chore: update pre-commit hooks

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ ci:
 repos:
 # Standard hooks
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v5.0.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -35,21 +35,21 @@ repos:
 
 # Black, the code formatter, natively supports pre-commit
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 23.7.0
+  rev: 25.1.0
   hooks:
   - id: black
     exclude: ^(docs)
 
 # Check linting and style issues
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: "v0.0.287"
+  rev: "v0.11.13"
   hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
 
 # Changes tabs to spaces
 - repo: https://github.com/Lucas-C/pre-commit-hooks
-  rev: v1.5.4
+  rev: v1.5.5
   hooks:
   - id: remove-tabs
     exclude: ^(docs)

.vscode/c_cpp_properties.json

@@ -24,4 +24,4 @@
         }
     ],
     "version": 4
-}
+}

.vscode/settings.json

@@ -71,4 +71,4 @@
     "valarray": "cpp",
     "variant": "cpp"
   }
-}
+}

CMakeLists.txt

@@ -11,7 +11,8 @@ find_package(pybind11 CONFIG REQUIRED)
 # Include the include/barry library
 include_directories(include/barry)
 
-python_add_library(_core MODULE src/main.cpp src/terms.cpp src/model.cpp WITH_SOABI)
+python_add_library(_core MODULE src/main.cpp src/terms.cpp src/model.cpp
+                   WITH_SOABI)
 target_link_libraries(_core PRIVATE pybind11::headers)
 target_compile_definitions(_core PRIVATE VERSION_INFO=${PROJECT_VERSION})
 

Makefile

@@ -1,5 +1,5 @@
 build:
-	pip3 install .
-	
+    pip3 install .
+
 update:
-	rsync -avz ../barry/include/barry include/
+    rsync -avz ../barry/include/barry include/

README.md

@@ -66,7 +66,7 @@ m.term_formula(obj, "{y0}")
 m.term_formula(obj, "{y1}")
 m.term_formula(obj, "{0y0, y1}")
 obj.init()
-obj.print() 
+obj.print()
 ```
 
     Num. of Arrays       : 6

README.qmd

@@ -42,7 +42,7 @@ ERGMs. More information in [this preprint](https://arxiv.org/abs/2211.00627).
 - `pip install ./pydefm`
 
 
-# Examples 
+# Examples
 
 ## Base setup
 
@@ -64,7 +64,7 @@ x = np.array([1, 2.0, 3.4, 3, 1, 2])
 id = np.array([1, 1, 1, 2, 2, 2])
 ```
 
