Merge pull request #2342 from oscar-system/lk/refactor/keyword_arguments

docs/src/DeveloperDocumentation/serialization.md

@@ -64,8 +64,8 @@ loading larger objects twice (or multiple times). Consider the following
 example code snippet:
 ```
 c = cube(3);
-LP0 = LinearProgram(c, [2,2,-3]);
-LP1 = LinearProgram(c, [2,2,4]);
+LP0 = linear_program(c, [2,2,-3]);
+LP1 = linear_program(c, [2,2,4]);
 v = [LP0, LP1];
 save("vector_of_lp.json", v)
 ```

docs/src/PolyhedralGeometry/Polyhedra/constructions.md

@@ -17,8 +17,8 @@ from other objects in OSCAR.
 ### Intersecting halfspaces: $H$-representation
 
 ```@docs
-Polyhedron{T}(A::AnyVecOrMat, b::AbstractVector) where T<:scalar_types
-Polyhedron{T}(I::Union{Nothing, AbstractCollection[AffineHalfspace]}, E::Union{Nothing, AbstractCollection[AffineHyperplane]} = nothing) where T<:scalar_types
+polyhedron(::Type{T}, A::AnyVecOrMat, b::AbstractVector) where T<:scalar_types
+polyhedron(::Type{T}, I::Union{Nothing, AbstractCollection[AffineHalfspace]}, E::Union{Nothing, AbstractCollection[AffineHyperplane]} = nothing) where T<:scalar_types
 ```
 
 The complete $H$-representation can be retrieved using [`facets`](@ref facets)

docs/src/PolyhedralGeometry/fans.md

@@ -25,7 +25,7 @@ To construct a polyhedral fan, you must pass the rays of each cone in the fan,
 along with an `IncidenceMatrix` encoding which rays generate which cones.
 
 ```@docs
-PolyhedralFan
+polyhedral_fan
 polyhedral_fan_from_rays_action
 ```
 

docs/src/PolyhedralGeometry/intro.md

@@ -125,7 +125,8 @@ row(i::IncidenceMatrix, n::Int)
 column(i::IncidenceMatrix, n::Int)
 ```
 
-A typical application is the assignment of rays to the cones of a polyhedral fan for its construction, see [`PolyhedralFan{T}`](@ref).
+A typical application is the assignment of rays to the cones of a polyhedral
+fan for its construction, see [`polyhedral_fan`](@ref).
 
 
 ## Visualization

docs/src/PolyhedralGeometry/linear_programs.md

@@ -22,7 +22,7 @@ which is described by a vector and (optionally) a translation. One can select wh
 problem is to maximize or to minimize the objective function.
 
 ```@docs
-LinearProgram
+linear_program
 ```
 
 ## Solving a linear program - an example
@@ -35,7 +35,7 @@ Computationally, this means first defining a linear program:
 julia> P = cube(3)
 Polyhedron in ambient dimension 3
 
-julia> LP = LinearProgram(P,[3,-2,4];k=2,convention = :min)
+julia> LP = linear_program(P,[3,-2,4];k=2,convention = :min)
 Linear program
    min{c⋅x + k | x ∈ P}
 where P is a Polyhedron{QQFieldElem} and
@@ -48,7 +48,7 @@ The information about the linear program `LP` can be easily extracted.
 ```jldoctest
 julia> P = cube(3);
 
-julia> LP = LinearProgram(P,[3,-2,4];k=2,convention = :min);
+julia> LP = linear_program(P,[3,-2,4];k=2,convention = :min);
 
 julia> c, k = objective_function(LP)
 (QQFieldElem[3, -2, 4], 2)
@@ -63,7 +63,7 @@ where the optimal value is `m`, and that value is attained at `v`.
 ```jldoctest
 julia> P = cube(3);
 
-julia> LP = LinearProgram(P,[3,-2,4];k=2,convention = :min);
+julia> LP = linear_program(P,[3,-2,4];k=2,convention = :min);
 
 julia> m, v = solve_lp(LP)
 (-7, QQFieldElem[-1, 1, -1])
@@ -84,7 +84,7 @@ The optimal value and an optimal vertex may be obtained individually as well.
 ```jldoctest
 julia> P = cube(3);
 
