Merge branch 'master' into gf/BasisLieHighestWeight

.bibtoolrsc

@@ -61,3 +61,27 @@ key.format =
     { %+8.1n(author) }
     { %2d(year) }
 }
+
+# Enforce "{...}" around fields
+rewrite.rule {"^\"\([^#]*\)\"$" "{\1}"}
+rewrite.rule {"^ *\([0-9]*\) *$" "{\1}"}
+
+# Remove empty fields
+rewrite.rule {"^{ *}$"}
+
+# Unify page range separator
+rewrite.rule {pages "\([0-9]+\) *\(-\|---\|–\) *\([0-9]+\)" "\1--\3"}
+
+# Check that 1800<=year<=2029
+check.rule { year "^[\"{]1[89][0-9][0-9][\"}]$" }
+check.rule { year "^[\"{]20[0-2][0-9][\"}]$" }
+check.error.rule { year "" "\@ \$: Year has to be a suitable number" }
+
+# Check that the doi field is not a URL
+check.error.rule { doi "\://" "\@ \$: doi field should not be a URL" }
+
+# Check that the url field is not a DOI
+check.error.rule { url "doi\.org/" "\@ \$: url field should not contain a doi. Use the doi field instead" }
+
+# Check that no field contains a LaTeX url command, as DocumenterCitations.jl prints them ugly
+check.error.rule { "\\url" "\@ \$: LaTeX's `\\url` commands are not supported" }

.codecov.yml

@@ -1,7 +1,7 @@
 codecov:
   notify:
     # Keep this in sync with the number of CI jobs uploading coverage.
-    after_n_builds: 3
+    after_n_builds: 4
 coverage:
   status:
     project:

.github/workflows/BibtoolCI.yml

@@ -25,7 +25,9 @@ jobs:
           sudo apt-get install -y bibtool
       - name: Execute bibtool and check for changes
         run: |
-          bibtool docs/oscar_references.bib -o docs/oscar_references.bib
+          bibtool docs/oscar_references.bib -o docs/oscar_references.bib 2>&1 | tee bibtool.log
+          test \! -s bibtool.log
+          rm bibtool.log
           if [ -n "$(git status --porcelain)" ]; then
             echo "We employ bibtool to standardize the bibtex entries of our reference list."
             echo "Your changes to the bibliography do not follow this standard."

.github/workflows/CI.yml

@@ -18,7 +18,6 @@ jobs:
   test:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 150
-    continue-on-error: ${{ matrix.julia-version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
@@ -27,9 +26,20 @@ jobs:
           - '1.9'
           - '~1.10.0-0'
           - 'nightly'
+        group: [ 'short', 'long' ]
         os:
           - ubuntu-latest
+        depwarn: [ '' ]
         include:
+          # Add a single job per group with deprecation errors on the most recent stable julia version
+          - julia-version: '1.9'
+            os: ubuntu-latest
+            group: 'short'
+            depwarn: 'depwarn=error'
+          - julia-version: '1.9'
+            os: ubuntu-latest
+            group: 'long'
+            depwarn: 'depwarn=error'
           # Add a few macOS jobs (not too many, the number we can run in parallel is limited)
           - julia-version: 'nightly'
             os: macOS-latest
@@ -50,26 +60,28 @@ jobs:
         if: runner.os == 'macOS'
         # restrict number of openMP threads on macOS due to oversubscription
         run: echo "OMP_NUM_THREADS=1" >> $GITHUB_ENV
+      - name: "set test subgroup"
+        if: ${{ matrix.group }} != ''
+        run: echo "OSCAR_TEST_SUBSET=${{matrix.group}}" >> $GITHUB_ENV
       - name: "Run tests"
         uses: julia-actions/julia-runtest@latest
         with:
           annotate: ${{ matrix.julia-version == '1.9' }}
           coverage: ${{ matrix.julia-version == '1.9' }}
-          depwarn: error
+          depwarn: ${{ matrix.depwarn == 'depwarn=error' && 'error' || 'no' }}
       - name: "Process code coverage"
-        if: matrix.julia-version == '1.9'
+        if: matrix.julia-version == '1.9' && matrix.depwarn != 'depwarn=error'
         uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src,experimental
       - name: "Upload coverage data to Codecov"
-        if: matrix.julia-version == '1.9'
+        if: matrix.julia-version == '1.9' && matrix.depwarn != 'depwarn=error'
         continue-on-error: true
         uses: codecov/codecov-action@v3
 