-Once we have the needed data -- the binary array `y`, the covariates `x` and the ids `id` -- we can create a `defm` object.  
+Once we have the needed data -- the binary array `y`, the covariates `x` and the ids `id` -- we can create a `defm` object.
 
 ```{python}
 # Creating the object
@@ -83,7 +83,7 @@ m.term_formula(obj, "{y0}")
 m.term_formula(obj, "{y1}")
 m.term_formula(obj, "{0y0, y1}")
 obj.init()
-obj.print() 
+obj.print()
 ```
 
 ```{python}
@@ -122,4 +122,4 @@ m.simulate(obj, par)
 
 # Acknowledgements
 
-This port work was supported by the Office of the Assistant Secretary of Defense for Health Affairs through the Epilepsy Research Program under Award No. HT94252310221. Opinions, interpretations, conclusions, and recommendations are those of the author and are not necessarily endorsed by the Department of Defense.
+This port work was supported by the Office of the Assistant Secretary of Defense for Health Affairs through the Epilepsy Research Program under Award No. HT94252310221. Opinions, interpretations, conclusions, and recommendations are those of the author and are not necessarily endorsed by the Department of Defense.

include/barry/barray-bones.hpp

@@ -4,7 +4,7 @@
 // #include "cell-bones.hpp"
 // #include "barraycell-bones.hpp"
 
-#ifndef BARRAY_BONES_HPP 
+#ifndef BARRAY_BONES_HPP
 #define BARRAY_BONES_HPP 1
 
 template<typename Cell_Type, typename Data_Type>
@@ -15,7 +15,7 @@ class BArrayCell_const;
 
 /**
  * @brief Baseline class for binary arrays.
- * 
+ *
  * `BArray` class objects are arbitrary arrays
  * in which non-empty cells hold data of type `Cell_Type`. The non-empty cells
  * are stored by row and indexed using `unordered_map`s, i.e.
@@ -43,34 +43,34 @@ class BArray {
     static const bool dense = false;
 
 public:
-    
-    /** 
+
+    /**
      * This is as a reference, if we need to iterate through the cells and we need
      * to keep track which were visited, we use this as a reference. So that if
      * cell.visited = true and visited = true, it means that we haven't been here
      * yet. Ideally, any routine using this->visited should switch it at the
      * beginning of the routine.
      */
     bool visited = false;
-    
+
 
     /**
      * @name Constructors
-     * 
+     *
      * @param N_ Number of rows
      * @param M_ Number of columns
      * @param source An unsigned vector ranging from 0 to N_
      * @param target An size_t vector ranging from 0 to M_
      * @param target When `true` tries to add repeated observations.
      */
     ///@{
-    
+
     /** @brief Zero-size array */
     BArray() : N(0u), M(0u), NCells(0u), el_ij(0u), el_ji(0u) {};
-    
+
     /** @brief Empty array */
     BArray (size_t N_, size_t M_) : N(N_), M(M_), NCells(0u), el_ij(N_), el_ji(M_) {};
-    
+
     /** @brief Edgelist with data */
     BArray (
         size_t N_, size_t M_,
@@ -79,18 +79,18 @@ class BArray {
         const std::vector< Cell_Type > & value,
         bool add = true
     );
-    
+
     /** @brief Edgelist with no data (simpler) */
     BArray (
         size_t N_, size_t M_,
         const std::vector< size_t > & source,
         const std::vector< size_t > & target,
         bool add = true
     );
-    
+
     /** @brief Copy constructor */
     BArray(const BArray<Cell_Type,Data_Type> & Array_, bool copy_data = false);
-    
+
     /** @brief Assignment constructor */
     BArray<Cell_Type,Data_Type> & operator=(const BArray<Cell_Type,Data_Type> & Array_);
 
@@ -100,20 +100,20 @@ class BArray {
     /** @brief Move assignment */
     BArray<Cell_Type,Data_Type> & operator=(BArray<Cell_Type,Data_Type> && x) noexcept;
     ///@}
-    
+
     bool operator==(const BArray<Cell_Type,Data_Type> & Array_);
 
     ~BArray();
-    
+
     // In principle, copy can be faster by using openmp on the rows
     // since those are independent.
     // BArray(BArray & A);
-    
+
     /**
      * @brief Set the data object
-     * 
-     * @param data_ 
-     * @param delete_data_ 
+     *
+     * @param data_
+     * @param delete_data_
      */
     ///@{
     void set_data(Data_Type * data_, bool delete_data_ = false);
@@ -123,11 +123,11 @@ class BArray {
     const Data_Type & D() const;
     void flush_data();
     ///@}
-    
+
     // Function to access the elements
     // bool check_cell
     void out_of_range(size_t i, size_t j) const;
-    Cell_Type get_cell(size_t i, size_t j, bool check_bounds = true) const; 
+    Cell_Type get_cell(size_t i, size_t j, bool check_bounds = true) const;
     std::vector< Cell_Type >      get_col_vec(size_t i, bool check_bounds = true) const;
     std::vector< Cell_Type >      get_row_vec(size_t i, bool check_bounds = true) const;