-julia> LP = LinearProgram(P,[3,-2,4];k=2,convention = :min);
+julia> LP = linear_program(P,[3,-2,4];k=2,convention = :min);
 
 julia> M = optimal_value(LP)
 -7

docs/src/PolyhedralGeometry/mixed_integer_linear_programs.md

@@ -23,7 +23,7 @@ to minimize the objective function. Furthermore one can optionally specify
 given as a set of integers, their respective indices.
 
 ```@docs
-MixedIntegerLinearProgram
+mixed_integer_linear_program
 ```
 
 ## Functions

docs/src/PolyhedralGeometry/polyhedral_complexes.md

@@ -24,7 +24,7 @@ along with an `IncidenceMatrix` encoding which points generate which
 polyhedron.
 
 ```@docs
-PolyhedralComplex
+polyhedral_complex
 ```
 
 

docs/src/PolyhedralGeometry/subdivisions_of_points.md

@@ -34,8 +34,8 @@ vector, but if it does, it is called `regular`.
 
 
 ```@docs
-SubdivisionOfPoints(Points::Union{Oscar.MatElem,AbstractMatrix}, Incidence::IncidenceMatrix)
-SubdivisionOfPoints(Points::Union{Oscar.MatElem,AbstractMatrix}, Weights::AbstractVector)
+subdivision_of_points(::Type{T}, Points::Union{Oscar.MatElem,AbstractMatrix}, Incidence::IncidenceMatrix) where T<:scalar_types
+subdivision_of_points(::Type{T}, Points::Union{Oscar.MatElem,AbstractMatrix}, Weights::AbstractVector) where T<:scalar_types
 ```
 
 From a subdivision of points one can construct the

experimental/FTheoryTools/src/auxiliary.jl

@@ -45,7 +45,7 @@ function _ambient_space_from_base(base::AbstractNormalToricVariety)
   ambient_space_max_cones = IncidenceMatrix(vcat(ambient_space_max_cones...))
 
   # Construct and return the ambient space
-  ambient_space = normal_toric_variety(PolyhedralFan(ambient_space_rays, ambient_space_max_cones; non_redundant = true))
+  ambient_space = normal_toric_variety(polyhedral_fan(ambient_space_rays, ambient_space_max_cones; non_redundant = true))
   set_coordinate_names(ambient_space, vcat([string(k) for k in gens(cox_ring(base))], ["x", "y", "z"]))
   return ambient_space
 
@@ -131,7 +131,7 @@ function sample_toric_variety()
           [5, 11, 12], [5, 6, 32], [5, 6, 12], [4, 31, 32], [4, 10, 11], [4, 5, 32],
           [4, 5, 11], [3, 30, 31], [3, 9, 10], [3, 4, 31], [3, 4, 10], [2, 29, 30],
           [2, 8, 9], [2, 3, 30], [2, 3, 9], [1, 8, 29], [1, 2, 29], [1, 2, 8]])
-  return normal_toric_variety(PolyhedralFan(rays, cones))
+  return normal_toric_variety(polyhedral_fan(rays, cones))
 end
 
 @doc raw"""

src/AlgebraicGeometry/ToricVarieties/NormalToricVarieties/attributes.jl

@@ -453,8 +453,8 @@ ideal(-x1*x2 + x3*x4)
 ```
 """
 function toric_ideal(R::MPolyRing, antv::AffineNormalToricVariety)
-    cone = Cone(pm_object(antv).WEIGHT_CONE)
-    gens = pm_object(cone).CONE_TORIC_IDEAL.BINOMIAL_GENERATORS
+    C = cone(pm_object(antv).WEIGHT_CONE)
+    gens = pm_object(C).CONE_TORIC_IDEAL.BINOMIAL_GENERATORS
     return binomial_exponents_to_ideal(R, gens)
 end
 
@@ -481,8 +481,8 @@ ideal(-x1*x2 + x3*x4)
 ```
 """
 @attr MPolyIdeal function toric_ideal(antv::AffineNormalToricVariety)
-    cone = Cone(pm_object(antv).WEIGHT_CONE)
-    n = length(hilbert_basis(cone))
+    C = cone(pm_object(antv).WEIGHT_CONE)
+    n = length(hilbert_basis(C))
     R, _ = polynomial_ring(coefficient_ring(antv), n, cached=false)
     return toric_ideal(R, antv)
 end
@@ -910,7 +910,7 @@ julia> dim(nef)
 1
 ```
 """
-@attr Cone nef_cone(v::NormalToricVariety) = Cone(pm_object(v).NEF_CONE)
+@attr Cone nef_cone(v::NormalToricVariety) = cone(pm_object(v).NEF_CONE)
 
 
 """
@@ -930,7 +930,7 @@ julia> dim(mori)
 1
 ```
 """
-@attr Cone mori_cone(v::NormalToricVariety) = Cone(pm_object(v).MORI_CONE)
+@attr Cone mori_cone(v::NormalToricVariety) = cone(pm_object(v).MORI_CONE)
 
