Merge remote-tracking branch 'cgal/releases/CGAL-5.0-branch'

Algebraic_kernel_d/include/CGAL/Algebraic_kernel_d/Algebraic_curve_kernel_2.h

@@ -430,7 +430,11 @@ public:
 
       Curve_analysis_2 operator()
         (const Polynomial_2& f) const {
-        return _m_kernel->curve_cache_2()(f);
+        if (_m_kernel->is_square_free_2_object()(f)) {
+          return _m_kernel->curve_cache_2()(f);
+        } else {
+          return _m_kernel->curve_cache_2()(_m_kernel->make_square_free_2_object()(f));
+        }
       }
 
     protected:

CGAL_Core/include/CGAL/CORE/extLong_impl.h

@@ -125,9 +125,9 @@ extLong& extLong::operator*= (const extLong& y) {
     if (std::fabs(d - p) <= std::fabs(d) * relEps) {
       val = p;
       flag = 0;
-    } else if (d > EXTLONG_MAX) {
+    } else if (d > static_cast<double>(EXTLONG_MAX)) {
       *this = CORE_posInfty;
-    } else if (d < EXTLONG_MIN) {
+    } else if (d < static_cast<double>(EXTLONG_MIN)) {
       *this = CORE_negInfty;
     } else {
 #ifdef CORE_DEBUG

Heat_method_3/include/CGAL/Heat_method_3/Surface_mesh_geodesic_distances_3.h

@@ -887,16 +887,6 @@ public:
     base().clear_sources();
   }
 
-  /**
-   * get estimated distance from the current source set to a vertex `vd`.
-   * \warning The return type is `double` even when used with an exact kernel.
-   */
-  double
-  estimate_geodesic_distance(vertex_descriptor vd) const
-  {
-    return base().estimate_geodesic_distance(vd);
-  }
-
   /**
    * returns the source set.
    */
@@ -906,7 +896,6 @@ public:
     return base().sources();
   }
 
-
   /**
    * fills the distance property map with the estimated geodesic distance of each vertex to the closest source vertex.
    * \tparam VertexDistanceMap a property map model of `WritablePropertyMap`

Heat_method_3/include/CGAL/Heat_method_3/internal/Intrinsic_Delaunay_triangulation_3.h

@@ -335,7 +335,6 @@ private:
         //then go back to top of the stack
       }
     }
-    std::cout<< a << " edges were flipped: " << std::endl;
   }
 
 

Periodic_3_triangulation_3/include/CGAL/Periodic_3_triangulation_ds_cell_base_3.h

@@ -180,9 +180,9 @@ public:
     int bit_offset = 3 * vhi;
 
     // first reset the bit to 0 (AND), then assign the value given in input (OR)
-    off = off & ~(1 <<  bit_offset)      | (offo[0] <<  bit_offset);
+    off = (off & ~(1 <<  bit_offset))      | (offo[0] <<  bit_offset);
-    off = off & ~(1 << (bit_offset + 1)) | (offo[1] << (bit_offset + 1));
+    off = (off & ~(1 << (bit_offset + 1))) | (offo[1] << (bit_offset + 1));
-    off = off & ~(1 << (bit_offset + 2)) | (offo[2] << (bit_offset + 2));
+    off = (off & ~(1 << (bit_offset + 2))) | (offo[2] << (bit_offset + 2));
 
     CGAL_postcondition(offset(vhi) == o);
   }

Point_set_processing_3/include/CGAL/Point_set_processing_3/internal/Rich_grid.h

@@ -186,15 +186,19 @@ void Rich_grid<Kernel>::init(std::vector<Rich_point<Kernel> > &vert,
 
   radius = _radius;
 
-  x_side = (unsigned int)ceil((bbox.xmax() - bbox.xmin()) / radius);
+  std::size_t x_size = (std::size_t)ceil((bbox.xmax() - bbox.xmin()) / radius);
-  y_side = (unsigned int)ceil((bbox.ymax() - bbox.ymin()) / radius);
+  std::size_t y_size = (std::size_t)ceil((bbox.ymax() - bbox.ymin()) / radius);
-  z_side = (unsigned int)ceil((bbox.zmax() - bbox.zmin()) / radius);
+  std::size_t z_size = (std::size_t)ceil((bbox.zmax() - bbox.zmin()) / radius);
 
