Improvement: Element data for mesh handle is now defined via mesh competence

.github/workflows/check_doxygen.yml

@@ -79,17 +79,21 @@ jobs:
       run: mkdir build && cd build && cmake ../ $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_doc_build.log
         path: build/config.log
     - name: check doxygen for errors / warnings
       run: |
         cd build && cd doc
         doxygen Doxyfile >> doxygen.out 2> doxygen.err
+    - name: Show doxygen log
+      if: failure()
+      run: |
+        cat build/doc/doxygen.err
     - name: Upload doxygen log
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: doxygen-log
         path: build/doc/doxygen.err

.github/workflows/check_indentation.yml

@@ -56,7 +56,7 @@ jobs:
     # Do this regardless of the result of the previous step.
     # We especially want to upload the result when the check fails.
       if: always()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: t8code indentation report
         path: scripts/indent_script_output.txt

.github/workflows/code_coverage.yml

@@ -57,7 +57,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -101,7 +101,7 @@ jobs:
       run: mkdir build && cd build && cmake ../ $CONFIG_OPTIONS -DCMAKE_Fortran_FLAGS="-fprofile-arcs -ftest-coverage" 
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/CMakeFiles/CMakeOutput.log

.github/workflows/spell_check.yml

@@ -38,11 +38,11 @@ jobs:
       - name: check macros
         run: |
           for file in $(git diff --name-only --diff-filter=A); do
-            ./scripts/check_macros.sh "$file" &>> check_macros.txt
+            ./scripts/internal/check_macros.sh "$file" &>> check_macros.txt
           done
       - name: Archive script output
         if: failure()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: t8code check macros report
           path: check_macros.txt

.github/workflows/test_preparation.yml

@@ -189,7 +189,7 @@ jobs:
 
     ## upload artifacts
     - name: Upload build artifacts
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
         path: ./artifact.tar

.github/workflows/test_sc_p4est.yml

@@ -52,7 +52,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -85,7 +85,7 @@ jobs:
       run: cd $SC_DEBUG && ninja test
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: sc_debug_MPI_${{ inputs.MPI }}.log
         path: $SC_DEBUG/Testing/Temporary/LastTest.log
@@ -94,7 +94,7 @@ jobs:
       run: cd $SC_RELEASE && ninja test
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: sc_release_MPI_${{ inputs.MPI }}.log
         path: $SC_RELEASE/Testing/Temporary/LastTest.log
@@ -106,7 +106,7 @@ jobs:
       run: cd $P4EST_DEBUG && ninja test
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: sp4est_debug_MPI_${{ inputs.MPI }}.log
         path: $P4EST_DEBUG/Testing/Temporary/LastTest.log
@@ -115,7 +115,7 @@ jobs:
       run: cd $P4EST_RELEASE && ninja test
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: sp4est_release_MPI_${{ inputs.MPI }}.log
         path: $P4EST_RELEASE/Testing/Temporary/LastTest.log

.github/workflows/test_t8code.yml

@@ -55,7 +55,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -97,7 +97,7 @@ jobs:
       run: mkdir build && cd build && cmake ../ $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/CMakeFiles/CMakeOutput.log
@@ -116,7 +116,7 @@ jobs:
       if: ${{ inputs.MPI == 'OFF' }}
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/Testing/Temporary/LastTest.log

.github/workflows/test_t8code_api.yml

@@ -55,7 +55,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -95,7 +95,7 @@ jobs:
       run: mkdir build_api && cd build_api && cmake ../ $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_api.log
         path: build_api/CMakeFiles/CMakeOutput.log
@@ -114,7 +114,7 @@ jobs:
       if: ${{ inputs.MPI == 'OFF' }}
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_api.log
         path: build_api/Testing/Temporary/LastTest.log

.github/workflows/test_t8code_linkage.yml

@@ -55,7 +55,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -96,7 +96,7 @@ jobs:
       run: mkdir build_occ && cd build_occ && cmake ../ $CONFIG_OPTIONS -DT8CODE_ENABLE_OCC=ON
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_OCC.log
         path: build_occ/CMakeFiles/CMakeOutput.log
@@ -115,7 +115,7 @@ jobs:
       if: ${{ inputs.MPI == 'OFF' }}
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_OCC.log
         path: build_occ/Testing/Temporary/LastTest.log
@@ -128,7 +128,7 @@ jobs:
       run: mkdir build_vtk && cd build_vtk && cmake ../ $CONFIG_OPTIONS -DT8CODE_ENABLE_VTK=ON -DVTK_DIR=/usr/local/lib/cmake/vtk-9.1
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_VTK.log
         path: build_vtk/CMakeFiles/CMakeOutput.log
@@ -147,7 +147,7 @@ jobs:
       if: ${{ inputs.MPI == 'OFF' }}
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_VTK.log
         path: build_vtk/Testing/Temporary/LastTest.log

.github/workflows/test_t8code_w_clang_and_ompi.yml

@@ -126,7 +126,7 @@ jobs:
     # On failure, upload logs
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_w_clang_and_ompi_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/CMakeFiles/CMakeOutput.log
@@ -158,7 +158,7 @@ jobs:
     # On failure, upload logs
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: test-suite_w_clang_and_ompi_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/Testing/Temporary/LastTest.log

.github/workflows/test_t8code_w_shipped_submodules.yml

@@ -94,7 +94,7 @@ jobs:
       run: mkdir build && cd build && cmake ../ $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_w_submodules_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/CMakeFiles/CMakeOutput.log
@@ -113,7 +113,7 @@ jobs:
       if: ${{ inputs.MPI == 'OFF' }}
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: test-suite_w_submodules_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/Testing/Temporary/LastTest.log

