Branch H - DO NOT MERGE - DO NOT REVIEW

.github/workflows/add_release_documentation.yml

@@ -93,7 +93,7 @@ jobs:
         && echo CXXFLAGS_var="-Wall -pedantic -O3" >> $GITHUB_ENV
     - name: build config variables
       if: ${{ env.MINOR_RELEASE == 'true' }}
-      run: export CONFIG_OPTIONS="--without-blas ${TEST_LEVEL_FLAG}"
+      run: export CONFIG_OPTIONS="--without-blas ${LESS_TEST_OPTION}"
            && export CONFIG_SERIAL_DEBUG="$CONFIG_OPTIONS --enable-debug --with-sc=$SC_SERIAL_DEBUG/install --with-p4est=$P4EST_SERIAL_DEBUG/install"
     - name: Check vars
       if: ${{ env.MINOR_RELEASE == 'true' }}

.github/workflows/build_cmake_tarball.yml

@@ -150,4 +150,3 @@ jobs:
         name: build_tar.log
         path: build_tar/test-suite.log
 
-

.github/workflows/check_indentation.yml

@@ -27,12 +27,20 @@ name: t8code indentation check
 # It is triggered for pull requests into main and develop and will also run once a day
 # on main.
 #
-# The script runs the scripts/check_if_all_files_indented.sh script of t8code.
+# The script runs the scripts/check_if_all_files_indented.scp script of t8code.
 # The output is uploaded as an artifact to the github page.
 
 on:
-  merge_group:
+  push:
+    branches:
+      - main
+      - develop
+      - feature-*CI* # for testing this script, all feature branches with "CI" in their name
   pull_request:
+    branches:
+      - main
+      - develop
+      - Branch_H
   workflow_dispatch: # Be able to trigger this manually on github.com
   # Run every night at 1:05
   schedule:
@@ -57,7 +65,7 @@ jobs:
     - name: Install indent
       run: pip install clang-format==17.0.1
     - name: Indentation check
-      run: cd scripts/ && ./check_if_all_files_indented.sh &> >(tee -a indent_script_output.txt)
+      run: cd scripts/ && ./check_if_all_files_indented.scp &> >(tee -a indent_script_output.txt)
     - name: Archive script output
     # Do this regardess of the result of the previous step.
     # We especially want to upload the result when the check fails.

.github/workflows/mattermost_pull_request.yml

@@ -28,7 +28,7 @@ name: Mattermost_message_pull_request
 on:
   # Triggers the workflow on pull request events on the feature-CI_mattermost_messages, develop or main branch
   pull_request:
-    branches:
+    branches: [ feature-CI_mattermost_messages, develop, main ]
     types: [ opened, synchronize, reopened, closed]
 
   # Allows you to run this workflow manually from the Actions tab

.github/workflows/spell_check.yml

@@ -1,7 +1,10 @@
 name: spell_check
 
 on:
-  merge_group:
+  push:
+    branches:
+      - main
+      - feature-*CI* # for testing this script, all feature branches with "CI" in their name
   pull_request:
   workflow_dispatch: # Be able to trigger this manually on github.com
 
@@ -14,14 +17,3 @@ jobs:
         uses: actions/checkout@v4
       - name: Check spelling
         uses: crate-ci/typos@master
-      - name: check macros
-        run: |
-          for file in $(git diff --name-only --diff-filter=A); do
-            ./scripts/check_macros.sh "$file" &>> check_macros.txt
-          done
-      - name: Archive script output
-        if: failure()
-        uses: actions/upload-artifact@v4
-        with:
-          name: t8code check macros report
-          path: check_macros.txt

.github/workflows/tests_cmake_t8code.yml

@@ -119,4 +119,4 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
-        path: build/Testing/Temporary/LastTest.log
+        path: build/Testing/Temporary/LastTest.log

