Script 'mail_helper' called by obssrc Hello community, here is the log from the commit of package python3-espressomd for openSUSE:Factory checked in at 2024-09-12 16:56:38 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/python3-espressomd (Old) and /work/SRC/openSUSE:Factory/.python3-espressomd.new.17570 (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python3-espressomd" Thu Sep 12 16:56:38 2024 rev:22 rq:1200197 version:4.2.2 Changes: -------- --- /work/SRC/openSUSE:Factory/python3-espressomd/python3-espressomd.changes 2024-05-23 15:35:40.384514363 +0200 +++ /work/SRC/openSUSE:Factory/.python3-espressomd.new.17570/python3-espressomd.changes 2024-09-12 16:58:01.761029025 +0200 @@ -1,0 +2,11 @@ +Wed Sep 11 19:01:36 UTC 2024 - Jean-Noel Grad <jg...@icp.uni-stuttgart.de> + +- Fix numpy.patch + +------------------------------------------------------------------- +Wed Sep 11 18:36:23 UTC 2024 - Jean-Noel Grad <jg...@icp.uni-stuttgart.de> + +- Add numpy.patch to improve NumPy 2.0 compatibility (gh#espressomd/espresso#4992) +- Add cmake.patch to address CMake warnings (gh#espressomd/espresso#4992) + +------------------------------------------------------------------- New: ---- cmake.patch numpy.patch BETA DEBUG BEGIN: New:- Add numpy.patch to improve NumPy 2.0 compatibility (gh#espressomd/espresso#4992) - Add cmake.patch to address CMake warnings (gh#espressomd/espresso#4992) New: - Fix numpy.patch BETA DEBUG END: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ python3-espressomd.spec ++++++ --- /var/tmp/diff_new_pack.hLL42M/_old 2024-09-12 16:58:02.889076019 +0200 +++ /var/tmp/diff_new_pack.hLL42M/_new 2024-09-12 16:58:02.889076019 +0200 @@ -28,6 +28,10 @@ License: GPL-3.0-or-later URL: http://espressomd.org Source: https://github.com/%{modname}/%{pkgname}/releases/download/%{version}/%{pkgname}-%{version}.tar.gz +# PATCH-FIX-UPSTREAM numpy.patch gh#espressomd/espresso#4992 +Patch0: numpy.patch +# PATCH-FIX-UPSTREAM cmake.patch gh#espressomd/espresso#4992 +Patch1: cmake.patch # According to gh#espressomd/espresso#4537 32bit architectures are not supported any more ExcludeArch: %{ix86} armv7l BuildRequires: cmake @@ -43,7 +47,7 @@ BuildRequires: libboost_mpi-devel BuildRequires: libboost_system-devel BuildRequires: libboost_test-devel -BuildRequires: python3-Cython < 3 +BuildRequires: python3-Cython < 3.0.10 BuildRequires: python3-devel BuildRequires: python3-h5py BuildRequires: python3-numpy-devel ++++++ cmake.patch ++++++ diff --git a/CMakeLists.txt b/CMakeLists.txt index ac0432c34..bff6f289b 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -38,7 +38,13 @@ if(POLICY CMP0148) cmake_policy(SET CMP0148 OLD) endif() +if(POLICY CMP0167) + # use BoostConfig.cmake shipped with Boost 1.70+ instead of the one in CMake + cmake_policy(SET CMP0167 NEW) +endif() # CMake modules/macros are in a subdirectory to keep this file cleaner set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake) +project(ESPResSo) + # C++ standard enable_language(CXX) @@ -49,5 +55,4 @@ set(CMAKE_CXX_EXTENSIONS OFF) include(FeatureSummary) include(GNUInstallDirs) -project(ESPResSo) include(option_enum) if(POLICY CMP0074) @@ -268,7 +273,5 @@ if(WITH_STOKESIAN_DYNAMICS) set(STOKESIAN_DYNAMICS 1) if(NOT stokesian_dynamics_POPULATED) - FetchContent_Populate(stokesian_dynamics) - add_subdirectory(${stokesian_dynamics_SOURCE_DIR} - ${stokesian_dynamics_BINARY_DIR}) + FetchContent_MakeAvailable(stokesian_dynamics) endif() endif(WITH_STOKESIAN_DYNAMICS) ++++++ numpy.patch ++++++ diff --git a/testsuite/python/brownian_dynamics.py b/testsuite/python/brownian_dynamics.py index 223340e15..f99d94018 100644 --- a/testsuite/python/brownian_dynamics.py +++ b/testsuite/python/brownian_dynamics.py @@ -161,5 +161,5 @@ class BrownianThermostat(ut.TestCase): system.integrator.run(3) np.testing.assert_allclose( - part.omega_lab, [0, 0, 1.3 / 1.5], atol=1e-14) + np.copy(part.omega_lab), [0, 0, 1.3 / 1.5], atol=1e-14) # noise only @@ -168,5 +168,5 @@ class BrownianThermostat(ut.TestCase): kT=1, gamma=1, gamma_rotation=1.5, act_on_virtual=False, seed=41) system.integrator.run(3) - self.assertGreater(np.linalg.norm(part.omega_lab), 0.) + self.assertGreater(np.linalg.norm(np.copy(part.omega_lab)), 0.) diff --git a/testsuite/python/lees_edwards.py b/testsuite/python/lees_edwards.py index 002340bd2..4539f1af5 100644 --- a/testsuite/python/lees_edwards.py +++ b/testsuite/python/lees_edwards.py @@ -397,5 +397,5 @@ class LeesEdwards(ut.TestCase): a=k_non_bonded / 2, n=-2, cutoff=r_cut) system.integrator.run(0) - r_12 = system.distance_vec(p1, p2) + r_12 = np.copy(system.distance_vec(p1, p2)) np.testing.assert_allclose( @@ -405,5 +405,5 @@ class LeesEdwards(ut.TestCase): np.testing.assert_allclose( np.copy(system.analysis.pressure_tensor()["non_bonded"]), - np.outer(r_12, p2.f) / system.volume()) + np.outer(r_12, np.copy(p2.f)) / system.volume()) np.testing.assert_almost_equal( @@ -438,5 +438,5 @@ class LeesEdwards(ut.TestCase): shear_direction="x", shear_plane_normal="y", protocol=lin_protocol) # Test position and velocity of VS with Le shift - old_p3_pos = p3.pos + old_p3_pos = np.copy(p3.pos) expected_p3_pos = old_p3_pos - \ np.array((get_lin_pos_offset(system.time, **params_lin), 0, 0)) @@ -444,5 +444,5 @@ class LeesEdwards(ut.TestCase): np.testing.assert_allclose(np.copy(p3.pos_folded), expected_p3_pos) np.testing.assert_allclose( - p3.v, p1.v + np.array((params_lin["shear_velocity"], 0, 0))) + np.copy(p3.v), np.copy(p1.v) + np.array((params_lin["shear_velocity"], 0, 0))) # Check distances diff --git a/testsuite/python/test_checkpoint.py b/testsuite/python/test_checkpoint.py index f295cec44..4b30aaefb 100644 --- a/testsuite/python/test_checkpoint.py +++ b/testsuite/python/test_checkpoint.py @@ -217,12 +217,12 @@ class CheckpointTest(ut.TestCase): np.testing.assert_allclose(np.copy(p3.ext_torque), [0.3, 0.5, 0.7]) if espressomd.has_features('ROTATIONAL_INERTIA'): - np.testing.assert_allclose(p3.rinertia, [2., 3., 4.]) + np.testing.assert_allclose(np.copy(p3.rinertia), [2., 3., 4.]) if espressomd.has_features('THERMOSTAT_PER_PARTICLE'): gamma = 2. if espressomd.has_features('PARTICLE_ANISOTROPY'): gamma = np.array([2., 3., 4.]) - np.testing.assert_allclose(p4.gamma, gamma) + np.testing.assert_allclose(np.copy(p4.gamma), gamma) if espressomd.has_features('ROTATION'): - np.testing.assert_allclose(p3.gamma_rot, 2. * gamma) + np.testing.assert_allclose(np.copy(p3.gamma_rot), 2. * gamma) if espressomd.has_features('ENGINE'): self.assertEqual(p3.swimming, {"f_swim": 0.03, "mode": "N/A", @@ -237,9 +237,11 @@ class CheckpointTest(ut.TestCase): q_ind = ([1, 2, 3, 0],) # convert from scalar-first to scalar-last vs_id, vs_dist, vs_quat = p2.vs_relative - d = p2.pos - p1.pos + d = np.copy(p2.pos - p1.pos) + vs_quat = np.copy(vs_quat) + p_quat = np.copy(p1.quat) theta = np.arccos(d[2] / np.linalg.norm(d)) assert abs(theta - 3. * np.pi / 4.) < 1e-8 q = np.array([0., 0., np.sin(theta / 2.), -np.cos(theta / 2.)]) - r = R.from_quat(p1.quat[q_ind]) * R.from_quat(vs_quat[q_ind]) + r = R.from_quat(p_quat[q_ind]) * R.from_quat(vs_quat[q_ind]) self.assertEqual(vs_id, p1.id) np.testing.assert_allclose(vs_dist, np.sqrt(2.)) @@ -500,5 +502,5 @@ class CheckpointTest(ut.TestCase): self.assertEqual(p_virt.vs_relative[1], np.sqrt(2.)) np.testing.assert_allclose( - p_real.vs_relative[2], [1., 0., 0., 0.], atol=1e-10) + np.copy(p_real.vs_relative[2]), [1., 0., 0., 0.], atol=1e-10) def test_mean_variance_calculator(self): @@ -785,6 +787,6 @@ class CheckpointTest(ut.TestCase): p2 = system.part.add(pos=[system.box_l[0] - 1., 1.6, 0.], type=6) system.integrator.run(0, recalc_forces=True) - np.testing.assert_allclose(p1.f, [0., 1e8, 0.], atol=1e-3) - np.testing.assert_allclose(p2.f, [0., 1e8, 0.], atol=1e-3) + np.testing.assert_allclose(np.copy(p1.f), [0., 1e8, 0.], atol=1e-3) + np.testing.assert_allclose(np.copy(p2.f), [0., 1e8, 0.], atol=1e-3) p1.remove() p2.remove()
