Accepting request 668739 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/668739
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=2

2255.patch

@@ -1,27 +0,0 @@
-diff --git a/src/core/unit_tests/ParallelScriptInterface_test.cpp b/src/core/unit_tests/ParallelScriptInterface_test.cpp
-index 7374ed99ca..0195b4f7d1 100644
---- a/src/core/unit_tests/ParallelScriptInterface_test.cpp
-+++ b/src/core/unit_tests/ParallelScriptInterface_test.cpp
-@@ -174,7 +174,7 @@ BOOST_AUTO_TEST_CASE(parameter_lifetime) {
- }
- 
- int main(int argc, char **argv) {
--  mpi::environment mpi_env;
-+  mpi::environment mpi_env(argc, argv);
-   mpi::communicator world;
-   callbacks = Utils::make_unique<Communication::MpiCallbacks>(
-       world, /* abort_on_exit */ false);
-diff --git a/src/python/espressomd/utils.pyx b/src/python/espressomd/utils.pyx
-index 9e29f0bd21..24ecb31c86 100644
---- a/src/python/espressomd/utils.pyx
-+++ b/src/python/espressomd/utils.pyx
-@@ -331,6 +331,8 @@ def is_valid_type(value, t):
-     if t == int:
-         return isinstance(value, (int, np.integer, np.long))
-     elif t == float:
--        return isinstance(value, (float, np.float16, np.float32, np.float64, np.float128, np.longdouble))
-+        if hasattr(np, 'float128'):
-+            return isinstance(value, (float, np.float16, np.float32, np.float64, np.float128, np.longdouble))
-+        return isinstance(value, (float, np.float16, np.float32, np.float64, np.longdouble))
-     else:
-         return isinstance(value, t)

2259.patch

@@ -1,37 +0,0 @@
-From 81f9b86cca275f053e914c7c42e864c3af9fed8e Mon Sep 17 00:00:00 2001
-From: Michael Kuron <mkuron@icp.uni-stuttgart.de>
-Date: Thu, 13 Sep 2018 11:09:40 +0200
-Subject: [PATCH] Fix PARTIAL_PERIODIC on big-endian platforms
-
----
- src/core/global.cpp                   | 2 +-
- src/core/utils/serialization/List.hpp | 3 +++
- 2 files changed, 4 insertions(+), 1 deletion(-)
-
-diff --git a/src/core/global.cpp b/src/core/global.cpp
-index 75959c3246..9164c5e0b4 100644
---- a/src/core/global.cpp
-+++ b/src/core/global.cpp
-@@ -147,7 +147,7 @@ const std::unordered_map<int, Datafield> fields{
-      {&nptiso.piston, Datafield::Type::DOUBLE, 1,
-       "npt_piston"}}, /* 27 from pressure.cpp */
-     {FIELD_PERIODIC,
--     {&periodic, Datafield::Type::BOOL, 3,
-+     {&periodic, Datafield::Type::INT, 1,
-       "periodicity"}}, /* 28 from grid.cpp */
-     {FIELD_SKIN,
-      {&skin, Datafield::Type::DOUBLE, 1, "skin"}}, /* 29 from integrate.cpp */
-diff --git a/src/core/utils/serialization/List.hpp b/src/core/utils/serialization/List.hpp
-index fdc2d172ee..ae7fc37db3 100644
---- a/src/core/utils/serialization/List.hpp
-+++ b/src/core/utils/serialization/List.hpp
-@@ -20,6 +20,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
- #define CORE_UTILS_SERIALIZATION_LIST_HPP
- 
- #include <boost/serialization/array.hpp>
-+#if BOOST_VERSION >= 106400 && BOOST_VERSION < 106500
-+#include <boost/serialization/array_wrapper.hpp>
-+#endif
- #include <boost/serialization/split_free.hpp>
- 
- #include "core/utils/List.hpp"