     void                          get_col_vec(std::vector< Cell_Type > * x, size_t i, bool check_bounds = true) const;
@@ -137,12 +137,12 @@ class BArray {
 
     /**
      * @brief Get the edgelist
-     * 
+     *
      * `Entries` is a class with three objects: Two `std::vector` with the row and
      * column coordinates respectively, and one `std::vector` with the corresponding
      * value of the cell.
-     * 
-     * @return Entries<Cell_Type> 
+     *
+     * @return Entries<Cell_Type>
      */
     Entries<Cell_Type> get_entries() const;
 
@@ -170,64 +170,64 @@ class BArray {
      * delete/add), or, in the case of `swap_cells`, check if either of both
      * cells exists/don't exist.
      */
-    ///@{  
+    ///@{
     BArray<Cell_Type,Data_Type> & operator+=(const std::pair<size_t, size_t> & coords);
     BArray<Cell_Type,Data_Type> & operator-=(const std::pair<size_t, size_t> & coords);
     BArrayCell<Cell_Type,Data_Type> operator()(size_t i, size_t j, bool check_bounds = true);
     const Cell_Type operator()(size_t i, size_t j, bool check_bounds = true) const;
-    
+
     void rm_cell(size_t i, size_t j, bool check_bounds = true, bool check_exists = true);
-    
+
     void insert_cell(size_t i, size_t j, const Cell< Cell_Type > & v, bool check_bounds, bool check_exists);
     void insert_cell(size_t i, size_t j, Cell< Cell_Type > && v, bool check_bounds, bool check_exists);
     void insert_cell(size_t i, size_t j, Cell_Type v, bool check_bounds, bool check_exists);
-    
+
     void swap_cells(
         size_t i0, size_t j0, size_t i1, size_t j1, bool check_bounds = true,
         int check_exists = CHECK::BOTH,
         int * report     = nullptr
         );
-    
+
     void toggle_cell(size_t i, size_t j, bool check_bounds = true, int check_exists = EXISTS::UKNOWN);
     void toggle_lock(size_t i, size_t j, bool check_bounds = true);
     ///@}
-    
+
     /**@name Column/row wise interchange*/
     ///@{
     void swap_rows(size_t i0, size_t i1, bool check_bounds = true);
     void swap_cols(size_t j0, size_t j1, bool check_bounds = true);
-    
+
     void zero_row(size_t i, bool check_bounds = true);
     void zero_col(size_t j, bool check_bounds = true);
     ///@}
-    
+
     void transpose();
     void clear(bool hard = true);
     void resize(size_t N_, size_t M_);
     void reserve();
 
     // Advances operators
     // void toggle_iterator
-    
+
     // Misc
     void print(const char * fmt = nullptr, ...) const;
     void print_n(size_t nrow, size_t ncol, const char * fmt = nullptr, ...) const;
 
     /**
      * @name Arithmetic operators
-     * 
+     *
      */
     ///@{
     BArray<Cell_Type,Data_Type>& operator+=(const BArray<Cell_Type,Data_Type>& rhs);
     BArray<Cell_Type,Data_Type>& operator+=(const Cell_Type & rhs);
 
     BArray<Cell_Type,Data_Type>& operator-=(const BArray<Cell_Type,Data_Type>& rhs);
     BArray<Cell_Type,Data_Type>& operator-=(const Cell_Type & rhs);
-    
+
     BArray<Cell_Type,Data_Type>& operator/=(const Cell_Type & rhs);
     BArray<Cell_Type,Data_Type>& operator*=(const Cell_Type & rhs);
     ///@}
-    
+
     // /**
     //  * @name Casting between types
     //  */

include/barry/barray-iterator.hpp

@@ -3,33 +3,33 @@
 // #include "typedefs.hpp"
 // #include "barray-bones.hpp"
 
-#ifndef BARRAY_ITERATOR_HPP 
+#ifndef BARRAY_ITERATOR_HPP
 #define BARRAY_ITERATOR_HPP 1
 
 template<typename Cell_Type, typename Data_Type>
 class ConstBArrayRowIter {
 public:
-    
+
     size_t current_row, current_col;
     typename Row_type<Cell_Type>::const_iterator iter;
     const BArray<Cell_Type,Data_Type> * Array;
-    
+
     ConstBArrayRowIter(const BArray<Cell_Type,Data_Type> * Array_) : Array(Array_) {
-        
+
         // Finding the first entry of the iterator
         for (size_t i = 0u; i < Array->nrow(); ++i)
             if (A_ROW(i).size() != 0u) {
                 iter = A_ROW(i).begin();
                 break;
             }
-        
+
         return;
 
     };
     ~ConstBArrayRowIter() {};
-    
+
     // operat
-      
+
 };
 
 #endif

include/barry/barray-meat-operators.hpp

@@ -35,7 +35,7 @@ BARRAY_TEMPLATE(BARRAY_TYPE()&, operator+=) (
 
     // Must be compatible
     checkdim_(*this, rhs);
-    
+
     for (size_t i = 0u; i < nrow(); ++i)
         for (size_t j = 0u; j < ncol(); ++j)
             this->operator()(i, j) += rhs.get_cell(i, j);
@@ -62,7 +62,7 @@ BARRAY_TEMPLATE(BARRAY_TYPE()&, operator-=) (
 
     // Must be compatible
     checkdim_(*this, rhs);
-    
+
     for (size_t i = 0u; i < nrow(); ++i) {
         for (size_t j = 0u; j < ncol(); ++j) {
             this->operator()(i, j) -= rhs.get_cell(i, j);
@@ -126,4 +126,4 @@ BARRAY_TEMPLATE(BARRAY_TYPE()&, operator/=) (
 #undef ROW
 #undef COL
 
-#endif
+#endif