Feature ghost interface restructuring overlap

.github/workflows/add_release_documentation.yml

@@ -62,7 +62,7 @@ jobs:
     # This step is necessary to get the newest package data
     - name: checkout
       if: ${{ env.MINOR_RELEASE == 'true' }}
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         path: t8code
         fetch-tags: true
@@ -116,7 +116,7 @@ jobs:
 # upload documentation
     - name: Checkout t8code-website repo
       if: ${{ env.MINOR_RELEASE == 'true' }}
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         ref: ${{ github.head_ref }}
         repository: DLR-AMR/t8code-website

.github/workflows/build_cmake_tarball.yml

@@ -49,7 +49,7 @@ jobs:
 #
 # Setup and bootstrap
 #
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-tags: true # required to get version tags
         fetch-depth: 0    # required to get all history, especially the version tags
@@ -98,7 +98,7 @@ jobs:
     timeout-minutes: 90
     steps:
     - name: Download tarball
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
           name: tarballs
           path: tarballs

.github/workflows/check_indentation.yml

@@ -44,7 +44,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 10
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-tags: true # required to get version tags
         fetch-depth: 0    # required to get all history, especially the version tags      

.github/workflows/code_coverage.yml

@@ -57,7 +57,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -91,7 +91,7 @@ jobs:
       run: export TEST_LEVEL_FLAG="-DT8CODE_TEST_LEVEL=${{ inputs.TEST_LEVEL }}"
            && echo TEST_LEVEL_FLAG="$TEST_LEVEL_FLAG" >> $GITHUB_ENV
     - name: build config variables
-      run: export CONFIG_OPTIONS="${TEST_LEVEL_FLAG} -DT8CODE_CODE_COVERAGE=ON -DT8CODE_USE_SYSTEM_SC=ON -DT8CODE_USE_SYSTEM_P4EST=ON -DT8CODE_BUILD_PEDANTIC=ON -DT8CODE_BUILD_WALL=ON -DT8CODE_BUILD_WERROR=ON -DT8CODE_ENABLE_MPI=$MPI -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DSC_DIR=$SC_PATH/install/cmake -DP4EST_DIR=$P4EST_PATH/install/cmake"
+      run: export CONFIG_OPTIONS="${TEST_LEVEL_FLAG} -DT8CODE_CODE_COVERAGE=ON -DT8CODE_USE_SYSTEM_SC=ON -DT8CODE_USE_SYSTEM_P4EST=ON -DT8CODE_BUILD_PEDANTIC=ON -DT8CODE_BUILD_WALL=ON -DT8CODE_BUILD_WERROR=ON -DT8CODE_ENABLE_MPI=$MPI -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DT8CODE_BUILD_FORTRAN_INTERFACE=ON -DSC_DIR=$SC_PATH/install/cmake -DP4EST_DIR=$P4EST_PATH/install/cmake -DT8CODE_BUILD_BENCHMARKS=OFF -DT8CODE_BUILD_DOCUMENTATION=OFF -DT8CODE_BUILD_EXAMPLES=OFF -DT8CODE_BUILD_TUTORIALS=OFF"
         && echo CONFIG_OPTIONS="$CONFIG_OPTIONS" >> $GITHUB_ENV
     # cmake
     - name: echo cmake line

.github/workflows/move_card.yml

@@ -111,6 +111,9 @@ jobs:
 
   evaluate_pr:
     runs-on: ubuntu-latest
+    # Don't run in parallel on the same PR. Otherwise multiple issues might be created for the same PR. 
+    concurrency:
+      group: pr-move-card-${{ github.event.pull_request.id }}
     outputs:
       NUMBER_IS_SET: ${{ steps.get_pr_issue_link.outputs.NUMBER_IS_SET }}
       CLEAN_ISSUE_NUMBER: ${{ steps.get_pr_issue_link.outputs.CLEAN_ISSUE_NUMBER }}

.github/workflows/quick_pr.yml

@@ -42,14 +42,12 @@ jobs:
         outputs:
             ISSUE_NUMBER: ${{ steps.create_issue_and_output_number.outputs.ISSUE_NUMBER }}
         steps:
-        - uses: actions/checkout@v4
+        - uses: actions/checkout@v5
           with:
-                repository: ${{ github.event.repository.full_name }}
-                ref: ${{ github.event.pull_request.head.ref }}
                 fetch-depth: 0
 
         - name: "Set up environment"
-          run: echo "GITHUB_TOKEN=${{ secrets.PAT }}" >> $GITHUB_ENV
+          run: echo "GH_TOKEN=${{ secrets.PAT }}" >> $GITHUB_ENV
 
