MAINT: Parameters of cg solver in scipy changed with version 1.12.0

matscipy/calculators/calculator.py

@@ -31,8 +31,7 @@
     nonaffine_elastic_contribution,
 )
 
-from ..numerical import numerical_nonaffine_forces
-
+from ..compat import compat_cg_parameters
 from ..numpy_tricks import mabincount
 
 
@@ -368,6 +367,8 @@ def get_non_affine_contribution_to_elastic_constants(self, atoms, eigenvalues=No
             "This function is deprecated and will be removed in the future. Use 'elasticity.nonaffine_elastic_contribution' instead.",
             DeprecationWarning)
 
+        cg_parameters = compat_cg_parameters(cg_parameters)
+
         nat = len(atoms)
 
         calc = self

matscipy/compat.py

@@ -0,0 +1,13 @@
+import scipy
+from packaging.version import Version
+
+
+def compat_cg_parameters(cg_parameters):
+    if Version(scipy.__version__) >= Version('1.12.0'):
+        return cg_parameters
+    else:
+        cg_parameters = cg_parameters.copy()
+        if 'rtol' in cg_parameters:
+            cg_parameters['tol'] = cg_parameters['rtol']
+            del cg_parameters['rtol']
+        return cg_parameters

matscipy/elasticity.py

@@ -37,6 +37,8 @@
 import ase.units as units
 from ase.atoms import Atoms
 
+from .compat import compat_cg_parameters
+
 ###
 
 # The indices of the full stiffness matrix of (orthorhombic) interest
@@ -1335,6 +1337,8 @@ def _sym(C_abab):
         symmetry_group = [(0, 1, 2, 3), (1, 0, 2, 3), (0, 1, 3, 2), (1, 0, 3, 2)]
         return 0.25 * np.add.reduce([C_abab.transpose(s) for s in symmetry_group])
 
+    cg_parameters = compat_cg_parameters(cg_parameters)
+
     nat = len(atoms)
     naforces_icab = atoms.calc.get_property('nonaffine_forces')
 

matscipy/io/opls.py

@@ -23,7 +23,7 @@
 import copy
 import re
 
-from looseversion import LooseVersion
+from packaging.version import Version
 
 import numpy as np
 import ase
@@ -359,7 +359,7 @@ def write_lammps_atoms(prefix, atoms, units='metal'):
                 fileobj.write('%d dihedral types\n' % (len(dtypes)))
 
             # cell
-            if LooseVersion(ase_version_str) > LooseVersion('3.11.0'):
+            if Version(ase_version_str) > Version('3.11.0'):
                 p = ase.calculators.lammpsrun.Prism(atoms.get_cell())
             else:
                 p = ase.calculators.lammpsrun.prism(atoms.get_cell())
@@ -385,9 +385,9 @@ def write_lammps_atoms(prefix, atoms, units='metal'):
                 molid = [1] * len(atoms)
 
             pos = ase.calculators.lammpsrun.convert(atoms.get_positions(), 'distance', 'ASE', units)
-            if LooseVersion(ase_version_str) > LooseVersion('3.17.0'):
+            if Version(ase_version_str) > Version('3.17.0'):
                 positions_lammps_str = p.vector_to_lammps(pos).astype(str)
-            elif LooseVersion(ase_version_str) > LooseVersion('3.13.0'):
+            elif Version(ase_version_str) > Version('3.13.0'):
                 positions_lammps_str = p.positions_to_lammps_strs(pos)
             else:
                 positions_lammps_str = map(p.pos_to_lammps_str, pos)

pyproject.toml

@@ -25,9 +25,9 @@ requires-python = ">=3.8.0"
 dynamic = ["version"]
 dependencies = [
     "numpy>=1.16.0",
-    "scipy>=1.12.0",  # rtol in scipy cg
+    "scipy>=1.2.3",
     "ase>=3.16.0",
-    "looseversion"
+    "packaging"
 ]
 
 [project.optional-dependencies]

tests/test_electrochemistry_cli.py

@@ -29,7 +29,7 @@
 import tempfile
 import unittest
 
-from looseversion import LooseVersion
+from packaging.version import Version
 
 
 class ElectrochemistryCliTest(matscipytest.MatSciPyTestCase):
@@ -116,7 +116,7 @@ def test_c2d_input_format_txt_output_format_xyz(self):
                 == self.ref_xyz.get_initial_charges() ).all() )
             self.assertTrue( ( xyz.cell == self.ref_xyz.cell ).all() )
 
-    @unittest.skipUnless(LooseVersion(ase.__version__) > LooseVersion('3.19.0'),
+    @unittest.skipUnless(Version(ase.__version__) > Version('3.19.0'),
         """ LAMMPS data file won't work for ASE version up until 3.18.1,
             LAMMPS data file input broken in ASE 3.19.0, skipped""")
     def test_c2d_input_format_npz_output_format_lammps(self):