allow passing nothing for undef values, update github actions

.github/workflows/Invalidations.yml

@@ -9,6 +9,11 @@ concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true
 
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+ actions: write
+ contents: read
+
 jobs:
  compare-invalidations:
  # Only run on PRs to the default branch.
@@ -19,15 +24,14 @@ jobs:
  - uses: julia-actions/setup-julia@v1
  with:
  version: '1'
- - uses: actions/checkout@v3
- - uses: julia-actions/julia-buildpkg@v1
+ - uses: actions/checkout@v4
+ - uses: julia-actions/cache@v1
  - uses: julia-actions/julia-invalidations@v1
  id: invs_pr
 
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  with:
  ref: ${{ github.event.repository.default_branch }}
- - uses: julia-actions/julia-buildpkg@v1
  - uses: julia-actions/julia-invalidations@v1
  id: invs_default
 

.github/workflows/createdocumentation.yml

@@ -8,6 +8,10 @@ on:
  pull_request:
  workflow_dispatch:
 
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+ actions: write
+
 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
@@ -20,16 +24,17 @@ jobs:
  runs-on: ubuntu-latest
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: "Set up Julia"
  uses: julia-actions/setup-julia@v1
  with:
- version: '1.6'
- - uses: julia-actions/julia-buildpkg@v1
+ version: '1.10'
+ - uses: julia-actions/cache@v1
  - name: "Add Documenter package"
  run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd()));
  Pkg.instantiate()'
  - name: "Build and deploy documentation"
  env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
  run: julia --project=docs/ docs/make.jl

.github/workflows/oscar.yml

@@ -23,7 +23,7 @@ jobs:
  JULIA_PKG_SERVER: ""
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: "Set up Julia"
  uses: julia-actions/setup-julia@v1
  with:
@@ -64,7 +64,7 @@ jobs:
  fail-fast: false
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: "Set up Julia"
  uses: julia-actions/setup-julia@v1
  with:

.github/workflows/runtests.yml

@@ -10,6 +10,11 @@ on:
  - master
  workflow_dispatch:
 
+# needed to allow julia-actions/cache to delete old caches that it has created
+permissions:
+ actions: write
+ contents: read
+
 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
@@ -21,22 +26,15 @@ jobs:
  # github services (for mongodb service) only works on linux
  test-with-mongodb:
  runs-on: ${{ matrix.os }}
- continue-on-error: ${{ matrix.julia-version == 'nightly' || matrix.julia-version == '~1.10.0-0' }}
+ continue-on-error: ${{ matrix.julia-version == 'nightly' }}
  strategy:
  matrix:
  julia-version:
  - '~1.6.0-0'
- - '~1.8.0-0'
  - '~1.10.0-0'
+ - 'nightly'
  os: ['ubuntu-latest']
  cxxwrap: [ '' ]
- include:
- - cxxwrap: '0.14'
- os: ubuntu-latest
- julia-version: 1.9
- - cxxwrap: '0.14'
- os: ubuntu-latest
- julia-version: nightly
 
  fail-fast: false
  # Service containers to run
@@ -56,11 +54,15 @@ jobs:
  JULIA_PKG_SERVER: ""
  POLYDB_TEST_URI: "mongodb://admin:admin@localhost:27017/?authSource=admin"
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: "Set up Julia"
  uses: julia-actions/setup-julia@v1
  with:
  version: ${{ matrix.julia-version }}
+ - uses: julia-actions/cache@v1
+ with:
+ cache-name: julia-cache;workflow=${{ github.workflow }};julia=${{ matrix.julia-version }};arch=${{ runner.arch }}
+ include-matrix: false
  - name: "pin CxxWrap"
  if: matrix.cxxwrap != ''
  run: julia --project -e 'using Pkg; pkg"add CxxWrap@${{ matrix.cxxwrap }}"; pkg"pin CxxWrap";'
@@ -73,40 +75,47 @@ jobs:
  mongorestore --host localhost -u admin -p admin --port 27017 .github/polydb_dump
  - uses: julia-actions/julia-runtest@v1
  - uses: julia-actions/julia-processcoverage@v1
- - uses: codecov/codecov-action@v2
+ - uses: codecov/codecov-action@v4
  with:
  file: ./lcov.info
  flags: unittests
  name: codecov-umbrella
  fail_ci_if_error: false
+ token: ${{ secrets.CODECOV_TOKEN }}
 
