Accepting request 1200197 from devel:languages:python:numeric
OBS-URL: https://build.opensuse.org/request/show/1200197 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python3-espressomd?expand=0&rev=22
This commit is contained in:
Ana Guerrero
Git OBS Bridge
commit
9ef8e4b0c4
33
cmake.patch
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33
cmake.patch
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@ -0,0 +1,33 @@
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diff --git a/CMakeLists.txt b/CMakeLists.txt
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index ac0432c34..bff6f289b 100644
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--- a/CMakeLists.txt
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+++ b/CMakeLists.txt
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@@ -38,7 +38,13 @@ if(POLICY CMP0148)
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cmake_policy(SET CMP0148 OLD)
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endif()
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+if(POLICY CMP0167)
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+ # use BoostConfig.cmake shipped with Boost 1.70+ instead of the one in CMake
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+ cmake_policy(SET CMP0167 NEW)
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+endif()
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# CMake modules/macros are in a subdirectory to keep this file cleaner
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set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
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+project(ESPResSo)
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+
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# C++ standard
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enable_language(CXX)
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@@ -49,5 +55,4 @@ set(CMAKE_CXX_EXTENSIONS OFF)
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include(FeatureSummary)
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include(GNUInstallDirs)
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-project(ESPResSo)
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include(option_enum)
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if(POLICY CMP0074)
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@@ -268,7 +273,5 @@ if(WITH_STOKESIAN_DYNAMICS)
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set(STOKESIAN_DYNAMICS 1)
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if(NOT stokesian_dynamics_POPULATED)
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- FetchContent_Populate(stokesian_dynamics)
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- add_subdirectory(${stokesian_dynamics_SOURCE_DIR}
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- ${stokesian_dynamics_BINARY_DIR})
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+ FetchContent_MakeAvailable(stokesian_dynamics)
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endif()
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endif(WITH_STOKESIAN_DYNAMICS)
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100
numpy.patch
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100
numpy.patch
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@ -0,0 +1,100 @@
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diff --git a/testsuite/python/brownian_dynamics.py b/testsuite/python/brownian_dynamics.py
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index 223340e15..f99d94018 100644
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--- a/testsuite/python/brownian_dynamics.py
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+++ b/testsuite/python/brownian_dynamics.py
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@@ -161,5 +161,5 @@ class BrownianThermostat(ut.TestCase):
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system.integrator.run(3)
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np.testing.assert_allclose(
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- part.omega_lab, [0, 0, 1.3 / 1.5], atol=1e-14)
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+ np.copy(part.omega_lab), [0, 0, 1.3 / 1.5], atol=1e-14)
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# noise only
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@@ -168,5 +168,5 @@ class BrownianThermostat(ut.TestCase):
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kT=1, gamma=1, gamma_rotation=1.5, act_on_virtual=False, seed=41)
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system.integrator.run(3)
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- self.assertGreater(np.linalg.norm(part.omega_lab), 0.)
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+ self.assertGreater(np.linalg.norm(np.copy(part.omega_lab)), 0.)
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diff --git a/testsuite/python/lees_edwards.py b/testsuite/python/lees_edwards.py
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index 002340bd2..4539f1af5 100644
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--- a/testsuite/python/lees_edwards.py
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+++ b/testsuite/python/lees_edwards.py
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@@ -397,5 +397,5 @@ class LeesEdwards(ut.TestCase):
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a=k_non_bonded / 2, n=-2, cutoff=r_cut)
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system.integrator.run(0)
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- r_12 = system.distance_vec(p1, p2)
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+ r_12 = np.copy(system.distance_vec(p1, p2))
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np.testing.assert_allclose(
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@@ -405,5 +405,5 @@ class LeesEdwards(ut.TestCase):
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np.testing.assert_allclose(
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np.copy(system.analysis.pressure_tensor()["non_bonded"]),
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- np.outer(r_12, p2.f) / system.volume())
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+ np.outer(r_12, np.copy(p2.f)) / system.volume())
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np.testing.assert_almost_equal(
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@@ -438,5 +438,5 @@ class LeesEdwards(ut.TestCase):
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shear_direction="x", shear_plane_normal="y", protocol=lin_protocol)
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# Test position and velocity of VS with Le shift
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- old_p3_pos = p3.pos
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+ old_p3_pos = np.copy(p3.pos)
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expected_p3_pos = old_p3_pos - \
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np.array((get_lin_pos_offset(system.time, **params_lin), 0, 0))
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@@ -444,5 +444,5 @@ class LeesEdwards(ut.TestCase):
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np.testing.assert_allclose(np.copy(p3.pos_folded), expected_p3_pos)
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np.testing.assert_allclose(
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- p3.v, p1.v + np.array((params_lin["shear_velocity"], 0, 0)))
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+ np.copy(p3.v), np.copy(p1.v) + np.array((params_lin["shear_velocity"], 0, 0)))
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# Check distances
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diff --git a/testsuite/python/test_checkpoint.py b/testsuite/python/test_checkpoint.py
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index f295cec44..4b30aaefb 100644
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--- a/testsuite/python/test_checkpoint.py
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+++ b/testsuite/python/test_checkpoint.py
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@@ -217,12 +217,12 @@ class CheckpointTest(ut.TestCase):
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np.testing.assert_allclose(np.copy(p3.ext_torque), [0.3, 0.5, 0.7])
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if espressomd.has_features('ROTATIONAL_INERTIA'):
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- np.testing.assert_allclose(p3.rinertia, [2., 3., 4.])
