Accepting request 1255106 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/1255106
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=23

espresso-cython.patch

@@ -0,0 +1,261 @@
+diff --git a/src/config/gen_featureconfig.py b/src/config/gen_featureconfig.py
+index 59cf81068d..b8d713e947 100644
+--- a/src/config/gen_featureconfig.py
++++ b/src/config/gen_featureconfig.py
+@@ -1,3 +1,4 @@
++#
+ # Copyright (C) 2013-2022 The ESPResSo project
+ # Copyright (C) 2012 Olaf Lenz
+ #
+@@ -16,9 +17,7 @@
+ # You should have received a copy of the GNU General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ #
+-# This script generates the files featureconfig.h and featureconfig.c.
+-#
+-import time
++
+ import string
+ import inspect
+ import sys
+@@ -32,67 +31,78 @@ if len(sys.argv) != 4:
+     print(f"Usage: {sys.argv[0]} DEFFILE HPPFILE CPPFILE", file=sys.stderr)
+     exit(2)
+ 
+-deffilename, hfilename, cfilename = sys.argv[1:5]
+-
+-print("Reading definitions from " + deffilename + "...")
+-defs = featuredefs.defs(deffilename)
+-print("Done.")
+-
+-print("Writing " + hfilename + "...")
+-hfile = open(hfilename, 'w')
+-
+-hfile.write("""/*
+-WARNING: This file was autogenerated by
++path_def, path_hpp, path_cpp = sys.argv[1:5]
+ 
+-   %s on %s
++print(f"Reading definitions from {path_def}")
++defs = featuredefs.defs(path_def)
+ 
+-   Do not modify it or your changes will be overwritten!
+-   Modify features.def instead.
++disclaimer = f"""/*
++    WARNING: This file was generated automatically.
++    Do not modify it or your changes will be overwritten!
++    Modify features.def instead.
+ */
+-#ifndef ESPRESSO_FEATURECONFIG_HPP
+-#define ESPRESSO_FEATURECONFIG_HPP
+-
+-#include "cmake_config.hpp"
+-#include "myconfig-final.hpp"
++"""
+ 
+-""" % (sys.argv[0], time.asctime()))
++print(f"Writing {path_hpp}")
++hfile = open(path_hpp, 'w')
++hfile.write(disclaimer)
++hfile.write("""
++#ifndef ESPRESSO_SRC_CONFIG_CONFIG_FEATURES_HPP
++#define ESPRESSO_SRC_CONFIG_CONFIG_FEATURES_HPP
++""")
+ 
+ # external features can only be set by the build
+ # system, so in case the user has defined some of
+ # them, we undef all external features and include
+ # the config from the build system again, to make
+ # sure only the detected ones are set.
+-hfile.write('/* Guards for externals */')
++hfile.write("""
++/*********************************/
++/* Handle definitions from CMake */
++/*********************************/
++
++#include "cmake_config.hpp"
++#include "myconfig-final.hpp"
++""")
+ external_template = string.Template("""
+ // $feature is external
+ #if defined($feature)
+ #undef $feature
+ #endif
+ """)
+-for feature in defs.externals:
++for feature in sorted(defs.externals):
+     hfile.write(external_template.substitute(feature=feature))
+ 
+ # Include definitions from CMake
+ hfile.write("""
+-/* Definitions from CMake */
+ #include "cmake_config.hpp"
+ 
+ """)
+ 
+ # handle implications
+-hfile.write('/* Handle implications */')
++hfile.write("""\
++/***********************/
++/* Handle implications */
++/***********************/
++""")
+ implication_template = string.Template("""
+ // $feature implies $implied
+ #if defined($feature) && !defined($implied)
+ #define $implied
+ #endif
+ """)
+-for feature, implied in defs.implications:
++for feature, implied in sorted(defs.implications):
+     hfile.write(implication_template.substitute(
+         feature=feature, implied=implied))
+ 
++hfile.write("\n")
++
+ # output warnings if internal features are set manually
+-hfile.write('/* Warn when derived switches are specified manually */')
++hfile.write("""\
++/*****************************************************/
