Merge branch 'master' into two_neighbor_step_in_char_0

.gitignore

@@ -6,7 +6,7 @@
 profile.pb.gz
 alloc-profile.pb.gz
 LocalPreferences.toml
-Manifest.toml
+Manifest*.toml
 .DS_Store
 *~
 *.swp

Artifacts.toml

@@ -1,10 +1,10 @@
 [QSMDB]
-git-tree-sha1 = "5c82e5ff3aa99f2aa660c9ffb3caa57ee535cc21"
+git-tree-sha1 = "52686066016440cf2e6e286a923aed887658543c"
 lazy = true
 
      [[QSMDB.download]]
-     sha256 = "3f69aae0fca02d74764f709c622388c564e6e144a8b11347dadef5725a65b0a2"
-     url = "https://github.com/oscar-system/Oscar.jl/releases/download/archive-tag-1/qsmdb.tar.gz"     
+     sha256 = "2b0a368c07d368f3973352b7f6e856214e25383d2cc3a78c70415afe247a997e"
+     url = "https://github.com/oscar-system/Oscar.jl/releases/download/archive-tag-1/QSMDB-2.tar.gz"     
 
 [gap_extraperfect]
 git-tree-sha1 = "084fa12573e5089ceb3299f9d341f244b415da52"

Project.toml

@@ -25,8 +25,8 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 cohomCalg_jll = "5558cf25-a90e-53b0-b813-cadaa3ae7ade"
 
 [compat]
-AbstractAlgebra = "0.43.1"
-AlgebraicSolving = "0.7.0"
+AbstractAlgebra = "0.43.7"
+AlgebraicSolving = "0.8.0"
 Distributed = "1.6"
 GAP = "0.12.0"
 Hecke = "0.34.3"

docs/src/CommutativeAlgebra/ModulesOverMultivariateRings/subquotients.md

@@ -354,6 +354,18 @@ sum(M::SubquoModule{T},N::SubquoModule{T}) where T
 intersect(M::SubquoModule{T}, N::SubquoModule{T}) where T
 ```
 
+```@docs
+annihilator(N::SubquoModule{T}) where T
+```
+
+```@docs
+quotient(M::SubquoModule{T}, N::SubquoModule{T}) where T
+```
+
+```@docs
+quotient(M::SubquoModule{T}, J::MPolyIdeal{T}) where T
+```
+
 ## Submodules and Quotients
 
 ```@docs

docs/src/CommutativeAlgebra/affine_algebras.md

@@ -171,6 +171,10 @@ simplify(f::MPolyQuoRingElem)
 ==(f::MPolyQuoRingElem{T}, g::MPolyQuoRingElem{T}) where T
 ```
 
+```@docs
+is_invertible_with_inverse(f::MPolyQuoRingElem)
+```
+
 In the graded case, we additionally have:
 
 ```@docs

docs/src/CommutativeAlgebra/ideals.md

@@ -134,7 +134,7 @@ Given two ideals $I, J$ of a ring $R$, the saturation of $I$ with respect to $J$
 $I:J^{\infty} = \bigl\{ f \in R \:\big|\: f J^k \!\subset I {\text{ for some }}k\geq 1 \bigr\} = \textstyle{\bigcup\limits_{k=1}^{\infty} (I:J^k)}.$
 
 ```@docs
-saturation(I::MPolyIdeal{T}, J::MPolyIdeal{T}) where T
+saturation(I::MPolyIdeal{T}, J::MPolyIdeal{T}; iteration::Bool=false) where T
 saturation_with_index(I::MPolyIdeal{T}, J::MPolyIdeal{T}) where T
 ```
 