.github/workflows/tests_cmake_t8code_api.yml

@@ -118,4 +118,4 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_fortran.log
-        path: build_fortran/Testing/Temporary/LastTest.log
+        path: build_fortran/Testing/Temporary/LastTest.log

.github/workflows/tests_cmake_t8code_linkage.yml

@@ -182,4 +182,4 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: test-suite_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}_VTK.log
-        path: build_vtk/Testing/Temporary/LastTest.log
+        path: build_vtk/Testing/Temporary/LastTest.log

.github/workflows/tests_cmake_t8code_w_shipped_submodules.yml

@@ -116,4 +116,4 @@ jobs:
       uses: actions/upload-artifact@v4
       with:
         name: test-suite_w_submodules_${{ inputs.BUILD_TYPE }}_MPI_${{ inputs.MPI }}.log
-        path: build/Testing/Temporary/LastTest.log
+        path: build/Testing/Temporary/LastTest.log

.github/workflows/tests_cmake_testsuite.yml

@@ -199,4 +199,4 @@ jobs:
     uses: ./.github/workflows/build_cmake_tarball.yml
     needs: [preparation, sc_p4est_tests, t8code_tests, t8code_linkage_tests, t8code_api_tests, t8code_w_shipped_submodules_tests]
     with:
-      TEST_LEVEL: ${{ github.event_name == 'pull_request' && 1 || 0 }} # Set TEST_LEVEL to 1 if the event is a PR, otherwise 0.
+      TEST_LEVEL: ${{ github.event_name == 'pull_request' && 1 || 0 }} # Set TEST_LEVEL to 1 if the event is a PR, otherwise 0.

.github/workflows/update_documentation.yml

@@ -67,7 +67,7 @@ jobs:
       run: echo CFLAGS_var="-Wall -pedantic -O3" >> $GITHUB_ENV
         && echo CXXFLAGS_var="-Wall -pedantic -O3" >> $GITHUB_ENV
     - name: build config variables
-      run: export CONFIG_OPTIONS="--without-blas ${TEST_LEVEL_FLAG}"
+      run: export CONFIG_OPTIONS="--without-blas ${LESS_TEST_OPTION}"
            && export CONFIG_SERIAL_DEBUG="$CONFIG_OPTIONS --enable-debug --with-sc=$SC_SERIAL_DEBUG/install --with-p4est=$P4EST_SERIAL_DEBUG/install"
     - name: Check vars
       run: echo "[$CONFIG_SERIAL_DEBUG]"

.typos.toml

@@ -3,4 +3,4 @@ eles = "eles"
 packageid = "packageid"
 
 [files]
-extend-exclude = ["scripts/t8indent.sh", "thirdparty/", "t8code_logo.png", "cmake/FindOpenCASCADE.cmake"]
+extend-exclude = ["scripts/t8indent", "thirdparty/", "t8code_logo.png", "cmake/FindOpenCASCADE.cmake"]

CMakeLists.txt

@@ -21,6 +21,7 @@ option( T8CODE_EXPORT_COMPILE_COMMANDS "Export the compile commands as json. Can
 
 option( T8CODE_BUILD_TESTS "Build t8code's automated tests" ON )
 cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" ON "T8CODE_BUILD_TESTS" OFF )
+cmake_dependent_option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF "T8CODE_BUILD_TESTS" OFF )
 
 option( T8CODE_BUILD_EXAMPLES "Build t8code's examples" ON )
 cmake_dependent_option( T8CODE_BUILD_TPL_EXAMPLES "Build the examples from libsc and p4est" OFF "T8CODE_BUILD_EXAMPLES" OFF )
@@ -40,8 +41,6 @@ option( T8CODE_USE_SYSTEM_P4EST "Use system-installed p4est library" OFF )
 option( T8CODE_BUILD_DOCUMENTATION "Build t8code's documentation" OFF )
 cmake_dependent_option( T8CODE_BUILD_DOCUMENTATION_SPHINX "Build t8code's documentation using sphinx" OFF "T8CODE_BUILD_DOCUMENTATION" OFF )
 
