Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose

package/AUTHORS

@@ -233,6 +233,8 @@ Chronological list of authors
   - Lawson Woods
   - Johannes Stöckelmaier
   - Jenna M. Swarthout Goddard
+  2024
+  - Aditya Keshari
 
 External code
 -------------

package/CHANGELOG

@@ -3336,3 +3336,8 @@ Testsuite
 
 11/12/07 naveen
   * prepared for release outside lab
+
+24/02/23 aditya292002
+  * "updated tests that used assert_almost_equal(..., decimal={N}) with equivalent assert_allclose(..., rtol=0, atol=1.5e-{N}) (issue modernize testing code #3743, PR Replaced numpy.testing.assert_almost_equal to numpy.testing.assert_allclose #4438)"
+
+  /workspaces/mdanalysis/package/CHANGELOG

testsuite/MDAnalysisTests/analysis/test_align.py

@@ -36,7 +36,6 @@
 from numpy.testing import (
     assert_equal,
     assert_array_equal,
-    assert_array_almost_equal,
     assert_allclose,
 )
 
@@ -318,7 +317,7 @@ def test_AlignTraj_custom_weights(self, universe, reference, tmpdir):
         x_weights = align.AlignTraj(universe, reference,
                                     filename=outfile, weights=weights).run()
 
-        assert_array_almost_equal(x.results.rmsd, x_weights.results.rmsd)
+        assert_allclose(x.results.rmsd, x_weights.results.rmsd, rtol=0, atol=1.5e-7)
 
     def test_AlignTraj_custom_mass_weights(self, universe, reference, tmpdir):
         outfile = str(tmpdir.join('align_test.dcd'))
@@ -393,8 +392,8 @@ def test_alignto_partial_universe(self, universe, reference):
         segB_free.translate(segB_bound.centroid() - segB_free.centroid())
 
         align.alignto(u_free, u_bound, select=selection)
-        assert_array_almost_equal(segB_bound.positions, segB_free.positions,
-                                  decimal=3)
+        assert_allclose(segB_bound.positions, segB_free.positions,
+                                  rtol=0, atol=1.5e-7)
 
 
 def _get_aligned_average_positions(ref_files, ref, select="all", **kwargs):

testsuite/MDAnalysisTests/analysis/test_contacts.py

@@ -29,7 +29,6 @@
 from numpy.testing import (
     assert_equal,
     assert_array_equal,
-    assert_array_almost_equal,
     assert_allclose,
 )
 import numpy as np
@@ -305,7 +304,7 @@ def test_hard_cut_method(self, universe):
                     0.48543689, 0.45631068, 0.46601942, 0.47572816, 0.51456311,
                     0.45631068, 0.37864078, 0.42718447]
         assert len(ca.results.timeseries) == len(expected)
-        assert_array_almost_equal(ca.results.timeseries[:, 1], expected)
+        assert_allclose(ca.results.timeseries[:, 1], expected, rtol=0, atol=1.5e-7)
 
     def test_radius_cut_method(self, universe):
         acidic = universe.select_atoms(self.sel_acidic)
@@ -365,7 +364,7 @@ def test_distance_box(self, pbc, expected):
         r = contacts.Contacts(u, select=(sel_acidic, sel_basic),
                         refgroup=(acidic, basic), radius=6.0, pbc=pbc)
         r.run()
-        assert_array_almost_equal(r.results.timeseries[:, 1], expected)
+        assert_allclose(r.results.timeseries[:, 1], expected,rtol=0, atol=1.5e-7)
 
     def test_warn_deprecated_attr(self, universe):
         """Test for warning message emitted on using deprecated `timeseries`
@@ -401,7 +400,7 @@ def test_q1q2():
                    0.93097184, 0.93006358, 0.93188011, 0.93278837, 0.93006358,
                    0.92915531, 0.92824705, 0.92733878, 0.92643052, 0.93188011,
                    0.93006358, 0.9346049, 0.93188011]
-    assert_array_almost_equal(q1q2.results.timeseries[:, 1], q1_expected)
+    assert_allclose(q1q2.results.timeseries[:, 1], q1_expected, rtol=0, atol=1.5e-7)
 
     q2_expected = [0.94649446, 0.94926199, 0.95295203, 0.95110701, 0.94833948,
                    0.95479705, 0.94926199, 0.9501845, 0.94926199, 0.95387454,
@@ -423,4 +422,4 @@ def test_q1q2():
                    0.97140221, 0.97601476, 0.97693727, 0.98154982, 0.98431734,
                    0.97601476, 0.9797048, 0.98154982, 0.98062731, 0.98431734,
                    0.98616236, 0.9898524, 1.]
-    assert_array_almost_equal(q1q2.results.timeseries[:, 2], q2_expected)
+    assert_allclose(q1q2.results.timeseries[:, 2], q2_expected, rtol=0, atol=1.5e-7)

testsuite/MDAnalysisTests/analysis/test_encore.py

@@ -32,7 +32,7 @@
 import platform
 
 import pytest
-from numpy.testing import assert_equal, assert_almost_equal, assert_allclose
+from numpy.testing import assert_equal, assert_allclose
 
 from MDAnalysisTests.datafiles import DCD, DCD2, PSF, TPR, XTC
 from MDAnalysisTests import block_import
@@ -412,8 +412,8 @@ def test_ces_error_estimation(self, ens1):
 
         assert_allclose(average, expected_average, rtol=0, atol=1.5e-1,
                             err_msg="Unexpected average value for bootstrapped samples in Clustering Ensemble similarity")
-        assert_almost_equal(stdev, expected_stdev, decimal=0,
-                            err_msg="Unexpected standard daviation  for bootstrapped samples in Clustering Ensemble similarity")
+        assert_allclose(stdev, expected_stdev, rtol=0, atol=1.5,
+                            err_msg="Unexpected standard deviation  for bootstrapped samples in Clustering Ensemble similarity")
 
     def test_ces_error_estimation_ensemble_bootstrap(self, ens1):
         # Error estimation using a method that does not take a distance
@@ -822,7 +822,7 @@ def test_dimensionality_reduction_three_ensembles_two_identical(self,
             encore.reduce_dimensionality([ens1, ens2, ens1])
         coordinates_ens1 = coordinates[:,np.where(details["ensemble_membership"]==1)]
         coordinates_ens3 = coordinates[:,np.where(details["ensemble_membership"]==3)]
-        assert_almost_equal(coordinates_ens1, coordinates_ens3, decimal=0,
+        assert_allclose(coordinates_ens1, coordinates_ens3, rtol=0, atol=1.5,
                      err_msg="Unexpected result in dimensionality reduction: {0}".format(coordinates))