  # this one is only for macos, ubuntu is run with mongodb in the other job
  test:
  runs-on: ${{ matrix.os }}
- continue-on-error: ${{ matrix.julia-version == 'nightly' || matrix.julia-version == '~1.10.0-0' }}
+ continue-on-error: ${{ matrix.julia-version == 'nightly' }}
  env:
  JULIA_PKG_SERVER: ""
  strategy:
  matrix:
  julia-version:
- - '~1.6.0-0'
- - '~1.9.0-0'
- - '~1.10.0-0'
+ - '1.6'
  - 'nightly'
- os: ['macOS-latest']
+ os: ['macos-latest']
+ include:
+ - os: 'macos-14'
+ julia-version: '1.10'
  fail-fast: false
 
  steps:
- - uses: actions/checkout@v3
+ - uses: actions/checkout@v4
  - name: "Set up Julia"
  uses: julia-actions/setup-julia@v1
  with:
  version: ${{ matrix.julia-version }}
+ - uses: julia-actions/cache@v1
+ with:
+ cache-name: julia-cache;workflow=${{ github.workflow }};julia=${{ matrix.julia-version }};arch=${{ runner.arch }}
+ include-matrix: false
  - uses: julia-actions/julia-runtest@v1
  - uses: julia-actions/julia-processcoverage@v1
- - uses: codecov/codecov-action@v2
+ - uses: codecov/codecov-action@v4
  with:
  file: ./lcov.info
  flags: unittests
  name: codecov-umbrella
  fail_ci_if_error: false
+ token: ${{ secrets.CODECOV_TOKEN }}

OscarCI.toml

@@ -1,8 +1,8 @@
 title = "metadata for oscar CI run"
 
 [env]
-os = [ "ubuntu-latest", "macos-latest" ]
-julia-version = [ "~1.6.0-0", "~1.9.0-0"]
+os = [ "ubuntu-latest" ]
+julia-version = [ "~1.6.0-0", "~1.10.0-0"]
 # branches = [ "release", "<matching>" ]
 
 [pkgs]
@@ -20,8 +20,14 @@ julia-version = [ "~1.6.0-0", "~1.9.0-0"]
  julia-version = "nightly"
  os = "ubuntu-latest"
 
- [include.julia_1_10]
+ [include.macamd64]
  Oscar = "<matching>"
  Polymake = ""
- julia-version = "~1.10.0-0"
- os = "ubuntu-latest"
+ julia-version = "1.6"
+ os = "macos-latest"
+
+ [include.macaarch64]
+ Oscar = "<matching>"
+ Polymake = ""
+ julia-version = "1.10"
+ os = "macos-14"

Project.toml

@@ -1,7 +1,7 @@
 name = "Polymake"
 uuid = "d720cf60-89b5-51f5-aff5-213f193123e7"
 repo = "https://github.com/oscar-system/Polymake.jl.git"
-version = "0.11.12"
+version = "0.11.13"
 
 [deps]
 BinaryWrappers = "f01c122e-0ea1-4f85-ad8f-907073ad7a9f"

src/convert.jl

@@ -28,6 +28,7 @@
 
 convert(::Type{PolymakeType}, x::T) where T = convert(convert_to_pm_type(T), x)
 convert(::Type{PolymakeType}, v::Visual) = v.obj
+convert(::Type{PolymakeType}, ::Nothing) = call_function(PropertyValue, :common, :get_undef)
 convert(::Type{OptionSet}, dict) = OptionSet(dict)
 
 ############### Adjusting type parameter to CxxWrap ##################
@@ -69,7 +70,7 @@
 convert_to_pm_type(::Type{T}) where T <: Union{Int64, Float64} = T
 convert_to_pm_type(::Type{T}) where T <: Union{BigObject, PropertyValue, OptionSet, TropicalNumber} = T
 
