Fix rdkit tests

MDAnalysis · Jul 22, 2024 · 10fc8df · 10fc8df
1 parent 1bf58cc
commit 10fc8df
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Showing 3 changed files with 14 additions and 28 deletions.
diff --git a/testsuite/MDAnalysisTests/converters/test_rdkit.py b/testsuite/MDAnalysisTests/converters/test_rdkit.py
@@ -27,7 +27,6 @@
 
 import MDAnalysis as mda
 import numpy as np
-from numpy.lib import NumpyVersion
 import pytest
 from MDAnalysis.topology.guessers import guess_atom_element
 from MDAnalysisTests.datafiles import GRO, PDB_full, PDB_helix, mol2_molecule
@@ -56,8 +55,6 @@
                     reason="only for min dependencies build")
 class TestRequiresRDKit(object):
     def test_converter_requires_rdkit(self):
-        if NumpyVersion(np.__version__) >= "2.0.0":
-            pytest.skip("RDKit not compatible with NumPy 2")
         u = mda.Universe(PDB_full)
         with pytest.raises(ImportError,
                            match="RDKit is required for the RDKitConverter"):

diff --git a/testsuite/MDAnalysisTests/converters/test_rdkit_parser.py b/testsuite/MDAnalysisTests/converters/test_rdkit_parser.py
@@ -24,7 +24,6 @@
 import warnings
 import pytest
 import numpy as np
-from numpy.lib import NumpyVersion
 from numpy.testing import assert_equal
 
 import MDAnalysis as mda
@@ -33,12 +32,9 @@
 
 # TODO: remove these shims when RDKit
 # has a release supporting NumPy 2
-if NumpyVersion(np.__version__) < "2.0.0":
-    Chem = pytest.importorskip('rdkit.Chem')
-    AllChem = pytest.importorskip('rdkit.Chem.AllChem')
-else:
-    Chem = pytest.importorskip("RDKit_does_not_support_NumPy_2")
-    AllChem = pytest.importorskip("RDKit_does_not_support_NumPy_2")
+Chem = pytest.importorskip('rdkit.Chem')
+AllChem = pytest.importorskip('rdkit.Chem.AllChem')
+
 
 class RDKitParserBase(ParserBase):
     parser = mda.converters.RDKitParser.RDKitParser

diff --git a/testsuite/MDAnalysisTests/core/test_universe.py b/testsuite/MDAnalysisTests/core/test_universe.py
@@ -30,7 +30,6 @@
 import warnings
 
 import numpy as np
-from numpy.lib import NumpyVersion
 from numpy.testing import (
     assert_allclose,
     assert_almost_equal,
@@ -224,12 +223,6 @@ def test_universe_empty_ROMol(self):
 
 
 class TestUniverseFromSmiles(object):
-    def setup_class(self):
-        if NumpyVersion(np.__version__) < "2.0.0":
-            pytest.importorskip("rdkit.Chem")
-        else:
-            pytest.importorskip("RDKit_does_not_support_NumPy_2")
-
     def test_default(self):
         smi = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
         u = mda.Universe.from_smiles(smi, format='RDKIT')
@@ -288,17 +281,17 @@ def test_coordinates(self):
                                      rdkit_kwargs=dict(randomSeed=42))
         assert u.trajectory.n_frames == 2
         expected = np.array([
-            [[-0.02209686,  0.00321505,  0.01651974],
-            [-0.6690088 ,  0.8893599 , -0.1009085 ],
-            [-0.37778795, -0.8577519 , -0.58829606],
-            [ 0.09642092, -0.3151253 ,  1.0637809 ],
-            [ 0.97247267,  0.28030226, -0.3910961 ]],
-            [[-0.0077073 ,  0.00435363,  0.01834692],
-            [-0.61228824, -0.83705765, -0.38619974],
-            [-0.41925883,  0.9689095 , -0.3415968 ],
-            [ 0.03148226, -0.03256683,  1.1267245 ],
-            [ 1.0077721 , -0.10363862, -0.41727486]]], dtype=np.float32)
-        assert_almost_equal(u.trajectory.coordinate_array, expected)
+        [[-0.02209686,  0.00321505,  0.01651974],
+         [-0.6664637 ,  0.8884155 , -0.10135844],
+         [-0.37778795, -0.8577519 , -0.58829606],
+         [ 0.09642092, -0.3151253 ,  1.0637809 ],
+         [ 0.96992755,  0.2812466 , -0.39064613]],
+        [[-0.0077073 ,  0.00435363,  0.01834692],
+         [-0.61228824, -0.83705765, -0.38619974],
+         [-0.41925883,  0.9689095 , -0.3415968 ],
+         [ 0.03148226, -0.03256683,  1.1267245 ],
+         [ 1.0077721 , -0.10363862, -0.41727486]]], dtype=np.float32)
+        assert_allclose(u.trajectory.coordinate_array, expected, rtol=1e-5)
 
 
 class TestUniverse(object):