Modernize test_base.py by replacing assert_almost_equal with assert_allclose per #3743

Author: Abdulrahman-PROG

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -27,7 +27,7 @@
 import numpy as np
 import pytest
 from MDAnalysis.analysis import backends, base
-from numpy.testing import assert_allclose, assert_almost_equal, assert_equal
+from numpy.testing import assert_allclose, assert_equal
 
 from MDAnalysisTests.datafiles import DCD, PSF, TPR, XTC
 from MDAnalysisTests.util import no_deprecated_call
@@ -279,7 +279,7 @@ def test_start_stop_step_parallel(u, run_kwargs, frames, client_FrameAnalysis):
     assert an.n_frames == len(frames)
     assert_equal(an.found_frames, frames)
     assert_equal(an.frames, frames, err_msg=FRAMES_ERR)
-    assert_almost_equal(an.times, frames + 1, decimal=4, err_msg=TIMES_ERR)
+    assert_allclose(an.times, frames + 1, rtol=0, atol=1e-4, err_msg=TIMES_ERR)
 
 
 def test_reset_n_parts_to_n_frames(u):
@@ -613,8 +613,8 @@ def test_AnalysisFromFunction_args_content(u, client_AnalysisFromFunction):
     ans = base.AnalysisFromFunction(mass_xyz, protein, another, masses)
     assert len(ans.args) == 3
     result = np.sum(ans.run(**client_AnalysisFromFunction).results.timeseries)
-    assert_allclose(result, -317054.67757345125, rtol=0, atol=1.5e-6)
-    assert_almost_equal(result, -317054.67757345125, decimal=6)
+    assert_allclose(result, -317054.67757345125, rtol=0, atol=1e-6)
+    assert_allclose(result, -317054.67757345125, rtol=0, atol=1e-6)
     assert (ans.args[0] is protein) and (ans.args[1] is another)
     assert ans._trajectory is protein.universe.trajectory
 
@@ -652,4 +652,4 @@ def distance(a, b):
     Distances = base.analysis_class(distance)
 
     with no_deprecated_call():
-        d = Distances(u.atoms[:10], u.atoms[10:20]).run()
+        d = Distances(u.atoms[:10], u.atoms[10:20]).run()