Accepting request 1301637 from devel:languages:python:numeric

- 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.

OBS-URL: https://build.opensuse.org/request/show/1301637
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-ase?expand=0&rev=6

ase-3.23.0.tar.gz

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

ase-3.26.0.tar.gz

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

ase-mr3400-numpy2.patch

@@ -1,222 +0,0 @@
-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

@@ -1,3 +1,34 @@
+-------------------------------------------------------------------
+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) 2024 SUSE LLC
+# Copyright (c) 2025 SUSE LLC and contributors
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -17,31 +17,29 @@
 
 
 Name:           python-ase
-Version:        3.23.0
+Version:        3.26.0
 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
-# PATCH-FIX-UPSTREAM ase-mr3400-numpy2.patch https://gitlab.com/ase/ase/-/merge_requests/3400
+BuildRequires:  %{python_module base >= 3.9}
-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 >= 3.1.0}
+BuildRequires:  %{python_module matplotlib >= 3.3.4}
-BuildRequires:  %{python_module numpy >= 1.15.0}
+BuildRequires:  %{python_module numpy >= 1.19.5}
-BuildRequires:  %{python_module pytest-mock}
+BuildRequires:  %{python_module pytest >= 7}
-BuildRequires:  %{python_module pytest-xdist}
+BuildRequires:  %{python_module pytest-xdist >= 2.1}
-BuildRequires:  %{python_module pytest}
+BuildRequires:  %{python_module scipy >= 1.6.0}
-BuildRequires:  %{python_module scipy >= 1.1.0}
 BuildRequires:  %{python_module tk}
 # /SECTION
 BuildRequires:  fdupes
-Requires:       python-matplotlib >= 3.1.0
+Requires:       python-matplotlib >= 3.3.4
-Requires:       python-numpy >= 1.15.0
+Requires:       python-numpy >= 1.19.5
-Requires:       python-scipy >= 1.1.0
+Requires:       python-scipy >= 1.6.0
 Requires(post): update-alternatives
 Requires(postun): update-alternatives
 BuildArch:      noarch