Accepting request 1198016 from devel:languages:python:numeric

OBS-URL: https://build.opensuse.org/request/show/1198016
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-ase?expand=0&rev=5

ase-3.23.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:91a2aa31d89bd90b0efdfe4a7e84264f32828b2abfc9f38e65e041ad76fec8ae
+size 2336462

ase-3.26.0.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a071a355775b0a8062d23e9266e9d811b19d9f6d9ec5215e8032f7d93dc65075
-size 2405567

ase-mr3400-numpy2.patch

@@ -0,0 +1,222 @@
+From 06c59143e7fdf15483491cf71800afba8b862bda Mon Sep 17 00:00:00 2001
+From: yuzie007 <yuji.ikeda.ac.jp@gmail.com>
+Date: Thu, 20 Jun 2024 17:44:31 +0200
+Subject: [PATCH 1/7] Use `np.exceptions.ComplexWarning`
+
+---
+ ase/test/vibrations/test_vib.py | 8 ++++++--
+ 1 file changed, 6 insertions(+), 2 deletions(-)
+
+Index: ase-3.23.0/ase/test/vibrations/test_vib.py
+===================================================================
+--- ase-3.23.0.orig/ase/test/vibrations/test_vib.py
++++ ase-3.23.0/ase/test/vibrations/test_vib.py
+@@ -6,6 +6,10 @@ import numpy as np
+ import pytest
+ from numpy.testing import (assert_array_almost_equal,
+                            assert_array_equal)
++try:
++    from numpy.exceptions import ComplexWarning  # NumPy 2.0.0
++except ImportError:
++    from numpy import ComplexWarning
+ 
+ import ase.io
+ from ase import Atoms, units
+@@ -438,14 +442,14 @@ def test_constrained_atoms(n2_data):
+ 
+ 
+ def test_dos(n2_vibdata):
+-    with pytest.warns(np.ComplexWarning):
++    with pytest.warns(ComplexWarning):
+         dos = n2_vibdata.get_dos()
+     assert_array_almost_equal(dos.get_energies(),
+                               n2_vibdata.get_energies())
+ 
+ 
+ def test_pdos(n2_vibdata):
+-    with pytest.warns(np.ComplexWarning):
++    with pytest.warns(ComplexWarning):
+         pdos = n2_vibdata.get_pdos()
+     assert_array_almost_equal(pdos[0].get_energies(),
+                               n2_vibdata.get_energies())
+Index: ase-3.23.0/ase/constraints.py
+===================================================================
+--- ase-3.23.0.orig/ase/constraints.py
++++ ase-3.23.0/ase/constraints.py
+@@ -1161,19 +1161,19 @@ class FixInternals(FixConstraint):
+         # Projection
+         hh = []
+         for i, constraint in enumerate(self.constraints):
+-            hh.append(aa[:, i] * np.row_stack(aa[:, i]))
++            hh.append(aa[:, i] * np.vstack(aa[:, i]))
+ 
+-        txx = aa[:, self.n] * np.row_stack(aa[:, self.n])
+-        tyy = aa[:, self.n + 1] * np.row_stack(aa[:, self.n + 1])
+-        tzz = aa[:, self.n + 2] * np.row_stack(aa[:, self.n + 2])
+-        rxx = aa[:, self.n + 3] * np.row_stack(aa[:, self.n + 3])
+-        ryy = aa[:, self.n + 4] * np.row_stack(aa[:, self.n + 4])
+-        rzz = aa[:, self.n + 5] * np.row_stack(aa[:, self.n + 5])
++        txx = aa[:, self.n] * np.vstack(aa[:, self.n])
++        tyy = aa[:, self.n + 1] * np.vstack(aa[:, self.n + 1])
++        tzz = aa[:, self.n + 2] * np.vstack(aa[:, self.n + 2])
++        rxx = aa[:, self.n + 3] * np.vstack(aa[:, self.n + 3])
++        ryy = aa[:, self.n + 4] * np.vstack(aa[:, self.n + 4])
++        rzz = aa[:, self.n + 5] * np.vstack(aa[:, self.n + 5])
+         T = txx + tyy + tzz + rxx + ryy + rzz
+         for vec in hh:
+             T += vec
+-        ff = np.dot(T, np.row_stack(ff))
+-        forces[:, :] -= np.dot(T, np.row_stack(ff)).reshape(-1, 3)
++        ff = np.dot(T, np.vstack(ff))
++        forces[:, :] -= np.dot(T, np.vstack(ff)).reshape(-1, 3)
+ 
+     def __repr__(self):
+         constraints = [repr(constr) for constr in self.constraints]
+Index: ase-3.23.0/ase/mep/autoneb.py
+===================================================================
+--- ase-3.23.0.orig/ase/mep/autoneb.py
++++ ase-3.23.0/ase/mep/autoneb.py
+@@ -544,7 +544,7 @@ class AutoNEB:
+             try:
+                 energies.append(a.get_potential_energy())
+             except RuntimeError:
+-                energies.append(np.NaN)
++                energies.append(np.nan)
+         return energies
+ 
+     def get_energies_one_image(self, image):
+@@ -553,7 +553,7 @@ class AutoNEB:
+         try:
+             energy = image.get_potential_energy()
+         except RuntimeError:
+-            energy = np.NaN
++            energy = np.nan
+         return energy
+ 
+     def get_highest_energy_index(self):
+Index: ase-3.23.0/ase/dft/__init__.py
+===================================================================
+--- ase-3.23.0.orig/ase/dft/__init__.py
++++ ase-3.23.0/ase/dft/__init__.py
+@@ -1,4 +1,8 @@
+ import numpy as np
++try:
++    from numpy import trapezoid  # NumPy 2.0.0
