From 6082f876db14a9ab1731c38d19bd2fdd3cfd06e4 Mon Sep 17 00:00:00 2001 From: Shubham Date: Fri, 12 Dec 2025 15:40:29 +0530 Subject: [PATCH 1/5] tests: modernize deprecated numpy assertions in test_gnm.py (ref #3743) --- .../MDAnalysisTests/analysis/test_gnm.py | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_gnm.py b/testsuite/MDAnalysisTests/analysis/test_gnm.py index 19d5a000937..9051ea228aa 100644 --- a/testsuite/MDAnalysisTests/analysis/test_gnm.py +++ b/testsuite/MDAnalysisTests/analysis/test_gnm.py @@ -27,7 +27,7 @@ import MDAnalysis.analysis.gnm import numpy as np import pytest -from numpy.testing import assert_almost_equal +from numpy.testing import assert_allclose from MDAnalysisTests.datafiles import GRO, XTC @@ -43,8 +43,8 @@ def test_gnm(universe, tmpdir, client_GNMAnalysis): gnm.run(**client_GNMAnalysis) result = gnm.results assert len(result.times) == 10 - assert_almost_equal(gnm.results.times, np.arange(0, 1000, 100), decimal=4) - assert_almost_equal( + assert_allclose(gnm.results.times, np.arange(0, 1000, 100), atol=1e-3,rtol=0) + assert_allclose( gnm.results.eigenvalues, [ 2.0287113e-15, @@ -57,7 +57,7 @@ def test_gnm(universe, tmpdir, client_GNMAnalysis): 4.0498182e-15, 4.2058769e-15, 3.9839431e-15, - ], + ],atol=1e-3,rtol=0 ) @@ -66,10 +66,10 @@ def test_gnm_run_step(universe, client_GNMAnalysis): gnm.run(step=3, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 4 - assert_almost_equal(gnm.results.times, np.arange(0, 1200, 300), decimal=4) - assert_almost_equal( + assert_allclose(gnm.results.times, np.arange(0, 1200, 300), atol=1e-3,rtol=0) + assert_allclose( gnm.results.eigenvalues, - [2.0287113e-15, 4.3810359e-15, 2.5501084e-15, 3.9839431e-15], + [2.0287113e-15, 4.3810359e-15, 2.5501084e-15, 3.9839431e-15],atol=1e-3,rtol=0 ) @@ -77,7 +77,7 @@ def test_generate_kirchoff(universe): gnm = mda.analysis.gnm.GNMAnalysis(universe) gen = gnm.generate_kirchoff() # fmt: off - assert_almost_equal( + assert_allclose( gen[0], [ 7,-1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, @@ -92,7 +92,7 @@ def test_generate_kirchoff(universe): 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 - ] + ],atol=1e-3,rtol=0 ) # fmt: on @@ -111,11 +111,11 @@ def test_closeContactGNMAnalysis(universe, client_GNMAnalysis): gnm.run(stop=2, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 2 - assert_almost_equal(gnm.results.times, (0, 100), decimal=4) - assert_almost_equal(gnm.results.eigenvalues, [0.1502614, 0.1426407]) + assert_allclose(gnm.results.times, (0, 100), atol=1e-3,rtol=0) + assert_allclose(gnm.results.eigenvalues, [0.1502614, 0.1426407],atol=1e-3,rtol=0) gen = gnm.generate_kirchoff() # fmt: off - assert_almost_equal( + assert_allclose( gen[0], [ 16.326744128018923, -2.716098853586913, -1.94736842105263, 0.0, @@ -138,7 +138,7 @@ def test_closeContactGNMAnalysis(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -2.263157894736841, -0.24333213169614382 - ] + ],atol=1e-3,rtol=0 ) # fmt: on @@ -148,11 +148,11 @@ def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis): gnm.run(stop=2, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 2 - assert_almost_equal(gnm.results.times, (0, 100), decimal=4) - assert_almost_equal(gnm.results.eigenvalues, [2.4328739, 2.2967251]) + assert_allclose(gnm.results.times, (0, 100), atol=1e-3,rtol=0) + assert_allclose(gnm.results.eigenvalues, [2.4328739, 2.2967251],atol=1e-3,rtol=0) gen = gnm.generate_kirchoff() # fmt: off - assert_almost_equal( + assert_allclose( gen[0], [ 303.0, -58.0, -37.