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here is the log from the commit of package python3-espressomd for
openSUSE:Factory checked in at 2023-04-19 17:43:06
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python3-espressomd (Old)
and /work/SRC/openSUSE:Factory/.python3-espressomd.new.2023 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python3-espressomd"
Wed Apr 19 17:43:06 2023 rev:17 rq:1080211 version:4.2.1
Changes:
--------
--- /work/SRC/openSUSE:Factory/python3-espressomd/python3-espressomd.changes
2023-01-28 19:03:30.696778213 +0100
+++
/work/SRC/openSUSE:Factory/.python3-espressomd.new.2023/python3-espressomd.changes
2023-04-19 17:43:16.644298254 +0200
@@ -1,0 +2,203 @@
+Tue Apr 18 10:43:03 UTC 2023 - Jean-Noel Grad <jg...@icp.uni-stuttgart.de>
+
+- Update to 4.2.1:
+ This release provides a number of corrections for the ESPResSo
+ 4.2 line. We recommend that this release be used for all
+ production simulations. The interface has not been changed
+ between ESPResSo 4.2.0 and 4.2.1. However, some bugs were
+ discovered which can affect simulation results. No further bug
+ fix releases will be provided for the 4.2 line.
+
+ Added functionality
+ -------------------
+
+ * P3M and DipolarP3M can now be used with the hybrid
+ decomposition cell system with 1 MPI rank (#4678).
+ * Lattice-Boltzmann can now be used with the N-square and
+ hybrid decomposition cell systems with 2 or more MPI ranks
+ (#4676).
+
+ Changed requirements
+ --------------------
+ * The nbconvert version requirement was bumped to 6.5.1 to
+ patch an XSS vulnerability (#4658).
+
+ Improved documentation
+ ----------------------
+ * The user guide now documents how to improve the
+ reproducibility of simulations that have checkpointing
+ enabled (#4677).
+ * The user guide now reflects that the lattice-Boltzmann
+ profile observables can be used in parallel (#4583).
+ * The active matter tutorial now uses an adequate engine
+ dipole for the swimmer particle (#4585).
+ * The error analysis tutorials have been improved (#4597).
+ * The tutorials can now be used in VS Code Jupyter (both the
+ desktop and web versions) and the mathematical formula are
+ now correctly displayed (#4531).
+ * All ESPResSo-specific CMake options are now documented in
+ the installation chapter of the user guide (#4608).
+ * Python package installation instructions no longer feature
+ package version numbers; instead, `requirements.txt` is used
+ as a constraint file (#4638).
+ * MMM1D algorithms now properly document their parameter names
+ (#4677).
+ * Reaction methods now cite the relevant literature (#4681).
+ * Caveats for chain analysis methods are now documented
+ (#4698).
+ * Minor formatting issues in Sphinx and typos in Python
+ docstrings were addressed (#4608).
+
+ Interface changes
+ -----------------
+ * A new boolean property
+ `System.virtual_sites.override_cutoff_check` was introduced
+ to allow disabling the cutoff range checks from virtual
+ sites (#4623).
+
+ Removed functionality
+ ---------------------
+ * The unused and untested `Analysis.v_kappa()` method was
+ removed (#4534).
+
+ Improved testing
+ ----------------
+ * Improve unit testing of core functionality: P3M, MMM1D, OIF,
+ virtual sites, script interface factory (#4631).
+
+ Bug fixes
+ ---------
+ * The checkpointing mechanism now properly restores the
+ particle quaternion and all derived quantities (#4637).
+ Release 4.2.0 introduced a regression that caused checkpoint
+ files to overwrite the particle quaternion/director by a
+ unit vector pointing along the z direction, when the
+ `DIPOLES` feature was part of the myconfig file. This lead
+ to incorrect trajectories when reloading a simulation from
+ a checkpoint file, if the particle director played a role in
+ the simulation (ex: relative virtual sites, Gay-Berne
+ potential, anisotropic particles, active particles, etc.).
+ In addition, the angular velocity in body frame was restored
+ with the wrong orientation. Since the default myconfig file
+ contains `DIPOLES`, most ESPResSo users were affected.
+ * The checkpointing mechanism now properly restores LB
+ boundaries (#4649). Release 4.2.0 introduced a regression
+ where reloading LB populations would accidentally reset LB
+ boundary flags.
+ * The checkpointing mechanism now restores P3M and DipolarP3M
+ solvers without triggering a re-tune (#4677). In previous
+ releases, the checkpointing code would automatically re-tune
+ these algorithms during a reload, causing tiny deviations in
+ the forces that were problematic for trajectory
+ reproducibility.
