diff --git a/espresso-4.1.1.tar.gz b/espresso-4.1.1.tar.gz deleted file mode 100644 index 28efde2..0000000 --- a/espresso-4.1.1.tar.gz +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:61f19f17469522d4aa480ff5254217668ba713589c6b74576e6305920d688f90 -size 22915050 diff --git a/espresso-4.1.2.tar.gz b/espresso-4.1.2.tar.gz new file mode 100644 index 0000000..7428eb8 --- /dev/null +++ b/espresso-4.1.2.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:00bc8e4cab8fc8f56d18978970b55f09168521ed5898a92769986f2157a81a2c +size 22921088 diff --git a/python3-espressomd.changes b/python3-espressomd.changes index 741124f..e84e70a 100644 --- a/python3-espressomd.changes +++ b/python3-espressomd.changes @@ -1,3 +1,69 @@ +------------------------------------------------------------------- +Wed Jan 15 23:35:14 CET 2020 - Matej Cepl + +- Update to 4.1.2: + - The interface has not been changed between ESPResSo 4.1.1 and + 4.1.2. + - General corrections and improvements: + - Remove correlation between the rotational noise and + translational noise in the Langevin thermostat (#3355) + - Fix a bug that may cause the wrong temperature to be set by + the Langevin and DPD thermostats in the first time step + after the system was altered from the Python level, e.g., + by changing particles or interactions (#3341) + - Fix a bug that caused the DPD thermostat to generate an + incorrect velocity distribution when used together with the + Langevin thermostat (#3352) + - Fix a bug in MMM2D and ELC with potential boundary + conditions, where one of the correction factors was + over-counted resulting in wrong energies (#3310) + - Fix a bug that caused the wrong bonds to be deleted when + removing particles from the system (#3356) + - Fix an ambiguity in `ParticleSlice`: the values in the + square brackets refer to particle ids, not array indices + (#3367). This means the ill-defined syntax + `system.part[0:-1]` is no longer valid. See the User Guide + section on Setting up particles for more information. + - Remove the mass prefactor in the `ComForce` observable and + use the correct Particle ids in the + `ParticleAngularVelocities` and `ParticleBodyVelocities` + observables (#3380) + - Fix a rounding error that caused debug builds of ESPResSo + running with multiple MPI threads to crash when a particle + was placed exactly on the boundary between two cells + (#3377) + - Fix `espressomd.has_features()` for the corner case where + the list of all compiled-in features is passed as argument, + returning ``False`` instead of ``True`` (#3318) + - Refactor the random number generator code (#3349) + - Documentation and tutorials corrections and improvements: + - Improve documentation of Monte Carlo methods (#3254, #3330) + - Build system and platform-related corrections and + improvements: + - List all Python dependencies in `requirements.txt` with the + supported version numbers (#3300). Please note that most of + them are optional. + - Add `MPIEXEC_PREFLAGS` and `MPIEXEC_POSTFLAGS` to the + command lines of parallel tests (#3221) + - Add the `-oversubscribe` flag to the command lines of + parallel tests running with OpenMPI v2.X to avoid exiting + early from a Python test configured without `MAX_NUM_PROC` + on a machine with a hyperthreaded CPU where OpenMPI is + configured such that the number of threads cannot exceed + the number of cores (#3335) + - Refactor the CI, maintainer, Doxygen and pypresso shell + scripts to make them more portable and support filepaths + containing whitespaces (#3326, #3373) + - Fix a nvcc compiler warning on the empty config (#3329) + - Improved testing: + - Add a test for ELC and MMM2D using analytic expressions of + the force and energy (#3331) + - Sped-up seven Python tests (#3319) + - Fix a test that broke on s390x architectures with Fedora 31 + (#3312) + - Fix tests that broke on i586 architectures with OpenSUSE + Tumbleweed (#3327, #3358) + ------------------------------------------------------------------- Fri Nov 15 16:24:45 UTC 2019 - Christoph Junghans diff --git a/python3-espressomd.spec b/python3-espressomd.spec index 4cfc51f..9bc10f0 100644 --- a/python3-espressomd.spec +++ b/python3-espressomd.spec @@ -1,7 +1,7 @@ # # spec file for package python3-espressomd # -# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. +# Copyright (c) 2020 SUSE LLC # Copyright (c) 2014 Christoph Junghans # # All modifications and additions to the file contributed by third parties @@ -16,6 +16,7 @@ # Please submit bugfixes or comments via https://bugs.opensuse.org/ # + # Build with OpenMPI %if 0%{?sle_version} == 0 %define mpiver openmpi2 @@ -34,7 +35,7 @@ %define pkgname espresso %define modname %{pkgname}md Name: python3-%{modname} -Version: 4.1.1 +Version: 4.1.2 Release: 0 Summary: Parallel simulation software for soft matter research License: GPL-3.0-or-later @@ -46,8 +47,8 @@ BuildRequires: fftw3-devel BuildRequires: gcc-c++ # Currently libboost_mpi-devel and hdf5 use different mpi versions # BuildRequires: hdf5-devel -BuildRequires: gsl-devel BuildRequires: %{mpiver}-devel +BuildRequires: gsl-devel BuildRequires: python3-Cython BuildRequires: python3-devel BuildRequires: python3-numpy-devel @@ -74,6 +75,8 @@ systems, for example DNA and lipid membranes. %build source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh +# gh#espressomd/espresso#3396 +%define _lto_cflags %{nil} # overwrite .so linker flags on SUSE distros: drop --no-undefined # we don't install {i,}pypresso scripts as they aren't needed when installing in /usr @@ -94,9 +97,9 @@ find %{buildroot}%{_prefix} -name "gen_pxiconfig" -exec chmod +x {} \; rm -f %{buildroot}%{_libdir}/lib*.so %check -# https://github.com/espressomd/espresso/issues/3315 +# https://github.com/espressomd/espresso/issues/3315 & gh#espressomd/espresso#3396 %ifarch i586 -%define testargs ARGS='-E \\(MpiCallbacks_test\\|matrix_vector_product\\|collision_detection\\)' +%define testargs ARGS='-E \\(matrix_vector_product\\|collision_detection\\)' %endif LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}} @@ -105,4 +108,4 @@ LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc %doc README AUTHORS NEWS ChangeLog %{python3_sitearch}/espressomd -%changelog \ No newline at end of file +%changelog