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+ np.testing.assert_allclose(np.copy(p3.rinertia), [2., 3., 4.])
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if espressomd.has_features('THERMOSTAT_PER_PARTICLE'):
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gamma = 2.
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if espressomd.has_features('PARTICLE_ANISOTROPY'):
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gamma = np.array([2., 3., 4.])
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- np.testing.assert_allclose(p4.gamma, gamma)
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+ np.testing.assert_allclose(np.copy(p4.gamma), gamma)
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if espressomd.has_features('ROTATION'):
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- np.testing.assert_allclose(p3.gamma_rot, 2. * gamma)
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+ np.testing.assert_allclose(np.copy(p3.gamma_rot), 2. * gamma)
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if espressomd.has_features('ENGINE'):
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self.assertEqual(p3.swimming, {"f_swim": 0.03, "mode": "N/A",
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@@ -237,9 +237,11 @@ class CheckpointTest(ut.TestCase):
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q_ind = ([1, 2, 3, 0],) # convert from scalar-first to scalar-last
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vs_id, vs_dist, vs_quat = p2.vs_relative
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- d = p2.pos - p1.pos
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+ d = np.copy(p2.pos - p1.pos)
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+ vs_quat = np.copy(vs_quat)
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+ p_quat = np.copy(p1.quat)
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theta = np.arccos(d[2] / np.linalg.norm(d))
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assert abs(theta - 3. * np.pi / 4.) < 1e-8
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q = np.array([0., 0., np.sin(theta / 2.), -np.cos(theta / 2.)])
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- r = R.from_quat(p1.quat[q_ind]) * R.from_quat(vs_quat[q_ind])
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+ r = R.from_quat(p_quat[q_ind]) * R.from_quat(vs_quat[q_ind])
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self.assertEqual(vs_id, p1.id)
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np.testing.assert_allclose(vs_dist, np.sqrt(2.))
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@@ -500,5 +502,5 @@ class CheckpointTest(ut.TestCase):
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self.assertEqual(p_virt.vs_relative[1], np.sqrt(2.))
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np.testing.assert_allclose(
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- p_real.vs_relative[2], [1., 0., 0., 0.], atol=1e-10)
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+ np.copy(p_real.vs_relative[2]), [1., 0., 0., 0.], atol=1e-10)
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def test_mean_variance_calculator(self):
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@@ -785,6 +787,6 @@ class CheckpointTest(ut.TestCase):
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p2 = system.part.add(pos=[system.box_l[0] - 1., 1.6, 0.], type=6)
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system.integrator.run(0, recalc_forces=True)
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- np.testing.assert_allclose(p1.f, [0., 1e8, 0.], atol=1e-3)
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- np.testing.assert_allclose(p2.f, [0., 1e8, 0.], atol=1e-3)
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+ np.testing.assert_allclose(np.copy(p1.f), [0., 1e8, 0.], atol=1e-3)
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+ np.testing.assert_allclose(np.copy(p2.f), [0., 1e8, 0.], atol=1e-3)
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p1.remove()
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p2.remove()
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@ -1,3 +1,14 @@
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-------------------------------------------------------------------
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Wed Sep 11 19:01:36 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
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- Fix numpy.patch
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-------------------------------------------------------------------
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Wed Sep 11 18:36:23 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
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- Add numpy.patch to improve NumPy 2.0 compatibility (gh#espressomd/espresso#4992)
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- Add cmake.patch to address CMake warnings (gh#espressomd/espresso#4992)
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-------------------------------------------------------------------
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Wed May 22 16:08:22 UTC 2024 - Jean-Noel Grad <jgrad@icp.uni-stuttgart.de>
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@ -28,6 +28,10 @@ Summary: Parallel simulation software for soft matter research
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License: GPL-3.0-or-later
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URL: http://espressomd.org
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Source: https://github.com/%{modname}/%{pkgname}/releases/download/%{version}/%{pkgname}-%{version}.tar.gz
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# PATCH-FIX-UPSTREAM numpy.patch gh#espressomd/espresso#4992
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Patch0: numpy.patch
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# PATCH-FIX-UPSTREAM cmake.patch gh#espressomd/espresso#4992
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Patch1: cmake.patch
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# According to gh#espressomd/espresso#4537 32bit architectures are not supported any more
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ExcludeArch: %{ix86} armv7l
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BuildRequires: cmake
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@ -43,7 +47,7 @@ BuildRequires: libboost_filesystem-devel
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BuildRequires: libboost_mpi-devel
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BuildRequires: libboost_system-devel
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BuildRequires: libboost_test-devel
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BuildRequires: python3-Cython < 3
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BuildRequires: python3-Cython < 3.0.10
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BuildRequires: python3-devel
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BuildRequires: python3-h5py
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BuildRequires: python3-numpy-devel
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