Merge branch 'master' into lg/dep-bump

docs/Project.toml

@@ -4,4 +4,4 @@ DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 
 [compat]
 Documenter = "1.1"
-DocumenterCitations = "~1.3.1"
+DocumenterCitations = "~1.3.4"

docs/citation_style.jl

@@ -11,7 +11,7 @@ const oscar_style = :oscar
 
 # The long reference string in the bibliography
 function DocumenterCitations.format_bibliography_reference(style::Val{oscar_style}, entry)
-  return DocumenterCitations.format_labeled_bibliography_reference(style, entry)
+  return DocumenterCitations.format_labeled_bibliography_reference(style, entry; article_link_doi_in_title=true)
 end
 
 # The label in the bibliography

docs/oscar_references.bib

@@ -114,7 +114,7 @@ @Article{BBS02
 }
 
 @Article{BCL21,
-  author        = {Bies, Martin and Cveti\v{c}, Mirjam and Liu, Muyang},
+  author        = {Bies, Martin and Cvetič, Mirjam and Liu, Muyang},
   title         = {Statistics of limit root bundles relevant for exact matter spectra of F-theory MSSMs},
   journal       = {Phys. Rev. D},
   volume        = {104},
@@ -193,12 +193,12 @@ @InProceedings{BES-E-D21
   location      = {Virtual Event, Russian Federation}
 }
 
-@Article{BES19,
+@Misc{BES19,
   author        = {Backman, Spencer and Eur, Christopher and Simpson, Connor},
   title         = {Simplicial generation of Chow rings of matroids},
-  journal       = {arXiv:1905.07114},
   year          = {2019},
-  doi           = {10.48550/arxiv.1905.07114},
+  eprint        = {1905.07114},
+  archiveprefix = {arXiv},
   primaryclass  = {math.CO}
 }
 
@@ -236,12 +236,12 @@ @Article{BH23
   doi           = {10.1017/fms.2023.50}
 }
 
-@Article{BHMPW20,
+@Misc{BHMPW20,
   author        = {Braden, Tom and Huh, June and Matherne, Jacob P. and Proudfoot, Nicholas and Wang, Botong},
   title         = {A semi-small decomposition of the Chow ring of a matroid},
-  journal       = {arXiv:2002.03341},
   year          = {2020},
-  doi           = {10.48550/arXiv.2002.03341},
+  eprint        = {2002.03341},
+  archiveprefix = {arXiv},
   primaryclass  = {math.AG}
 }
 
@@ -386,7 +386,7 @@ @PhDThesis{Bie18
 
 @Article{Bie24,
   author        = {Bies, Martin},
-  title         = {{Root bundles: Applications to F-theory Standard Models}},
+  title         = {Root bundles: Applications to F-theory Standard Models},
   journal       = {Proc. Symp. Pure Math.},
   volume        = {107},
   pages         = {17--44},
@@ -450,8 +450,8 @@ @Book{CCNPW85
 }
 
 @Article{CHLLT19,
-  author        = {Cveti\v{c}, Mirjam and Halverson, James and Lin, Ling and Liu, Muyang and Tian, Jiahua},
-  title         = {{Quadrillion $F$-Theory Compactifications with the Exact Chiral Spectrum of the Standard Model}},
+  author        = {Cvetič, Mirjam and Halverson, James and Lin, Ling and Liu, Muyang and Tian, Jiahua},
+  title         = {Quadrillion $F$-Theory Compactifications with the Exact Chiral Spectrum of the Standard Model},
   journal       = {Phys. Rev. Lett.},
   volume        = {123},
   number        = {10},
@@ -560,12 +560,12 @@ @Article{CSZ15
   doi           = {10.1007/s00493-014-2959-9}
 }
 
