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Package is "python3-espressomd" Thu Jul 21 11:35:31 2022 rev:14 rq:990492 version:4.2.0 Changes: -------- --- /work/SRC/openSUSE:Factory/python3-espressomd/python3-espressomd.changes 2022-04-30 00:46:10.878984882 +0200 +++ /work/SRC/openSUSE:Factory/.python3-espressomd.new.1523/python3-espressomd.changes 2022-07-21 11:35:46.987089093 +0200 @@ -1,0 +2,70 @@ +Tue Jul 19 19:40:59 UTC 2022 - Matej Cepl <[email protected]> + +- Update to 4.2.0: + This is a feature release, i.e., new functionality is added + to ESPResSo. New thermostats, cell systems and boundary + conditions have been introduced to simulate systems with + Stokesian Dynamics, Brownian Dynamics, strongly inhomogeneous + particle sizes or translation-invariant shear flow. The + interface underwent (non-silent) changes, therefore scripts + will have to be slightly adapted. Most notably, particle + access by id and particle slices have a new syntax, and + electrostatic/magnetostatic layer correction and reaction + methods have a different setup. All errors are also now + emitted as Python exceptions and are recoverable with minimal + effort. An additional focus of this release is the + simplification of both the C++ core and the Python script + interface to facilitate future extensions of ESPResSo. The + testing of ESPResSo's functionality has been extended + considerably. We recommend that this release be used for all + production simulations. No further bug fix releases will be + provided for the 4.1 line, and not all fixes are present in + ESPResSo 4.1.4. + + Added functionality + ------------------- + + * `P3MGPU` now supports energy and pressure calculation via + the CPU kernels (#4506). + * `ELC` now works with `P3MGPU` (#4506). + * The LB grid now supports slicing operations (#4195) and LB + slices are equality comparable (#4268). + * Lees-Edwards boundary conditions can be used for + particle-based simulations (#4457). Lattice-Boltzmann + support will be added in the 4.3.0 release. + * The non-bonded energy of a single particle can be calculated + (#4401). + * The list of close neighbors of a single particle can be + extracted (#4401). + * Brownian Dynamics simulations can be carried out with the + newly added Brownian integrator and Brownian thermostat + (#1842). + * Stokesian Dynamics simulations can be carried out with the + newly added Stokesian integrator and Stokesian thermostat + (#3790, #3987). + * Bonded interactions can now be automatically broken when the + bond length exceeds a critical value (#4456). This feature + can be combined with collision detection to model reversible + bonds (#4464). + * A new cell system `HybridDecomposition` was introduced to + speed up simulations with inhomogeneous particle interaction + ranges (#4373). + * Shapes can be merged into meta-shapes (#3493, #3538). + * The `HollowConicalFrustum` can now be sliced open, made + thick and rotated to model quarter pipes in any orientation + (#4179). The main application is in the construction of + complex microchannel geometries via `LBBoundaries`. + * A parametric weight function was added to the DPD + interaction (#3570). + * H5MD output files now support a unit system (#3751). + * H5MD output files now support custom specifications to + control which particle and box properties to write to disk + (#4480). + * The `H5md` class is now checkpointable and usable in an + interactive Python session (#3751). + * MDAnalysis integration now provides bond information + (#3801). +- Give up on building on 32bit architectures (gh#espressomd/espresso#4537). +- Fix rpath in provided libraries and shebang in pypresso. + +------------------------------------------------------------------- Old: ---- espresso-4.1.4.tar.gz New: ---- espresso-4.2.0.