diff --git a/.github/workflows/push_pull.yml b/.github/workflows/push_pull.yml index e6e24fded3c..3cbd6fc2d46 100644 --- a/.github/workflows/push_pull.yml +++ b/.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: ${{ secrets.github_token }} diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 563c1b62c1f..ee19040ea36 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,4 +1,4 @@ -image: ghcr.io/espressomd/docker/ubuntu:7843821c7cfe66dc8b718bb4041eba52adaa2df0 +image: ghcr.io/espressomd/docker/ubuntu:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b stages: - prepare @@ -18,7 +18,7 @@ stages: .notification_job_template: ¬ification_job_definition <<: *global_job_definition - image: ghcr.io/espressomd/docker/fedora:7843821c7cfe66dc8b718bb4041eba52adaa2df0 + image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b variables: GIT_SUBMODULE_STRATEGY: none before_script: @@ -145,7 +145,7 @@ no_rotation: fedora:40: <<: *global_job_definition stage: build - image: ghcr.io/espressomd/docker/fedora:7843821c7cfe66dc8b718bb4041eba52adaa2df0 + image: ghcr.io/espressomd/docker/fedora:f7f8ef2c0ca93c67aa16b9f91785492fb04ecc1b variables: with_cuda: 'false' with_gsl: 'false' diff --git a/CMakeLists.txt b/CMakeLists.txt index def6da778e1..91298f02c66 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -669,14 +669,14 @@ if(ESPRESSO_BUILD_WITH_CALIPER) endif() set(CALIPER_BUILD_SHARED_LIBS on CACHE BOOL "") add_subdirectory("${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 $<$:-Wno-maybe-uninitialized>) - endif() + target_compile_options( + caliper-services + PRIVATE + $<$:-Wno-deprecated-declarations>) + target_compile_options( + caliper-runtime + PRIVATE $<$:-Wno-maybe-uninitialized> + $<$:-Wno-volatile>) endif() # diff --git a/maintainer/CI/build_cmake.sh b/maintainer/CI/build_cmake.sh index 9e967814d25..90d4fa5b9f3 100755 --- a/maintainer/CI/build_cmake.sh +++ b/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 "" diff --git a/maintainer/CI/jupyter_warnings.py b/maintainer/CI/jupyter_warnings.py index 8b286395df4..8c7b6ec161a 100755 --- a/maintainer/CI/jupyter_warnings.py +++ b/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' diff --git a/requirements.txt b/requirements.txt index 796992dc913..d8472b2a3dd 100644 --- a/requirements.txt +++ b/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 diff --git a/src/python/espressomd/analyze.py b/src/python/espressomd/analyze.py index 42d0b229df0..7345c739a04 100644 --- a/src/python/espressomd/analyze.py +++ b/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" diff --git a/src/scafacos/CMakeLists.txt b/src/scafacos/CMakeLists.txt index 222f05c4944..b6e4350a37d 100644 --- a/src/scafacos/CMakeLists.txt +++ b/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)