-
+convert_to_pm_type(::Nothing) = Nothing
 convert_to_pm_type(::Type{Int32}) = Int64
 convert_to_pm_type(::Type{<:AbstractFloat}) = Float64
 convert_to_pm_type(::Type{<:AbstractString}) = String

src/polymake/julia.rules

@@ -51,6 +51,11 @@ function is_boolean_wrapper($) {
  return is_boolean($c);
 }
 
+# helper function for converting `nothing`
+function get_undef() {
+ return undef;
+}
+
 function jupyter_visual_threejs(Visual::Object+) {
  my $string = "";
  local $ThreeJS::is_used_in_jupyter=1;

test/matrices.jl

@@ -199,7 +199,9 @@ using Polymake.CxxWrap
  @test V[2] = T(10)//T(3) isa typeof(T(10)//T(3))
  V[2] = T(10)//T(3)
  @test V[2] == 10//3
- @test string(V) == "pm::Matrix<pm::QuadraticExtension<pm::Rational> >\n5/3 2 3\n10/3 5 6\n"
+ type = "pm::Matrix<pm::QuadraticExtension<pm::Rational>>"
+ mat = "5/3 2 3\n10/3 5 6\n"
+ @test string(V) in typename_variants("$type\n$mat")
  end
  end
 
@@ -545,7 +547,9 @@ using Polymake.CxxWrap
  @test (V[2, 1] = T([4, 5], [1 0 0; 0 0 1])) isa T
  V[2, 1] = T([4, 5], [1 0 0; 0 0 1])
  @test V[2, 1] == T([4, 5], [1 0 0; 0 0 1])
- @test string(V) == "pm::Matrix<pm::Polynomial<pm::Rational, long> >\n2*x_0^2*x_1^3 + 3*x_1^2*x_2^3 0 0 0\n4*x_0 + 5*x_2 0 0 0\n0 0 0 x_0 + x_1 + x_2\n"
+ type = "pm::Matrix<pm::Polynomial<pm::Rational, long>>"
+ mat = "2*x_0^2*x_1^3 + 3*x_1^2*x_2^3 0 0 0\n4*x_0 + 5*x_2 0 0 0\n0 0 0 x_0 + x_1 + x_2\n"
+ @test string(V) in typename_variants("$type\n$mat")
  end
  end
  end

test/oscarnumber.jl

@@ -25,7 +25,9 @@
 
  @test Polymake.OscarNumber(m) isa Polymake.OscarNumber
  if isdefined(@__MODULE__, :_with_oscar) && _with_oscar
- @test Polymake.unwrap(M) isa Hecke.EmbeddedNumFieldElem{NfAbsNSElem}
+ if isdefined(Hecke, :EmbeddedNumFieldElem)
+ @test Polymake.unwrap(M) isa Hecke.EmbeddedNumFieldElem
+ end
  end
  @test Polymake.unwrap(M) == m
  @test M == Polymake.OscarNumber(m)
@@ -113,10 +115,12 @@
  @test M * A2 == A2 * M == Polymake.OscarNumber(a1*a2 + 15 + 7*a2)
  @test Polymake.OscarNumber(5) // A2 == Polymake.OscarNumber(a2^2)
  # avoid test error for older oscar versions
- if length(methods(Polymake._fieldelem_to_float, (EmbeddedElem,), Oscar)) > 0
- @test Polymake.common.convert_to{Float64}(A2) isa Float64
- fa2 = Polymake.common.convert_to{Float64}(A2)
- @test isapprox(fa2, 1.71; rtol=0.001)
+ if isdefined(Hecke, :EmbeddedNumFieldElem)
+ if length(methods(Polymake._fieldelem_to_float, (EmbeddedNumFieldElem,), Oscar)) > 0
+ @test Polymake.common.convert_to{Float64}(A2) isa Float64
+ fa2 = Polymake.common.convert_to{Float64}(A2)
+ @test isapprox(fa2, 1.71; rtol=0.001)
+ end
  end
  end
  end

test/perlobj.jl

@@ -152,6 +152,9 @@
  @test i.VERTICES[1, :] == [1, 0, Polymake.QuadraticExtension{Polymake.Rational}(1//4, 1//4, 5), 1//2]
  @test i.VOLUME == Polymake.QuadraticExtension{Polymake.Rational}(5//4, 5//12, 5)
  @test Polymake.bigobject_eltype(i) == "QuadraticExtension"
+
+ undefobj = Polymake.polytope.Polytope(POINTS=nothing)
+ @test undefobj.POINTS === nothing
  end
 
