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

2582.patch

@@ -1,26 +0,0 @@
-From 5e733253d9e791ed1568076ede93a983f27979f6 Mon Sep 17 00:00:00 2001
-From: "Adam J. Jackson" <a.j.jackson@physics.org>
-Date: Tue, 30 Nov 2021 09:51:47 +0000
-Subject: [PATCH] TST: Vibration slab test should check for movement in ANY
- direction
-
-It is possible for a perfectly good eigenvector to be zero in some
-Cartesian direction; this was encountered in #976 and appears to be
-architecture-dependent.
----
- ase/test/vibrations/test_vib.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ase/test/vibrations/test_vib.py b/ase/test/vibrations/test_vib.py
-index fe28ff13e5..7786a47aec 100644
---- a/ase/test/vibrations/test_vib.py
-+++ b/ase/test/vibrations/test_vib.py
-@@ -524,4 +524,4 @@ class TestSlab:
-             assert_array_almost_equal(vibs.get_mode(i)[0], [0., 0., 0.])
- 
-             # The N atoms should have finite displacement
--            assert np.all(vibs.get_mode(i)[-2:, :])
-+            assert np.all(np.any(vibs.get_mode(i)[-2:, :], axis=1))
--- 
-GitLab
-

ase-3.22.1.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432
-size 2807134

ase-3.26.0.tar.gz

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

deprecated-importlib-find_loader.patch

@@ -1,32 +0,0 @@
-Index: ase-3.22.1/ase/calculators/autodetect.py
-===================================================================
---- ase-3.22.1.orig/ase/calculators/autodetect.py
-+++ ase-3.22.1/ase/calculators/autodetect.py
-@@ -45,11 +45,11 @@ def detect(name):
-         return d
- 
-     if name in python_modules:
--        loader = importlib.find_loader(python_modules[name])
--        if loader is not None:
-+        spec = importlib.util.find_spec(python_modules[name])
-+        if spec is not None:
-             d['type'] = 'python'
-             d['module'] = python_modules[name]
--            d['path'] = loader.get_filename()
-+            d['path'] = spec.loader.get_filename()
-             return d
- 
-     envvar = get_executable_env_var(name)
-Index: ase-3.22.1/ase/test/testsuite.py
-===================================================================
---- ase-3.22.1.orig/ase/test/testsuite.py
-+++ ase-3.22.1/ase/test/testsuite.py
-@@ -53,7 +53,7 @@ def test(calculators=tuple(), jobs=0, ve
- 
- 
- def have_module(module):
--    return importlib.find_loader(module) is not None
-+    return importlib.util.find_spec(module) is not None
- 
- 
- MULTIPROCESSING_MAX_WORKERS = 32

python-ase.changes

@@ -1,3 +1,107 @@
+-------------------------------------------------------------------
+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>
+
+- Unpin numpy
+- Add ase-mr3400-numpy2.patch gl#ase/ase#3400
+
+-------------------------------------------------------------------
+Thu Jul 18 03:49:28 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com>
+
+- Update to 3.23.0:
+  * Add FixSubsetCom to fix the center of mass of the specified subset
+    of atoms.
+  * Add the indices option to ase.Atoms.get_center_of_mass() to compute
+    the center of mass of the specified subset of atoms.
+  * All saddle-point search and minimum-energy path methods have been
+    moved into a new ase.mep module. You should start importing from this
+    location; e.g., from ase.mep import NEB, DyNEB.
+  * Fix ase.constraints.FixCom.adjust_momenta() to have no center-of-mass
+    momentum
+  * ase.build.surface.graphene() now takes a thickness argument
+  * ase.build.bulk() now assigns initial magnetic moments to BCC Fe, Co,
+    and Ni.
+  * ase.build.make_supercell() can now control how to order the atoms in
+    the supercell via the option order
+  * mask() returns the mask of nonzero cell vectors, an array of three
+    booleans.
+  * reciprocal() now guarantees that cell vectors which are zero correspond
+    to reciprocal cell vectors that are also zero. Previously the
+    reciprocal cell vectors could have small nonzero values due to floating
+    point tolerance.
+  * The Cell object now has normal() and normals() which calculate normal
+    vectors to one or all pairs of cell vectors. Also added area() and
+    areas(), which return the area spanned by one or all pairs of cell
+    vectors.
+  * New a2b and periodic formats for Formula objects. The abc format has
+    been renamed to ab2.
+  * IO formats can now be implemented in separate packages and registered
+    in ase with the entry point ase.ioformats in the external package
+    configuration.
+  * ase.phonons.Displacement now has a comm keyword argument to better
+    support parallelization.
+  * Fix ase.build.rotate.minimize_rotation_and_translation() for systems
+    with periodic boundary conditions.
+  * Fix ase.io.db.row.AtomsRow.charge(), which was looking for
+    inital_charges instead of initial_charges.
+  * Fixed definition of the Lennard-Jones potential in ase.utils.ff
+  * The x3d viewer has improved aesthetics
+  * Added a function, ase.dft.kpoints.mindistance2monkhorstpack(), to
+    construct a Monkhorst-Pack grid
+  * Fixed turbomole calculator parsing issues when = are present in data
+    groups
+  * Fixed round-trip dict (de)serialization with FixedMode constraint
+  * Show total number of rows in ASE database
+  * Fix units of magnetic moments in ASE database
+  * General improvements to POVRay colors
+  * Remove deprecated CLI functions, such as the old ase-gui command
+  * Fix calculation of stresses in ase.stress.full_3x3_to_voigt_6_stress()
+  * Add polarization parser for FHI-AIMS calculator
+  * Fix bug in ase.atoms.Atoms.get_center_of_mass()
+  * Fix multiprocessing bug with ase.neb.NEB
+  * NEB calculations now call get_forces() instead of get_potential_energy()
+    followed by get_forces() to prevent duplicate work
+  * Improve performance of ase.build.supercells.make_supercell() for large
+    supercells
+  * Fix conservation of momentum in ase.md.langevin.Langevin
+  * Fix bug in ase.vibrations.Vibrations causing property calculations to
+    always use the default method
+- Switch to pyproject macros.
+- Remove patches, included upstream:
+  * support-matplotlib-36.patch
+  * 2582.patch
+  * deprecated-importlib-find_loader.patch
+
 -------------------------------------------------------------------
 Tue Feb  6 18:08:22 UTC 2024 - Daniel Garcia <daniel.garcia@suse.com>
 