-@Article{CW16,
+@Misc{CW16,
   author        = {Cébron, Guillaume and Weber, Moritz},
   title         = {Quantum groups based on spatial partitions},
-  journal       = {arXiv:1609.02321},
   year          = {2016},
-  doi           = {10.48550/arXiv.1609.02321},
+  eprint        = {1609.02321},
+  archiveprefix = {arXiv},
   primaryclass  = {math.QA}
 }
 
@@ -651,13 +651,13 @@ @Article{DES93
   zbmath        = {404355}
 }
 
-@Article{DF20,
+@Misc{DF20,
   bibkey        = {DF20},
   author        = {De Franceschi, G.},
   title         = {Centralizers and conjugacy classes in finite classical groups},
-  journal       = {arXiv:2008.12651},
   year          = {2020},
-  doi           = {10.48550/arXiv.2008.12651},
+  eprint        = {2008.12651},
+  archiveprefix = {arXiv},
   primaryclass  = {math.GR}
 }
 
@@ -801,7 +801,7 @@ @Book{DSS09
   zbl           = {1166.13001},
   series        = {Oberwolfach Semin.},
   volume        = {39},
-  publisher     = {Basel: Birkh{\"a}user},
+  publisher     = {Basel: Birkhäuser},
   year          = {2009},
   fseries       = {Oberwolfach Seminars},
   language      = {English},
@@ -821,7 +821,7 @@ @Article{Der99
 }
 
 @Article{EFS03,
-  author        = {Eisenbud, David and Fl{\o}ystad, Gunnar and Schreyer, Frank-Olaf},
+  author        = {Eisenbud, David and Fløystad, Gunnar and Schreyer, Frank-Olaf},
   title         = {Sheaf cohomology and free resolutions over exterior algebras},
   zbl           = {1063.14021},
   journal       = {Trans. Am. Math. Soc.},
@@ -896,7 +896,7 @@ @Article{EM19
 }
 
 @Article{EMSS16,
-  author        = {Er{\"o}cal, Bur{\c{c}}in and Motsak, Oleksandr and Schreyer, Frank-Olaf and Steenpa{\ss}, Andreas},
+  author        = {Eröcal, Burçin and Motsak, Oleksandr and Schreyer, Frank-Olaf and Steenpaß, Andreas},
   title         = {Refined algorithms to compute syzygies},
   zbl           = {1405.14138},
   journal       = {J. Symb. Comput.},
@@ -1325,7 +1325,7 @@ @Misc{HRR23
 
 @Article{HT17,
   author        = {Halverson, James and Tian, Jiahua},
-  title         = {{Cost of seven-brane gauge symmetry in a quadrillion F-theory compactifications}},
+  title         = {Cost of seven-brane gauge symmetry in a quadrillion F-theory compactifications},
   journal       = {Phys. Rev. D},
   volume        = {95},
   number        = {2},
@@ -1590,12 +1590,12 @@ @Article{KMSS11
   reportnumber  = {UCSB-MATH-2011-09, IPMU11-0107, NSF-KITP-11-110, KCL-MTH-11-13}
 }
 
-@Article{KO14,
+@Misc{KO14,
   author        = {Kelleher, Jerome and O'Sullivan, Barry},
   title         = {Generating All Partitions: A Comparison Of Two Encodings},
-  journal       = {arXiv:0909.2331},
   year          = {2014},
-  doi           = {10.48550/arXiv.0909.2331},
+  eprint        = {0909.2331},
+  archiveprefix = {arXiv},
   primaryclass  = {cs.DS}
 }
 
@@ -1655,12 +1655,12 @@ @Article{Kem99
   doi           = {10.1006/jsco.1998.0247}
 }
 
-@Article{Kin07,
+@Misc{Kin07,
   author        = {King, Simon},
   title         = {Fast computation of secondary invariants},
-  journal       = {arXiv:math/0701270},
   year          = {2007},
-  doi           = {10.48550/arXiv.math/0701270},
+  eprint        = {math/0701270},
+  archiveprefix = {arXiv},
   primaryclass  = {math.AC}
 }
 