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python3-espressomd.spec ++++++ --- /var/tmp/diff_new_pack.hWlrdp/_old 2022-07-21 11:35:48.471090556 +0200 +++ /var/tmp/diff_new_pack.hWlrdp/_new 2022-07-21 11:35:48.471090556 +0200 @@ -35,7 +35,7 @@ %define pkgname espresso %define modname %{pkgname}md Name: python3-%{modname} -Version: 4.1.4 +Version: 4.2.0 Release: 0 Summary: Parallel simulation software for soft matter research License: GPL-3.0-or-later @@ -50,16 +50,21 @@ Patch2: hdf5.patch # PATCH-FIX-OPENSUSE rpath.patch boo#1198352 Patch3: rpath.patch +# According to gh#espressomd/espresso#4537 32bit architectures are not supported any more +ExcludeArch: %{ix86} BuildRequires: cmake BuildRequires: fftw3-devel BuildRequires: gcc-c++ # Currently libboost_mpi-devel and hdf5 use different mpi versions # BuildRequires: hdf5-devel BuildRequires: %{mpiver}-devel +BuildRequires: chrpath BuildRequires: gsl-devel BuildRequires: python3-Cython BuildRequires: python3-devel BuildRequires: python3-numpy-devel +BuildRequires: python3-scipy +BuildRequires: python3-setuptools %if 0%{?suse_version} > 1325 BuildRequires: hdf5-%{mpiver}-devel BuildRequires: libboost_filesystem-devel @@ -71,6 +76,7 @@ %else BuildRequires: boost-devel %endif +Provides: libEspresso4 = %{version}-%{release} Obsoletes: libEspresso4 < 4.1 Requires: python3-h5py Requires: python3-numpy @@ -86,11 +92,10 @@ systems, for example DNA and lipid membranes. %prep -%setup -q -n %{pkgname} -%patch0 -p1 -%patch1 -p1 -%patch2 -p1 -%patch3 -p1 +%autosetup -p1 -n %{pkgname} + +# Fix shebang line for pypresso +sed -i -E '1s@^#!/usr/bin/env[[:blank:]]+sh@#!/bin/sh@' src/python/pypresso.cmakein %build source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh @@ -103,16 +108,16 @@ # we don't install {i,}pypresso scripts as they aren't needed when installing in /usr %cmake \ -DCMAKE_SHARED_LINKER_FLAGS='-Wl,--as-needed -Wl,-z,now' \ - -DLIBDIR=%{_lib} \ + -DLIBDIR=%{_libdir} \ -DPYTHON_EXECUTABLE=%{_bindir}/python3 \ - -DINSTALL_PYPRESSO=OFF + -DPYTHON_INSTDIR=%{python3_sitearch} \ + -DINSTALL_PYPRESSO=ON %make_jobs %install %cmake_install - -# no devel package -rm -f %{buildroot}%{_libdir}/lib*.so +find %{buildroot}%{python3_sitearch} -name \*.so \ + -exec chrpath -r %{python3_sitearch} '{}' \; %check # gh#espressomd/espresso#3315 @@ -123,7 +128,8 @@ %files %license COPYING -%doc README AUTHORS NEWS ChangeLog +%doc Readme.md AUTHORS NEWS ChangeLog +%{_bindir}/pypresso %{python3_sitearch}/espressomd %changelog ++++++ boost-1.74.patch ++++++ --- /var/tmp/diff_new_pack.hWlrdp/_old 2022-07-21 11:35:48.491090576 +0200 +++ /var/tmp/diff_new_pack.hWlrdp/_new 2022-07-21 11:35:48.495090579 +0200 @@ -10,14 +10,16 @@ https://github.com/boostorg/serialization/issues/210 https://github.com/boostorg/serialization/issues/217 -diff --git a/src/core/grid_based_algorithms/lb_particle_coupling.hpp b/src/core/grid_based_algorithms/lb_particle_coupling.hpp -index de12cb4..13111ab 100644 +--- + src/core/grid_based_algorithms/lb_particle_coupling.hpp | 9 +++++++++ + 1 file changed, 9 