 
 @doc raw"""
@@ -1039,7 +1039,7 @@ julia> affine_open_covering(p2)
 @attr Vector{AffineNormalToricVariety} function affine_open_covering(v::AbstractNormalToricVariety)
     charts = Vector{AffineNormalToricVariety}(undef, pm_object(v).N_MAXIMAL_CONES)
     for i in 1:pm_object(v).N_MAXIMAL_CONES
-        charts[i] = affine_normal_toric_variety(Cone(Polymake.fan.cone(pm_object(v), i-1)))
+        charts[i] = affine_normal_toric_variety(cone(Polymake.fan.cone(pm_object(v), i-1)))
     end
     return charts
 end

src/AlgebraicGeometry/ToricVarieties/NormalToricVarieties/constructors.jl

@@ -36,7 +36,7 @@ Normal, affine toric variety
 ```
 """
 function affine_normal_toric_variety(C::Cone; set_attributes::Bool = true)
-    fan = PolyhedralFan(C)
+    fan = polyhedral_fan(C)
     pmntv = Polymake.fulton.NormalToricVariety(Oscar.pm_object(fan))
     variety = AffineNormalToricVariety(pmntv)
 
@@ -71,7 +71,7 @@ Normal, affine toric variety
 ```
 """
 function normal_toric_variety(C::Cone; set_attributes::Bool = true)
-    fan = PolyhedralFan(C)
+    fan = polyhedral_fan(C)
     pmntv = Polymake.fulton.NormalToricVariety(Oscar.pm_object(fan))
     variety = NormalToricVariety(pmntv)
 