@@ -1731,8 +1731,8 @@ @InCollection{LS03
 }
 
 @Article{LS13,
-  author        = {Lawrie, Craig and Sch\"afer-Nameki, Sakura},
-  title         = {{The Tate Form on Steroids: Resolution and Higher Codimension Fibers}},
+  author        = {Lawrie, Craig and Schäfer-Nameki, Sakura},
+  title         = {The Tate Form on Steroids: Resolution and Higher Codimension Fibers},
   journal       = {JHEP},
   volume        = {04},
   pages         = {061},
@@ -2058,7 +2058,7 @@ @Article{RSS03
 }
 
 @Article{Rin13,
-  author        = {Rinc{\'o}n, Felipe},
+  author        = {Rincón, Felipe},
   title         = {Computing tropical linear spaces},
   zbl           = {1319.14060},
   journal       = {J. Symb. Comput.},
@@ -2197,7 +2197,7 @@ @Article{Sta79
 @Misc{Stacks,
   bibkey        = {Stacks},
   author        = {{The Stacks Project Authors}},
-  title         = {{S}tacks {P}roject},
+  title         = {Stacks Project},
   howpublished  = {Published electronically},
   url           = {https://stacks.math.columbia.edu/}
 }
@@ -2384,7 +2384,7 @@ @Article{Wit88
 
 @Article{Wit97,
   author        = {Witten, Edward},
-  title         = {{On flux quantization in M theory and the effective action}},
+  title         = {On flux quantization in M theory and the effective action},
   journal       = {J. Geom. Phys.},
   volume        = {22},
   pages         = {1--13},

docs/src/DeveloperDocumentation/documentation.md

@@ -137,4 +137,4 @@ Please follow the additional guidelines below, that are not checked by bibtool:
 - You do not need to use braces to preserve capitalization as `DocumenterCitations.jl` keeps entries as is (in contrast to `bibtex`). In some cases, braces can even be harmful, i.e., show up in the output.
 - If a DOI is available for your reference, please add it as a `doi` field to the BibTeX entry. In this case, please refrain from adding an additional `url` field.
 - If your reference has no DOI or the paper is not open-access, but is available as an arXiv preprint, you can add the arXiv link as a `eprint` field (even additionally to a `doi` field). For other preprint servers (e.g. HAL), please refer to the [DocumenterCitations.jl docs](https://juliadocs.org/DocumenterCitations.jl/stable/syntax/#Preprint-support).
-- Documents available only as an arXiv preprint should be added as `@Article` entries with, e.g., `arXiv:2003.10132` in the `journal` field, and, e.g., `10.48550/arxiv.2003.10132` in the `doi` field, but without an `eprint` field.
+- Documents available only as an arXiv preprint should be added as `@Misc` entries with the arXiv-ID in the `eprint` field, e.g., `archiveprefix = {arXiv}` and `eprint = {2008.12651}`.