-  x_side = (x_side > 0) ? x_side : 1;
+  x_size = (x_size > 0) ? x_size : 1;
-  y_side = (y_side > 0) ? y_side : 1;
+  y_size = (y_size > 0) ? y_size : 1;
-  z_side = (z_side > 0) ? z_side : 1;
+  z_size = (z_size > 0) ? z_size : 1;
 
-  indices.resize(x_side * y_side * z_side + 1, -1);
+  indices.resize(x_size * y_size * z_size + 1, -1);
+
+  x_side = int(x_size);
+  y_side = int(y_size);
+  z_side = int(z_size);
 
   std::sort(rich_points.begin(), rich_points.end(), Z_Sort<Kernel>());
 

Point_set_processing_3/include/CGAL/edge_aware_upsample_point_set.h

@@ -377,7 +377,7 @@ edge_aware_upsample_point_set(
 
   // copy rich point set
   std::vector<Rich_point> rich_point_set(number_of_input);
-  CGAL::Bbox_3 bbox(0., 0., 0., 0., 0., 0.);
+  CGAL::Bbox_3 bbox;
 
   typename PointRange::const_iterator it = begin; // point iterator
   for(unsigned int i = 0; it != end; ++it, ++i)

Solver_interface/doc/Solver_interface/Concepts/DiagonalizeTraits.h

@@ -21,7 +21,6 @@ follows:
 
 \cgalHasModel `CGAL::Eigen_diagonalize_traits`
 */
-
 template <typename FT, unsigned int dim = 3>
 class DiagonalizeTraits
 {

Solver_interface/doc/Solver_interface/Concepts/MixedIntegerProgramTraits.h

@@ -1,16 +1,13 @@
-
-
 class MixedIntegerProgramTraits
 
-
 /*!
+\ingroup PkgSolverInterfaceConcepts
 \cgalConcept
 
 `MixedIntegerProgramVariable` is a concept of a variable in
 a Mixed Integer Programming (MIP) problem.
 
 \cgalHasModel `CGAL::Variable<FT>`
-
 */
 template <typename FT>
 class MixedIntegerProgramVariable
@@ -25,7 +22,7 @@ public:
         typedef unspecified_type FT;
 
         /*!
-        A variable can be continuous, integer, or binary
+        A variable can be continuous, integer, or binary.
         */
         enum Variable_type { CONTINUOUS, INTEGER, BINARY };
 
@@ -43,10 +40,10 @@ public:
         /// \name Operations
         /// @{
 
-        /// Returns the variable type
+        /// Returns the variable type.
         Variable_type variable_type() const;
 
-        /// Sets/Changes the variable type
+        /// Sets/Changes the variable type.
         void set_variable_type(Variable_type t);
 
         /*!
@@ -69,26 +66,26 @@ public:
         */
         void set_index(int idx);
 
-        /// Returns the solver that owns this variable
+        /// Returns the solver that owns this variable.
         const MixedIntegerProgramTraits* solver() const;
         MixedIntegerProgramTraits* solver();
 
-        /// Sets the lower bound
+        /// Sets the lower bound.
         void set_lower_bound(FT lb);
 
-        /// Sets the upper bound
+        /// Sets the upper bound.
         void set_upper_bound(FT ub);
 
-        /// Sets both lower and upper bounds
+        /// Sets both lower and upper bounds.
         void set_bounds(FT lb, FT ub);
 
-        /// Gets the lower bound
+        /// Gets the lower bound.
         FT lower_bound() const;
 
-        /// Gets the upper bound
+        /// Gets the upper bound.
         FT upper_bound() const;
 
-        /// Gets both lower and upper bounds
+        /// Gets both lower and upper bounds.
         void get_bounds(FT& lb, FT& ub) const;
 
         /// Gets the infinity threshold (e.g., 1e20).
@@ -108,17 +105,15 @@ public:
 
 }; /* end MixedIntegerProgramVariable */
 
+/*!
+\ingroup PkgSolverInterfaceConcepts
+\cgalConcept
 
+`MixedIntegerProgramLinearConstraint` is a concept of a linear
+constraint in a Mixed Integer Programming (MIP) problem.
 
