaticStructureFactor
     unsigned int m_frame_counter {0}; //!< Number of frames calculated
 };
 
-}; };  // namespace freud::diffraction
+}; }; // namespace freud::diffraction
 
 #endif // STATIC_STRUCTURE_FACTOR_DEBYE_H

cpp/diffraction/StaticStructureFactorDirect.h

@@ -97,11 +97,11 @@ class StaticStructureFactorDirect : public StaticStructureFactor
     std::vector<vec3<float>> m_k_points; //!< k-vectors used for sampling
     KBinHistogram m_k_histogram;         //!< Histogram of sampled k bins, used to normalize S(q)
     KBinHistogram::ThreadLocalHistogram
-        m_local_k_histograms;            //!< Thread local histograms of sampled k bins for TBB parallelism
-    box::Box previous_box;               //!< box assigned to the system
-    bool box_assigned {false};           //!< Whether to reuse the box
+        m_local_k_histograms;  //!< Thread local histograms of sampled k bins for TBB parallelism
+    box::Box previous_box;     //!< box assigned to the system
+    bool box_assigned {false}; //!< Whether to reuse the box
 };
 
-}; };  // namespace freud::diffraction
+}; }; // namespace freud::diffraction
 
 #endif // STATIC_STRUCTURE_FACTOR_DIRECT_H

cpp/environment/AngularSeparation.h

@@ -83,6 +83,6 @@ class AngularSeparationNeighbor
     locality::NeighborList m_nlist;     //!< The NeighborList used in the last call to compute.
 };
 
-}; };  // end namespace freud::environment
+}; }; // end namespace freud::environment
 
 #endif // ANGULAR_SEPARATION_H

cpp/environment/BondOrder.h

@@ -60,6 +60,6 @@ class BondOrder : public locality::BondHistogramCompute
     BondOrderMode m_mode;                 //!< The mode to calculate with.
 };
 
-}; };  // end namespace freud::environment
+}; }; // end namespace freud::environment
 
 #endif // BOND_ORDER_H

cpp/environment/LocalBondProjection.h

@@ -57,12 +57,12 @@ class LocalBondProjection
     }
 
 private:
-    locality::NeighborList m_nlist;                   //!< The NeighborList used in the last call to compute.
+    locality::NeighborList m_nlist; //!< The NeighborList used in the last call to compute.
 
     util::ManagedArray<float> m_local_bond_proj;      //!< Local bond projection array computed
     util::ManagedArray<float> m_local_bond_proj_norm; //!< Normalized local bond projection array computed
 };
 
-}; };  // end namespace freud::environment
+}; }; // end namespace freud::environment
 
 #endif // LOCAL_BOND_PROJECTION_H

cpp/environment/LocalDescriptors.h

@@ -96,6 +96,6 @@ class LocalDescriptors
     util::ManagedArray<std::complex<float>> m_sphArray;
 };
 
-}; };  // end namespace freud::environment
+}; }; // end namespace freud::environment
 
 #endif // LOCAL_DESCRIPTORS_H

cpp/environment/MatchEnv.h

@@ -312,7 +312,7 @@ class EnvironmentCluster : public MatchEnv
     unsigned int m_num_clusters {0};              //!< Last number of local environments computed
     util::ManagedArray<unsigned int> m_env_index; //!< Cluster index determined for each particle
     std::vector<std::vector<vec3<float>>>
-        m_cluster_environments;                   //!< Dictionary of (cluster id, vectors) pairs
+        m_cluster_environments; //!< Dictionary of (cluster id, vectors) pairs
 };
 
 //! Match local point environments to a specific motif.
@@ -441,6 +441,6 @@ class EnvironmentRMSDMinimizer : public MatchEnv
         m_rmsds; //!< Boolean array indicating whether or not a particle's environment matches the motif.
 };
 
-}; };  // end namespace freud::environment
+}; }; // end namespace freud::environment
 
 #endif // MATCH_ENV_H

cpp/environment/Registration.h

@@ -146,7 +146,7 @@ inline void AlignVectorSets(matrix& P, matrix& Q, matrix* pRotation = nullptr)
     // back to its original dimensionality.
     P = (rotation * P.transpose()).transpose(); // Apply the transformation.
 
