commit: 2d4dc553811d221a3fd4f86ce55e6910b638fbc4
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 9 18:00:16 2025 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Tue Sep 9 20:52:39 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2d4dc553
sci-physics/espresso: backport upstream fix for numpy 2.x
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
sci-physics/espresso/espresso-4.2.2.ebuild | 5 +-
.../espresso/files/espresso-4.2.2-numpy-2.x.patch | 105 +++++++++++++++++++++
2 files changed, 109 insertions(+), 1 deletion(-)
diff --git a/sci-physics/espresso/espresso-4.2.2.ebuild
b/sci-physics/espresso/espresso-4.2.2.ebuild
index faa88fa89fb1..392c61bed0bf 100644
--- a/sci-physics/espresso/espresso-4.2.2.ebuild
+++ b/sci-physics/espresso/espresso-4.2.2.ebuild
@@ -32,7 +32,7 @@ RDEPEND="
${PYTHON_DEPS}
$(python_gen_cond_dep '
>=dev-python/cython-0.26.1[${PYTHON_USEDEP}]
- <dev-python/numpy-2[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
')
cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
fftw? ( sci-libs/fftw:3.0 )
@@ -58,6 +58,9 @@ DOCS=( AUTHORS NEWS Readme.md ChangeLog )
PATCHES=(
"${FILESDIR}/${PN}-4.2.0-fix-disable-test.patch"
"${FILESDIR}"/0001-allow-building-test-deps-without-running-ctest-indir.patch
+ # https://github.com/espressomd/espresso/pull/4992
+ #
https://src.fedoraproject.org/rpms/espresso/c/1c764324a21a92d6500289b4d72043471b5f3840
+ "${FILESDIR}"/${P}-numpy-2.x.patch
)
src_prepare() {
diff --git a/sci-physics/espresso/files/espresso-4.2.2-numpy-2.x.patch
b/sci-physics/espresso/files/espresso-4.2.2-numpy-2.x.patch
new file mode 100644
index 000000000000..af3dea9ed5b8
--- /dev/null
+++ b/sci-physics/espresso/files/espresso-4.2.2-numpy-2.x.patch
@@ -0,0 +1,105 @@
+https://github.com/espressomd/espresso/pull/4992
+
+backported by upstream to fedora:
+https://src.fedoraproject.org/rpms/espresso/c/1c764324a21a92d6500289b4d72043471b5f3840
+
+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()