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, @@ -172,7 +172,7 @@ def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -43.0, -3.0 - ] + ],atol=1e-3,rtol=0 ) # fmt: on @@ -185,18 +185,18 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): gnm.run(stop=2, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 2 - assert_almost_equal(gnm.results.times, (0, 100), decimal=4) + assert_allclose(gnm.results.times, (0, 100), atol=1e-3,rtol=0) # without Issue #4924 fix, eigenvalues are [3.20010632e-16, 4.27574601e-16] # but use big totolerance to make sure PASS in each platform - assert_almost_equal( + assert_allclose( gnm.results.eigenvalues, - [3.57984776e-16, 3.53892581e-16], + [3.57984776e-16, 3.53892581e-16],atol=1e-3,rtol=0 ) gen = gnm.generate_kirchoff() # without Issue #4924 fix, gnm only use 0~14 residues for this data assert np.abs(gen[15]).sum() > 0 # fmt: off - assert_almost_equal( + assert_allclose( gen[0], [ 1.0, -1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, @@ -216,6 +216,6 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, - ] + ],atol=1e-3,rtol=0 ) # fmt: on From 0ab0be428ed7aaa2e789df9efa9fb09b5be55b85 Mon Sep 17 00:00:00 2001 From: Shubham Date: Sat, 13 Dec 2025 16:11:32 +0530 Subject: [PATCH 2/5] added my name' --- package/AUTHORS | 1 + 1 file changed, 1 insertion(+) diff --git a/package/AUTHORS b/package/AUTHORS index e23f2afcf2c..6816564c6ec 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -265,6 +265,7 @@ Chronological list of authors - Raúl Lois-Cuns - Pranay Pelapkar - Shreejan Dolai + - Shubham Mittal External code ------------- From 30245d0ca709e94930e2a40cfc1494aa0cf911c0 Mon Sep 17 00:00:00 2001 From: Shubham Date: Sat, 13 Dec 2025 16:50:25 +0530 Subject: [PATCH 3/5] formatted the test_gnm file --- .../MDAnalysisTests/analysis/test_gnm.py | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_gnm.py b/testsuite/MDAnalysisTests/analysis/test_gnm.py index 9051ea228aa..fe1aaa90dfd 100644 --- a/testsuite/MDAnalysisTests/analysis/test_gnm.py +++ b/testsuite/MDAnalysisTests/analysis/test_gnm.py @@ -43,7 +43,7 @@ def test_gnm(universe, tmpdir, client_GNMAnalysis): gnm.run(**client_GNMAnalysis) result = gnm.results assert len(result.times) == 10 - assert_allclose(gnm.results.times, np.arange(0, 1000, 100), atol=1e-3,rtol=0) + assert_allclose(gnm.results.times, np.arange(0, 1000, 100), atol=1e-3, rtol=0) assert_allclose( gnm.results.eigenvalues, [ @@ -57,7 +57,7 @@ def test_gnm(universe, tmpdir, client_GNMAnalysis): 4.0498182e-15, 4.2058769e-15, 3.9839431e-15, - ],atol=1e-3,rtol=0 + ], atol=1e-3, rtol=0 ) @@ -66,10 +66,10 @@ def test_gnm_run_step(universe, client_GNMAnalysis): gnm.run(step=3, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 4 - assert_allclose(gnm.results.times, np.arange(0, 1200, 