-    if (pRotation != nullptr)                   // optionally copy the rotation.
+    if (pRotation != nullptr) // optionally copy the rotation.
     {
         *pRotation = rotation;
     }
@@ -477,6 +477,6 @@ class RegisterBruteForce
                    //! those passed to Fit).
 };
 
-}; };  // end namespace freud::environment
+}; }; // end namespace freud::environment
 
 #endif // REGISTRATION_H

cpp/locality/AABB.h

@@ -368,6 +368,6 @@ inline AABB merge(const AABB& a, const AABB& b)
     return new_aabb;
 }
 
-}; };  // end namespace freud::locality
+}; }; // end namespace freud::locality
 
 #endif // AABB_H

cpp/locality/AABBQuery.h

@@ -199,6 +199,6 @@ class AABBQueryBallIterator : public AABBIterator
     unsigned int
         cur_ref_p; //!< The current index into the reference particles in the current node of the tree.
 };
-}; };              // end namespace freud::locality
+}; }; // end namespace freud::locality
 
-#endif             // AABBQUERY_H
+#endif // AABBQUERY_H

cpp/locality/AABBTree.h

@@ -52,8 +52,8 @@ struct CACHE_ALIGN AABBNode
 
     std::array<unsigned int, NODE_CAPACITY> particles; //!< Indices of the particles contained in the node
     std::array<unsigned int, NODE_CAPACITY>
-        particle_tags;                                 //!< Corresponding particle tags for particles in node
-    unsigned int num_particles;                        //!< Number of particles contained in the node
+        particle_tags;          //!< Corresponding particle tags for particles in node
+    unsigned int num_particles; //!< Number of particles contained in the node
 };
 
 //! AABB Tree
@@ -616,6 +616,6 @@ inline unsigned int AABBTree::allocateNode()
     return m_num_nodes - 1;
 }
 
-}; };  // end namespace freud::locality
+}; }; // end namespace freud::locality
 
 #endif // AABB_TREE_H

cpp/locality/BondHistogramCompute.h

@@ -115,18 +115,18 @@ class BondHistogramCompute
 
 protected:
     box::Box m_box;
-    unsigned int m_frame_counter {0};          //!< Number of frames calculated.
-    unsigned int m_n_points {0};               //!< The number of points.
-    unsigned int m_n_query_points {0};         //!< The number of query points.
-    bool m_reduce {true};                      //!< Whether or not the histogram needs to be reduced.
+    unsigned int m_frame_counter {0};  //!< Number of frames calculated.
+    unsigned int m_n_points {0};       //!< The number of points.
+    unsigned int m_n_query_points {0}; //!< The number of query points.
+    bool m_reduce {true};              //!< Whether or not the histogram needs to be reduced.
 
     util::Histogram<unsigned int> m_histogram; //!< Histogram of interparticle distances (bond lengths).
     util::Histogram<unsigned int>::ThreadLocalHistogram
-        m_local_histograms;                    //!< Thread local bin counts for TBB parallelism
+        m_local_histograms; //!< Thread local bin counts for TBB parallelism
 
     using BondHistogram = util::Histogram<unsigned int>;
 };
 
-}; };  // namespace freud::locality
+}; }; // namespace freud::locality
 
 #endif // BOND_HISTOGRAM_COMPUTE_H

cpp/locality/Filter.h

@@ -94,6 +94,6 @@ class Filter
     }
 };
 
-}; };  // namespace freud::locality
+}; }; // namespace freud::locality
 
 #endif // __FILTER_H__

cpp/locality/FilterRAD.h

@@ -29,6 +29,6 @@ class FilterRAD : public Filter
     bool m_terminate_after_blocked;
 };
 
-}; };  // namespace freud::locality
+}; }; // namespace freud::locality
 
 #endif // __FILTERRAD_H__

cpp/locality/FilterSANN.h

@@ -31,6 +31,6 @@ class FilterSANN : public Filter
     void warnAboutUnfilledNeighborShells(const std::vector<unsigned int>& unfilled_qps) const;
 };
 
-}; };  // namespace freud::locality
+}; }; // namespace freud::locality
 
 #endif // __FILTERSANN_H__