   doctest:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 150
-    continue-on-error: ${{ matrix.julia-version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
@@ -79,7 +91,12 @@ jobs:
           - 'nightly'
         os:
           - ubuntu-latest
+        depwarn: [ '' ]
         include:
+          # Add a single job with deprecation errors on the most recent stable julia version
+          - julia-version: '1.9'
+            os: ubuntu-latest
+            depwarn: 'depwarn=error'
           # Add macOS jobs (not too many, the number we can run in parallel is limited)
           - julia-version: '1.9'
             os: macOS-latest
@@ -108,7 +125,7 @@ jobs:
         with:
           annotate: ${{ matrix.julia-version == '1.9' }}
           coverage: ${{ matrix.julia-version == '1.9' }}
-          depwarn: error
+          depwarn: ${{ matrix.depwarn == 'depwarn=error' && 'error' || 'no' }}
       - name: "Setup package"
         run: |
           julia --project=docs --color=yes -e '
@@ -118,18 +135,18 @@ jobs:
       - name: "Run doctests"
         run: |
           julia ${{ matrix.julia-version == '1.9' && '--code-coverage' || '' }} \
-            --project=docs --depwarn=error --color=yes -e'
+            --project=docs --depwarn=${{ matrix.depwarn == 'depwarn=error' && 'error' || 'no' }} --color=yes -e'
               using Documenter
               include("docs/documenter_helpers.jl")
               using Oscar
               DocMeta.setdocmeta!(Oscar, :DocTestSetup, Oscar.doctestsetup(); recursive = true)
               doctest(Oscar)'
       - name: "Process code coverage"
-        if: matrix.julia-version == '1.9'
+        if: matrix.julia-version == '1.9' && matrix.depwarn != 'depwarn=error'
         uses: julia-actions/julia-processcoverage@v1
         with:
           directories: src,experimental
       - name: "Upload coverage data to Codecov"
-        if: matrix.julia-version == '1.9'
+        if: matrix.julia-version == '1.9' && matrix.depwarn != 'depwarn=error'
         continue-on-error: true
         uses: codecov/codecov-action@v3

docs/oscar_references.bib

@@ -128,7 +128,7 @@ @Article{BDLPSS13
   journal       = {Journal of Symbolic Computation},
   volume        = {51},
   note          = {Effective Methods in Algebraic Geometry},
-  pages         = {99-114},
+  pages         = {99--114},
   year          = {2013},
   doi           = {10.1016/j.jsc.2012.07.002}
 }
@@ -695,7 +695,7 @@ @Article{FGLM93
   journal       = {Journal of Symbolic Computation},
   volume        = {16},
   number        = {4},
-  pages         = {329-344},
+  pages         = {329--344},
   year          = {1993},
   doi           = {10.1006/jsco.1993.1051}
 }
@@ -707,7 +707,7 @@ @Article{FJR17
   volume        = {22},
   number        = {1},
   publisher     = {Mathematical Sciences Publishers},
-  pages         = {235-303},
+  pages         = {235--303},
   year          = {2017},
   month         = {Oct},
   doi           = {10.2140/gt.2018.22.235}
@@ -736,7 +736,7 @@ @Article{FY04
   number        = {3},
   publisher     = {Springer Science and Business Media {LLC}},
   pages         = {515--536},
-  year          = 2004,
+  year          = {2004},
   month         = {mar},
   doi           = {10.1007/s00222-003-0327-2}
 }
@@ -1011,7 +1011,7 @@ @InCollection{IR96
   title         = {The {M}c{K}ay correspondence for finite subgroups of ${\rm SL}(3,\mathbb C)$},
   booktitle     = {Higher-dimensional complex varieties ({T}rento, 1994)},
   publisher     = {de Gruyter},
-  pages         = {221-240},
+  pages         = {221--240},
   year          = {1996},
   location      = {Berlin}
 }
@@ -1509,8 +1509,8 @@ @MastersThesis{Peg14
   title         = {Chow Rings of Toric Varieties},
   note          = {Refereed by Prof. Dr. Eva Maria Feichtner and Dr. Emanuele Delucchi},
   address       = {Faculty of Mathematics},
-  year          = 2014,
-  month         = 9,
+  year          = {2014},
+  month         = {9},
   school        = {University of Bremen}
 }
 

docs/src/CommutativeAlgebra/FrameWorks/ring_localizations.md

@@ -21,7 +21,7 @@ localized rings should belong to the `AbsLocalizedRing` abstract type.
 The basic functionality that has to be realized for any concrete instance of `AbsMultSet`
 is the containment check for elements in multiplicatively closed subsets via the `in` function.
 