+ * Brownian dynamics now integrates the rotational dynamics of
+ rotatable particles whose position is fixed in 3D space
+ (#4548).
+ * Langevin dynamics now properly integrates particles with
+ anisotropic friction (#4683, #4690).
+ * A regression that caused virtual sites to incorrectly count
+ their image box when crossing a periodic boundary has been
+ fixed (#4564, #4707).
+ * Particles can no longer be created or updated with a
+ negative mass or a null mass (#4679).
+ * Particles created without a user-specified type can now
+ participate in reactions (#4589).
+ * When a Monte Carlo displacement move is rejected, the
+ original particle velocity is now restored (#4589).
+ * Reaction methods now raise an exception when accidentally
+ calling `method.reaction(steps=20)` instead of
+ `method.reaction(reaction_steps=20)` (#4666). Since 4.2.0
+ the `steps` argument was ignored, in which case the default
+ value `reaction_steps=1` would used by the core. Note that
+ in the next minor release of ESPResSo, the `reaction_steps`
+ argument will be renamed to `steps`.
+ * Reaction methods now rebuild the list of free particle ids
+ every time
`WidomInsertion::calculate_particle_insertion_potential_energy()`
+ and `ReactionAlgorithm::do_reaction()` are called (#4609).
+ This was needed to allow multiple concurrent reactions, as
+ well as avoiding subtle bugs when both the user and a
+ reaction method tried to create a new particle with an id
+ that used to belong to a deleted particle.
+ * When all particles are cleared, the reaction methods type
+ map is now also cleared (#4645). In the past, it was
+ possible to attempt a reaction on particles that had just
+ been cleared from the system, which would raise an
+ exception. This bug affected all ESPResSo releases since
+ 4.0.
+ * The `System.part.pairs()` method now returns the correct
+ particle pairs when particle ids aren't both contiguous and
+ starting from 0 (#4628). The regression was introduced in
+ release 4.2.0.
+ * The auto-exclusions feature no longer adds spurious
+ exclusions to particle ids in the range [1, distance]
+ (#4654). This bug would potentially break the physics of the
+ system and potentially raise an exception in a system with
+ non-contiguous particle ids. This regression was introduced
+ in release 2.2.0b.
+ * The structure factor analysis code no longer double-counts
+ particles when the same particle type is provided twice
+ (#4534).
+ * The minimal distance distribution analysis code no longer
+ has an arbitrary cutoff distance when the simulation box is
+ aperiodic (open boundaries); this would cause spurious
+ artifacts to appear in the histogram at
+ `r = np.sum(system.box_l)` when particles were further apart
+ than this arbitrary distance (#4534).
+ * The cluster analysis functions are now disabled for systems
+ with Lees-Edwards periodic boundaries, since the cluster
+ analysis position wrapping code doesn't properly handle the
+ shear offset (#4698).
+ * The chain analysis methods now raise an error when the
+ number of chains or beads per chain is invalid (#4708).
+ * The observable tests now longer rely on deprecated numpy
+ options that were removed in numpy 1.24 (#4635).
+ * The visualizer `*_arrows_type_materials` options now have an
+ effect on arrow materials (#4686).
+ * The visualizer exception handling mechanism has been made
+ less brittle (#4686).
+ * The visualizer no longer raises exception when the optional
+ dependency `freeglut` isn't installed (#4691).
+ * The visualizer can randomly freeze when using collision
+ detection or bond breakage; a temporary workaround has been
+ introduced that fixes the issue for simulations that use
+ only 1 MPI rank (#4686).
+ * The `__dir__()` method of script interface objects no longer
+ raises an exception (#4674).
+ * Compilation and testsuite issues involving missing or
+ incorrect feature guards were addressed (#4562, #4648).
+ * The build system no longer silently ignores invalid external
+ feature definitions in `myconfig.hpp` and CMake files
+ (#4608). This issue would only affect feature developers,
+ as well as users of very old compilers, and would lead to
+ ESPResSo builds missing features.
+
+ Under the hood changes
+ ----------------------
+ * The Clang 14 and AppleClang 14 compilers are now supported
+ (#4601).
+ * Several Clang 14 compiler diagnostics have been addressed
+ (#4606).
+ * Boost 1.81 and later versions are now supported (#4655).
+ * Compiler errors on non-x86 architectures were addressed
+ (#4538).
+ * Test tolerances were adjusted for non-x86 architectures
+ (#4708).
+ * The pypresso script now prints a warning when running with
+ MCA binding policy "numa" on NUMA architectures that are not
+ supported in singleton mode by Open MPI 4.x (#4607).