-   /*!
+\cgalHasModel `CGAL::Linear_constraint<FT>`
-
+*/
-   \cgalConcept
-
-   `MixedIntegerProgramLinearConstraint` is a concept of a linear
-   constraint in a Mixed Integer Programming (MIP) problem.
-
-   \cgalHasModel `CGAL::Linear_constraint<FT>`
-   */
 template <typename FT>
 class MixedIntegerProgramLinearConstraint
 {
@@ -155,26 +150,26 @@ public:
         */
         void set_index(int idx);
 
-        /// Returns the solver that owns this constraint
+        /// Returns the solver that owns this constraint.
         const MixedIntegerProgramTraits* solver() const;
         MixedIntegerProgramTraits* solver();
 
-        /// Sets the lower bound
+        /// Sets the lower bound.
         void set_lower_bound(FT lb);
 
-        /// Sets the upper bound
+        /// Sets the upper bound.
         void set_upper_bound(FT ub);
 
-        /// Sets both lower and upper bounds
+        /// Sets both lower and upper bounds.
         void set_bounds(FT lb, FT ub);
 
-        /// Gets the lower bound
+        /// Gets the lower bound.
         FT lower_bound() const;
 
-        /// Gets the upper bound
+        /// Gets the upper bound.
         FT upper_bound() const;
 
-        /// Gets both lower and upper bounds
+        /// Gets both lower and upper bounds.
         void get_bounds(FT& lb, FT& ub) const;
 
         /// Gets the infinity threshold (e.g., 1e20).
@@ -207,17 +202,15 @@ public:
 
 }; /* end MixedIntegerProgramLinearConstraint */
 
+/*!
+\ingroup PkgSolverInterfaceConcepts
+\cgalConcept
 
+`MixedIntegerProgramLinearObjective` is a concept of the linear
+objective function in a Mixed Integer Programming (MIP) problem.
 
-   /*!
+\cgalHasModel `CGAL::Linear_objective<FT>`
-
+*/
-   \cgalConcept
-
-   `MixedIntegerProgramLinearObjective` is a concept of the linear
-   objective function in a Mixed Integer Programming (MIP) problem.
-
-   \cgalHasModel `CGAL::Linear_objective<FT>`
-   */
 template <typename FT>
 class MixedIntegerProgramLinearObjective
 {
@@ -225,7 +218,7 @@ public:
         /// \name Types
         /// @{
 
-        /// The objective sense (i.e., optimization direction)
+        /// The objective sense (i.e., optimization direction).
         enum Sense { MINIMIZE, MAXIMIZE, UNDEFINED };
 
         /// @}
@@ -275,10 +268,8 @@ public:
 
 }; /* end MixedIntegerProgramLinearObjective */
 
-
-
 /*!
-\ingroup PkgSolverConcepts
+\ingroup PkgSolverInterfaceConcepts
 \cgalConcept
 
 @brief Concept describing the set of requirements for (constrained or unconstrained)
@@ -290,12 +281,10 @@ to solve the problem.
 \cgalHasModel `CGAL::GLPK_mixed_integer_program_traits<T>`
 \cgalHasModel `CGAL::SCIP_mixed_integer_program_traits<T>`
 */
-
 template <typename FT>
 class MixedIntegerProgramTraits
 {
 public:
-
         /// \name Creation
         /// @{
 
@@ -335,42 +324,42 @@ public:
         ///                  solver is destroyed.
         MixedIntegerProgramLinearObjective* create_objective(Sense sense);
 
-        /// Returns the number of variables
+        /// Returns the number of variables.
         std::size_t number_of_variables() const;
 