@@ -123,7 +123,7 @@ Normal toric variety
 ```
 """
 function normal_toric_variety(rays::Vector{Vector{Int64}}, max_cones::Vector{Vector{Int64}}; non_redundant::Bool = false, set_attributes::Bool = true)
-    fan = PolyhedralFan(transpose(hcat(rays...)), IncidenceMatrix(max_cones); non_redundant = non_redundant)
+    fan = polyhedral_fan(transpose(hcat(rays...)), IncidenceMatrix(max_cones); non_redundant = non_redundant)
     return normal_toric_variety(fan; set_attributes = set_attributes)
 end
 
@@ -234,7 +234,7 @@ Normal, affine, 2-dimensional toric variety
 """
 function affine_space(::Type{NormalToricVariety}, d::Int; set_attributes::Bool = true)
     C = positive_hull(identity_matrix(ZZ, d))
-    fan = PolyhedralFan(C)
+    fan = polyhedral_fan(C)
     pmntv = Polymake.fulton.NormalToricVariety(Oscar.pm_object(fan))
     variety = NormalToricVariety(pmntv)
 
@@ -342,7 +342,7 @@ function weighted_projective_space(::Type{NormalToricVariety}, w::Vector{T}; set
     tr,_ = pseudo_inv(lattice_gens)
     ray_gens = ray_gens * transpose(tr)
     mc = IncidenceMatrix(subsets(Vector{Int}(1:length(w)), length(w)-1))
-    variety = normal_toric_variety(PolyhedralFan(ray_gens, mc; non_redundant=true ))
+    variety = normal_toric_variety(polyhedral_fan(ray_gens, mc; non_redundant=true ))
 
     # make standard choice for the weights of the cox ring
     set_attribute!(variety, :torusinvariant_weil_divisor_group, free_abelian_group(length(w)))
@@ -381,7 +381,7 @@ Normal, non-affine, smooth, projective, gorenstein, non-fano, 2-dimensional tori
 function hirzebruch_surface(::Type{NormalToricVariety}, r::Int; set_attributes::Bool = true)
     fan_rays = [1 0; 0 1; -1 r; 0 -1]
     cones = IncidenceMatrix([[1, 2], [2, 3], [3, 4], [4, 1]])
-    variety = normal_toric_variety(PolyhedralFan(fan_rays, cones; non_redundant = true))
+    variety = normal_toric_variety(polyhedral_fan(fan_rays, cones; non_redundant = true))
 
     # make standard choice for the weights of the cox ring
     set_attribute!(variety, :torusinvariant_cartier_divisor_group, free_abelian_group(4))
@@ -457,7 +457,7 @@ function del_pezzo_surface(::Type{NormalToricVariety}, b::Int; set_attributes::B
         fan_rays = [1 0; 0 1; -1 -1; 1 1; 0 -1; -1 0]
         cones = IncidenceMatrix([[1, 4], [2, 4], [1, 5], [5, 3], [2, 6], [6, 3]])
     end
-    variety = normal_toric_variety(PolyhedralFan(fan_rays, cones; non_redundant = true))
+    variety = normal_toric_variety(polyhedral_fan(fan_rays, cones; non_redundant = true))
 
     # make standard choice for weights of the cox ring
     if b == 1
@@ -754,7 +754,7 @@ function normal_toric_varieties_from_star_triangulations(P::Polyhedron; set_attr
     max_cones = [IncidenceMatrix([[c[i]-1 for i in 2:length(c)] for c in t]) for t in max_cones]
 
     # construct the varieties
-    return [normal_toric_variety(PolyhedralFan(integral_rays, cones; non_redundant = true), set_attributes = set_attributes) for cones in max_cones]
+    return [normal_toric_variety(polyhedral_fan(integral_rays, cones; non_redundant = true), set_attributes = set_attributes) for cones in max_cones]
 end
 
 

src/AlgebraicGeometry/ToricVarieties/ToricDivisors/attributes.jl

@@ -37,7 +37,7 @@ julia> is_feasible(polyhedron(td2))
 false
 ```
 """
-@attr Polyhedron polyhedron(td::ToricDivisor) = Polyhedron(pm_tdivisor(td).SECTION_POLYTOPE)
+@attr Polyhedron polyhedron(td::ToricDivisor) = polyhedron(pm_tdivisor(td).SECTION_POLYTOPE)
 
 
 @doc raw"""

src/AlgebraicGeometry/ToricVarieties/ToricMorphisms/constructors.jl

@@ -145,7 +145,7 @@ function toric_morphism(domain::AbstractNormalToricVariety, grid_morphism::GrpAb
     # compute the image
     image_rays = matrix(ZZ, rays(domain)) * matrix(grid_morphism)
     image_rays = hcat([[Int(image_rays[i, j]) for i in 1:nrows(image_rays)] for j in 1:ncols(image_rays)]...)
-    image = normal_toric_variety(PolyhedralFan(image_rays, ray_indices(maximal_cones(domain))))
+    image = normal_toric_variety(polyhedral_fan(image_rays, ray_indices(maximal_cones(domain))))
 
     # compute the morphism
     if codomain === nothing

src/AlgebraicGeometry/ToricVarieties/ToricMorphisms/special_attributes.jl

@@ -16,7 +16,7 @@ A toric morphism
     mapping_matrix = matrix(ZZ, rays(fan(variety)))
     max_cones_for_cox_variety = ray_indices(maximal_cones(variety))
     rays_for_cox_variety = matrix(ZZ, [[if i==j 1 else 0 end for j in 1:nrays(variety)] for i in 1:nrays(variety)])
-    cox_variety = normal_toric_variety(PolyhedralFan(rays_for_cox_variety, max_cones_for_cox_variety))
+    cox_variety = normal_toric_variety(polyhedral_fan(rays_for_cox_variety, max_cones_for_cox_variety))
     return toric_morphism(cox_variety, mapping_matrix, variety)
 end
 

src/AlgebraicGeometry/TropicalGeometry/curve.jl

@@ -82,7 +82,7 @@ end
 function TropicalCurve(graph::IncidenceMatrix, M::Union{typeof(min),typeof(max)}=min)
     # Columns correspond to nodes
     # Rows correpons to edges
-    empty = PolyhedralComplex(Polymake.fan.PolyhedralComplex())
+    empty = polyhedral_complex(Polymake.fan.PolyhedralComplex())
     result = TropicalCurve{M, false}(empty)
     set_attribute!(result, :graph, graph)
     return result

src/AlgebraicGeometry/TropicalGeometry/groebner_polyhedron.jl

@@ -90,5 +90,5 @@ function groebner_polyhedron(GB::Vector{<:MPolyRingElem}, inGB::Vector{<:MPolyRi
     end
   end
 
