Merge branch 'oscar-system:master' into ep/cox_ring_strict_transform

.github/workflows/Docstrings.yml

@@ -0,0 +1,29 @@
+name: docstring test
+
+on:
+  push:
+    branches:
+      - master
+      - 'release-*'
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  # group by workflow and ref; the last slightly strange component ensures that for pull
+  # requests, we limit to 1 concurrent job, but for the master branch we don't
+  group: ${{ github.workflow }}-${{ github.ref }}-${{ github.ref != 'refs/heads/master' || github.run_number }}
+  # Cancel intermediate builds, but only if it is a pull request build.
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+
+jobs:
+  check-docstrings:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: julia-actions/setup-julia@v2
+    - uses: julia-actions/cache@v2
+    - name: Build package
+      uses: julia-actions/julia-buildpkg@v1
+    - name: 'Check issues in docstrings'
+      run: |
+        julia --project=. -e 'using Oscar; include("etc/check_docstrings.jl")'

CITATION.cff

@@ -41,7 +41,6 @@ preferred-citation:
     interested researchers from graduate students through established
     experts.
   year: 2024
-  month: 8
   edition: 1
   issn: "1431-1550"
   url: "https://link.springer.com/book/9783031621260"

LICENSE.md

@@ -1,6 +1,11 @@
 The Oscar.jl package is licensed under the GNU Public License, Version 3.0+:
 
-> Copyright (c) 2019 The OSCAR Development Team.
+> Copyright (c) 2019-2024 The OSCAR Development Team
+>
+> See <https://www.oscar-system.org/contributors/> for a list of OSCAR
+> Development Team members. Note that this list may occasionally be slightly
+> outdated. Additional contributors may be found in the `git log` of the main
+> OSCAR repository and other related repositories.
 > This program is free software: you can redistribute it and/or modify
 > it under the terms of the GNU General Public License as published by
 > the Free Software Foundation, either version 3 of the License, or

Project.toml

@@ -1,7 +1,7 @@
 name = "Oscar"
 uuid = "f1435218-dba5-11e9-1e4d-f1a5fab5fc13"
 authors = ["The OSCAR Team <[email protected]>"]
-version = "1.2.0-DEV"
+version = "1.3.0-DEV"
 
 [deps]
 AbstractAlgebra = "c3fe647b-3220-5bb0-a1ea-a7954cac585d"
@@ -25,11 +25,11 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 cohomCalg_jll = "5558cf25-a90e-53b0-b813-cadaa3ae7ade"
 
 [compat]
-AbstractAlgebra = "0.43.7"
+AbstractAlgebra = "0.43.11"
 AlgebraicSolving = "0.8.0"
 Distributed = "1.6"
 GAP = "0.12.0"
-Hecke = "0.34.3"
+Hecke = "0.34.7"
 JSON = "^0.20, ^0.21"
 JSON3 = "1.13.2"
 LazyArtifacts = "1.6"

README.md

@@ -37,7 +37,7 @@ julia> using Oscar
  / _ \ / ___| / ___|  / \  |  _ \   |  Combining ANTIC, GAP, Polymake, Singular
 | | | |\___ \| |     / _ \ | |_) |  |  Type "?Oscar" for more information
 | |_| | ___) | |___ / ___ \|  _ <   |  Manual: https://docs.oscar-system.org
- \___/ |____/ \____/_/   \_\_| \_\  |  Version 1.2.0-DEV
+ \___/ |____/ \____/_/   \_\_| \_\  |  Version 1.3.0-DEV
 
 julia> k, a = quadratic_field(-5)
 (Imaginary quadratic field defined by x^2 + 5, sqrt(-5))
@@ -70,34 +70,28 @@ Free module of rank 1 over R
 
 julia> s = sub(F, [f*F[1]])[1]
 Submodule with 1 generator
-1 -> (x1^2 + x2)*e[1]
-represented as subquotient with no relations.
+  1: (x1^2 + x2)*e[1]
+represented as subquotient with no relations
 
 julia> H, mH = hom(s, quo(F, s)[1])
-(hom of (s, Subquotient of
-1 -> e[1]
-by
-1 -> (x1^2 + x2)*e[1]), Map: H -> set of all homomorphisms from s to subquotient of Submodule with 1 generator
-1 -> e[1]
-by Submodule with 1 generator
-1 -> (x1^2 + x2)*e[1])
+(hom of (s, Subquotient of submodule with 1 generator
+  1: e[1]
+by submodule with 1 generator
+  1: (x1^2 + x2)*e[1]), Map: H -> set of all homomorphisms from s to subquotient of submodule with 1 generator
+  1: e[1]
+by submodule with 1 generator
+  1: (x1^2 + x2)*e[1])
 
 julia> mH(H[1])
-Map with following data
-Domain:
-=======
-Submodule with 1 generator
-1 -> (x1^2 + x2)*e[1]
-represented as subquotient with no relations.
-Codomain:
-=========
-Subquotient of Submodule with 1 generator
-1 -> e[1]
-by Submodule with 1 generator
-1 -> (x1^2 + x2)*e[1]
+Module homomorphism
+  from s
+  to subquotient of submodule with 1 generator
+    1: e[1]
+  by submodule with 1 generator
+    1: (x1^2 + x2)*e[1]
 ```
 
-Of course, the cornerstones are also available directly:
+Of course, the cornerstones are also available directly. For example:
 
