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

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-3.23.0.tar.gz

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

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
+ 

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 +1,76 @@
+-------------------------------------------------------------------
+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

@@ -17,19 +17,17 @@
 
 
 Name:           python-ase
-Version:        3.22.1
+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
-# PATCH-FIX-UPSTREAM https://gitlab.com/ase/ase/-/merge_requests/2826
+# PATCH-FIX-UPSTREAM ase-mr3400-numpy2.patch https://gitlab.com/ase/ase/-/merge_requests/3400
-Patch0:         support-matplotlib-36.patch
+Patch0:         ase-mr3400-numpy2.patch
-# PATCH-FIX-UPSTREAM https://gitlab.com/ase/ase/-/merge_requests/2582
+BuildRequires:  %{python_module pip}
-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 setuptools}
+BuildRequires:  %{python_module wheel}
 BuildRequires:  python-rpm-macros
 # SECTION test requirements
 BuildRequires:  %{python_module matplotlib >= 3.1.0}
@@ -44,6 +42,8 @@ BuildRequires:  fdupes
 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
 %python_subpackages
 
@@ -54,24 +54,22 @@ 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 +78,7 @@ 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
-