experimental/FTheoryTools/src/AbstractFTheoryModels/methods.jl

@@ -157,18 +157,18 @@ function blow_up(m::AbstractFTheoryModel, I::AbsIdealSheaf; coordinate_name::Str
   # Construct the new model
   if m isa GlobalTateModel
     if isdefined(m, :tate_polynomial) && new_ambient_space isa NormalToricVariety
-      new_tate_polynomial = _strict_transform(bd, tate_polynomial(m); coordinate_name)
+      new_tate_polynomial = _strict_transform(bd, tate_polynomial(m))
       model = GlobalTateModel(explicit_model_sections(m), defining_section_parametrization(m), new_tate_polynomial, base_space(m), new_ambient_space)
     else
-      new_tate_ideal_sheaf = _strict_transform(bd, tate_ideal_sheaf(m); coordinate_name)
+      new_tate_ideal_sheaf = _strict_transform(bd, tate_ideal_sheaf(m))
       model = GlobalTateModel(explicit_model_sections(m), defining_section_parametrization(m), new_tate_ideal_sheaf, base_space(m), new_ambient_space)
     end
   else
     if isdefined(m, :weierstrass_polynomial) && new_ambient_space isa NormalToricVariety
-      new_weierstrass_polynomial = _strict_transform(bd, weierstrass_polynomial(m); coordinate_name)
+      new_weierstrass_polynomial = _strict_transform(bd, weierstrass_polynomial(m))
       model = WeierstrassModel(explicit_model_sections(m), defining_section_parametrization(m), new_weierstrass_polynomial, base_space(m), new_ambient_space)
     else
-      new_weierstrass_ideal_sheaf = _strict_transform(bd, weierstrass_ideal_sheaf(m); coordinate_name)
+      new_weierstrass_ideal_sheaf = _strict_transform(bd, weierstrass_ideal_sheaf(m))
       model = WeierstrassModel(explicit_model_sections(m), defining_section_parametrization(m), new_weierstrass_ideal_sheaf, base_space(m), new_ambient_space)
     end
   end

experimental/FTheoryTools/src/auxiliary.jl

@@ -460,15 +460,15 @@ eval_poly(n::Number, R) = R(n)
 ### 10 strict_transform helpers
 ##########################################
 
-_strict_transform(bd::AbsCoveredSchemeMorphism, II::AbsIdealSheaf; coordinate_name = "e") = strict_transform(bd, II)
+_strict_transform(bd::AbsCoveredSchemeMorphism, II::AbsIdealSheaf) = strict_transform(bd, II)
 
-function _strict_transform(bd::ToricBlowdownMorphism, II::ToricIdealSheafFromCoxRingIdeal; coordinate_name = "e")
+function _strict_transform(bd::ToricBlowdownMorphism, II::ToricIdealSheafFromCoxRingIdeal)
   center_ideal = ideal_in_cox_ring(center_unnormalized(bd))
   if (ngens(ideal_in_cox_ring(II)) != 1) || (all(x -> x in gens(base_ring(center_ideal)), gens(center_ideal)) == false)
     return strict_transform(bd, II)
   end
   S = cox_ring(domain(bd))
-  _e = eval_poly(coordinate_name, S)
+  _e = gen(S, index_of_new_ray(bd))
   images = MPolyRingElem[]
   g_list = gens(S)
   g_center = [string(k) for k in gens(ideal_in_cox_ring(center_unnormalized(bd)))]
@@ -487,9 +487,9 @@ function _strict_transform(bd::ToricBlowdownMorphism, II::ToricIdealSheafFromCox
   return ideal_sheaf(domain(bd), strict_transform)
 end
 
-function _strict_transform(bd::ToricBlowdownMorphism, tate_poly::MPolyRingElem; coordinate_name = "e")
+function _strict_transform(bd::ToricBlowdownMorphism, tate_poly::MPolyRingElem)
   S = cox_ring(domain(bd))
-  _e = eval_poly(coordinate_name, S)
+  _e = gen(S, index_of_new_ray(bd))
   g_list = string.(gens(S))
   g_center = [string(k) for k in gens(ideal_in_cox_ring(center_unnormalized(bd)))]
   position_of_center_variables = [findfirst(==(g), g_list) for g in g_center]