++/* Warn when derived switches are specified manually */
++/*****************************************************/
++""")
+ derivation_template = string.Template("""
+ // $feature equals $expr
+ #ifdef $feature
+@@ -101,58 +111,52 @@ derivation_template = string.Template("""
+ #define $feature
+ #endif
+ """)
+-for feature, expr, cppexpr in defs.derivations:
++for feature, expr, cppexpr in sorted(defs.derivations):
+     hfile.write(derivation_template.substitute(
+         feature=feature, cppexpr=cppexpr, expr=expr))
+ 
+-# write footer
+-# define external FEATURES and NUM_FEATURES
+ hfile.write("""
+-extern const char* FEATURES[];
+-extern const int NUM_FEATURES;
+ 
+-#endif /* of _FEATURECONFIG_HPP */""")
+-hfile.close()
+-print("Done.")
++extern char const *const FEATURES[];
++extern char const *const FEATURES_ALL[];
++extern unsigned int const NUM_FEATURES;
++extern unsigned int const NUM_FEATURES_ALL;
+ 
+-print("Writing " + cfilename + "...")
+-cfile = open(cfilename, 'w')
+-
+-# handle requirements
+-
+-cfile.write(f"""/*
+-WARNING: This file was autogenerated by
++#endif
++""")
+ 
+-   {sys.argv[0]}
+-   on
+-   {time.asctime()}
++hfile.close()
+ 
+-   Do not modify it or your changes will be overwritten!
+-   Modify features.def instead.
+-*/
++print(f"Writing {path_cpp}")
++cfile = open(path_cpp, "w")
+ 
+-/* config.hpp includes config-features.hpp and myconfig.hpp */
++cfile.write(disclaimer)
++cfile.write(f"""
++#include "config-features.hpp"
+ #include "config.hpp"
+ 
++/***********************/
++/* Handle requirements */
++/***********************/
+ """)
+ 
+-cfile.write('/* Handle requirements */')
+-
+ requirement_string = """
+ // {feature} requires {expr}
+ #if defined({feature}) && !({cppexpr})
+ #error Feature {feature} requires {expr}
+ #endif
+ """
+-for feature, expr, cppexpr in defs.requirements:
++for feature, expr, cppexpr in sorted(defs.requirements):
+     cfile.write(
+         requirement_string.format(
+             feature=feature, cppexpr=cppexpr, expr=expr))
+ 
+ cfile.write("""
+-
++/****************/
+ /* Feature list */
+-const char* FEATURES[] = {
++/****************/
++
++char const *const FEATURES[] = {
+ """)
+ 
+ feature_string = """
+@@ -161,14 +165,31 @@ feature_string = """
+ #endif
+ """
+ 
+-for feature in defs.externals.union(defs.features, defs.derived):
++for feature in sorted(defs.externals.union(defs.features, defs.derived)):
+     cfile.write(feature_string.format(feature=feature))
+ 
+ cfile.write("""
+ };
++unsigned int const NUM_FEATURES = sizeof(FEATURES) / sizeof(char*);
++""")
+ 
+-const int NUM_FEATURES = sizeof(FEATURES)/sizeof(char*);
++cfile.write("""
++/*********************/
++/* Feature full list */
++/*********************/
++
++char const *const FEATURES_ALL[] = {\
++""")
++
++feature_string = """
++  "{feature}","""
++
++for feature in sorted(defs.allfeatures):
++    cfile.write(feature_string.format(feature=feature))
++
++cfile.write("""
++};
++unsigned int const NUM_FEATURES_ALL = sizeof(FEATURES_ALL) / sizeof(char*);
+ """)
+ 
+ cfile.close()
+-print("Done.")
+diff --git a/src/python/espressomd/gen_code_info.py b/src/python/espressomd/gen_code_info.py
+index 4314d5e3c..2f14582b8 100644
+--- a/src/python/espressomd/gen_code_info.py
++++ b/src/python/espressomd/gen_code_info.py
+@@ -53,14 +53,14 @@ def features():
+     f = []
+ """)
+ 
+-for feature in defs.allfeatures:
++for feature in sorted(defs.allfeatures):
+     cfile.write(f"\n    IF {feature} == 1:\n        f.append(\"{feature}\")\n")
+ 
+ cfile.write(f"""
+     return sorted(f)
+ 
+ def all_features():
+-    return {defs.allfeatures}
++    return {{{str(sorted(defs.allfeatures))[1:-1]}}}
+ 
+ 
+ cdef extern from "version.hpp":