docs/src/DeveloperDocumentation/design_decisions.md

@@ -90,7 +90,7 @@ software frameworks on a lower level:
  - Gap
 
 So: Please use it. It is safe to assume all can be improved, however, if we try
-to perfect every single line of code again and again, we we won't get anywhere;
+to perfect every single line of code again and again, we won't get anywhere;
 there is a balance to be found.
 For preference: 
 ```

docs/src/Groups/action.md

@@ -61,7 +61,7 @@ action_function(Omega::GSetByElements)
 action_homomorphism(Omega::GSetByElements{T}) where T<:GAPGroup
 is_conjugate(Omega::GSet, omega1, omega2)
 is_conjugate_with_data(Omega::GSet, omega1, omega2)
-orbit(Omega::GSetByElements{<:GAPGroup}, omega::T) where T
+orbit(Omega::GSetByElements{<:GAPGroup, S}, omega::S) where S
 orbit(G::PermGroup, omega)
 orbits(Omega::T) where T <: GSetByElements{TG} where TG <: GAPGroup
 ```
@@ -70,5 +70,6 @@ orbits(Omega::T) where T <: GSetByElements{TG} where TG <: GAPGroup
 ## Stabilizers
 
 ```@docs
-stabilizer(G::Oscar.GAPGroup, pnt::Any, actfun::Function)
+stabilizer(G::GAPGroup, pnt::Any, actfun::Function)
+stabilizer(Omega::GSet)
 ```

docs/src/PolyhedralGeometry/Polyhedra/constructions.md

@@ -26,13 +26,13 @@ julia> P = polyhedron(([-1 0; 1 0], [0,1]), ([0 1], [0]))
 Polyhedron in ambient dimension 2
 
 julia> facets(P)
-2-element SubObjectIterator{AffineHalfspace{QQFieldElem}} over the Halfspaces of R^2 described by:
+2-element SubObjectIterator{AffineHalfspace{QQFieldElem}} over the halfspaces of R^2 described by:
 -x_1 <= 0
 x_1 <= 1
 
 
 julia> affine_hull(P)
-1-element SubObjectIterator{AffineHyperplane{QQFieldElem}} over the Hyperplanes of R^2 described by:
+1-element SubObjectIterator{AffineHyperplane{QQFieldElem}} over the hyperplanes of R^2 described by:
 x_2 = 0
 
 

docs/src/PolyhedralGeometry/intro.md

@@ -159,7 +159,13 @@ Some methods will require input or return output in form of an `IncidenceMatrix`
 IncidenceMatrix
 ```
 
-From the example it can be seen that this type supports `julia`'s matrix functionality. There are also functions to retrieve specific rows or columns as a `Set` over the non-zero indices.
+The unique nature of the `IncidenceMatrix` allows for different ways of construction:
+
+```@docs
+incidence_matrix
+```
+
+From the examples it can be seen that this type supports `julia`'s matrix functionality. There are also functions to retrieve specific rows or columns as a `Set` over the non-zero indices.
 
 ```@docs
 row(i::IncidenceMatrix, n::Int)

etc/test_formatting.jl

@@ -1,7 +1,7 @@
 using Pkg
 Pkg.activate(; temp=true)
 Pkg.add("Test")
-Pkg.add("JuliaFormatter")
+Pkg.add(name="JuliaFormatter", version="1")
 using Test
 using JuliaFormatter
 

experimental/FTheoryTools/src/AbstractFTheoryModels/attributes.jl

@@ -1052,7 +1052,7 @@ julia> qsm_model = literature_model(arxiv_id = "1903.00009", model_parameters =
 Hypersurface model over a concrete base
 