experimental/Schemes/src/ToricBlowups/constructors.jl

@@ -50,7 +50,8 @@ and exceptional divisor
       4a: Ideal (x_1_4*x_2_4)
 ```
 """
-function blow_up(m::NormalToricVariety, I::ToricIdealSheafFromCoxRingIdeal; coordinate_name::String = "e")
+function blow_up(m::NormalToricVarietyType, I::ToricIdealSheafFromCoxRingIdeal; coordinate_name::Union{String, Nothing} = nothing)
+  coordinate_name = _find_blowup_coordinate_name(m, coordinate_name)
   defining_ideal = ideal_in_cox_ring(I)
   if all(x -> x in gens(base_ring(defining_ideal)), gens(defining_ideal))
     return blow_up(m, defining_ideal; coordinate_name) # Apply toric method
@@ -59,9 +60,28 @@ function blow_up(m::NormalToricVariety, I::ToricIdealSheafFromCoxRingIdeal; coor
   end
 end
 
+function _find_blowup_coordinate_name(m::NormalToricVarietyType, coordinate_name::Union{String, Nothing} = nothing)
+  if coordinate_name !== nothing
+    @req !(coordinate_name in coordinate_names(m)) "Coordinate name already exists"
+    return coordinate_name
+  else
+    return _find_blowup_coordinate_name(coordinate_names(m))
+  end
+end
+
+function _find_blowup_coordinate_name(vs::Vector{String})
+  i = 1
+  coordinate_name = "e"
+  while coordinate_name in vs
+    coordinate_name = string("e", i)
+    i = i+1
+  end
+  return coordinate_name
+end
+
 
 @doc raw"""
-    blow_up(v::NormalToricVariety, new_ray::AbstractVector{<:IntegerUnion}; coordinate_name::String = "e")
+    blow_up(v::NormalToricVariety, new_ray::AbstractVector{<:IntegerUnion}; coordinate_name::String)
 
 Blow up the toric variety by subdividing the fan of the variety with the
 provided new ray. This function returns the corresponding morphism.
@@ -137,9 +157,9 @@ julia> typeof(center_unnormalized(f))
 IdealSheaf{NormalToricVariety, AbsAffineScheme, Ideal, Map}
 ```
 """
-function blow_up(v::NormalToricVariety, new_ray::AbstractVector{<:IntegerUnion}; coordinate_name::String = "e")
+function blow_up(v::NormalToricVarietyType, new_ray::AbstractVector{<:IntegerUnion}; coordinate_name::Union{String, Nothing} = nothing)
+  coordinate_name = _find_blowup_coordinate_name(v, coordinate_name)
   new_variety = normal_toric_variety(star_subdivision(v, new_ray))
-  @req n_rays(v) != n_rays(new_variety) "New ray already a ray of the given toric variety"
   if is_smooth(v) == false
     return ToricBlowdownMorphism(v, new_variety, coordinate_name, new_ray, new_ray)
   end
@@ -188,7 +208,8 @@ Multivariate polynomial ring in 5 variables over QQ graded by
   e -> [1 -1]
 ```
 """
-function blow_up(v::NormalToricVariety, n::Int; coordinate_name::String = "e")
+function blow_up(v::NormalToricVarietyType, n::Int; coordinate_name::Union{String, Nothing} = nothing)
+  coordinate_name = _find_blowup_coordinate_name(v, coordinate_name)
   gens_S = gens(cox_ring(v))
   center_unnormalized = ideal_sheaf(v, ideal([gens_S[i] for i in 1:number_of_rays(v) if cones(v)[n,i]]))
   new_variety = normal_toric_variety(star_subdivision(v, n))
@@ -247,7 +268,8 @@ julia> codomain(b2P3) === P3
 true
 ```
 """
-function blow_up(v::NormalToricVariety, I::MPolyIdeal; coordinate_name::String = "e")
+function blow_up(v::NormalToricVarietyType, I::MPolyIdeal; coordinate_name::Union{String, Nothing} = nothing)
+  coordinate_name = _find_blowup_coordinate_name(v, coordinate_name)
   cox = cox_ring(v)
   indices = [findfirst(y -> y == x, gens(cox)) for x in gens(I)]
   if all(index -> index !== nothing, indices)
@@ -266,6 +288,6 @@ function _generic_blow_up(v::Any, I::Any)
   error("Not yet supported")
 end
 
-function _generic_blow_up(v::NormalToricVariety, I::MPolyIdeal)
+function _generic_blow_up(v::NormalToricVarietyType, I::MPolyIdeal)
   return blow_up(ideal_sheaf(v, I))
 end