-        /// Returns the variables
+        /// Returns the variables.
         const std::vector<MixedIntegerProgramVariable*>& variables() const;
         std::vector<MixedIntegerProgramVariable*>& variables();
 
-        /// Returns the number of constraints
+        /// Returns the number of constraints.
         std::size_t number_of_constraints() const;
 
-        /// Returns the constraints
+        /// Returns the constraints.
         const std::vector<MixedIntegerProgramLinearConstraint*>& constraints() const;
         std::vector<MixedIntegerProgramLinearConstraint*>& constraints();
 
-        /// Returns the number of continuous variables
+        /// Returns the number of continuous variables.
         std::size_t number_of_continuous_variables() const;
 
-        /// Returns the number of integer variables
+        /// Returns the number of integer variables.
         std::size_t number_of_integer_variables() const;
 
-        /// Returns the number of binary variables
+        /// Returns the number of binary variables.
         std::size_t number_of_binary_variables() const;
 
-        /// Returns true if all variables are continuous
+        /// Returns true if all variables are continuous.
         bool is_continuous() const;
 
-        /// Returns true if this is a mixed integer program
+        /// Returns true if this is a mixed integer program.
         bool is_mixed_integer_program() const;
 
-        /// Returns true if this is an integer program
+        /// Returns true if this is an integer program.
         bool is_integer_program() const;
 
-        /// Returns true if binary program
+        /// Returns true if binary program.
         bool is_binary_program() const;
 
-        /// Returns the objective
+        /// Returns the objective.
         const MixedIntegerProgramLinearObjective * objective() const;
         MixedIntegerProgramLinearObjective * objective();
 
@@ -391,4 +380,5 @@ public:
         void clear();
 
         /// @}
+
 }; /* end MixedIntegerProgramTraits */

Solver_interface/doc/Solver_interface/Concepts/NormalEquationSparseLinearAlgebraTraits_d.h

@@ -1,6 +1,5 @@
 /*!
 \ingroup PkgSolverInterfaceConcepts
-
 \cgalConcept
 
 Concept describing the set of requirements for solving the normal equation \f$ A^t A X = A^t B \f$,
@@ -10,7 +9,6 @@ Concept describing the set of requirements for solving the normal equation \f$ A
 
 \cgalHasModel `CGAL::Eigen_solver_traits<T>`
 */
-
 class NormalEquationSparseLinearAlgebraTraits_d
 {
 public:
@@ -70,4 +68,3 @@ bool normal_equation_solver(const Matrix& A, const Vector& B, Vector& X);
 /// @}
 
 }; /* end NormalEquationSparseLinearAlgebraTraits_d */
-

Solver_interface/doc/Solver_interface/Concepts/SparseLinearAlgebraTraits_d.h

@@ -1,13 +1,11 @@
 /*!
 \ingroup PkgSolverInterfaceConcepts
-
 \cgalConcept
 
 The concept `SparseLinearAlgebraTraits_d` is used to solve sparse linear systems <I>A\f$ \times \f$ X = B</I>.
 
 \cgalHasModel `CGAL::Eigen_solver_traits<T>`
 */
-
 class SparseLinearAlgebraTraits_d
 {
 public:
@@ -68,7 +66,6 @@ by a sparse matrix.
 
 \sa `SparseLinearAlgebraTraits_d`
 \sa `SparseLinearAlgebraTraits_d::Matrix`
-
 */
 class SparseLinearAlgebraTraits_d::Vector
 {
@@ -126,7 +123,6 @@ NT& operator[](Index row);
 }; /* end Vector */
 
 /*!
-
 \cgalConcept
 
 `SparseLinearAlgebraTraits_d::Matrix` is a concept of a sparse matrix class.
@@ -150,7 +146,6 @@ Index type
 */
 typedef unspecified_type Index;
 
-
 /*!
 
 */
@@ -214,8 +209,8 @@ in the matrix by setting `new_coef` to `true`.
 void set_coef(Index row, Index column, NT value, bool new_coef = false);
 
 /*!
-swaps the content of `*this` and `m`
+Swaps the content of `*this` and `m`.
- */
+*/
 void swap(Matrix& m);
 
 /// Multiplication with a scalar.