300), atol=1e-3,rtol=0) + assert_allclose(gnm.results.times, np.arange(0, 1200, 300), atol=1e-3, rtol=0) assert_allclose( gnm.results.eigenvalues, - [2.0287113e-15, 4.3810359e-15, 2.5501084e-15, 3.9839431e-15],atol=1e-3,rtol=0 + [2.0287113e-15, 4.3810359e-15, 2.5501084e-15, 3.9839431e-15], atol=1e-3, rtol=0 ) @@ -92,7 +92,7 @@ def test_generate_kirchoff(universe): 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 - ],atol=1e-3,rtol=0 + ], atol=1e-3, rtol=0 ) # fmt: on @@ -111,8 +111,8 @@ def test_closeContactGNMAnalysis(universe, client_GNMAnalysis): gnm.run(stop=2, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 2 - assert_allclose(gnm.results.times, (0, 100), atol=1e-3,rtol=0) - assert_allclose(gnm.results.eigenvalues, [0.1502614, 0.1426407],atol=1e-3,rtol=0) + assert_allclose(gnm.results.times, (0, 100), atol=1e-3, rtol=0) + assert_allclose(gnm.results.eigenvalues, [0.1502614, 0.1426407], atol=1e-3, rtol=0) gen = gnm.generate_kirchoff() # fmt: off assert_allclose( @@ -138,7 +138,7 @@ def test_closeContactGNMAnalysis(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -2.263157894736841, -0.24333213169614382 - ],atol=1e-3,rtol=0 + ], atol=1e-3, rtol=0 ) # fmt: on @@ -148,8 +148,8 @@ def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis): gnm.run(stop=2, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 2 - assert_allclose(gnm.results.times, (0, 100), atol=1e-3,rtol=0) - assert_allclose(gnm.results.eigenvalues, [2.4328739, 2.2967251],atol=1e-3,rtol=0) + assert_allclose(gnm.results.times, (0, 100), atol=1e-3, rtol=0) + assert_allclose(gnm.results.eigenvalues, [2.4328739, 2.2967251], atol=1e-3, rtol=0) gen = gnm.generate_kirchoff() # fmt: off assert_allclose( @@ -172,7 +172,7 @@ def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, -43.0, -3.0 - ],atol=1e-3,rtol=0 + ], atol=1e-3, rtol=0 ) # fmt: on @@ -185,12 +185,12 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): gnm.run(stop=2, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 2 - assert_allclose(gnm.results.times, (0, 100), atol=1e-3,rtol=0) + assert_allclose(gnm.results.times, (0, 100), atol=1e-3, rtol=0) # without Issue #4924 fix, eigenvalues are [3.20010632e-16, 4.27574601e-16] # but use big totolerance to make sure PASS in each platform assert_allclose( gnm.results.eigenvalues, - [3.57984776e-16, 3.53892581e-16],atol=1e-3,rtol=0 + [3.57984776e-16, 3.53892581e-16], atol=1e-3, rtol=0 ) gen = gnm.generate_kirchoff() # without Issue #4924 fix, gnm only use 0~14 residues for this data @@ -216,6 +216,6 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, - ],atol=1e-3,rtol=0 + ], atol=1e-3, rtol=0 ) # fmt: on From 85e5ff471c151ae2c4d94302163e5bd43ae1b222 Mon Sep 17 00:00:00 2001 From: Shubham Date: Sat, 13 Dec 2025 17:06:31 +0530 Subject: [PATCH 4/5] formatted --- testsuite/MDAnalysisTests/analysis/test_gnm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_gnm.py b/testsuite/MDAnalysisTests/analysis/test_gnm.py index fe1aaa90dfd..2ae630234f1 100644 --- a/testsuite/MDAnalysisTests/analysis/test_gnm.py +++ b/testsuite/MDAnalysisTests/analysis/test_gnm.py @@ -218,4 +218,4 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ], atol=1e-3, rtol=0 ) - # fmt: on + # fmt: on \ No newline at end of file From bf6388b372d630226c1d4c41e35777caf9826cd1 Mon Sep 17 00:00:00 2001 From: Shubham Date: Sat, 13 Dec 2025 17:55:40 +0530 Subject: [PATCH 5/5] black formatting --- .../MDAnalysisTests/analysis/test_gnm.py | 30 ++++++++++++++----- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/testsuite/MDAnalysisTests/analysis/test_gnm.py b/testsuite/MDAnalysisTests/analysis/test_gnm.py index 2ae630234f1..dcc625e5b49 100644 --- a/testsuite/MDAnalysisTests/analysis/test_gnm.py +++ b/testsuite/MDAnalysisTests/analysis/test_gnm.py @@ -43,7 +43,9 @@ def test_gnm(universe, tmpdir, client_GNMAnalysis): gnm.run(**client_GNMAnalysis) result = gnm.results assert len(result.times) == 10 - assert_allclose(gnm.results.times, np.arange(0, 1000, 100), atol=1e-3, rtol=0) + assert_allclose( + gnm.results.times, np.arange(0, 1000, 100), atol=1e-3, rtol=0 + ) assert_allclose( gnm.results.eigenvalues, [ @@ -57,7 +59,9 @@ def test_gnm(universe, tmpdir, client_GNMAnalysis): 4.0498182e-15, 4.2058769e-15, 3.9839431e-15, - ], atol=1e-3, rtol=0 + ], + atol=1e-3, + rtol=0, ) @@ -66,10 +70,14 @@ def test_gnm_run_step(universe, client_GNMAnalysis): gnm.run(step=3, **client_GNMAnalysis) result = gnm.results assert len(result.times) == 4 - assert_allclose(gnm.results.times, np.arange(0, 1200, 300), atol=1e-3, rtol=0) + assert_allclose( + gnm.results.times, np.arange(0, 1200, 300), atol=1e-3, rtol=0 + ) assert_allclose( gnm.results.eigenvalues, - [2.0287113e-15, 4.3810359e-15, 2.5501084e-15, 3.9839431e-15], atol=1e-3, rtol=0 + [2.0287113e-15, 4.3810359e-15, 2.5501084e-15, 3.9839431e-15], + atol=1e-3, + rtol=0, ) @@ -112,7 +120,9 @@ def test_closeContactGNMAnalysis(universe, client_GNMAnalysis): result = gnm.results assert len(result.times) == 2 assert_allclose(gnm.results.times, (0, 100), atol=1e-3, rtol=0) - assert_allclose(gnm.results.eigenvalues, [0.1502614, 0.1426407], atol=1e-3, rtol=0) + assert_allclose( + gnm.results.eigenvalues, [0.1502614, 0.1426407], atol=1e-3, rtol=0 + ) gen = gnm.generate_kirchoff() # fmt: off assert_allclose( @@ -149,7 +159,9 @@ def test_closeContactGNMAnalysis_weights_None(universe, client_GNMAnalysis): result = gnm.results assert len(result.times) == 2 assert_allclose(gnm.results.times, (0, 100), atol=1e-3, rtol=0) - assert_allclose(gnm.results.eigenvalues, [2.4328739, 2.2967251], atol=1e-3, rtol=0) + assert_allclose( + gnm.results.eigenvalues, [2.4328739, 2.2967251], atol=1e-3, rtol=0 + ) gen = gnm.generate_kirchoff() # fmt: off assert_allclose( @@ -190,7 +202,9 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): # but use big totolerance to make sure PASS in each platform assert_allclose( gnm.results.eigenvalues, - [3.57984776e-16, 3.53892581e-16], atol=1e-3, rtol=0 + [3.57984776e-16, 3.53892581e-16], + atol=1e-3, + rtol=0, ) gen = gnm.generate_kirchoff() # without Issue #4924 fix, gnm only use 0~14 residues for this data @@ -218,4 +232,4 @@ def test_closeContactGNMAnalysis_select_CA(universe, client_GNMAnalysis): 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, ], atol=1e-3, rtol=0 ) - # fmt: on \ No newline at end of file + # fmt: on