 ```
 julia> C = Polymake.polytope.cube(3);
@@ -120,7 +114,7 @@ pm::Array<topaz::HomologyGroup<pm::Integer> >
 If you have used OSCAR in the preparation of a paper please cite it as described below:
 
     [OSCAR]
-        OSCAR -- Open Source Computer Algebra Research system, Version 1.2.0-DEV,
+        OSCAR -- Open Source Computer Algebra Research system, Version 1.3.0-DEV,
         The OSCAR Team, 2024. (https://www.oscar-system.org)
     [OSCAR-book]
         Wolfram Decker, Christian Eder, Claus Fieker, Max Horn, Michael Joswig, eds.
@@ -133,7 +127,7 @@ If you are using BibTeX, you can use the following BibTeX entries:
       key          = {OSCAR},
       organization = {The OSCAR Team},
       title        = {OSCAR -- Open Source Computer Algebra Research system,
-                      Version 1.2.0-DEV},
+                      Version 1.3.0-DEV},
       year         = {2024},
       url          = {https://www.oscar-system.org},
       }
@@ -147,7 +141,6 @@ If you are using BibTeX, you can use the following BibTeX entries:
       volume = {32},
       edition = {1},
       url = {https://link.springer.com/book/9783031621260},
-      month = {8},
       issn = {1431-1550},
     }
 

docs/Project.toml

@@ -1,7 +1,9 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 
 [compat]
 Documenter = "1.1"
 DocumenterCitations = "~1.3.4"
+JSON = "0.21.4"

docs/doc.main

@@ -198,6 +198,7 @@
      ],
      "Surfaces" => [
         "AlgebraicGeometry/Surfaces/K3Surfaces.md",
+        "AlgebraicGeometry/Surfaces/EllipticSurface.md",
 	"AlgebraicGeometry/Surfaces/AdjunctionProcess.md",
 	"AlgebraicGeometry/Surfaces/ParametrizationSurfaces.md",
         "AlgebraicGeometry/Surfaces/SurfacesP4.md",

docs/make_work.jl

@@ -4,7 +4,7 @@
 #
 module BuildDoc
 
-using Documenter, DocumenterCitations
+using Documenter, DocumenterCitations, JSON
 
 include("documenter_helpers.jl")
 include("citation_style.jl")
@@ -210,6 +210,56 @@ function doit(
     dstbase = normpath(Oscar.oscardir, "docs", "src", string(nameof(pkg)))
     rm(dstbase; recursive=true, force=true)
   end
+
+  # postprocessing, for the search index
+  docspath = normpath(joinpath(Oscar.oscardir, "docs"))
+  @info "Patching search index."
+  # extract valid json from search_index.js
+  run(pipeline(`sed -n '2p;3q' $(joinpath(docspath, "build", "search_index.js"))`, stdout=(joinpath(docspath, "build", "search_index.json")))) # imperfect file, but JSON parses it
+
+  # extract paths from doc.main
+  filelist=String[]
+  docmain = include(joinpath(docspath, "doc.main"))
+  while !isempty(docmain)
+    n = pop!(docmain)
+    if n isa Pair
+      push!(docmain, last(n))
+    elseif n isa String
+      push!(filelist, n)
+    elseif n isa Array{String}
+      append!(filelist,n)
+    elseif n isa Array
+      append!(docmain,n)
+    else
+      error("err: $(typeof(n))")
+    end
+  end
+  suffix = local_build ? ".html" : "/"
+  filelist = replace.(filelist, r"\.md$"=>suffix)
+
+  # read these files
+  iosearchindex = open(joinpath(docspath, "build", "search_index.json"), "r")
+  searchindex = JSON.parse(iosearchindex)
+  close(iosearchindex)
+
+  newsearchindex = []
+
+  for item in searchindex
+    if split(item["location"], "#")[1] in filelist
+      push!(newsearchindex, item)
+    end
+  end
+
+
+  # combine this to valid javascript again, and overwrite input
+  ionewsearchindex = open(joinpath(docspath, "build", "search_index.js"), "w")
+  write(ionewsearchindex, """var documenterSearchIndex = {"docs":\n""")
+  JSON.print(ionewsearchindex, newsearchindex)
+  write(ionewsearchindex, "\n}")
+  close(ionewsearchindex)
+
+  # clean up
+  rm(joinpath(docspath, "build", "search_index.json"))
 end
 
 end # module BuildDoc