Solver_interface/doc/Solver_interface/Concepts/SparseLinearAlgebraWithFactorTraits_d.h

@@ -1,4 +1,3 @@
-
 /*!
 \ingroup PkgSolverInterfaceConcepts
 \cgalConcept
@@ -11,7 +10,6 @@ method to solve the system for different right-hand vectors.
 
 \cgalHasModel `CGAL::Eigen_solver_traits<T>`
 */
-
 class SparseLinearAlgebraWithFactorTraits_d {
 public:
 
@@ -48,4 +46,3 @@ bool linear_solver(const Matrix& B, Vector& X);
 /// @}
 
 }; /* end SparseLinearAlgebraWithFactorTraits_d */
-

Solver_interface/doc/Solver_interface/Concepts/SvdTraits.h

@@ -101,12 +101,12 @@ public:
 
   /*!
     Return the number of rows of the matrix.
-   */
+  */
   size_t number_of_rows();
 
   /*!
     Return the number of columns of the matrix.
-   */
+  */
   size_t number_of_columns();
 
   /*!
@@ -120,4 +120,3 @@ public:
   */
   void set(size_t i, size_t j, const FT value);
 };
-

Solver_interface/doc/Solver_interface/Solver_interface.txt

@@ -27,6 +27,7 @@ high performance libraries, e.g.,
 <a href = "http://www.gurobi.com/"> Gurobi </a>.
 
 
+
 \section SectionSolverDiagonalize Matrix Diagonalization
 
 The concept `DiagonalizeTraits<T,dim>` defines an interface for the
@@ -41,6 +42,7 @@ class:
 \cgalExample{Solver_interface/diagonalize_matrix.cpp}
 
 
+
 \section SectionSolverSVD Singular Value Decomposition
 
 The concept `SvdTraits` defines an interface for solving in the least
@@ -55,7 +57,6 @@ and this solver:
 
 
 
-
 \section SectionSolverSparse Sparse Solvers
 
 We define 3 concepts for sparse linear algebra:
@@ -102,17 +103,16 @@ formulating and solving (constrained or unconstrained) mixed integer
 programs. It can also be used for general linear programs.
 
 The field type is `double`. We provide two models of this concept:
-`GLPK_mixed_integer_program_traits` using \ref thirdpartyGLPK and
+`CGAL::GLPK_mixed_integer_program_traits` using \ref thirdpartyGLPK and
-`SCIP_mixed_integer_program_traits` using \ref thirdpartySCIP.
+`CGAL::SCIP_mixed_integer_program_traits` using \ref thirdpartySCIP.
 
 Here is an example that shows how to formulate and solve a simple
-mixed integer programs using this solver.
+mixed integer program using this solver.
 
 \cgalExample{Solver_interface/mixed_integer_program.cpp}
 
 
 
-
 \section SolversHistory Implementation History
 This package is the result of the increasing needs for linear solvers
 in \cgal.  The first packages that introduced the solver concepts were
@@ -132,4 +132,3 @@ with the help of Andreas Fabri.
 
 */
 } /* namespace CGAL */
-

Solver_interface/include/CGAL/GLPK_mixed_integer_program_traits.h

@@ -46,15 +46,15 @@ int bound_type(FT lb, FT ub)
 
 } // namespace internal
 
-/// \ingroup PkgSolver
+/// \ingroup PkgSolverInterfaceRef
 ///
 /// This class provides an interface for formulating and solving
 /// constrained or unconstrained mixed integer programs using
 /// \ref thirdpartyGLPK, which must be available on the system.
 ///
 /// \note For better performance, please consider using
-///      `SCIP_mixed_integer_program_traits`, or derive a new
+///      `CGAL::SCIP_mixed_integer_program_traits`, or derive a new
-///      model from `Mixed_integer_program_traits`.
+///      model from `CGAL::Mixed_integer_program_traits`.
 ///
 /// \cgalModels `MixedIntegerProgramTraits`
 ///