++except ImportError:
++    from numpy import trapz as trapezoid
+ 
+ from ase.dft.dos import DOS
+ from ase.dft.kpoints import monkhorst_pack
+@@ -19,9 +23,9 @@ def get_distribution_moment(x, y, order=
+     y = np.asarray(y)
+ 
+     if order == 0:
+-        return np.trapz(y, x)
++        return trapezoid(y, x)
+     elif isinstance(order, int):
+-        return np.trapz(x**order * y, x) / np.trapz(y, x)
++        return trapezoid(x**order * y, x) / trapezoid(y, x)
+     elif hasattr(order, '__iter__'):
+         return [get_distribution_moment(x, y, n) for n in order]
+     else:
+Index: ase-3.23.0/ase/md/switch_langevin.py
+===================================================================
+--- ase-3.23.0.orig/ase/md/switch_langevin.py
++++ ase-3.23.0/ase/md/switch_langevin.py
+@@ -1,6 +1,10 @@
+ from typing import Any, List, Optional
+ 
+ import numpy as np
++try:
++    from numpy import trapezoid  # NumPy 2.0.0
++except ImportError:
++    from numpy import trapz as trapezoid
+ 
+ from ase import Atoms
+ from ase.calculators.mixing import MixedCalculator
+@@ -117,7 +121,7 @@ class SwitchLangevin(Langevin):
+         lambdas = self.path_data[:, 1]
+         U1 = self.path_data[:, 2]
+         U2 = self.path_data[:, 3]
+-        delta_F = np.trapz(U2 - U1, lambdas)
++        delta_F = trapezoid(U2 - U1, lambdas)
+         return delta_F
+ 
+ 
+Index: ase-3.23.0/ase/test/calculator/test_harmonic.py
+===================================================================
+--- ase-3.23.0.orig/ase/test/calculator/test_harmonic.py
++++ ase-3.23.0/ase/test/calculator/test_harmonic.py
+@@ -1,6 +1,10 @@
+ import numpy as np
+ import pytest
+ from numpy.testing import assert_array_almost_equal
++try:
++    from numpy import trapezoid  # NumPy 2.0.0
++except ImportError:
++    from numpy import trapz as trapezoid
+ 
+ from ase import Atoms
+ from ase.calculators.calculator import CalculationFailed, CalculatorSetupError
+@@ -266,7 +270,7 @@ def test_thermodynamic_integration():
+                 e0, e1 = calc_linearCombi.get_energy_contributions(atoms)
+                 ediffs[lamb].append(float(e1) - float(e0))
+             ediffs[lamb] = np.mean(ediffs[lamb])
+-    dA = np.trapz([ediffs[lamb] for lamb in lambs], x=lambs)  # anharm. corr.
++    dA = trapezoid([ediffs[lamb] for lamb in lambs], x=lambs)  # anharm. corr.
+     assert -0.005 < dA < 0.005  # the MD run is to short for convergence
+     if dA == 0.0:
+         raise ValueError('there is most likely something wrong, but it could '
+Index: ase-3.23.0/ase/io/octopus/input.py
+===================================================================
+--- ase-3.23.0.orig/ase/io/octopus/input.py
++++ ase-3.23.0/ase/io/octopus/input.py
+@@ -516,7 +516,7 @@ def atoms2kwargs(atoms, use_ase_cell):
+ 
+         if atoms.cell.orthorhombic:
+             Lsize = 0.5 * np.diag(cell)
+-            kwargs['lsize'] = [[repr(size) for size in Lsize]]
++            kwargs['lsize'] = [[str(size) for size in Lsize]]
+             # ASE uses (0...cell) while Octopus uses -L/2...L/2.
+             # Lsize is really cell / 2, and we have to adjust our
+             # positions by subtracting Lsize (see construction of the coords
+@@ -533,7 +533,7 @@ def atoms2kwargs(atoms, use_ase_cell):
+             if sym is None:
+                 raise ValueError('Cannot represent atom X without tags and '
+                                  'species info in atoms.info')
+-        coord_block.append([repr(sym)] + [repr(x) for x in pos])
++        coord_block.append([repr(sym)] + [str(x) for x in pos])
+ 
+     kwargs[coordtype] = coord_block
+     npbc = sum(atoms.pbc)
+Index: ase-3.23.0/ase/dft/band_structure.py
+===================================================================
+--- ase-3.23.0.orig/ase/dft/band_structure.py
++++ ase-3.23.0/ase/dft/band_structure.py
+@@ -1,6 +1,9 @@
+ import warnings
+ 
+-from numpy import VisibleDeprecationWarning
++try:
++    from numpy.exceptions import VisibleDeprecationWarning  # NumPy 2.0.0
++except ImportError:
++    from numpy import VisibleDeprecationWarning
+ 
+ from ase.spectrum.band_structure import *  # noqa: F401,F403
+ 
+Index: ase-3.23.0/ase/test/test_imports.py
+===================================================================
+--- ase-3.23.0.orig/ase/test/test_imports.py
++++ ase-3.23.0/ase/test/test_imports.py
+@@ -3,7 +3,10 @@ from importlib import import_module
+ from pathlib import Path
+ 
+ import pytest
+-from numpy import VisibleDeprecationWarning
++try:
++    from numpy.exceptions import VisibleDeprecationWarning  # NumPy 2.0.0
++except ImportError:
++    from numpy import VisibleDeprecationWarning
+ 
+ import ase
+ 