-set(T8CODE_TEST_LEVEL 0 CACHE STRING "Test level: 0 for full tests, 1 for less thorough tests, 2 for minimal tests. (WARNING: Use with care.)")
-add_definitions(-DT8CODE_TEST_LEVEL=${T8CODE_TEST_LEVEL})
 set(T8CODE_CUSTOM_PARALLEL_TEST_COMMAND "" CACHE STRING "Define a custom command for parallel tests , e.g.: mpirun -np 8 (overwrites standard mpirun -np 4 if build with mpi)")
 set(T8CODE_CUSTOM_SERIAL_TEST_COMMAND "" CACHE STRING "Define a custom command for serial tests.")
 

NEWS.md

@@ -108,7 +108,7 @@ A list of all renamings (without considering the deletion of the prefix) is here
 - `t8_element_vertex_integer_coords` -> `element_get_vertex_integer_coords`
 - `t8_element_vertex_reference_coords` -> `element_get_vertex_reference_coords`
 - `t8_element_refines_irregular` -> `refines_irregular`
-- `t8_element_root` -> `t8_element_set_to_root`
+- `t8_element_root` -> `t8_element_get_root`
 
 
 ### Usage of the default scheme

README.md

@@ -72,10 +72,15 @@ We provide a short guide to install t8code in our Wiki [Installation guide](http
 
 ### Documentation
 
-t8code uses [Doxygen](https://doxygen.nl/) to generate the code documentation. 
-You can find the documentation of our releases on the [t8code website](https://dlr-amr.github.io/t8code/pages/documentation.html).
-Follow the steps described in our Wiki [Documentation](https://github.com/DLR-AMR/t8code/wiki/Documentation) to create the documentation locally.
+t8code uses [Doxygen](https://doxygen.nl/) to generate the code documentation. You can build the documentation with
 
+```
+make doxygen
+```
+
+and then find the generated files in the `/doc` subfolder.
+
+You can also find the documentation of our releases on the [t8code website](https://dlr-amr.github.io/t8code/pages/documentation.html).
 
 ### License and contributing
 t8code is licensed under GPLv2 (see [COPYING](COPYING)). We appreciate

benchmarks/t8_time_forest_partition.cxx

@@ -38,8 +38,7 @@
 #include <t8_forest/t8_forest_geometrical.h>
 #include <t8_forest/t8_forest_profiling.h>
 #include <t8_schemes/t8_default/t8_default.hxx>
-#include <example/common/t8_example_common.hxx>
-#include <t8_types/t8_vec.hxx>
+#include <example/common/t8_example_common.h>
 
 /* This is the user defined data used to define the
  * region in which we partition.
@@ -49,11 +48,29 @@
 typedef struct
 {
   double c_min, c_max; /* constants that define the thickness of the refinement region */
-  t8_3D_vec normal;    /* normal vector to the plane E */
+  double normal[3];    /* normal vector to the plane E */
   int base_level;      /* A given level that is not coarsend further, see -l argument */
   int max_level;       /* A max level that is not refined further, see -L argument */
 } adapt_data_t;
 