  @testset verbose=true "attachments" begin

test/runtests.jl

@@ -26,6 +26,11 @@ struct MyInt x::Int end # needed in test/convert.jl
 
 include("Aqua.jl")
 
+function typename_variants(s::AbstractString)
+ r = replace(s, ">>" => "> >")
+ return [r, s]
+end
+
 include("integers.jl")
 include("rationals.jl")
 include("quadraticextension.jl")

test/sparsevector.jl

@@ -112,7 +112,7 @@ using Polymake.SparseArrays
  end
 
  @testset verbose=true "Low-level operations" begin
- for (E,s) in [(Int64, "long"), (Polymake.Integer, "pm::Integer"), (Polymake.Rational, "pm::Rational"), (Float64, "double"), (Polymake.QuadraticExtension{Polymake.Rational}, "pm::QuadraticExtension<pm::Rational> "), (Polymake.OscarNumber, "common::OscarNumber")]
+ for (E,s) in [(Int64, "long"), (Polymake.Integer, "pm::Integer"), (Polymake.Rational, "pm::Rational"), (Float64, "double"), (Polymake.QuadraticExtension{Polymake.Rational}, "pm::QuadraticExtension<pm::Rational>"), (Polymake.OscarNumber, "common::OscarNumber")]
  @testset verbose=true "Polymake.SparseVector{$E}" begin
  V = Polymake.SparseVector{E}(jl_v)
 
@@ -124,6 +124,8 @@ using Polymake.SparseArrays
  @test length(V) == 3
  @test size(V) == (3,)
 
+ type = "pm::SparseVector<$s>"
+
  for T in [IntTypes; Polymake.Integer]
  V = Polymake.SparseVector{E}(jl_v) # local copy
  setindex!(V, T(5), 1)
@@ -134,17 +136,11 @@ using Polymake.SparseArrays
  @test V[2] = T(10) isa T
  V[2] = T(10)
  @test V[2] == 10
- if E == Polymake.OscarNumber
- @test string(V) == string("pm::SparseVector<", s, ">\n(5) (10) (3)")
- else
- @test string(V) == string("pm::SparseVector<", s, ">\n5 10 3")
- end
- end
- if E == Polymake.OscarNumber
- @test string(Polymake.SparseVector{E}(jl_s)) == string("pm::SparseVector<", s, ">\n(3) (1 (1))")
- else
- @test string(Polymake.SparseVector{E}(jl_s)) == string("pm::SparseVector<", s, ">\n(3) (1 1)")
+ vec = E != Polymake.OscarNumber ? "5 10 3" : "(5) (10) (3)"
+ @test string(V) in typename_variants("$type\n$vec")
  end
+ vec = E != Polymake.OscarNumber ? "(3) (1 1)" : "(3) (1 (1))"
+ @test string(Polymake.SparseVector{E}(jl_s)) in typename_variants("$type\n$vec")
  end
  end
 

test/vectors.jl

@@ -213,7 +213,9 @@ using Polymake.CxxWrap
  end
  V[2] = T(10)//T(3)
  @test V[2] == 10//3
- @test string(V) == "pm::Vector<pm::QuadraticExtension<pm::Rational> >\n5/3 10/3 3"
+ type = "pm::Vector<pm::QuadraticExtension<pm::Rational>>"
+ vec = "5/3 10/3 3"
+ @test string(V) in typename_variants("$type\n$vec")
  end
  end
 
@@ -494,7 +496,9 @@ using Polymake.CxxWrap
  @test (W[3] = T([4, 5], [1 0 0; 0 0 1])) isa Polymake.to_cxx_type(T)
  W[3] = T([4, 5], [1 0 0; 0 0 1])
  @test W[3] == T([4, 5], [1 0 0; 0 0 1])
- @test string(W) == "pm::Vector<pm::Polynomial<pm::Rational, long> >\n2*x_0^2*x_1^3 + 3*x_1^2*x_2^3 0 4*x_0 + 5*x_2"
+ type = "pm::Vector<pm::Polynomial<pm::Rational, long>>"
+ polystr = "2*x_0^2*x_1^3 + 3*x_1^2*x_2^3 0 4*x_0 + 5*x_2"
+ @test string(W) in typename_variants("$type\n$polystr")
  end
  end
  end