Solver_interface/include/CGAL/Mixed_integer_program_traits.h

@@ -96,7 +96,9 @@ namespace CGAL {
         };
         /// \endcond
 
-        /// The variables of mixed integer programs.
+        /// \ingroup PkgSolverInterfaceRef
+        ///
+        /// The variable of a mixed integer program.
         ///
         /// \cgalModels `MixedIntegerProgramVariable`
         template <typename FT>
@@ -193,7 +195,10 @@ namespace CGAL {
         };
         /// \endcond
 
-        /// The linear constraint.
+        /// \ingroup PkgSolverInterfaceRef
+        ///
+        /// The linear constraint of a mixed integer program.
+        ///
         /// \cgalModels `MixedIntegerProgramLinearConstraint`
         template <typename FT>
         class Linear_constraint : public Linear_expression<FT>, public Bound<FT>
@@ -222,7 +227,9 @@ namespace CGAL {
         };
 
 
-        /// The linear objective.
+        /// \ingroup PkgSolverInterfaceRef
+        ///
+        /// The linear objective of a mixed integer program.
         ///
         /// \cgalModels `MixedIntegerProgramLinearObjective`
         ///
@@ -256,16 +263,16 @@ namespace CGAL {
                 /// \endcond
         };
 
-        /// \ingroup PkgSolver
+        /// \ingroup PkgSolverInterfaceRef
         ///
-        /// The class `Mixed_integer_program_traits` provides an interface for
+        /// The class `CGAL::Mixed_integer_program_traits` provides an interface for
         /// formulating and solving (constrained or unconstrained) mixed integer
         /// programs. It can also be used for general linear programs.
         /// \note The solve() function is virtual and thus this class cannot be
         ///                  instantiated directly. Client code should use the inherited
-        ///       classes, i.e., `GLPK_mixed_integer_program_traits` or
+        ///       classes, i.e., `CGAL::GLPK_mixed_integer_program_traits` or
-        ///                  `SCIP_mixed_integer_program_traits`. Alternatively, use
+        ///                  `CGAL::SCIP_mixed_integer_program_traits`. Alternatively, use
-        ///       `Mixed_integer_program_traits` as a base to derive a new model
+        ///       `CGAL::Mixed_integer_program_traits` as a base to derive a new model
         ///       (using e.g., <a href = "https://projects.coin-or.org/Cbc"> CBC </a>,
         ///       <a href = "http://www.gurobi.com/"> Gurobi </a> for better
         ///       performance).
@@ -275,7 +282,6 @@ namespace CGAL {
         /// \endcond
         ///
         /// \cgalModels `MixedIntegerProgramTraits`
-
         template <typename FT>
         class Mixed_integer_program_traits
         {

Solver_interface/include/CGAL/SCIP_mixed_integer_program_traits.h

@@ -25,7 +25,7 @@
 
 namespace CGAL {
 
-/// \ingroup PkgSolver
+/// \ingroup PkgSolverInterfaceRef
 ///
 /// This class provides an interface for formulating and solving
 /// constrained or unconstrained mixed integer programs using

Surface_mesher/include/CGAL/Surface_mesher/Surface_mesher.h

@@ -479,11 +479,15 @@ namespace CGAL {
       // On enleve la facette de la liste des mauvaises facettes
 #ifdef CGAL_SURFACE_MESHER_TAG_BAD
       if(f.first->is_bad(f.second))
+      {
+#endif // CGAL_SURFACE_MESHER_TAG_BAD
+      if(f.first < other_side.first)
+        facets_to_refine.erase(f);
+      else
+        facets_to_refine.erase(other_side);
+#ifdef CGAL_SURFACE_MESHER_TAG_BAD
+      }
 #endif // CGAL_SURFACE_MESHER_TAG_BAD
-        if(f.first < other_side.first)
-          facets_to_refine.erase(f);
-        else
-          facets_to_refine.erase(other_side);
       // Le compteur des visites est remis a zero
        reset_visited(f);
        reset_visited(other_side);