insertions(+) + --- a/src/core/grid_based_algorithms/lb_particle_coupling.hpp +++ b/src/core/grid_based_algorithms/lb_particle_coupling.hpp -@@ -21,6 +21,15 @@ - - #include "ParticleRange.hpp" - +@@ -25,6 +25,15 @@ + + #include <boost/serialization/access.hpp> + +/* This <boost/serialization/version.hpp> include guards against an issue + * in boost::serialization from boost 1.74.0 that leads to compiler error + * "explicit specialization of undeclared template struct 'version'" when @@ -27,7 +29,7 @@ + */ +#include <boost/serialization/version.hpp> + - #include <boost/serialization/optional.hpp> - - #include "ParticleRange.hpp" + #include <cstdint> + #include <unordered_set> + ++++++ espresso-4.1.4.tar.gz -> espresso-4.2.0.tar.gz ++++++ /work/SRC/openSUSE:Factory/python3-espressomd/espresso-4.1.4.tar.gz /work/SRC/openSUSE:Factory/.python3-espressomd.new.1523/espresso-4.2.0.tar.gz differ: char 5, line 1 ++++++ hdf5.patch ++++++ --- /var/tmp/diff_new_pack.hWlrdp/_old 2022-07-21 11:35:48.515090600 +0200 +++ /var/tmp/diff_new_pack.hWlrdp/_new 2022-07-21 11:35:48.515090600 +0200 @@ -1,15 +1,18 @@ -diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt -index c956b9de1..b68208eaa 100644 +--- + src/core/CMakeLists.txt | 4 ++++ + 1 file changed, 4 insertions(+) + --- a/src/core/CMakeLists.txt +++ b/src/core/CMakeLists.txt -@@ -189,6 +189,9 @@ endif(SCAFACOS) - # Subdirectories - add_subdirectory(io) +@@ -127,6 +127,10 @@ add_subdirectory(reaction_methods) + add_subdirectory(scafacos) + add_subdirectory(virtual_sites) +if(H5MD) + target_link_libraries(EspressoCore PUBLIC ${HDF5_LIBRARIES}) +endif(H5MD) - - if(WITH_UNIT_TESTS) ++ + if(WITH_TESTS) add_subdirectory(unit_tests) + endif(WITH_TESTS) ++++++ missing_size_t.patch ++++++ --- /var/tmp/diff_new_pack.hWlrdp/_old 2022-07-21 11:35:48.523090607 +0200 +++ /var/tmp/diff_new_pack.hWlrdp/_new 2022-07-21 11:35:48.527090611 +0200 @@ -1,5 +1,7 @@ -diff --git a/src/config/config.hpp b/src/config/config.hpp -index 78ec14b78..139c1f97a 100644 +--- + src/config/config.hpp | 2 ++ + 1 file changed, 2 insertions(+) + --- a/src/config/config.hpp +++ b/src/config/config.hpp @@ -37,6 +37,8 @@ @@ -10,17 +12,5 @@ + #include "config-features.hpp" - /** P3M: Default for number of interpolation points of the charge -diff --git a/src/utils/include/utils/NumeratedContainer.hpp b/src/utils/include/utils/NumeratedContainer.hpp -index 1d99098f0..36602b203 100644 ---- a/src/utils/include/utils/NumeratedContainer.hpp -+++ b/src/utils/include/utils/NumeratedContainer.hpp -@@ -25,6 +25,7 @@ - */ - - #include <cassert> -+#include <cstddef> - #include <set> - #include <unordered_map> - + /** P3M: Default for offset of first mesh point from the origin (left ++++++ rpath.patch ++++++ --- /var/tmp/diff_new_pack.hWlrdp/_old 2022-07-21 11:35:48.539090623 +0200 +++ /var/tmp/diff_new_pack.hWlrdp/_new 2022-07-21 11:35:48.539090623 +0200 @@ -1,14 +1,16 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 238e6dac3..96cbaa9a9 100644 +--- + CMakeLists.txt | 2 ++ + 1 file changed, 2 insertions(+) + --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -20,6 +20,7 @@ +@@ -21,6 +21,8 @@ - cmake_minimum_required(VERSION 3.4) + cmake_minimum_required(VERSION 3.16) message(STATUS "CMake version: ${CMAKE_VERSION}") +set(CMAKE_SKIP_RPATH ON) - - # C++ standard - enable_language(CXX) - ++ + if(POLICY CMP0076) + # make target_sources() convert relative paths to absolute + cmake_policy(SET CMP0076 NEW)
