4.2.2rc

.clang-tidy

@@ -10,6 +10,8 @@ Checks: |
    -bugprone-implicit-widening-of-multiplication-result,
    -bugprone-macro-parentheses,
    -bugprone-reserved-identifier,
+   -bugprone-switch-missing-default-case,
+   -bugprone-unchecked-optional-access,
    clang-analyzer-alpha.*,
    modernize-deprecated-headers,
    modernize-make-shared,
@@ -41,7 +43,6 @@ Checks: |
    readability-function-size'
 WarningsAsErrors: '*,-clang-analyzer-core.StackAddrEscapeBase,-clang-analyzer-optin.mpi.MPI-Checker'
 HeaderFilterRegex: '.*'
-AnalyzeTemporaryDtors: false
 FormatStyle:     none
 User: espresso
 CheckOptions:    

.github/actions/build_and_check/action.yml

@@ -1,24 +1,15 @@
 name: 'Build and check'
-description: 'Build espresso and run checks'
-inputs:
-  asan:  # id of input
-    description: 'Whether to build with address sanitizer'
-    required: true
-    default: 'false'
-  ubsan:
-    description: 'Whether to build with undefined behavior sanitizer'
-    required: true
-    default: 'false'
+description: 'Build ESPResSo and run checks'
 runs:
   using: "composite"
   steps:
     - run: |
        brew install boost boost-mpi fftw
        brew install hdf5-mpi
-       pip3 install -c requirements.txt numpy cython h5py scipy
+       pip3 install -c requirements.txt "cython<3.0" numpy scipy h5py packaging
       shell: bash
     - run: |
-        export myconfig=maxset with_cuda=false test_timeout=800 with_asan=${{ inputs.asan }} with_ubsan=${{ inputs.ubsan }} check_skip_long=true
+        export myconfig=maxset with_cuda=false with_gsl=false test_timeout=800 check_skip_long=true
         bash maintainer/CI/build_cmake.sh
       shell: bash
       # This is a workaround for the unfortunate interaction of MacOS and OpenMPI 4

.github/workflows/deploy.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Install pandoc
         uses: r-lib/actions/setup-pandoc@v2
       - name: Setup SSH agent
-        uses: webfactory/ssh-agent@v0.7.0
+        uses: webfactory/ssh-agent@v0.9.0
         with:
           ssh-private-key: ${{ secrets.GH_PAGES_SSH_PRIVATE_KEY }}
       - name: Checkout

.github/workflows/push_pull.yml

@@ -1,57 +1,24 @@
-name: run tests on mac
+name: run tests on macOS
 
 on:
   push:
   pull_request:
-  schedule:
-    - cron: '0 3 * * *'
 
 permissions:
   contents: read # to fetch code (actions/checkout)
 
 jobs:
-  regular_check:
-    runs-on: macos-12
-    if: github.event_name != 'schedule'
+  macos:
+    runs-on: macos-13
     steps:
       - name: Checkout
         uses: actions/checkout@main
       - name: Setup Python environment
-        uses: actions/setup-python@v4.3.1
+        uses: actions/setup-python@v5.1.0
         with:
-          python-version: '3.8'
-      - name: Check without sanitizer
+          python-version: '3.9'
+      - name: Build and check
         uses: ./.github/actions/build_and_check
-        with:
-          asan: false
-          ubsan: false
-
-  sanitizer_check:
-    permissions:
-      contents: read # to fetch code (actions/checkout)
-      issues: write # to create an issue
-
-    runs-on: macos-12
-    if: (github.event_name == 'schedule' && github.repository == 'espressomd/espresso')
-    steps:
-      - name: Checkout
-        uses: actions/checkout@main
-      - name: Setup Python environment
-        uses: actions/setup-python@v4.3.1
-        with:
-          python-version: '3.8'
-      - name: Check with sanitizer
-        uses: ./.github/actions/build_and_check
-        with:
-          asan: true
-          ubsan: true
-      - name: Setting job link variable
-        if: ${{ failure() }}
-        run: |
-          echo "job_link=${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}" >> $GITHUB_ENV
-      - uses: alialaa/issue-action@v1
-        if: ${{ failure() }}
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          title: Scheduled CI job has failed
-          body: ${{ env.job_link }}
+        env:
+          build_procs: 4
+          check_procs: 4

