Merge branch 'master' into minimal_associated_primes

.github/workflows/CI.yml

@@ -6,6 +6,9 @@ on:
  - master
  - 'release-*'
  pull_request:
+ schedule:
+ # Every day at 3:10 AM UTC
+ - cron: '10 3 * * *'
  workflow_dispatch:
 
 # needed to allow julia-actions/cache to delete old caches that it has created
@@ -56,6 +59,9 @@ jobs:
  - julia-version: '1.10'
  group: 'book'
  os: ubuntu-latest
+ - julia-version: 'nightly'
+ group: 'book'
+ os: ubuntu-latest
  # nightly on macos is disabled for now since the macos jobs take too long
  # with just 5 runners
  #- julia-version: 'nightly'

.gitignore

@@ -4,6 +4,7 @@
 /docs/src/Nemo/
 /docs/src/Experimental/
 profile.pb.gz
+alloc-profile.pb.gz
 LocalPreferences.toml
 Manifest.toml
 .DS_Store

Project.toml

@@ -25,22 +25,22 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 cohomCalg_jll = "5558cf25-a90e-53b0-b813-cadaa3ae7ade"
 
 [compat]
-AbstractAlgebra = "0.42.0"
-AlgebraicSolving = "0.5.1"
+AbstractAlgebra = "0.43.1"
+AlgebraicSolving = "0.7.0"
 Distributed = "1.6"
-GAP = "0.10.2"
-Hecke = "0.33.0"
+GAP = "0.12.0"
+Hecke = "0.34.3"
 JSON = "^0.20, ^0.21"
 JSON3 = "1.13.2"
 LazyArtifacts = "1.6"
 Markdown = "1.6"
-Nemo = "0.46.2"
+Nemo = "0.47.1"
 Pkg = "1.6"
 Polymake = "0.11.20"
 Random = "1.6"
 RandomExtensions = "0.4.3"
 Serialization = "1.6"
-Singular = "0.23.4"
+Singular = "0.23.8"
 TOPCOM_jll = "0.17.8"
 UUIDs = "1.6"
 cohomCalg_jll = "0.32.0"

README.md

@@ -38,6 +38,7 @@ julia> using Oscar
 | | | |\___ \| | / _ \ | |_) | | Type "?Oscar" for more information
 | |_| | ___) | |___ / ___ \| _ < | Manual: https://docs.oscar-system.org
  \___/ |____/ \____/_/ \_\_| \_\ | Version 1.2.0-DEV
+
 julia> k, a = quadratic_field(-5)
 (Imaginary quadratic field defined by x^2 + 5, sqrt(-5))
 

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/doc.main

@@ -83,7 +83,8 @@
  "Hecke/manual/quad_forms/genusherm.md",
  "Hecke/manual/quad_forms/integer_lattices.md",
  "Hecke/manual/quad_forms/Zgenera.md",
- "Hecke/manual/quad_forms/discriminant_group.md"
+ "Hecke/manual/quad_forms/discriminant_group.md",
+ "NumberTheory/vinberg.md",
  ],
  ],
 
@@ -132,6 +133,7 @@
  "CommutativeAlgebra/ModulesOverMultivariateRings/intro.md",
  "CommutativeAlgebra/ModulesOverMultivariateRings/free_modules.md",
  "CommutativeAlgebra/ModulesOverMultivariateRings/subquotients.md",
+ "CommutativeAlgebra/ModulesOverMultivariateRings/ideals_quorings_as_modules.md",
  "CommutativeAlgebra/ModulesOverMultivariateRings/module_operations.md",
  "CommutativeAlgebra/ModulesOverMultivariateRings/hom_operations.md",
  "CommutativeAlgebra/ModulesOverMultivariateRings/complexes.md",
@@ -172,6 +174,8 @@
  "AlgebraicGeometry/Schemes/ProjectiveSchemes.md",
  "AlgebraicGeometry/Schemes/MorphismsOfProjectiveSchemes.md",
  "AlgebraicGeometry/Schemes/RationalPointsProjective.md",
+ "AlgebraicGeometry/Schemes/Sheaves.md",
+ "AlgebraicGeometry/Schemes/Cycles.md",
  ],
  "Algebraic Sets" => [
  "AlgebraicGeometry/AlgebraicSets/AffineAlgebraicSet.md",
@@ -192,6 +196,7 @@
  "AlgebraicGeometry/Surfaces/AdjunctionProcess.md",
  "AlgebraicGeometry/Surfaces/ParametrizationSurfaces.md",
  "AlgebraicGeometry/Surfaces/SurfacesP4.md",
+ "AlgebraicGeometry/Surfaces/duValSing.md",
  ],
  "Sheaf Cohomology" => [
  "AlgebraicGeometry/SheafCohomology/sheaf_cohomology.md",
@@ -210,7 +215,7 @@
  "AlgebraicGeometry/ToricVarieties/ToricMorphisms.md",
  "AlgebraicGeometry/ToricVarieties/ToricSchemes.md",
  "AlgebraicGeometry/ToricVarieties/ToricIdealSheaves.md",
- "AlgebraicGeometry/ToricVarieties/BlowdownMorphisms.md",
+ "AlgebraicGeometry/ToricVarieties/BlowupMorphisms.md",
  ],
  "Miscellaneous" => [
  "AlgebraicGeometry/Miscellaneous/miscellaneous.md",