-For each concrete instance of `AbsLocalizedRing`, the `Localization` constructor as well as the
+For each concrete instance of `AbsLocalizedRing`, the `localization` constructor as well as the
 functions `base_ring` and `inverted_set` need to be implemented. Moreover, as for any other type
 of rings in OSCAR, methods for the standardized set of functions of OSCAR's
 general [Ring Interface](@ref) must be supplied.

docs/src/CommutativeAlgebra/ideals.md

@@ -167,13 +167,13 @@ is_monomial(f::MPolyRingElem)
 ### Containment of Ideals
 
 ```@docs
-is_subset(I::MPolyIdeal{T}, J::MPolyIdeal{T}) where T
+is_subset(I::MPolyIdeal, J::MPolyIdeal)
 ```
 
 ### Equality of Ideals
 
 ```@docs
-==(I::MPolyIdeal{T}, J::MPolyIdeal{T}) where T
+==(I::MPolyIdeal, J::MPolyIdeal)
 ```
 
 ### Ideal Membership

docs/src/CommutativeAlgebra/localizations.md

@@ -237,7 +237,7 @@ Complement
 
 julia> RQ, p = quo(R, I);
 
-julia> RQL, iota = Localization(RQ, U);
+julia> RQL, iota = localization(RQ, U);
 
 julia> phi = compose(p, iota);
 
@@ -340,7 +340,7 @@ Complement
 
 julia> RQ, p = quo(R, I);
 
-julia> RQL, iota = Localization(RQ, U);
+julia> RQL, iota = localization(RQ, U);
 
 julia> phi = compose(p, iota);
 