         - name: "Create Issue"
           id: create_issue_and_output_number
@@ -69,12 +67,21 @@ jobs:
                 # Create the new issue. Use the DEFAULT_PROJECT to directly add it to the project. 
                 # Letting GH add the Issue to the project by automatization can lead to a delay, 
                 # and the following worfkflows will try to move a card that doesn't exist yet.
-                new_issue_url=$(gh issue create \
-                    --title "$TITLE" \
-                    --assignee "$AUTHOR" \
-                    --body "$ISSUE_BODY" \
-                    --project "${{ inputs.DEFAULT_PROJECT }}"
-                )
+                # Only assign the issue if the author is not a bot
+                if [[ "$AUTHOR" == *"[bot]"* ]]; then
+                  new_issue_url=$(gh issue create \
+                  --title "$TITLE" \
+                  --body "$ISSUE_BODY" \
+                  --project "${{ inputs.DEFAULT_PROJECT }}"
+                  )
+                else
+                  new_issue_url=$(gh issue create \
+                  --title "$TITLE" \
+                  --assignee "$AUTHOR" \
+                  --body "$ISSUE_BODY" \
+                  --project "${{ inputs.DEFAULT_PROJECT }}"
+                  )
+                fi
                 echo "new_issue_url=$new_issue_url"
                 # Extract the issue number from the URL. 
                 # The URL is in the format https://github.com/orga-name/repo-name/issues/issues_number

.github/workflows/spell_check.yml

@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Actions Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Check spelling
         uses: crate-ci/typos@master
       - name: check macros

.github/workflows/tests_cmake_preparation.yml

@@ -60,7 +60,7 @@ jobs:
 #
 # Setup
 #
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with: 
         fetch-depth: 0
     - name: Update packages

.github/workflows/tests_cmake_sc_p4est.yml

@@ -52,7 +52,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact

.github/workflows/tests_cmake_t8code.yml

@@ -55,7 +55,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact

.github/workflows/tests_cmake_t8code_api.yml

@@ -55,7 +55,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact

.github/workflows/tests_cmake_t8code_linkage.yml

@@ -55,7 +55,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact

.github/workflows/tests_cmake_t8code_w_shipped_submodules.yml

@@ -54,7 +54,7 @@ jobs:
 #
 # Setup
 #
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with: 
         fetch-depth: 0
     - name: Update packages

.github/workflows/tests_cmake_testsuite.yml

@@ -56,7 +56,7 @@ jobs:
     outputs:
       run_ci: ${{ steps.set_run_ci.outputs.RUN_CI }}
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         repository: ${{ github.event.pull_request.head.repo.full_name }}
         ref: ${{ github.event.pull_request.head.ref }}

.github/workflows/tests_cmake_valgrind.yml

@@ -51,7 +51,7 @@ jobs:
 # Setup
 #
     - name: Download artifacts
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v5
       with:
         name: SC_P4EST_MPI_${{ inputs.MPI }}
     - name: untar artifact
@@ -86,7 +86,7 @@ jobs:
       run: export TEST_LEVEL_FLAG="-DT8CODE_TEST_LEVEL=${{ inputs.TEST_LEVEL }}"
            && echo TEST_LEVEL_FLAG="$TEST_LEVEL_FLAG" >> $GITHUB_ENV
     - name: build config variables
-      run: export CONFIG_OPTIONS="${TEST_LEVEL_FLAG} -GNinja -DT8CODE_USE_SYSTEM_SC=ON -DT8CODE_USE_SYSTEM_P4EST=ON -DT8CODE_BUILD_PEDANTIC=ON -DT8CODE_BUILD_WALL=ON -DT8CODE_BUILD_WERROR=ON -DT8CODE_ENABLE_MPI=$MPI -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DSC_DIR=$SC_PATH/install/cmake -DP4EST_DIR=$P4EST_PATH/install/cmake"
+      run: export CONFIG_OPTIONS="${TEST_LEVEL_FLAG} -GNinja -DT8CODE_USE_SYSTEM_SC=ON -DT8CODE_USE_SYSTEM_P4EST=ON -DT8CODE_BUILD_PEDANTIC=ON -DT8CODE_BUILD_WALL=ON -DT8CODE_BUILD_WERROR=ON -DT8CODE_ENABLE_MPI=$MPI -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DSC_DIR=$SC_PATH/install/cmake -DP4EST_DIR=$P4EST_PATH/install/cmake -DT8CODE_BUILD_FORTRAN_INTERFACE=ON"
         && echo CONFIG_OPTIONS="$CONFIG_OPTIONS" >> $GITHUB_ENV
     # cmake
     - name: echo cmake line

.github/workflows/update_documentation.yml

@@ -44,7 +44,7 @@ jobs:
 #
 # Setup and bootstrap
 #
-    - uses: actions/checkout@v4    
+    - uses: actions/checkout@v5    
       with:
         fetch-tags: true # required to get version tags
         fetch-depth: 0    # required to get all history, especially the version tags
@@ -81,7 +81,7 @@ jobs:
 
 # upload documentation
     - name: Checkout t8code-website repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         ref: ${{ github.head_ref }}
         repository: DLR-AMR/t8code-website

