Merge branch 'python' of ssh://github.com/espressomd/espresso into dds_gpu_replica_field_tracking

Author: RudolfWeeber

.github/workflows/push_pull.yml

@@ -21,12 +21,23 @@ jobs:
           save: ${{ github.ref == 'refs/heads/python' }}
       - name: Get runner specifications
         run: system_profiler SPHardwareDataType
-      - run: |
-         brew install boost boost-mpi fftw ccache
-         # https://mac.r-project.org/openmp/
-         curl -O https://mac.r-project.org/openmp/openmp-17.0.6-darwin20-Release.tar.gz
-         sudo tar fvxz openmp-17.0.6-darwin20-Release.tar.gz -C /
+      - name: Install dependencies
+        run: |
+         echo '' > Brewfile
+         for dep in boost boost-mpi fftw ccache ninja; do echo "brew \"${dep}\"" >> Brewfile; done
+         brew bundle check >/dev/null 2>&1 || brew bundle --verbose --no-upgrade
+         # set up Xcode compiler
+         echo "::group::List available Xcode compilers"
+         ls /Applications | grep Xcode
+         echo "::endgroup::"
+         sudo xcode-select -switch /Applications/Xcode_16.4.app
+         echo "::group::Install OpenMP (https://mac.r-project.org/openmp/)"
+         curl -s -o ${{ runner.temp }}/openmp.tar.gz https://mac.r-project.org/openmp/openmp-19.1.0-darwin20-Release.tar.gz
+         sudo tar fvxz ${{ runner.temp }}/openmp.tar.gz -C /
+         rm ${{ runner.temp }}/openmp.tar.gz
          codesign -d -vv /usr/local/lib/libomp.dylib
+         echo "::endgroup::"
+         # Python dependencies
          python3 -m venv venv
          . venv/bin/activate
          pip3 install -c requirements.txt cython numpy scipy packaging
@@ -38,11 +49,14 @@ jobs:
           build_procs: 3
           check_procs: 3
           with_ccache: 'true'
+          with_walberla: 'true'
+          with_walberla_fft: 'false'
+          with_walberla_avx: 'false'
 
   debian:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/espressomd/docker/debian:77a3823c5c4c2338c39eb0e0f054b5802f0f2a5e-base-layer
+      image: ghcr.io/espressomd/docker/debian:17ae5d9f6217a5653be3ec409178f0ee15cb519f-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}
@@ -64,8 +78,8 @@ jobs:
         env:
           build_procs: 4
           check_procs: 4
-          CC: 'gcc-12'
-          CXX: 'g++-12'
+          CC: 'gcc-14'
+          CXX: 'g++-14'
           myconfig: 'maxset'
           with_ccache: 'true'
           with_cuda: 'false'
@@ -83,7 +97,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.repository == 'espressomd/espresso' }}
     container:
-      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:77a3823c5c4c2338c39eb0e0f054b5802f0f2a5e-base-layer
+      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:17ae5d9f6217a5653be3ec409178f0ee15cb519f-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu:77a3823c5c4c2338c39eb0e0f054b5802f0f2a5e
+image: ghcr.io/espressomd/docker/ubuntu:17ae5d9f6217a5653be3ec409178f0ee15cb519f
 
 stages:
   - prepare
@@ -16,7 +16,7 @@ stages:
 
 .notification_job_template: &notification_job_definition
   <<: *global_job_definition
-  image: ghcr.io/espressomd/docker/fedora:77a3823c5c4c2338c39eb0e0f054b5802f0f2a5e
+  image: ghcr.io/espressomd/docker/fedora:17ae5d9f6217a5653be3ec409178f0ee15cb519f
   variables:
     GET_SOURCES_ATTEMPTS: 3
   before_script:
@@ -108,7 +108,7 @@ maxset:
      with_stokesian_dynamics: 'true'
      with_caliper: 'true'
      check_skip_long: 'true'
-     cmake_params: '-D CMAKE_CXX_STANDARD=23 -D ESPRESSO_TEST_NP=8'
+     cmake_params: '-D CMAKE_CXX_STANDARD=23 -D CMAKE_CXX_EXTENSIONS=OFF -D ESPRESSO_TEST_NP=8'
   script:
     - bash maintainer/CI/build_cmake.sh
   tags:
@@ -137,10 +137,10 @@ no_rotation:
     - no-cuda
     - numa
 