.github/workflows/test_tarball.yml

@@ -85,7 +85,7 @@ jobs:
       run: mkdir build && cd build && cmake ../ $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: config.log
         path: build/config.log
@@ -94,7 +94,7 @@ jobs:
       run: cd build && ninja GenerateVersionFile && ninja package_source && mkdir tarballs && mv package/*Source.tar.gz tarballs
 # Upload the tarball
     - name: upload tarball
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: tarballs
         path: build/tarballs
@@ -106,7 +106,7 @@ jobs:
     timeout-minutes: 15
     steps:
     - name: Download tarball
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
           name: tarballs
           path: tarballs
@@ -129,7 +129,7 @@ jobs:
       run: mkdir build_tar && cd build_tar && cmake $TAR_DIR $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: build_tar.log
         path: build_tar/config.log
@@ -143,7 +143,7 @@ jobs:
       run: cd build_tar && ctest -R _parallel
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: build_tar.log
         path: build_tar/test-suite.log

.github/workflows/test_valgrind.yml

@@ -69,7 +69,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v7
+      uses: actions/download-artifact@v8
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -113,7 +113,7 @@ jobs:
       run: mkdir build && cd build && cmake ../ $CONFIG_OPTIONS
     - name: OnFailUploadLog
       if: failure()
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: cmake_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
         path: build/CMakeFiles/CMakeOutput.log
@@ -122,4 +122,4 @@ jobs:
     # Execute script that runs a Valgrind check for all test binaries.
     # We use 4 parallel processes to run the binaries in parallel with MPI.
     - name: Valgrind check
-      run: cd scripts && bash ./check_all_test_binaries_valgrind.sh --ntasks=4
+      run: cd scripts && bash ./check_all_test_binaries_valgrind.sh ../build/test/ --ntasks=4

.gitignore

@@ -26,59 +26,5 @@ Testing/
 *.vtu
 *.pvtu
 *~
-
-# ------------------------------------------------------------ #
-# Following list of files can be easily generated with:
-# $ git status --porcelain | grep '^??' | cut -c4- >> .gitignore
-
-benchmarks/t8_time_forest_partition
-benchmarks/t8_time_partition
-benchmarks/t8_time_prism_adapt
-example/IO/cmesh/gmsh/t8_load_and_refine_square_w_hole
-example/IO/cmesh/gmsh/t8_read_msh_file
-example/IO/cmesh/t8_cmesh_load_save
-example/IO/cmesh/tetgen/t8_forest_tetgen
-example/IO/cmesh/tetgen/t8_read_tetgen
-example/IO/cmesh/tetgen/t8_time_tetgen
-example/IO/cmesh/triangle/t8_read_triangle
-example/advect/t8_advection
-example/cmesh/t8_cmesh_create_partitioned
-example/cmesh/t8_cmesh_partition
-example/forest/t8_face_neighbor
-example/forest/t8_test_face_iterate
-example/forest/t8_test_ghost
-example/forest/t8_test_ghost_large_level_diff
-example/geometry/t8_example_geometries
-example/version/t8_version
-tutorials/t8_step0_helloworld
-tutorials/t8_step1_coarsemesh
-tutorials/t8_step2_uniform_forest
-tutorials/t8_step3_adapt_forest
-tutorials/t8_step4_partition_balance_ghost
-tutorials/t8_step5_element_data
-tutorials/t8_tutorial_search
-test/t8_cmesh/t8_test_cmesh_copy
-test/t8_cmesh/t8_test_cmesh_face_is_boundary
-test/t8_cmesh/t8_test_cmesh_partition
-test/t8_cmesh/t8_test_cmesh_readmshfile
-test/t8_cmesh/t8_test_hypercube
-test/t8_data/t8_test_shmem
-test/t8_forest/t8_test_find_owner
-test/t8_forest/t8_test_forest_commit
-test/t8_forest/t8_test_ghost_and_owner
-test/t8_forest/t8_test_ghost_exchange
-test/t8_forest/t8_test_half_neighbors
-test/t8_forest/t8_test_search
-test/t8_forest/t8_test_transform
-test/t8_forest/t8_test_user_data
-test/t8_geometry/t8_test_geometry
-test/t8_geometry/t8_test_point_inside
-test/t8_gtest_main
-test/t8_schemes/t8_test_descendant
-test/t8_schemes/t8_test_element_count_leaves
-test/t8_schemes/t8_test_find_parent
-test/t8_schemes/t8_test_init_linear_id
-test/t8_schemes/t8_test_pyra_face_descendant
-test/t8_schemes/t8_test_pyra_face_neigh
-test/t8_schemes/t8_test_successor
-test/t8_test_vtk_linkage
+*.brep
+*.msh

.typos.toml

@@ -3,4 +3,4 @@ eles = "eles"
 packageid = "packageid"
 
 [files]
-extend-exclude = ["scripts/t8indent.sh", "thirdparty/", "t8code_logo.png", "cmake/FindOpenCASCADE.cmake", "src/t8_with_macro_error.h", "doc/Doxyfile.in"]
+extend-exclude = ["scripts/indent.sh", "thirdparty/", "t8code_logo.png", "cmake/FindOpenCASCADE.cmake", "src/t8_misc/t8_with_macro_error.h", "doc/Doxyfile.in"]

README.md

@@ -186,7 +186,7 @@ to install the package on your system.
 
   [K] **Hanging node resolution 3D**:
   Tabea Leistikow (2024) *Derivation and implementation of a hanging nodes resolution scheme for hexahedral non-conforming meshes in t8code*. Master's thesis, Universität zu Köln.
-  Full text currently not available.
+  [Full text available](https://elib.dlr.de/204843/)
 
   ### Citing t8code