+/* Simple 3 dimensional vector product */
+static double
+t8_vec3_dot (double *v1, double *v2)
+{
+  return v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2];
+}
+
+/* Set x = x - alpha*y
+ * for 2 3dim vectors x,y and a constant alpha */
+static void
+t8_vec3_xmay (double *x, double alpha, double *y)
+{
+  int i;
+  for (i = 0; i < 3; i++) {
+    x[i] -= alpha * y[i];
+  }
+}
+
 #if 0
 /* TODO: deprecated. was replaced by t8_common_midpoint. */
 static void
@@ -85,36 +102,37 @@ t8_anchor_element (t8_forest_t forest, t8_locidx_t which_tree,
  * c_min, c_max. We refine the cells in the band c_min*E, c_max*E */
 static int
 t8_band_adapt (t8_forest_t forest, t8_forest_t forest_from, t8_locidx_t which_tree, t8_eclass_t tree_class,
-               [[maybe_unused]] t8_locidx_t lelement_id, const t8_scheme *scheme, const int is_family,
-               [[maybe_unused]] const int num_elements, t8_element_t *elements[])
+               t8_locidx_t lelement_id, const t8_scheme *scheme, const int is_family, const int num_elements,
+               t8_element_t *elements[])
 {
   int level, base_level, max_level;
-  t8_3D_vec elem_midpoint;
+  double elem_midpoint[3];
+  double *normal;
   adapt_data_t *adapt_data;
 
   T8_ASSERT (!is_family || num_elements == scheme->element_get_num_children (tree_class, elements[0]));
   level = scheme->element_get_level (tree_class, elements[0]);
   /* Get the minimum and maximum x-coordinate from the user data pointer of forest */
   adapt_data = (adapt_data_t *) t8_forest_get_user_data (forest);
-  t8_3D_vec normal = adapt_data->normal;
+  normal = adapt_data->normal;
   base_level = adapt_data->base_level;
   max_level = adapt_data->max_level;
   /* Compute the coordinates of the anchor node. */
-  t8_forest_element_centroid (forest_from, which_tree, elements[0], elem_midpoint.data ());
+  t8_forest_element_centroid (forest_from, which_tree, elements[0], elem_midpoint);
 
   /* Calculate elem_midpoint - c_min n */
-  t8_axy (elem_midpoint, normal, adapt_data->c_min);
+  t8_vec3_xmay (elem_midpoint, adapt_data->c_min, normal);
 
   /* The purpose of the factor C*h is that the levels get smaller, the
    * closer we get to the interface. We refine a cell if it is at most
    * C times its own height away from the interface */
-  if (t8_dot (elem_midpoint, normal) >= 0) {
+  if (t8_vec3_dot (elem_midpoint, normal) >= 0) {
     /* if the anchor node is to the right of c_min*E,
      * check if it is to the left of c_max*E */
 
     /* set elem_midpoint to the original anchor - c_max*normal */
-    t8_axy (elem_midpoint, normal, adapt_data->c_max - adapt_data->c_min);
-    if (t8_dot (elem_midpoint, normal) <= 0) {
+    t8_vec3_xmay (elem_midpoint, adapt_data->c_max - adapt_data->c_min, normal);
+    if (t8_vec3_dot (elem_midpoint, normal) <= 0) {
       if (level < max_level) {
         /* We do refine if level smaller 1+base level and the anchor is
          * to the left of c_max*E */
@@ -136,6 +154,16 @@ t8_band_adapt (t8_forest_t forest, t8_forest_t forest_from, t8_locidx_t which_tr
   return 0;
 }
 