.gitlab-ci.yml

@@ -166,6 +166,21 @@ debian:10:
     - espresso
     - no-cuda
 
+debian:12:
+  <<: *global_job_definition
+  stage: build
+  image: ghcr.io/espressomd/docker/debian:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+  variables:
+     with_cuda: 'false'
+     myconfig: 'maxset'
+     make_check_python: 'false'
+     with_stokesian_dynamics: 'true'
+  script:
+    - bash maintainer/CI/build_cmake.sh
+  tags:
+    - espresso
+    - no-cuda
+
 fedora:36:
   <<: *global_job_definition
   stage: build
@@ -181,6 +196,23 @@ fedora:36:
     - espresso
     - no-cuda
 
+fedora:40:
+  <<: *global_job_definition
+  stage: build
+  image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+  variables:
+     with_cuda: 'false'
+     with_gsl: 'false'
+     myconfig: 'maxset'
+     make_check_python: 'true'
+     with_stokesian_dynamics: 'true'
+     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
+  tags:
+    - espresso
+    - no-cuda
+
 ### Builds with CUDA
 
 clang-sanitizer:
@@ -195,7 +227,7 @@ clang-sanitizer:
      with_coverage: 'false'
      with_static_analysis: 'true'
      check_skip_long: 'true'
-     with_asan: 'true'
+     with_asan: 'false'
      with_ubsan: 'true'
      with_scafacos: 'true'
      with_stokesian_dynamics: 'true'
@@ -227,6 +259,28 @@ fast_math:
     - cuda
   when: manual
 
+cuda12-maxset-ubuntu24.04:
+  <<: *global_job_definition
+  stage: build
+  image: ghcr.io/espressomd/docker/ubuntu:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
+  variables:
+     CC: 'gcc-12'
+     CXX: 'g++-12'
+     GCOV: 'gcov-12'
+     myconfig: 'maxset'
+     with_cuda: 'true'
+     with_coverage: 'false'
+     with_coverage_python: 'false'
+     check_skip_long: 'false'
+     with_scafacos: 'true'
+     with_stokesian_dynamics: 'true'
+  script:
+    - bash maintainer/CI/build_cmake.sh
+  tags:
+    - espresso
+    - cuda
+    - numa
+
 cuda11-maxset-ubuntu20.04:
   <<: *global_job_definition
   stage: build
@@ -238,6 +292,7 @@ cuda11-maxset-ubuntu20.04:
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'true'
+     with_coverage_python: 'true'
      check_skip_long: 'true'
      with_scafacos: 'true'
      with_stokesian_dynamics: 'true'
@@ -259,6 +314,7 @@ cuda11-maxset-ubuntu22.04:
      myconfig: 'maxset'
      with_cuda: 'true'
      with_coverage: 'true'
+     with_coverage_python: 'true'
      check_skip_long: 'true'
      with_scafacos: 'true'
      with_stokesian_dynamics: 'true'
@@ -489,6 +545,7 @@ run_tutorials:
     paths:
     - build/doc/tutorials
     expire_in: 1 week
+  timeout: 2h
   tags:
     - espresso
     - cuda

CMakeLists.txt

@@ -29,6 +29,14 @@ if(POLICY CMP0025)
   # make CXX_COMPILER_ID return "AppleClang" instead of "Clang" for Apple Clang
   cmake_policy(SET CMP0025 NEW)
 endif()
+if(POLICY CMP0146)
+  # make FindCUDA available
+  cmake_policy(SET CMP0146 OLD)
+endif()
+if(POLICY CMP0148)
+  # make FindPythonInterp available
+  cmake_policy(SET CMP0148 OLD)
+endif()
 # CMake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
@@ -47,7 +55,7 @@ if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
 
-set(PROJECT_VERSION "4.2.1")
+set(PROJECT_VERSION "4.2-dev")
 
 #
 # CMake internal vars

Readme.md

@@ -1,6 +1,6 @@
 # ESPResSo
 
-[![GitLab CI](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/badges/python/pipeline.svg)](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/commits/python)
+[![GitLab CI](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/badges/4.2/pipeline.svg)](https://gitlab.icp.uni-stuttgart.de/espressomd/espresso/-/commits/4.2)
 [![codecov](https://codecov.io/gh/espressomd/espresso/branch/python/graph/badge.svg)](https://codecov.io/gh/espressomd/espresso)
 
 This is the Molecular Dynamics software ESPResSo ("Extensible