python-ase.changes

@@ -1,34 +1,3 @@
--------------------------------------------------------------------
-Thu Aug 28 04:31:25 UTC 2025 - Steve Kowalik <steven.kowalik@suse.com>
-
-- Update to 3.26.0:
-  * Requirements
-    + The minimum supported Python version has increased to 3.9
-  * Breaking changes
-    + Removed unused IOFormat.open() method.
-    + The Optimizable interface now works in terms of arbitrary degrees of
-      freedom rather than Cartesian (Nx3) ones.
-    + ase.io.orca.read_orca_output now returns Atoms with attached
-      properties. ase.io.read() will use this function.
-    + The master parameter to each Optimizer is now passed via **kwargs and
-      so becomes keyword-only.
-    + Removed legacy read_cell and write_cell functions from ase.io.castep.
-    + Removed deprecated force_consistent option from Optimizer.
-    + ase.spectrum.band_structure.BandStructurePlot: the plot_with_colors()
-      has been removed and its features merged into the plot() method.
-  * Highlights
-   + Changed ELK based on GenericFileIOCalculator.
-   + The “heavy-weight” database backends in ase.db have been moved to a
-     separate project.
-   + Major improvements to find_optimal_cell_shape(): improve target metric;
-     ensure rotationally invariant results; avoid negative determinants;
-     improved performance via vectorisation.
-   + Added new FiniteDifferenceCalculator, which wraps other calculator for
-     finite-difference forces and strains.
-   + Added two new MD thermostats: ase.md.bussi.Bussi and
-     ase.md.nose_hoover_chain.NoseHooverChainNVT.
-- Drop patch ase-mr3400-numpy2.patch, included upstream.
-
 -------------------------------------------------------------------
 Fri Aug 30 12:50:49 UTC 2024 - Ben Greiner <code@bnavigator.de>
 

python-ase.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python-ase
 #
-# Copyright (c) 2025 SUSE LLC and contributors
+# Copyright (c) 2024 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -17,29 +17,31 @@
 
 
 Name:           python-ase
-Version:        3.26.0
+Version:        3.23.0
 Release:        0
 Summary:        Atomic Simulation Environment
 License:        LGPL-2.1-or-later
 URL:            https://wiki.fysik.dtu.dk/ase
 Source:         https://files.pythonhosted.org/packages/source/a/ase/ase-%{version}.tar.gz
-BuildRequires:  %{python_module base >= 3.9}
+# PATCH-FIX-UPSTREAM ase-mr3400-numpy2.patch https://gitlab.com/ase/ase/-/merge_requests/3400
+Patch0:         ase-mr3400-numpy2.patch
 BuildRequires:  %{python_module pip}
 BuildRequires:  %{python_module setuptools}
 BuildRequires:  %{python_module wheel}
 BuildRequires:  python-rpm-macros
 # SECTION test requirements
-BuildRequires:  %{python_module matplotlib >= 3.3.4}
-BuildRequires:  %{python_module numpy >= 1.19.5}
-BuildRequires:  %{python_module pytest >= 7}
-BuildRequires:  %{python_module pytest-xdist >= 2.1}
-BuildRequires:  %{python_module scipy >= 1.6.0}
+BuildRequires:  %{python_module matplotlib >= 3.1.0}
+BuildRequires:  %{python_module numpy >= 1.15.0}
+BuildRequires:  %{python_module pytest-mock}
+BuildRequires:  %{python_module pytest-xdist}
+BuildRequires:  %{python_module pytest}
+BuildRequires:  %{python_module scipy >= 1.1.0}
 BuildRequires:  %{python_module tk}
 # /SECTION
 BuildRequires:  fdupes
-Requires:       python-matplotlib >= 3.3.4
-Requires:       python-numpy >= 1.19.5
-Requires:       python-scipy >= 1.6.0
+Requires:       python-matplotlib >= 3.1.0
+Requires:       python-numpy >= 1.15.0
+Requires:       python-scipy >= 1.1.0
 Requires(post): update-alternatives
 Requires(postun): update-alternatives
 BuildArch:      noarch