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
@@ -17,33 +17,31 @@
 
 
 Name:           python-ase
-Version:        3.22.1
+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 https://gitlab.com/ase/ase/-/merge_requests/2826
-Patch0:         support-matplotlib-36.patch
-# PATCH-FIX-UPSTREAM https://gitlab.com/ase/ase/-/merge_requests/2582
-Patch1:         2582.patch
-# PATCH-FIX-UPSTREAM deprecated-importlib-find_loader.patch https://gitlab.com/ase/ase/-/merge_requests/2938
-Patch2:         deprecated-importlib-find_loader.patch
+BuildRequires:  %{python_module base >= 3.9}
+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 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 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 tk}
 # /SECTION
 BuildRequires:  fdupes
-Requires:       python-matplotlib >= 3.1.0
-Requires:       python-numpy >= 1.15.0
-Requires:       python-scipy >= 1.1.0
+Requires:       python-matplotlib >= 3.3.4
+Requires:       python-numpy >= 1.19.5
+Requires:       python-scipy >= 1.6.0
+Requires(post): update-alternatives
+Requires(postun): update-alternatives
 BuildArch:      noarch
 %python_subpackages
 
@@ -54,24 +52,22 @@ Atomic Simulation Environment
 %autosetup -p1 -n ase-%{version}
 
 %build
-%python_build
+%pyproject_wheel
 
 %install
-%python_install
+%pyproject_install
 %python_clone -a %{buildroot}%{_bindir}/ase
-%python_clone -a %{buildroot}%{_bindir}/ase-db
-%python_clone -a %{buildroot}%{_bindir}/ase-gui
-%python_clone -a %{buildroot}%{_bindir}/ase-run
-%python_clone -a %{buildroot}%{_bindir}/ase-info
-%python_clone -a %{buildroot}%{_bindir}/ase-build
 %python_expand %fdupes %{buildroot}%{$python_sitelib}
 
 %check
 # No scipy CODATA
-%pytest -k 'not test_units'
+donttest="test_units"
+# Broken with current release, remove on upgrade
+donttest+=" or test_pw_input_write_nested_flat or test_fix_scaled"
+%pytest -k "not ($donttest)"
 
 %post
-%python_install_alternative ase ase-db ase-gui ase-run ase-info ase-build
+%python_install_alternative ase
 
 %postun
 %python_uninstall_alternative ase
@@ -80,12 +76,7 @@ Atomic Simulation Environment
 %doc CHANGELOG.rst README.rst
 %license COPYING COPYING.LESSER LICENSE
 %python_alternative %{_bindir}/ase
-%python_alternative %{_bindir}/ase-db
-%python_alternative %{_bindir}/ase-gui
-%python_alternative %{_bindir}/ase-run
-%python_alternative %{_bindir}/ase-info
-%python_alternative %{_bindir}/ase-build
 %{python_sitelib}/ase
-%{python_sitelib}/ase*info
+%{python_sitelib}/ase-%{version}.dist-info
 
 %changelog

support-matplotlib-36.patch

@@ -1,37 +0,0 @@
-From 3d4fff328ba9a06d9799563f357cfe5968f1f79c Mon Sep 17 00:00:00 2001
-From: Ask Hjorth Larsen <asklarsen@gmail.com>
-Date: Mon, 16 Jan 2023 16:41:15 +0100
-Subject: [PATCH] set window title in way that will not crash on matplotlib
- 3.6+
-
----
- ase/cli/band_structure.py | 6 ++++--
- 1 file changed, 4 insertions(+), 2 deletions(-)
-
-diff --git a/ase/cli/band_structure.py b/ase/cli/band_structure.py
-index 303c64b88..603ad659a 100644
---- a/ase/cli/band_structure.py
-+++ b/ase/cli/band_structure.py
-@@ -16,15 +16,17 @@ def read_band_structure(filename):
- 
- def main(args, parser):
-     import matplotlib.pyplot as plt
-+
-     bs = read_band_structure(args.calculation)
-     emin, emax = (float(e) for e in args.range)
--    fig = plt.gcf()
--    fig.canvas.set_window_title(args.calculation)
-+    fig = plt.figure(args.calculation)
-     ax = fig.gca()
-+
-     bs.plot(ax=ax,
-             filename=args.output,
-             emin=emin + bs.reference,
-             emax=emax + bs.reference)
-+
-     if args.output is None:
-         plt.show()
- 
--- 
-GitLab
-