+static void
+t8_vec3_normalize (double *v)
+{
+  double norm = sqrt (t8_vec3_dot (v, v));
+
+  v[0] /= norm;
+  v[1] /= norm;
+  v[2] /= norm;
+}
+
 /* Create a cmesh from a .msh files uniform level 0
  * partitioned. */
 static void
@@ -184,7 +212,7 @@ t8_time_forest_cmesh_mshfile (t8_cmesh_t cmesh, const char *vtu_prefix, sc_MPI_C
   adapt_data.normal[0] = 0.8;
   adapt_data.normal[1] = 0.3;
   adapt_data.normal[2] = 0.0;
-  t8_normalize (adapt_data.normal);
+  t8_vec3_normalize (adapt_data.normal);
   adapt_data.base_level = init_level;
   adapt_data.max_level = max_level;
   /* Start the time loop, in each time step the refinement front  moves
@@ -313,7 +341,7 @@ main (int argc, char *argv[])
   int level, level_diff;
   int help = 0, no_vtk, do_ghost, do_balance, use_cad;
   int dim, num_files;
-  int test_tet, test_linear_cylinder, test_cad_cylinder;
+  int test_tet, test_linear_cylinder, test_cad_cylinder, test_hybrid_cube, test_hex_cube;
   int stride;
   int cmesh_level;
   double T, delta_t, cfl;
@@ -363,6 +391,12 @@ main (int argc, char *argv[])
   sc_options_add_switch (opt, 'O', "test-cad-cylinder", &test_cad_cylinder,
                          "Use a cad cmesh to compare linear and cad geometry performance."
                          " If this option is used -o is enabled automatically. Not allowed with -f and -c.");
+  sc_options_add_switch (opt, 'C', "test-hybridcube", &test_hybrid_cube,
+                         "Use a hypercube with Tet, Prism and Hex elements as cmesh."
+                         " If this option is used -o is enabled automatically. Not allowed with -f and -c.");
+  sc_options_add_switch (opt, 'H', "test-hexcube", &test_hex_cube,
+                         "Use a hypercube with Hex elements as cmesh."
+                         " If this option is used -o is enabled automatically. Not allowed with -f and -c.");
   sc_options_add_int (opt, 'l', "level", &level, 0, "The initial uniform refinement level of the forest.");
   sc_options_add_int (opt, 'r', "rlevel", &level_diff, 1,
                       "The number of levels that the forest is refined from the initial level.");
@@ -388,11 +422,12 @@ main (int argc, char *argv[])
   /* check for wrong usage of arguments */
   if (first_argc < 0 || first_argc != argc || dim < 2 || dim > 3
       || (cmeshfileprefix == NULL && mshfileprefix == NULL && test_tet == 0 && test_cad_cylinder == 0
-          && test_linear_cylinder == 0)
+          && test_linear_cylinder == 0 && test_hybrid_cube == 0 && test_hex_cube == 0)
       || stride <= 0 || (num_files - 1) * stride >= mpisize || cfl < 0 || T <= 0
-      || test_tet + test_linear_cylinder + test_cad_cylinder > 1
-      || (cmesh_level >= 0 && (!test_linear_cylinder && !test_cad_cylinder))
-      || ((mshfileprefix != NULL || cmeshfileprefix != NULL) && (test_linear_cylinder || test_cad_cylinder || test_tet))
+      || test_tet + test_linear_cylinder + test_cad_cylinder + test_hybrid_cube + test_hex_cube > 1
+      || (cmesh_level >= 0 && (!test_linear_cylinder && !test_cad_cylinder && !test_hybrid_cube && !test_hex_cube))
+      || ((mshfileprefix != NULL || cmeshfileprefix != NULL)
+          && (test_linear_cylinder || test_cad_cylinder || test_tet || test_hybrid_cube || test_hex_cube))
       || (mshfileprefix == NULL && use_cad)) {
     sc_options_print_usage (t8_get_package_id (), SC_LP_ERROR, opt, NULL);
     return 1;
@@ -427,6 +462,14 @@ main (int argc, char *argv[])
                                             sc_intpow (2, cmesh_level), sc_intpow (2, cmesh_level), test_cad_cylinder);
       test_linear_cylinder ? vtu_prefix = "test_linear_cylinder" : vtu_prefix = "test_cad_cylinder";
     }
+    else if (test_hybrid_cube) {
+      cmesh = t8_cmesh_new_hypercube_hybrid (sc_MPI_COMM_WORLD, 0, 0);
+      vtu_prefix = "test_hypercube_hybrid";
+    }
+    else if (test_hex_cube) {
+      cmesh = t8_cmesh_new_hypercube (T8_ECLASS_HEX, sc_MPI_COMM_WORLD, 0, 0, 0);
+      vtu_prefix = "test_hypercube_hex";
+    }
     else {
       T8_ASSERT (cmeshfileprefix != NULL);
       cmesh