Bugfix for Julia 1.12

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/ci-jll.yml

@@ -9,25 +9,18 @@ jobs:
       matrix:
         version:
           - '1.9'
+          - 'lts'
+          - '1'
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v3
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest

.github/workflows/ci.yml

@@ -11,26 +11,18 @@ jobs:
       matrix:
         version:
           - '1.9'
+          - 'lts'
+          - '1'
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      #- uses: actions/cache@v1
-      #  env:
-      #    cache-name: cache-artifacts
-      #  with:
-      #    path: ~/.julia/artifacts
-      #    key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-      #    restore-keys: |
-      #      ${{ runner.os }}-test-${{ env.cache-name }}-
-      #      ${{ runner.os }}-test-
-      #      ${{ runner.os }}-
       - name: Install p4est dependencies
         run: |
            sudo apt-get update 
@@ -69,12 +61,12 @@ jobs:
           using MPIPreferences
           MPIPreferences.use_system_binary()
 
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v6
         with:
-          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
   # docs:
   #   name: Documentation
   #   runs-on: ubuntu-latest

src/common_fixes.jl

@@ -47,22 +47,22 @@ const sc_array_t = sc_array
 ################################################################
 
 function _pointer_to_c_memory(obj::S) where {S}
-    Base.unsafe_convert(Ptr{Cvoid}, [obj])
+    ref = Ref{S}(obj)
+    GC.@preserve ref Ptr{Cvoid}(Base.unsafe_convert(Ptr{S}, ref))
 end
 
 function _unsafe_reinterpret(::Type{T}, obj::S) where {T,S}
-# Use unsafe_wrap to avoid copy from unsafe_load 
-# unsafe_load(Ptr{T}(Base.unsafe_convert(Ptr{Cvoid}, Ref{S}(obj))))
-    unsafe_wrap(Array, Ptr{T}(_pointer_to_c_memory(obj)), 1)[]
+    ref = Ref{S}(obj)
+    GC.@preserve ref unsafe_load(Ptr{T}(Base.unsafe_convert(Ptr{S}, ref)))
 end
 
-    ############################################
-    # Primitive type: quadrant_data 
-    # represents the following p4est C-Unions:
-    #   - p4est_quadrant_data
-    #   - p6est_quadrant_data
-    #   - p8est_quadrant_data
-    ############################################
+############################################
+# Primitive type: quadrant_data 
+# represents the following p4est C-Unions:
+#   - p4est_quadrant_data
+#   - p6est_quadrant_data
+#   - p8est_quadrant_data
+############################################
 struct piggy1 which_tree::p4est_topidx_t; owner_rank::Cint; end
 struct piggy2 which_tree::p4est_topidx_t; from_tree::p4est_topidx_t; end
 struct piggy3 which_tree::p4est_topidx_t; local_num::p4est_locidx_t; end
@@ -108,7 +108,10 @@ iter_side_data_properties = (:full, :hanging)
 
 # Biggest data size in union (24 bytes - 192 bits)
 iter_side_data_2_union = Union{full, hanging{2}}
-primitive type iter_side_data_2 8*sizeof(iter_side_data_2_union) end
+struct iter_side_data_2
+    head::UInt64
+    tail::NTuple{24,UInt8}
+end
 
 function Base.getproperty(x::iter_side_data_2, name::Symbol)
     if name == :full
@@ -125,15 +128,18 @@ Base.propertynames(x::iter_side_data_2) = (iter_side_data_properties..., fieldna
 const p4est_iter_face_side_data = iter_side_data_2
 const p8est_iter_edge_side_data = iter_side_data_2
 
-    ############################################
-    # Primitive type: iter_side_data_4 
-    # represents the following p4est C-Unions:
-    #   - p8est_iter_face_side_data
-    ############################################
+############################################
+# Primitive type: iter_side_data_4 
+# represents the following p4est C-Unions:
+#   - p8est_iter_face_side_data
+############################################
 
 # Biggest data size in union (32 bytes - 256 bits) 
 iter_side_data_4_union = Union{full, hanging{4}}
-primitive type iter_side_data_4 8*sizeof(iter_side_data_4_union) end 
+struct iter_side_data_4
+    head::UInt64
+    tail::NTuple{48,UInt8}
+end
 
 function Base.getproperty(x::iter_side_data_4, name::Symbol)
     if name == :full
@@ -148,4 +154,3 @@ end
 Base.propertynames(x::iter_side_data_4) = (iter_side_data_properties..., fieldnames(DataType)...)
 
 const p8est_iter_face_side_data = iter_side_data_4
-

test/test_p8est_bindings.jl

@@ -2,6 +2,13 @@ using MPI
 using P4est_wrapper
 using Test
 
+@test Base.datatype_alignment(P4est_wrapper.iter_side_data_4) == 8
+@test Base.datatype_alignment(P4est_wrapper.iter_side_data_2) == 8
+@test sizeof(P4est_wrapper.p8est_iter_face_side_t) == 64
+@test fieldoffset(P4est_wrapper.p8est_iter_face_side_t, 4) == 8
+@test sizeof(P4est_wrapper.p8est_iter_edge_side_t) == 48
+@test fieldoffset(P4est_wrapper.p8est_iter_edge_side_t, 5) == 8
+
 # Initialize MPI if not initialized yet
 if !MPI.Initialized()
     MPI.Init()