-  return Polyhedron(A,b)
+  return polyhedron(A,b)
 end

src/AlgebraicGeometry/TropicalGeometry/hypersurface.jl

@@ -82,7 +82,7 @@ function TropicalHypersurface(f::AbstractAlgebra.Generic.MPoly{Oscar.TropicalSem
     pmpoly = Polymake.common.totropicalpolynomial(fstr...)
     pmhypproj = Polymake.tropical.Hypersurface{M}(POLYNOMIAL=pmpoly)
     pmhyp = Polymake.tropical.affine_chart(pmhypproj)
-    Vf = TropicalHypersurface{M, true}(PolyhedralComplex(pmhyp))
+    Vf = TropicalHypersurface{M, true}(polyhedral_complex(pmhyp))
     w = pmhypproj.WEIGHTS
     set_attribute!(Vf,:polymake_bigobject,pmhypproj)
     set_attribute!(Vf,:tropical_polynomial,f)

src/AlgebraicGeometry/TropicalGeometry/links.jl

@@ -36,7 +36,7 @@ function homogeneity_space(I; compute_groebner_basis::Bool=false)
     end
   end
 
-  return Polyhedron((zeros(Int,0,n),zeros(Int,0)),(A,b))
+  return polyhedron((zeros(Int,0,n),zeros(Int,0)),(A,b))
 end
 
 

src/AlgebraicGeometry/TropicalGeometry/variety.jl

@@ -81,7 +81,7 @@ julia> VR = [0 0; 1 0; 0 1; -1 -1];
 
 julia> far_vertices = [2,3,4];
 
-julia> Sigma = PolyhedralComplex(IM, VR, far_vertices);
+julia> Sigma = polyhedral_complex(IM, VR, far_vertices);
 
 julia> tropicalLine = TropicalVariety{min,true}(Sigma)
 """
@@ -277,7 +277,7 @@ function tropical_variety(I::MPolyIdeal, val::TropicalSemiringMap, convention::U
     # 3.0.1: dehomogenize Groebner polyhedra
     zeroth_unit_vector_as_row_vector = zeros(Int,1,n)
     zeroth_unit_vector_as_row_vector[1,1] = 1
-    dehomogenising_hyperplane = Polyhedron((zeros(Int,0,n),zeros(Int,0)),
+    dehomogenising_hyperplane = polyhedron((zeros(Int,0,n),zeros(Int,0)),
                                            (zeroth_unit_vector_as_row_vector,[1]))
     for wCG in working_list_done
       wCG[2] = intersect(wCG[2],dehomogenising_hyperplane)
@@ -333,7 +333,7 @@ function tropical_variety(I::MPolyIdeal, val::TropicalSemiringMap, convention::U
 
 
 
-  PC = PolyhedralComplex(IncidenceMatrix(incidence_matrix),
+  PC = polyhedral_complex(IncidenceMatrix(incidence_matrix),
   verts_rays_matrix,
   far_vertices,
   lineality_space_gens)

src/Combinatorics/Graphs.jl

@@ -927,7 +927,7 @@ julia> fractional_cut_polytope(G)
 Polyhedron in ambient dimension 6
 ```
 """
-fractional_cut_polytope(G::Graph{Undirected}) = Polyhedron(Polymake.polytope.fractional_cut_polytope(pm_object(G)))
+fractional_cut_polytope(G::Graph{Undirected}) = polyhedron(Polymake.polytope.fractional_cut_polytope(pm_object(G)))
 
 
 @doc raw"""
@@ -944,4 +944,4 @@ julia> fractional_matching_polytope(G)
 Polyhedron in ambient dimension 6
 ```
 """
-fractional_matching_polytope(G::Graph{Undirected}) = Polyhedron(Polymake.polytope.fractional_matching_polytope(pm_object(G)))
+fractional_matching_polytope(G::Graph{Undirected}) = polyhedron(Polymake.polytope.fractional_matching_polytope(pm_object(G)))