docs/src/DeveloperDocumentation/new_developers.md

@@ -106,6 +106,11 @@ Oscar.test_module
 Oscar.get_seeded_rng
 ```
 
+If a test folder contains a file called `setup_tests.jl` it is included
+automatically before each file (directly) in this directory. This can be used
+to define helper functions that are used in multiple test files, for example
+`test_save_load_roundtrip` for serialization.
+
 ### Adding documentation
 For more information on docstrings, please read our page on [Documenting OSCAR
 code](@ref).  There are two places where documentation can be added:

docs/src/DeveloperDocumentation/styleguide.md

@@ -194,6 +194,63 @@ end
 
 However, as always, rules sometimes should be broken.
 
+## Optional arguments for parents of return values
+
+Several objects in OSCAR have `parent`s, e.g. polynomials, group elements, ... 
+Whenever a function creates such objects from an input which does not involve 
+the output's parent, we strongly recommend that 
+the user should have the possibility to pass on this 
+parent as a keyword argument under the name `parent`.
+Beyond that you can make more entry points for such parents available for 
+the user's convenience.
+
+Let's see an example. Say, you want to implement the characteristic 
+polynomial of a matrix. You could do it as follows:
+```julia
+  function characteristic_polynomial(A::MatrixElem)
+    kk = base_ring(A)
+    P, x = kk["x"]
+    AP = change_base_ring(P, A)
+    return det(AP - x*one(AP))
+  end
+```
+You can see that the polynomial ring `P`, i.e. the parent of the output, 
+is newly created in the body of the function. In particular, calling this 
+function two times on two different matrices `A` and `B` might produce 
+incompatible polynomials `p = det(A - x*one(A))` and `q = det(B - x*one(B))` 
+with different parents. Calling `p + q` will result in an error. 
+
+To solve this, we should have implemented the function differently:
+```julia
+  # Implementation of the recommended keyword argument signature:
+  function characteristic_polynomial(
+      A::MatrixElem;
+      parent::AbstractAlgebra.Ring=polynomial_ring(base_ring(A), :t)[1]
+    )
+    AP = change_base_ring(parent, A)
+    x = first(gens(ring))
+    return det(AP - x*one(AP))
+  end
+
+  # Optional second signature to also allow for the specification of the 
+  # output's parent as the first argument:
+  function characteristic_polynomial(
+      P::PolyRing,
+      A::MatrixElem
+    )
+    coefficient_ring(P) === base_ring(A) || error("coefficient rings incompatible")
+    return characteristic_polynomial(A, parent=P)
+  end
+```
+In fact this now allows for two different entry points for the parent ring `P` 
+of the output: First as the required `parent` keyword argument and second 
+as the first argument of a method of `characteristic_polynomial` with 
+an extended signature. Note that within the scope of the first method's body 
+the OSCAR function `parent` is necessarily overwritten by the name of the 
+keyword argument. Hence to call the actual parent of any other object, you 
+must then use `Oscar.parent`. E.g. to get the `MatrixSpace` of the 
+matrix `A`, write `Oscar.parent(A)`.
+
 
 ## Documentation
 

docs/src/Experimental/intro.md

@@ -34,14 +34,18 @@ experimental/PACKAGE_NAME/
 ├── src
 │   └── PACKAGE_NAME.jl
 └── test
-    └── runtests.jl
+    └── *.jl
 ```
-The files `src/PACKAGE_NAME.jl` and `test/runtests.jl` are mandatory as they
-are used by Oscar.jl to find your code and tests. The file `docs/doc.main` is
-used for integrating your documentation in the Oscar manual under the
-`Experimental` section. Optionally please provide a `README.md` describing your
-project and its goals, especially if you are starting from scratch and don't
-have any documentation yet.
+The file `src/PACKAGE_NAME.jl` and at least one `.jl` file in the `test/`
+directory are mandatory and are used by Oscar.jl to find your code and tests.
+If there is a `test/runtests.jl` then only this file is executed during
+testing, otherwise all `.jl` files will be run automatically (in a random
+order).
+
+The file `docs/doc.main` is used for integrating your documentation in the
+Oscar manual under the `Experimental` section. Optionally please provide a
+`README.md` describing your project and its goals, especially if you are
+starting from scratch and don't have any documentation yet.
 
 !!! note
     There are still older projects in `experimental` from before the

docs/src/PolyhedralGeometry/linear_programs.md

@@ -101,6 +101,7 @@ julia> V = optimal_vertex(LP)
 
 ```@docs
 feasible_region(lp::LinearProgram)
+ambient_dim(lp::LinearProgram)
 objective_function(lp::LinearProgram{T}; as::Symbol = :pair) where T<:scalar_types
 solve_lp(LP::LinearProgram)
 optimal_value(lp::LinearProgram{T}) where T<:scalar_types

docs/src/PolyhedralGeometry/mixed_integer_linear_programs.md

@@ -28,6 +28,8 @@ mixed_integer_linear_program
 
 ## Functions
 ```@docs
+feasible_region(milp::MixedIntegerLinearProgram)
+ambient_dim(milp::MixedIntegerLinearProgram)
 optimal_value(milp::MixedIntegerLinearProgram{T}) where T<:scalar_types
 optimal_solution
 solve_milp

experimental/Experimental.jl

@@ -28,8 +28,9 @@ for pkg in exppkgs
   if !isfile(joinpath(expdir, pkg, "src", "$pkg.jl"))
     error("experimental/$pkg is incomplete: $pkg/src/$pkg.jl missing. See the documentation at https://docs.oscar-system.org/dev/Experimental/intro/ for details.")
   end
-  if !isfile(joinpath(expdir, pkg, "test", "runtests.jl"))
-    error("experimental/$pkg is incomplete: $pkg/test/runtests.jl missing. See the documentation at https://docs.oscar-system.org/dev/Experimental/intro/ for details.")
+  path = joinpath(expdir, pkg, "test")
+  if !isdir(path) || length(filter(endswith(".jl"), readdir(path))) == 0
+    error("experimental/$pkg is incomplete: $pkg/test/ missing or empty. See the documentation at https://docs.oscar-system.org/dev/Experimental/intro/ for details.")
   end
 end