python3-espressomd.changes

@@ -1,3 +1,24 @@
+-------------------------------------------------------------------
+Fri Mar 21 14:41:09 UTC 2025 - Bernhard Wiedemann <bwiedemann@suse.com>
+
+- Add espresso-cython.patch to drop build date (boo#1047218)
+
+-------------------------------------------------------------------
+Thu Mar 13 15:25:08 UTC 2025 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
+
+- Fix Python executable path hint
+
+-------------------------------------------------------------------
+Thu Mar 13 15:10:17 UTC 2025 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
+
+- Disable HDF5 feature
+
+-------------------------------------------------------------------
+Thu Mar 13 15:04:19 UTC 2025 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
+
+- Fix breaking builds
+- Disable features that rely on unmet dependencies (h5py, scipy)
+
 -------------------------------------------------------------------
 Wed Sep 11 19:01:36 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
 

python3-espressomd.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python3-espressomd
 #
-# Copyright (c) 2024 SUSE LLC
+# Copyright (c) 2025 SUSE LLC
 # Copyright (c) 2014 Christoph Junghans
 #
 # All modifications and additions to the file contributed by third parties
@@ -18,6 +18,15 @@
 
 
 # Build with OpenMPI
+%if 0%{?suse_version} > 1600 && 0%{?is_opensuse}
+%define is_tumbleweed 1
+%define boostver      %{nil}
+%define pyver         3
+%else
+%define is_tumbleweed 0
+%define boostver      1_75_0
+%define pyver         311
+%endif
 %define mpiver  openmpi4
 %define pkgname espresso
 %define modname %{pkgname}md
@@ -32,34 +41,31 @@ Source:         https://github.com/%{modname}/%{pkgname}/releases/download/%{ver
 Patch0:         numpy.patch
 # PATCH-FIX-UPSTREAM cmake.patch gh#espressomd/espresso#4992
 Patch1:         cmake.patch
+# PATCH-FIX-UPSTREAM https://github.com/espressomd/espresso/commit/2111342
+Patch2:         espresso-cython.patch
 # According to gh#espressomd/espresso#4537 32bit architectures are not supported any more
 ExcludeArch:    %{ix86} armv7l
+BuildRequires:  %{mpiver}-devel
+BuildRequires:  chrpath
 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:  hdf5-%{mpiver}-devel
-BuildRequires:  libboost_filesystem-devel
-BuildRequires:  libboost_mpi-devel
-BuildRequires:  libboost_system-devel
-BuildRequires:  libboost_test-devel
-BuildRequires:  python3-Cython < 3.0.10
-BuildRequires:  python3-devel
-BuildRequires:  python3-h5py
-BuildRequires:  python3-numpy-devel
-BuildRequires:  python3-scipy
-BuildRequires:  python3-setuptools
+BuildRequires:  libboost_filesystem%{boostver}-devel
+BuildRequires:  libboost_mpi%{boostver}-devel
+BuildRequires:  libboost_system%{boostver}-devel
+BuildRequires:  libboost_test%{boostver}-devel
+BuildRequires:  python%{pyver}-Cython < 3.0.13
+BuildRequires:  python%{pyver}-devel
+BuildRequires:  python%{pyver}-numpy-devel
+BuildRequires:  python%{pyver}-setuptools
+%if 0%{?is_tumbleweed}
+BuildRequires:  python%{pyver}-scipy
+%endif
 BuildRequires:  zlib-devel
 Provides:       libEspresso4 = %{version}-%{release}
 Obsoletes:      libEspresso4 < 4.1
-Requires:       python3-h5py
 Requires:       python3-numpy
-# make sure rpm pulls in the right dependency
-Requires:       libhdf5-%{mpiver}
 
 %description
 ESPResSo is a highly versatile software package for performing and analyzing
@@ -73,23 +79,39 @@ systems, for example DNA and lipid membranes.
 %autosetup -p1 -n %{pkgname}
 # Fix shebang line for pypresso
 sed -i -E '1s@^#!/usr/bin/env[[:blank:]]+sh@#!/bin/sh@' src/python/pypresso.cmakein
-# skip mpiio test - it fails if inwoked with cmake, direct run with python3 -m unittest pass
+# skip mpiio test - it fails if invoked with cmake, directly run with python3 -m unittest pass
 sed -i '/mpiio\.py/d' testsuite/python/CMakeLists.txt
+%if 0%{?is_tumbleweed} == 0
+# remove tests that depend on scipy (unavailable in Leap 15.6)
+sed -i '/checkpoint_test(/d' testsuite/python/CMakeLists.txt
+sed -i '/                MAX_NUM_PROC 1)/d' testsuite/python/CMakeLists.txt
+sed -i '/rotation\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/reaction_complex\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/canonical_ensemble\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/lb_pressure_tensor\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/analyze_acf\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/analyze_distribution\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/random_pairs\.py/d' testsuite/python/CMakeLists.txt
+sed -i '/oif_volume_conservation\.py/d' testsuite/python/CMakeLists.txt
+%endif
 
 %build
 source %{_libdir}/mpi/gcc/%{mpiver}/bin/mpivars.sh
 # gh#espressomd/espresso#3396
 %define _lto_cflags %{nil}
 
-#force usage of shared hdf5
-export HDF5_USE_SHLIB=yes
 # 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
 %cmake \
   -DCMAKE_SHARED_LINKER_FLAGS='-Wl,--as-needed -Wl,-z,now' \
   -DCMAKE_SKIP_RPATH=ON \
+  -DWITH_HDF5=OFF \
   -DLIBDIR=%{_libdir} \
+%if 0%{?is_tumbleweed}
   -DPYTHON_EXECUTABLE=%{_bindir}/python3 \
+%else
+  -DPYTHON_EXECUTABLE=%{_bindir}/python3.11 \
+%endif
   -DPYTHON_INSTDIR=%{python3_sitearch} \
   -DINSTALL_PYPRESSO=ON
 %make_jobs