diff --git a/package/AUTHORS b/package/AUTHORS index 5b347d08539..43028566a9a 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -206,6 +206,7 @@ Chronological list of authors - Christian Pfaendner - Pratham Chauhan - Meet Brijwani + - Vishal Parmar External code diff --git a/package/CHANGELOG b/package/CHANGELOG index 9a2aea6e9b4..00a5a6b8b63 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -13,12 +13,13 @@ The rules for this file: * release numbers follow "Semantic Versioning" http://semver.org ------------------------------------------------------------------------------ - + ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, - ooprathamm, MeetB7, BFedder + ooprathamm, MeetB7, BFedder, v-parmar * 2.5.0 Fixes + * Fix tests should use results.rmsf to avoid DeprecationWarning (Issue #3695) * Fix EDRReader failing when parsing single-frame EDR files (Issue #3999) * Fix element parsing from PSF files tests read via Parmed (Issue #4015) * Fix test clobbering in lib/test_util.py (PR #4000) diff --git a/testsuite/MDAnalysisTests/analysis/test_encore.py b/testsuite/MDAnalysisTests/analysis/test_encore.py index 110f7252e37..afcd490e648 100644 --- a/testsuite/MDAnalysisTests/analysis/test_encore.py +++ b/testsuite/MDAnalysisTests/analysis/test_encore.py @@ -152,7 +152,7 @@ def test_rmsd_matrix_with_superimposition(self, ens1): err_msg = ( "Calculated RMSD values differ from " "the reference implementation") - for i, rmsd in enumerate(reference.rmsd): + for i, rmsd in enumerate(reference.results.rmsd): assert_almost_equal(conf_dist_matrix[0, i], rmsd[2], 3, err_msg) def test_rmsd_matrix_with_superimposition_custom_weights(self, ens1): @@ -211,8 +211,10 @@ def test_ensemble_superimposition(self): rmsfs2 = rms.RMSF(aligned_ensemble2.select_atoms('name *')) rmsfs2.run() - assert sum(rmsfs1.rmsf) > sum(rmsfs2.rmsf),"Ensemble aligned on all " \ - "atoms should have lower full-atom RMSF than ensemble aligned on only CAs." + assert sum(rmsfs1.results.rmsf) > sum(rmsfs2.results.rmsf), ( + "Ensemble aligned on all " + "atoms should have lower full-atom RMSF than ensemble aligned on only CAs." + ) def test_ensemble_superimposition_to_reference_non_weighted(self): aligned_ensemble1 = mda.Universe(PSF, DCD) @@ -230,8 +232,10 @@ def test_ensemble_superimposition_to_reference_non_weighted(self): rmsfs2 = rms.RMSF(aligned_ensemble2.select_atoms('name *')) rmsfs2.run() - assert sum(rmsfs1.rmsf) > sum(rmsfs2.rmsf), "Ensemble aligned on all " \ - "atoms should have lower full-atom RMSF than ensemble aligned on only CAs." + assert sum(rmsfs1.results.rmsf) > sum(rmsfs2.results.rmsf), ( + "Ensemble aligned on all " + "atoms should have lower full-atom RMSF than ensemble aligned on only CAs." + ) def test_covariance_matrix(self, ens1): reference_cov = np.array([