+ * The config file generator has been rewritten to properly
+ handle external features and compiler errors (#4608).
+ * Security hardening for GitHub Workflows (#4577, #4638) and
+ Codecov (#4600).
+ * Deployment of the user guide to GitHub Pages now relies on
+ cloud providers to fetch JavaScript dependencies (#4656).
+- Removed upstreamed patches:
+ - fix-broken-fft-check.patch
+ - boost-1.74.patch
+ - numpy-1.24.patch
++++ 6 more lines (skipped)
++++ between
/work/SRC/openSUSE:Factory/python3-espressomd/python3-espressomd.changes
++++ and
/work/SRC/openSUSE:Factory/.python3-espressomd.new.2023/python3-espressomd.changes
Old:
----
boost-1.74.patch
espresso-4.2.0.tar.gz
fix-broken-fft-check.patch
hdf5.patch
missing_size_t.patch
numpy-1.24.patch
rpath.patch
New:
----
espresso-4.2.1.tar.gz
setuptools.patch
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python3-espressomd.spec ++++++
--- /var/tmp/diff_new_pack.0T06U6/_old 2023-04-19 17:43:23.356337248 +0200
+++ /var/tmp/diff_new_pack.0T06U6/_new 2023-04-19 17:43:23.364337294 +0200
@@ -35,25 +35,15 @@
%define pkgname espresso
%define modname %{pkgname}md
Name: python3-%{modname}
-Version: 4.2.0
+Version: 4.2.1
Release: 0
Summary: Parallel simulation software for soft matter research
License: GPL-3.0-or-later
Group: Productivity/Scientific/Chemistry
URL: http://espressomd.org
Source:
https://github.com/%{modname}/%{pkgname}/releases/download/%{version}/%{pkgname}-%{version}.tar.gz
-# PATCH-FIX-UPSTREAM boost-1.74.patch gh#espressomd/espresso#3864
-Patch0: boost-1.74.patch
-# PATCH-FIX-OPENSUSE missing_size_t.patch gh#espressomd/espresso#4274
-Patch1: missing_size_t.patch
-# PATCH-FIX-OPENSUSE hdf5.patch gh#espressomd/espresso#3543
-Patch2: hdf5.patch
-# PATCH-FIX-OPENSUSE rpath.patch boo#1198352
-Patch3: rpath.patch
-# PATCH-FIX-UPSTREAM fix-broken-fft-check.patch gh#espressomd/espresso#4567
-Patch4: fix-broken-fft-check.patch
-# PATCH-FIX-UPSTREAM numpy-1.24.patch gh#espressomd/espresso#4635
-Patch5: numpy-1.24.patch
+# PATCH-FIX-UPSTREAM setuptools.patch gh#espressomd/espresso#4709
+Patch0: setuptools.patch
# According to gh#espressomd/espresso#4537 32bit architectures are not
supported any more
ExcludeArch: %{ix86}
BuildRequires: cmake
@@ -112,6 +102,7 @@
# 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' \
+ -DCMAKE_SKIP_RPATH=ON \
-DLIBDIR=%{_libdir} \
-DPYTHON_EXECUTABLE=%{_bindir}/python3 \
-DPYTHON_INSTDIR=%{python3_sitearch} \
@@ -124,10 +115,6 @@
-exec chrpath -r %{python3_sitearch} '{}' \;
%check
-# gh#espressomd/espresso#3315
-%ifarch i586
-%define testargs ARGS='-E 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}}
%files
++++++ espresso-4.2.0.tar.gz -> espresso-4.2.1.tar.gz ++++++
/work/SRC/openSUSE:Factory/python3-espressomd/espresso-4.2.0.tar.gz
/work/SRC/openSUSE:Factory/.python3-espressomd.new.2023/espresso-4.2.1.tar.gz
differ: char 5, line 1
++++++ setuptools.patch ++++++
diff --git a/testsuite/python/unittest_decorators.py
b/testsuite/python/unittest_decorators.py
index 109f89cc8..a9a0e5200 100644
--- a/testsuite/python/unittest_decorators.py
+++ b/testsuite/python/unittest_decorators.py
@@ -20,5 +20,5 @@
import sys
import importlib
-import setuptools
+import pkg_resources
import unittest
@@ -75,5 +75,5 @@ def skipIfUnmetModuleVersionRequirement(module,
version_requirement):
except ImportError:
return skipIfMissingModules(module)
- if not setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet(
+ if not pkg_resources.packaging.specifiers.SpecifierSet(
version_requirement).contains(_module.__version__):
return unittest.skip(