.readthedocs.yaml

@@ -0,0 +1,65 @@
+#  This file is part of t8code.
+#  t8code is a C library to manage a collection (a forest) of multiple
+#  connected adaptive space-trees of general element types in parallel.
+#
+#  Copyright (C) 2025 the developers
+#
+#  t8code is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  t8code is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with t8code; if not, write to the Free Software Foundation, Inc.,
+#  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  apt_packages:
+    - cmake
+  jobs:
+    post_checkout:
+      # Fetch all tags to ensure we can build documentation for any version
+      # The tags are needed to determine the version number of the documentation
+      - git fetch --unshallow --tags || true  
+    post_install:
+      - bash ./scripts/configure_for_rtd.sh
+
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "doc/" directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: doc/requirements.txt

CMakeLists.txt

@@ -75,7 +75,7 @@ elseif(T8CODE_TEST_LEVEL STREQUAL "T8_TEST_LEVEL_MEDIUM" )
     set(T8_TEST_LEVEL_INT 1)
 elseif(T8CODE_TEST_LEVEL STREQUAL "T8_TEST_LEVEL_FULL" )
     set(T8_TEST_LEVEL_INT 0)
-else() 
+else()
     message( FATAL_ERROR "Invalid string for T8CODE_TEST_LEVEL: ${T8CODE_TEST_LEVEL}. Valid options are T8_TEST_LEVEL_FULL, T8_TEST_LEVEL_MEDIUM, or T8_TEST_LEVEL_BASIC.")
 endif()
 
@@ -131,11 +131,11 @@ if( T8CODE_ENABLE_OCC )
 endif( T8CODE_ENABLE_OCC )
 
 if( T8CODE_ENABLE_NETCDF )
-    find_package( netCDF REQUIRED )
-    if(netCDF_FOUND)
-        message("Found netCDF")
+    find_package( NetCDF REQUIRED )
+    if(NetCDF_FOUND)
+        message("Found NetCDF")
         include(cmake/CheckNetCDFPar.cmake)
-    endif (netCDF_FOUND)
+    endif (NetCDF_FOUND)
 endif( T8CODE_ENABLE_NETCDF )
 
 # Override default for this libsc option
@@ -162,7 +162,10 @@ else()
 
     # Capture the list of variables before adding the subdirectory to mark the added ones as advanced.
     get_cmake_property(_vars_before_sc VARIABLES )
+    list( APPEND CMAKE_MESSAGE_CONTEXT "sc" )
     add_subdirectory( ${CMAKE_CURRENT_LIST_DIR}/sc )
+    list( POP_BACK CMAKE_MESSAGE_CONTEXT )
+    add_library(SC INTERFACE)
     # Capture the list of variables after adding the subdirectory
     get_cmake_property(_vars_after_sc VARIABLES )
     # Compute the difference (new variables added by the subdirectory)
@@ -175,6 +178,38 @@ else()
 
     # Mark the new variables as advanced
     mark_as_advanced( FORCE ${_new_sc_vars} )
+
+    ########################## Fix for OpenMPI ############################################
+    # OpenMPI sometimes has a mismatch between their C and CXX interface which produces a warning in SC.
+    # The warning makes t8codes build fail when Werror is activated. This fix checks if t8code
+    # is linked against OpenMPI and then suppresses that Werror treats this warning as error.
+    # The warning is still displayed while compiling.
+    # We compile a test program mich checks if a OpenMPI specific macro is defined and then apply the fix.
+
+    include(CheckIncludeFile)
+
+    # Check if mpi.h is available
+    check_include_file("mpi.h" MPI_HEADER_FOUND)
+
+    if(MPI_HEADER_FOUND)
+        # Create a temporary C++ source file to check for OpenMPI-specific macros
+        include(CheckCXXSourceCompiles)
+        check_cxx_source_compiles("
+        #include <mpi.h>
+        #ifndef OPEN_MPI
+        #error 'Not OpenMPI'
+        #endif
+        int main() { return 0; }" HAS_OPENMPI)
+
+        if(HAS_OPENMPI)
+            message(STATUS "OpenMPI detected via mpi.h")
+            # Suppress warning
+            target_compile_options(SC::SC INTERFACE -Wno-error=cast-function-type)
+        endif()
+    else()
+        message(WARNING "mpi.h not found!")
+    endif()
+    ########################## End of fix for OpenMPI ############################################
 endif()
 
 if ( T8CODE_USE_SYSTEM_P4EST )
@@ -185,7 +220,9 @@ else()
 
     # Capture the list of variables before adding the subdirectory to mark the added ones as advanced.
     get_cmake_property( _vars_before_p4est VARIABLES )
+    list( APPEND CMAKE_MESSAGE_CONTEXT "p4est" )
     add_subdirectory( ${CMAKE_CURRENT_LIST_DIR}/p4est )
+    list( POP_BACK CMAKE_MESSAGE_CONTEXT )
     # Capture the list of variables after adding the subdirectory
     get_cmake_property( _vars_after_p4est VARIABLES )
     # Compute the difference (new variables added by the subdirectory)