Merge pull request #1094 from glotzerlab/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -66,7 +66,7 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: '23.1.0'
+    rev: '23.3.0'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
@@ -83,7 +83,7 @@ repos:
     hooks:
       - id: cmake-format
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: 'v15.0.7'
+    rev: 'v16.0.0'
     hooks:
       - id: clang-format
         types_or: [c, c++]

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

@@ -50,6 +50,6 @@ class Filter
     std::shared_ptr<NeighborList> m_filtered_nlist;
 };
 
-}; }; // namespace freud::locality
+}; };  // namespace freud::locality
 
 #endif // __FILTER_H__

cpp/locality/FilterSANN.h

@@ -36,6 +36,6 @@ class FilterSANN : public Filter
     bool m_allow_incomplete_shell;
 };
 
-}; }; // namespace freud::locality
+}; };  // namespace freud::locality
 
 #endif // __FILTERSANN_H__

cpp/locality/LinkCell.h

@@ -242,13 +242,13 @@ class LinkCell : public NeighborQuery
     //! Helper function to compute cell neighbors
     const std::vector<unsigned int>& computeCellNeighbors(unsigned int cell) const;
 
-    float m_cell_width {0};                 //!< Minimum necessary cell width cutoff
-    vec3<unsigned int> m_celldim {0, 0, 0}; //!< Cell dimensions
-    unsigned int m_size {0};                //!< The size of cell list.
+    float m_cell_width {0};                       //!< Minimum necessary cell width cutoff
+    vec3<unsigned int> m_celldim {0, 0, 0};       //!< Cell dimensions
+    unsigned int m_size {0};                      //!< The size of cell list.
 
     util::ManagedArray<unsigned int> m_cell_list; //!< The cell list last computed
     using CellNeighbors = tbb::concurrent_hash_map<unsigned int, std::vector<unsigned int>>;
-    mutable CellNeighbors m_cell_neighbors; //!< Hash map of cell neighbors for each cell
+    mutable CellNeighbors m_cell_neighbors;       //!< Hash map of cell neighbors for each cell
 };
 
 //! Parent class of LinkCell iterators that knows how to traverse general cell-linked list structures.
@@ -271,7 +271,7 @@ class LinkCellIterator : public NeighborQueryPerPointIterator
     ~LinkCellIterator() override = default;
 
 protected:
-    const LinkCell* m_linkcell; //!< Link to the LinkCell object
+    const LinkCell* m_linkcell;   //!< Link to the LinkCell object
     IteratorCellShell
         m_neigh_cell_iter;        //!< The shell iterator indicating how far out we're currently searching.
     IteratorLinkCell m_cell_iter; //!< The cell iterator indicating which cell we're currently searching.
@@ -334,6 +334,6 @@ class LinkCellQueryBallIterator : public LinkCellIterator
 protected:
     int m_extra_search_width; //!< The extra shell distance to search, always 0 or 1.
 };
-}; }; // end namespace freud::locality
+}; };                         // end namespace freud::locality
 
-#endif // LINKCELL_H
+#endif                        // LINKCELL_H

cpp/locality/NeighborBond.h

@@ -96,6 +96,6 @@ struct NeighborBond
     float weight {0};                 //! The weight of this bond.
 };
 
-}; }; // end namespace freud::locality
+}; };  // end namespace freud::locality
 
 #endif // NEIGHBOR_BOND_H

cpp/locality/NeighborComputeFunctional.h

@@ -86,7 +86,7 @@ class NeighborListPerPointIterator : public NeighborPerPointIterator
     const NeighborList* m_nlist; //! The NeighborList being iterated over.
     size_t m_current_index;      //! The row of m_nlist where the iterator is currently located.
     size_t m_returned_point_index {
-        0xffffffff}; //! The index of the last returned point (i.e. the value of
+        0xffffffff};             //! The index of the last returned point (i.e. the value of
                      //! m_nlist.getNeighbors()(m_current_index, 0)). Initialized to an arbitrary sentinel in
                      //! case the user ever tries to access this for an iterator built from an empty nlist.
     bool m_finished; //! Flag to indicate that the iterator has been exhausted.
@@ -221,6 +221,6 @@ void loopOverNeighbors(const NeighborQuery* neighbor_query, const vec3<float>* q
     }
 }
 
-}; }; // end namespace freud::locality
+}; };  // end namespace freud::locality
 
 #endif // NEIGHBOR_COMPUTE_FUNCTIONAL_H

cpp/locality/NeighborList.h

@@ -164,6 +164,6 @@ bool compareNeighborBond(const NeighborBond& left, const NeighborBond& right);
 bool compareNeighborDistance(const NeighborBond& left, const NeighborBond& right);
 bool compareFirstNeighborPairs(const std::vector<NeighborBond>& left, const std::vector<NeighborBond>& right);
 
-}; }; // end namespace freud::locality
+}; };  // end namespace freud::locality
 
 #endif // NEIGHBOR_LIST_H

cpp/locality/NeighborPerPointIterator.h

@@ -57,6 +57,6 @@ class NeighborPerPointIterator
     unsigned int m_query_point_idx; //!< The index of the query point.
 };
 
-}; }; // end namespace freud::locality
+}; };  // end namespace freud::locality
 
 #endif // NEIGHBOR_PER_POINT_ITERATOR_H