Merge pull request #469 from oscar-system/bl/undef

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 @@ struct PolymakeType end
 
 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(T::Type) = throw(ArgumentError("Unrecognized argument type: $
 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