2265.patch

@@ -1,56 +0,0 @@
-From be29174ad76db081ff0111ac3b96c0a8f64aea5b Mon Sep 17 00:00:00 2001
-From: Michael Kuron <mkuron@users.noreply.github.com>
-Date: Fri, 14 Sep 2018 13:14:01 +0200
-Subject: [PATCH 1/2] Fix unit test on 32-bit platform
-
----
- src/core/unit_tests/field_coupling_couplings_test.cpp | 8 ++++----
- 1 file changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/src/core/unit_tests/field_coupling_couplings_test.cpp b/src/core/unit_tests/field_coupling_couplings_test.cpp
-index 268d666eff..1dd7809eb8 100644
---- a/src/core/unit_tests/field_coupling_couplings_test.cpp
-+++ b/src/core/unit_tests/field_coupling_couplings_test.cpp
-@@ -78,10 +78,10 @@ BOOST_AUTO_TEST_CASE(scaled) {
-       const int m_id;
-     };
- 
--    BOOST_CHECK((1.23 * 2.) == scaled_coupling(Particle(0), 2.));
--    BOOST_CHECK((default_val * 3.) == scaled_coupling(Particle(1), 3.));
--    BOOST_CHECK((3.45 * 4.) == scaled_coupling(Particle(2), 4.));
--    BOOST_CHECK((default_val * 5.) == scaled_coupling(Particle(3), 5.));
-+    BOOST_CHECK_CLOSE(1.23 * 2., scaled_coupling(Particle(0), 2.), 1e-14);
-+    BOOST_CHECK_CLOSE(default_val * 3., scaled_coupling(Particle(1), 3.), 1e-14);
-+    BOOST_CHECK_CLOSE(3.45 * 4., scaled_coupling(Particle(2), 4.), 1e-14);
-+    BOOST_CHECK_CLOSE(default_val * 5., scaled_coupling(Particle(3), 5.), 1e-14);
-   }
- }
- 
-
-From 005380040f5d7d9a50c450cdaf46639b333b8683 Mon Sep 17 00:00:00 2001
-From: Michael Kuron <mkuron@users.noreply.github.com>
-Date: Fri, 14 Sep 2018 14:20:59 +0200
-Subject: [PATCH 2/2] formatting
-
----
- src/core/unit_tests/field_coupling_couplings_test.cpp | 6 ++++--
- 1 file changed, 4 insertions(+), 2 deletions(-)
-
-diff --git a/src/core/unit_tests/field_coupling_couplings_test.cpp b/src/core/unit_tests/field_coupling_couplings_test.cpp
-index 1dd7809eb8..b14fad8e5e 100644
---- a/src/core/unit_tests/field_coupling_couplings_test.cpp
-+++ b/src/core/unit_tests/field_coupling_couplings_test.cpp
-@@ -79,9 +79,11 @@ BOOST_AUTO_TEST_CASE(scaled) {
-     };
- 
-     BOOST_CHECK_CLOSE(1.23 * 2., scaled_coupling(Particle(0), 2.), 1e-14);
--    BOOST_CHECK_CLOSE(default_val * 3., scaled_coupling(Particle(1), 3.), 1e-14);
-+    BOOST_CHECK_CLOSE(default_val * 3., scaled_coupling(Particle(1), 3.),
-+                      1e-14);
-     BOOST_CHECK_CLOSE(3.45 * 4., scaled_coupling(Particle(2), 4.), 1e-14);
--    BOOST_CHECK_CLOSE(default_val * 5., scaled_coupling(Particle(3), 5.), 1e-14);
-+    BOOST_CHECK_CLOSE(default_val * 5., scaled_coupling(Particle(3), 5.),
-+                      1e-14);
-   }
- }
- 

espresso-4.0.0.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8e128847447eebd843de24be9b4ad14aa19c028ae48879a5a4535a9683836e6b
-size 25767191

espresso-4.0.1.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:17b7268eeba652a77f861bc534cdd05d206e7641d203a9dd5029b44bd422304b
+size 25793301

python3-espressomd.changes

@@ -1,3 +1,10 @@
+-------------------------------------------------------------------
+Fri Jan 25 16:28:37 UTC 2019 - Christoph Junghans <junghans@votca.org>
+
+- Version bump to 4.0.1 
+  * Many small bugfixes
+- Drop 2255.patch, 2259.patch and 2265.patch - merged upstream
+
 -------------------------------------------------------------------
 Fri Sep 28 23:13:13 UTC 2018 - Christoph Junghans <junghans@votca.org>
 

python3-espressomd.spec

@@ -32,19 +32,13 @@
 %define modname %{pkgname}md
 %define sonum 4
 Name:           python3-%{modname}
-Version:        4.0.0
+Version:        4.0.1
 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 2255.patch https://github.com/espressomd/espresso/pull/2255 - fix numpy issue on i586
-Patch0:         2255.patch
-# PATCH-FIX-UPSTREAM 2259.patch https://github.com/espressomd/espresso/pull/2259 - fix numpy issue on big-endian platforms
-Patch1:         2259.patch
-# PATCH-FIX-UPSTREAM 2265.patch https://github.com/espressomd/espresso/pull/2265 - fix test on i586
-Patch2:         2265.patch
 BuildRequires:  cmake
 BuildRequires:  fftw3-devel
 BuildRequires:  gcc-c++
@@ -81,10 +75,6 @@ This package provides shared libraries for ESPResSo.
 
 %prep
 %setup -q -n %{pkgname}-%{version}
-%patch0 -p1
-%patch1 -p1
-%patch2 -p1
-chmod -x AUTHORS COPYING README NEWS ChangeLog
 
 %build
 source %{_libdir}/mpi/gcc/%{mpi_implem}/bin/mpivars.sh
@@ -107,10 +97,16 @@ find %{buildroot}%{_prefix} -name "gen_pxiconfig" -exec chmod +x {} \;
 rm -f %{buildroot}%{_libdir}/lib*.so
 
 %check
-# https://github.com/espressomd/espresso/issues/2258
+# https://github.com/espressomd/espresso/issues/2468
-%ifnarch i586 %arm ppc64le
+%ifarch ppc64 ppc64le
-LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/%{mpi_implem}/%{_lib}' make -C build check
+%global testargs ARGS='-E npt'
 %endif
+# https://github.com/espressomd/espresso/issues/2469
+%ifarch aarch64
+%global testargs ARGS='-E analyze_gyration_tensor'
+%endif
+
+LD_LIBRARY_PATH='%{buildroot}/%{_libdir}::%{_libdir}/mpi/gcc/%{mpi_implem}/%{_lib}' make -C build check CTEST_OUTPUT_ON_FAILURE=1 %{?testargs:%{testargs}}
 
 %post -n libEspresso%{sonum} -p /sbin/ldconfig
 %postun -n libEspresso%{sonum} -p /sbin/ldconfig