-fedora:41:
+fedora:42:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/fedora:77a3823c5c4c2338c39eb0e0f054b5802f0f2a5e
+  image: ghcr.io/espressomd/docker/fedora:17ae5d9f6217a5653be3ec409178f0ee15cb519f
   variables:
      with_cuda: 'false'
      with_gsl: 'false'
@@ -149,7 +149,6 @@ fedora:41:
      myconfig: 'maxset'
      make_check_python: 'true'
      with_stokesian_dynamics: 'true'
-     with_fftw: 'false'
      cmake_params: '-D CMAKE_INCLUDE_PATH=/usr/include/mpich-x86_64 -D CMAKE_PREFIX_PATH=/usr/lib64/mpich/lib/'
   script:
     - bash maintainer/CI/build_cmake.sh
@@ -176,6 +175,7 @@ clang-sanitizer:
      with_scafacos: 'true'
      with_walberla: 'true'
      with_stokesian_dynamics: 'true'
+     with_shared_memory_parallelism: 'true'
      with_coverage: 'false'
      with_coverage_python: 'false'
   script:
@@ -398,12 +398,12 @@ installation:
   script:
     - bash maintainer/CI/build_cmake.sh
     - cd build
-    - make install
+    - ninja install
     - cmake . -D ESPRESSO_BUILD_TESTS=ON
     - sed -i "s|$(pwd)/pypresso|/tmp/espresso-unit-tests/bin/pypresso|" testsuite/{python,samples,tutorials}/CTestTestfile.cmake
-    - make check_python_skip_long
-    - make check_samples
-    - make check_tutorials
+    - ninja check_python_skip_long
+    - ninja check_samples
+    - ninja check_tutorials
   tags:
     - espresso
     - cuda
@@ -442,8 +442,8 @@ check_sphinx:
       artifacts: true
   script:
     - cd ${CI_PROJECT_DIR}/build
-    - make -t && make sphinx
-    - make -j2 tutorials
+    - ninja sphinx
+    - ninja -j2 tutorials
     - bash ${CI_PROJECT_DIR}/maintainer/CI/doc_warnings.sh
     - python3 ${CI_PROJECT_DIR}/maintainer/CI/jupyter_warnings.py
   artifacts:
@@ -464,9 +464,9 @@ run_tutorials:
       artifacts: true
   script:
     - cd ${CI_PROJECT_DIR}/build
-    - make -t
-    - make tutorials
-    - make -j1 tutorials_html
+    - ninja -t restat
+    - ninja tutorials
+    - ninja -j1 tutorials_html
     - cd doc/tutorials
     - mkdir html
     - ${CI_PROJECT_DIR}/maintainer/CI/deploy_tutorials.py
@@ -492,7 +492,7 @@ run_doxygen:
       artifacts: true
   script:
     - cd ${CI_PROJECT_DIR}/build
-    - make -t && make doxygen
+    - ninja doxygen
   artifacts:
     paths:
     - build/doc/doxygen
@@ -515,7 +515,8 @@ maxset_no_gpu:
   script:
     - export CUDA_VISIBLE_DEVICES=""
     - cd ${CI_PROJECT_DIR}/build
-    - make -t && make check
+    - ninja -t restat
+    - ninja check
   tags:
     - espresso
     - no-cuda

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
         language: system
         always_run: false
         files: '.*\.(cpp|hpp|h|cu|cuh)'
-        exclude: '^libs/|^src/walberla_bridge/src/.*/generated_kernels/.*\.(cpp|cu)|^maintainer/walberla_kernels/templates/.*\.tmpl\.(cpp|hpp|h|cu|cuh)'
+        exclude: '^libs/|^src/config/include/config/version.hpp.in|^src/walberla_bridge/src/.*/generated_kernels/.*\.(cpp|cu)|^maintainer/walberla_kernels/templates/.*\.tmpl\.(cpp|hpp|h|cu|cuh)'
         args: ["-i", "-style=file"]
 
     -   id: autopep8
@@ -27,7 +27,7 @@ repos:
         language: system
         always_run: false
         files: 'CMakeLists.txt'
-        exclude: '^libs/h5xx/|^libs/Random123-1\.09/'
+        exclude: '^libs/Random123-1\.09/'
         args: ["-i"]
 
     -   id: ex-flags