 julia> zero_section_class(qsm_model)
-Cohomology class on a normal toric variety given by x32 + 2*x33 + 3*x34 + x35 - x36
+Cohomology class on a normal toric variety given by e2 + 2*u + 3*e4 + e1 - w
 ```
 """
 function zero_section_class(m::AbstractFTheoryModel)
@@ -1741,7 +1741,7 @@ end
 
 
 @doc raw"""
-    simplified dual_graph(m::AbstractFTheoryModel)
+    simplified_dual_graph(m::AbstractFTheoryModel)
 
 This method returns the simplified dual graph of the QSM model in question.
 Note that no labels are (currently) attached to the vertices/nodes or edges.

experimental/FTheoryTools/src/AbstractFTheoryModels/methods.jl

@@ -118,7 +118,7 @@ julia> x1, x2, x3, x4, x, y, z = gens(cox_ring(ambient_space(t)))
 
 julia> blowup_center = ideal_sheaf(ambient_space(t), ideal([x, y, x1]))
 Sheaf of ideals
-  on normal toric variety
+  on normal, simplicial toric variety
 with restrictions
    1: Ideal (x_5_1, x_4_1, x_1_1)
    2: Ideal (1)

experimental/FTheoryTools/src/HypersurfaceModels/constructors.jl

@@ -72,7 +72,7 @@ function hypersurface_model(base::NormalToricVariety, fiber_ambient_space::Norma
   @req length(ds) == 1 "Inconsistency in determining the degree of the hypersurface equation"
   @req ds[1] == divisor_class(anticanonical_divisor_class(ambient_space)).coeff "Degree of hypersurface equation differs from anticanonical bundle"
   explicit_model_sections = Dict{String, MPolyRingElem}()
-  gens_S = gens(cox_ring(ambient_space))
+  gens_S = gens(cox_ring(base))
   for k in 1:length(gens_S)
     explicit_model_sections[string(gens_S[k])] = gens_S[k]
   end

experimental/FTheoryTools/src/LiteratureModels/Models/model1511_03209.json

@@ -48,7 +48,7 @@
             [1, 2, 3, 4, 6]
         ],
         "zero_section_class": "z",
-        "zero_section": ["1", "1", "0"]
+        "zero_section": ["1", "1", "0"],
         "resolutions": [
             [
                 [
@@ -289,11 +289,8 @@
                 ["e99_4", "e99_8"],
                 ["e99_4", "e99_9"],
                 ["e99_8", "e99_9"],
-                ["e99_9", "e99_11"],
+                ["e99_9", "e99_11"]
 
-                ["y", "z"],
-                ["x", "ea_1"],
-                ["z", "ea_2"]
                 ],
                 [
                 "e9_1", "e9_2", "e9_3", "e9_4",
@@ -328,8 +325,7 @@
                 "e63_1", "e63_2", "e63_3", "e63_4", "e63_5", "e63_6", "e63_7", "e63_8", "e63_9", "e63_10", "e63_11", "e63_12", "e63_13", "e63_14",
                 "e75_1", "e75_2", "e75_3", "e75_4", "e75_5", "e75_6", "e75_7", "e75_8", "e75_9", "e75_10", "e75_11", "e75_12", "e75_13", "e75_14",
                 "e87_1", "e87_2", "e87_3", "e87_4", "e87_5", "e87_6", "e87_7", "e87_8", "e87_9", "e87_10", "e87_11", "e87_12", "e87_13", "e87_14",
-                "e99_1", "e99_2", "e99_3", "e99_4", "e99_5", "e99_6", "e99_7", "e99_8", "e99_9", "e99_10", "e99_11", "e99_12", "e99_13", "e99_14",
-                "ea_1", "ea_2", "ea_3"
+                "e99_1", "e99_2", "e99_3", "e99_4", "e99_5", "e99_6", "e99_7", "e99_8", "e99_9", "e99_10", "e99_11", "e99_12", "e99_13", "e99_14"
                 ]
             ]
         ]

experimental/FTheoryTools/src/LiteratureModels/constructors.jl

@@ -203,7 +203,7 @@ function literature_model(model_dict::Dict{String, Any}; model_parameters::Dict{
   if model_dict["arxiv_data"]["id"] == "1903.00009"
 
     # Read in the QSM-model form the database
-    model_dict["literature_identifier"] = "1903.00009"
+    model_dict["literature_identifier"] = "1903_00009"
     k = model_parameters["k"]
     qsmd_path = artifact"QSMDB"
     qsm_model = load(joinpath(qsmd_path, "$k.mrdi"))
