Use latest Docker images

Several regressions were addressed in the ScaFaCoS, Caliper, and
Kokkos dependencies. New Python packages are available: pandas, ase.
CTest wall time was increased to avoid LB tests timeouts.

.github/workflows/push_pull.yml

@@ -35,7 +35,7 @@ jobs:
   debian:
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/espressomd/docker/debian:7843821c7cfe66dc8b718bb4041eba52adaa2df0-base-layer
+      image: ghcr.io/espressomd/docker/debian:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}
@@ -74,7 +74,7 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.repository == 'espressomd/espresso' }}
     container:
-      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:7843821c7cfe66dc8b718bb4041eba52adaa2df0-base-layer
+      image: ghcr.io/espressomd/docker/ubuntu-wo-dependencies:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b-base-layer
       credentials:
          username: ${{ github.actor }}
          password: ${{ secrets.github_token }}

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: ghcr.io/espressomd/docker/ubuntu:7843821c7cfe66dc8b718bb4041eba52adaa2df0
+image: ghcr.io/espressomd/docker/ubuntu:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
 
 stages:
   - prepare
@@ -18,7 +18,7 @@ stages:
 
 .notification_job_template: &notification_job_definition
   <<: *global_job_definition
-  image: ghcr.io/espressomd/docker/fedora:7843821c7cfe66dc8b718bb4041eba52adaa2df0
+  image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
   variables:
     GIT_SUBMODULE_STRATEGY: none
   before_script:
@@ -145,7 +145,7 @@ no_rotation:
 fedora:40:
   <<: *global_job_definition
   stage: build
-  image: ghcr.io/espressomd/docker/fedora:7843821c7cfe66dc8b718bb4041eba52adaa2df0
+  image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b
   variables:
      with_cuda: 'false'
      with_gsl: 'false'

CMakeLists.txt

@@ -669,14 +669,14 @@ if(ESPRESSO_BUILD_WITH_CALIPER)
   endif()
   set(CALIPER_BUILD_SHARED_LIBS on CACHE BOOL "")
   add_subdirectory("${caliper_SOURCE_DIR}")
-  if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR CMAKE_CXX_COMPILER_ID STREQUAL
-                                              "GNU")
-    target_compile_options(caliper-services
-                           PRIVATE -Wno-deprecated-declarations)
-    target_compile_options(
-      caliper-runtime
-      PRIVATE $<$<CXX_COMPILER_ID:GNU>:-Wno-maybe-uninitialized>)
-  endif()
+  target_compile_options(
+    caliper-services
+    PRIVATE
+      $<$<CXX_COMPILER_ID:GNU,Clang,AppleClang>:-Wno-deprecated-declarations>)
+  target_compile_options(
+    caliper-runtime
+    PRIVATE $<$<CXX_COMPILER_ID:GNU>:-Wno-maybe-uninitialized>
+            $<$<CXX_COMPILER_ID:GNU,Clang,AppleClang>:-Wno-volatile>)
 endif()
 
 #

maintainer/CI/build_cmake.sh

@@ -130,7 +130,7 @@ set_default_value with_scafacos false
 set_default_value with_walberla false
 set_default_value with_walberla_avx false
 set_default_value with_stokesian_dynamics false
-set_default_value test_timeout 400
+set_default_value test_timeout 500
 set_default_value hide_gpu false
 set_default_value mpiexec_preflags ""
 

maintainer/CI/jupyter_warnings.py

@@ -66,7 +66,7 @@ def detect_invalid_urls(nb, build_root='.', html_exporter=None):
             if filepath.is_file():
                 with open(filepath) as f:
                     config = json.load(f)
-                kwargs = config.get("Exporter", {})
+                kwargs = config.get("HTMLExporter", {})
                 break
         html_exporter = nbconvert.HTMLExporter(**kwargs)
     html_exporter.template_name = 'classic'

requirements.txt

@@ -7,10 +7,12 @@ numpy>=1.26.4
 h5py>=3.10.0
 # optional scientific packages
 scipy>=1.11.4
+pandas>=1.3.5
 pint>=0.19.2
+ase>=3.22.1
 # optional packages for graphics and external devices
 matplotlib>=3.6.3
-vtk==9.1.0
+vtk>=9.1.0
 PyOpenGL>=3.1.5
 pygame>=2.1.2
 # waLBerla dependencies

src/python/espressomd/analyze.py

@@ -285,14 +285,17 @@ class Analysis(ScriptInterfaceHelper):
             and [1] contains the structure factors S(q)
 
     distribution()
-        Calculates the distance distribution of particles (probability of
-        finding a particle of type A at a certain distance around a particle of
+        Calculate the minimal distance distribution of particles (probability of
+        finding a particle of type A at a certain distance to the nearest particle of
         type B, disregarding the fact that a spherical shell of a larger radius
         covers a larger volume). The distance is defined as the minimal distance
         between a particle of group ``type_list_a`` to any of the group
         ``type_list_b``. Returns two arrays, the bins and the (normalized)
         distribution.
 
+        For the radial distribution function,
+        use :class:`espressomd.observables.RDF` instead.
+
         Parameters
         ----------
         type_list_a : list of :obj:`int`
@@ -319,7 +322,7 @@ class Analysis(ScriptInterfaceHelper):
         -------
         :obj:`ndarray`
             Where [0] contains the midpoints of the bins,
-            and [1] contains the values of the rdf.
+            and [1] contains the values of the minimal distance distribution function.
 
     """
     _so_name = "Analysis::Analysis"

src/scafacos/CMakeLists.txt

@@ -22,12 +22,6 @@ add_library(espresso_scafacos SHARED src/Scafacos.cpp src/Coulomb.cpp
 add_library(espresso::scafacos ALIAS espresso_scafacos)
 set_target_properties(espresso_scafacos PROPERTIES CXX_CLANG_TIDY
                                                    "${ESPRESSO_CXX_CLANG_TIDY}")
-if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10
-   AND ESPRESSO_INSIDE_DOCKER AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS_EQUAL
-                                  11 AND ESPRESSO_BUILD_WITH_COVERAGE)
-  target_link_libraries(espresso_scafacos
-                        PRIVATE "-L/usr/lib/gcc/x86_64-linux-gnu/10")
-endif()
 target_link_libraries(espresso_scafacos PUBLIC MPI::MPI_CXX
                       PRIVATE ${SCAFACOS_LDFLAGS} espresso::cpp_flags)