docs/documenter_helpers.jl

@@ -23,3 +23,11 @@ else
  end
  end
 end
+
+# We monkey-patch Base.walkdir to use true as default value for follow_symlinks
+# (normally false is the default), in order to "trick" the Documenter code into
+# following those symlinks.
+# See also:
+# https://github.com/JuliaDocs/Documenter.jl/pull/552
+# https://github.com/JuliaLang/julia/blob/master/doc/make.jl#L19
+Base.walkdir(str::String) = Base.walkdir(str; follow_symlinks=true)

docs/make_work.jl

@@ -26,14 +26,6 @@ include("citation_style.jl")
 # Remove the module prefix
 Base.print(io::IO, b::Base.Docs.Binding) = print(io, b.var)
 
-# We monkey-patch Base.walkdir to use true as default value for follow_symlinks
-# (normally false is the default), in order to "trick" the Documenter code into
-# following those symlinks.
-# See also:
-# https://github.com/JuliaDocs/Documenter.jl/pull/552
-# https://github.com/JuliaLang/julia/blob/master/doc/make.jl#L19
-Base.walkdir(str::String) = Base.walkdir(str; follow_symlinks=true)
-
 # When we read a `doc.main` from an experimental package, we need to equip all
 # its entries with a prefix to fit with our docs. The doc.main of an
 # experimental package will contain paths relative to
@@ -83,22 +75,13 @@ function setup_experimental_package(Oscar::Module, package_name::String)
  return []
  end
 
- # Set symlink inside docs/src/experimental
- symlink_link = joinpath(Oscar.oscardir, "docs/src/Experimental", package_name)
- symlink_target = joinpath(Oscar.oscardir, "experimental", package_name, "docs", "src")
-
- if !ispath(symlink_target)
+ # Assumes that a symbolic link from `experimental/package_name/docs/src`
+ # to `docs/src/Experimental/package_name` has been created (or there is no
+ # documentation for this package)
+ if !ispath(joinpath(Oscar.oscardir, "docs/src/Experimental", package_name))
  return []
  end
 
- if !ispath(symlink_link)
- symlink(symlink_target, symlink_link)
- elseif !islink(symlink_link) || readlink(symlink_link) != symlink_target
- error("""$symlink_link already exists, but is not a symlink to $symlink_target
- Please investigate the contents of $symlink_link,
- optionally move them somewhere else and delete the directory once you are done.""")
- end
-
  # Read doc.main of package
  exp_s = read(doc_main_path, String)
  exp_doc = eval(Meta.parse(exp_s))
@@ -116,15 +99,12 @@ function doit(
  doctest::Union{Bool,Symbol}=true,
 )
 
- # Remove symbolic links from earlier runs
- expdocdir = joinpath(Oscar.oscardir, "docs", "src", "Experimental")
- for x in readdir(expdocdir; join=true)
- islink(x) && rm(x)
- end
-
  # include the list of pages, performing substitutions
  s = read(joinpath(Oscar.oscardir, "docs", "doc.main"), String)
  doc = eval(Meta.parse(s))
+
+ # Link experimental docs to `docs/src` and collect the documentation pages
+ Oscar.link_experimental_docs()
  collected = Any["Experimental/intro.md"]
  for pkg in Oscar.exppkgs
  pkgdocs = setup_experimental_package(Oscar, pkg)