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Accepting request 764825 from devel:languages:python:numeric

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- 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      `system.part[0:-1]` is no longer valid.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)

OBS-URL: https://build.opensuse.org/request/show/764825
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=5
This commit is contained in:
Dominique Leuenberger 2020-01-16 17:21:54 +00:00 committed by Git OBS Bridge
commit 04927dd7d6
4 changed files with 78 additions and 9 deletions
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3
espresso-4.1.1.tar.gz
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oid sha256:61f19f17469522d4aa480ff5254217668ba713589c6b74576e6305920d688f90
size 22915050

3
espresso-4.1.2.tar.gz Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:00bc8e4cab8fc8f56d18978970b55f09168521ed5898a92769986f2157a81a2c
size 22921088

66
python3-espressomd.changes
View File

@ -1,3 +1,69 @@
-------------------------------------------------------------------
Wed Jan 15 23:35:14 CET 2020 - Matej Cepl <mcepl@suse.com>
- 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 <junghans@votca.org> Fri Nov 15 16:24:45 UTC 2019 - Christoph Junghans <junghans@votca.org>

15
python3-espressomd.spec
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@ -1,7 +1,7 @@
# #
# spec file for package python3-espressomd # spec file for package python3-espressomd
# #
# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany. # Copyright (c) 2020 SUSE LLC
# Copyright (c) 2014 Christoph Junghans # Copyright (c) 2014 Christoph Junghans
# #
# All modifications and additions to the file contributed by third parties # 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/ # Please submit bugfixes or comments via https://bugs.opensuse.org/
# #
# Build with OpenMPI # Build with OpenMPI
%if 0%{?sle_version} == 0 %if 0%{?sle_version} == 0
%define mpiver openmpi2 %define mpiver openmpi2
@ -34,7 +35,7 @@
%define pkgname espresso %define pkgname espresso
%define modname %{pkgname}md %define modname %{pkgname}md
Name: python3-%{modname} Name: python3-%{modname}
Version: 4.1.1 Version: 4.1.2
Release: 0 Release: 0
Summary: Parallel simulation software for soft matter research Summary: Parallel simulation software for soft matter research
License: GPL-3.0-or-later License: GPL-3.0-or-later
@ -46,8 +47,8 @@ BuildRequires: fftw3-devel
BuildRequires: gcc-c++ BuildRequires: gcc-c++
# Currently libboost_mpi-devel and hdf5 use different mpi versions # Currently libboost_mpi-devel and hdf5 use different mpi versions
# BuildRequires: hdf5-devel # BuildRequires: hdf5-devel
BuildRequires: gsl-devel
BuildRequires: %{mpiver}-devel BuildRequires: %{mpiver}-devel
BuildRequires: gsl-devel
BuildRequires: python3-Cython BuildRequires: python3-Cython
BuildRequires: python3-devel BuildRequires: python3-devel
BuildRequires: python3-numpy-devel BuildRequires: python3-numpy-devel
@ -74,6 +75,8 @@ systems, for example DNA and lipid membranes.
%build %build
source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh 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 # 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 # 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 rm -f %{buildroot}%{_libdir}/lib*.so
%check %check
# https://github.com/espressomd/espresso/issues/3315 # https://github.com/espressomd/espresso/issues/3315 & gh#espressomd/espresso#3396
%ifarch i586 %ifarch i586
%define testargs ARGS='-E \\(MpiCallbacks_test\\|matrix_vector_product\\|collision_detection\\)' %define testargs ARGS='-E \\(matrix_vector_product\\|collision_detection\\)'
%endif %endif
LD_LIBRARY_PATH='%{buildroot}/%{python3_sitearch}/espressomd::%{_libdir}/mpi/gcc/%{mpiver}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}} 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 %doc README AUTHORS NEWS ChangeLog
%{python3_sitearch}/espressomd %{python3_sitearch}/espressomd
%changelog %changelog