@@ -276,6 +276,11 @@ function literature_model(model_dict::Dict{String, Any}; model_parameters::Dict{
       @req dim(base_space) == Int(model_dict["model_data"]["base_dim"]) "Model requires base dimension different from dimension of provided base"
     end
 
+    # Add additional information that is always known for weierstrass/tate 
+    if (model_dict["model_descriptors"]["type"] == "weierstrass") || (model_dict["model_descriptors"]["type"] == "tate")
+      model_dict["model_data"]["zero_section_class"] = "z"
+    end
+
     # Construct the model
     model = _construct_literature_model_over_concrete_base(model_dict, base_space, defining_classes_provided, completeness_check)
     @vprint :FTheoryModelPrinter 0 "Construction over concrete base may lead to singularity enhancement. Consider computing singular_loci. However, this may take time!\n\n"
@@ -634,7 +639,7 @@ function _set_all_attributes(model::AbstractFTheoryModel, model_dict::Dict{Strin
     set_zero_section(model, string.(model_dict["model_data"]["zero_section"]))
   end
 
-  if haskey(model_dict["model_data"], "zero_section_class")
+  if haskey(model_dict["model_data"], "zero_section_class") && base_space(model) isa NormalToricVariety
     set_zero_section_class(model, string.(model_dict["model_data"]["zero_section_class"]))
   end
 

experimental/FTheoryTools/src/LiteratureModels/create_index.jl

@@ -95,6 +95,6 @@ function _create_literature_model_index()
     JSON.print(file, index)
   end
   open(joinpath(@__DIR__,"model_indices.json"), "w") do file
-    JSON.print(file, sort(model_indices), 2)
+    JSON.print(file, model_indices, 2)
   end
 end

experimental/FTheoryTools/src/LiteratureModels/model_indices.json

@@ -1,48 +1,48 @@
 {
-  "model1109_3454.json": "1",
-  "model1208_2695-1.json": "2",
-  "model1208_2695-2.json": "3",
-  "model1212_2949-1.json": "4",
-  "model1212_2949-2.json": "5",
-  "model1212_2949-3.json": "6",
-  "model1212_2949-4.json": "7",
-  "model1212_2949-5.json": "8",
-  "model1212_2949-6.json": "9",
-  "model1212_2949-7.json": "10",
-  "model1408_4808-1-WSF.json": "13",
+  "model1511_03209.json": "46",
   "model1408_4808-1.json": "14",
-  "model1408_4808-10-WSF.json": "31",
-  "model1408_4808-10.json": "32",
-  "model1408_4808-11-WSF.json": "33",
-  "model1408_4808-11.json": "34",
+  "model1408_4808-1-WSF.json": "13",
+  "model1212_2949-6.json": "9",
+  "model1408_4808-14.json": "40",
   "model1408_4808-12-WSF.json": "35",
   "model1408_4808-12.json": "36",
-  "model1408_4808-13-WSF.json": "37",
-  "model1408_4808-13.json": "38",
-  "model1408_4808-14-WSF.json": "39",
-  "model1408_4808-14.json": "40",
   "model1408_4808-15-WSF.json": "41",
-  "model1408_4808-15.json": "42",
-  "model1408_4808-16-WSF.json": "43",
-  "model1408_4808-16.json": "44",
-  "model1408_4808-2-WSF.json": "15",
-  "model1408_4808-2.json": "16",
-  "model1408_4808-3-WSF.json": "17",
-  "model1408_4808-3.json": "18",
-  "model1408_4808-4-WSF.json": "19",
-  "model1408_4808-4.json": "20",
-  "model1408_4808-5-WSF.json": "21",
+  "model1212_2949-2.json": "5",
+  "model1212_2949-7.json": "10",
   "model1408_4808-5.json": "22",
-  "model1408_4808-6-WSF.json": "23",
-  "model1408_4808-6.json": "24",
+  "model1212_2949-1.json": "4",
   "model1408_4808-7-WSF.json": "25",
   "model1408_4808-7.json": "26",
-  "model1408_4808-8-WSF.json": "27",
-  "model1408_4808-8.json": "28",
+  "model1208_2695-2.json": "3",
+  "model1408_4808-14-WSF.json": "39",
+  "model1903_00009.json": "45",
+  "model1408_4808-4-WSF.json": "19",
   "model1408_4808-9-WSF.json": "29",
-  "model1408_4808-9.json": "30",
+  "model1408_4808-6-WSF.json": "23",
+  "model1408_4808-13-WSF.json": "37",
+  "model1408_4808-11-WSF.json": "33",
+  "model1408_4808-10-WSF.json": "31",
+  "model1212_2949-3.json": "6",
   "model1507_05954-1.json": "11",
+  "model1212_2949-4.json": "7",
+  "model1408_4808-8.json": "28",
   "model1507_05954-2.json": "12",
-  "model1511_03209.json": "46",
-  "model1903_00009.json": "45"
+  "model1408_4808-4.json": "20",
+  "model1408_4808-13.json": "38",
+  "model1408_4808-6.json": "24",
+  "model1408_4808-15.json": "42",
+  "model1109_3454.json": "1",
+  "model1408_4808-5-WSF.json": "21",
+  "model1408_4808-11.json": "34",
+  "model1208_2695-1.json": "2",
+  "model1408_4808-8-WSF.json": "27",
+  "model1408_4808-10.json": "32",
+  "model1408_4808-9.json": "30",
+  "model1408_4808-16.json": "44",
+  "model1408_4808-3.json": "18",
+  "model1408_4808-2.json": "16",
+  "model1408_4808-3-WSF.json": "17",
+  "model1212_2949-5.json": "8",
+  "model1408_4808-2-WSF.json": "15",
+  "model1408_4808-16-WSF.json": "43"
 }

experimental/FTheoryTools/src/Serialization/hypersurface_models.jl

@@ -56,6 +56,13 @@ function save_object(s::SerializerState, h::HypersurfaceModel)
         attrs_dict[key] = value
       end
     end
+    if has_resolutions(h)
+      res = resolutions(h)
+      resolution_loci = [k[1] for k in res]
+      exceptional_divisors = [k[2] for k in res]
+      attrs_dict[:resolution_loci] = resolution_loci
+      attrs_dict[:exceptional_divisors] = exceptional_divisors
+    end
     !isempty(attrs_dict) && save_typed_object(s, attrs_dict, :__attrs)
   end
 end
@@ -66,16 +73,25 @@ end
 ##########################################
 
 function load_object(s::DeserializerState, ::Type{<:HypersurfaceModel}, params::Tuple{NormalToricVariety, NormalToricVariety, NormalToricVariety, <:MPolyRing, <:MPolyRing})
-  base_space, ambient_space, fiber_ambient_space, R1, R2 = params
+  base_space, amb_space, fiber_ambient_space, R1, R2 = params
   defining_equation = load_object(s, MPolyRingElem, R1, :hypersurface_equation)
   defining_equation_parametrization = load_object(s, MPolyRingElem, R2, :hypersurface_equation_parametrization)
   explicit_model_sections = haskey(s, :explicit_model_sections) ? load_typed_object(s, :explicit_model_sections) : Dict{String, MPolyRingElem}()
   defining_classes = haskey(s, :defining_classes) ? load_typed_object(s, :defining_classes) : Dict{String, ToricDivisorClass}()
-  model = HypersurfaceModel(explicit_model_sections, defining_equation_parametrization, defining_equation, base_space, ambient_space, fiber_ambient_space)
+  model = HypersurfaceModel(explicit_model_sections, defining_equation_parametrization, defining_equation, base_space, amb_space, fiber_ambient_space)
   model.defining_classes = defining_classes
   attrs_data = haskey(s, :__attrs) ? load_typed_object(s, :__attrs) : Dict{Symbol, Any}()
   for (key, value) in attrs_data
-    set_attribute!(model, Symbol(key), value)
+    if (key != :resolution_loci) && (key != :exceptional_divisors)
+      set_attribute!(model, Symbol(key), value)
+    end
+  end
+  if haskey(attrs_data, :resolution_loci)
+    resolution_loci = attrs_data[:resolution_loci]
+    exceptional_divisors = attrs_data[:exceptional_divisors]
+    @req length(exceptional_divisors) == length(exceptional_divisors) "Inconsistency upon loading resolutions"
+    set_attribute!(model, :resolutions, [[resolution_loci[i], exceptional_divisors[i]] for i in 1:length(resolution_loci)])
   end
+  @req cox_ring(ambient_space(model)) == parent(hypersurface_equation(model)) "Hypersurface polynomial not in Cox ring of toric ambient space"
   return model
 end