From 5ab9a394358cf9342feee9ecbd94b22abd96eeaa Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Thu, 22 Apr 2021 21:34:45 -0700 Subject: [PATCH 1/4] rm ParmEd ts --- package/MDAnalysis/coordinates/ParmEd.py | 5 +++-- .../MDAnalysisTests/coordinates/test_parmed.py | 15 +++++++++++++++ 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/package/MDAnalysis/coordinates/ParmEd.py b/package/MDAnalysis/coordinates/ParmEd.py index 8b28bb47ca3..a02041fea8c 100644 --- a/package/MDAnalysis/coordinates/ParmEd.py +++ b/package/MDAnalysis/coordinates/ParmEd.py @@ -173,9 +173,10 @@ def convert(self, obj): ag_or_ts = obj.atoms except AttributeError: if isinstance(obj, base.Timestep): - ag_or_ts = obj.copy() + raise ValueError("Writing Timesteps to ParmEd " + "objects is not supported") else: - raise_from(TypeError("No Timestep found in obj argument"), None) + raise TypeError("No atoms found in obj argument") from None # Check for topology information missing_topology = [] diff --git a/testsuite/MDAnalysisTests/coordinates/test_parmed.py b/testsuite/MDAnalysisTests/coordinates/test_parmed.py index 907c35135ed..4c73f94518b 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_parmed.py +++ b/testsuite/MDAnalysisTests/coordinates/test_parmed.py @@ -29,6 +29,7 @@ from MDAnalysisTests.coordinates.base import _SingleFrameReader from MDAnalysisTests.coordinates.reference import RefAdKSmall +from MDAnalysis.coordinates.ParmEd import ParmEdConverter from MDAnalysisTests.datafiles import ( GRO, @@ -286,3 +287,17 @@ class TestParmEdConverterPDB(BaseTestParmEdConverter): def test_equivalent_coordinates(self, ref, output): assert_almost_equal(ref.coordinates, output.coordinates, decimal=3) + +def test_pass_ts_error(): + u = mda.Universe(PDB_small) + err = "Writing Timesteps to ParmEd objects is not supported" + with pytest.raises(ValueError, match=err): + c = ParmEdConverter() + c.convert(u.trajectory.ts) + + +def test_incorrect_object_passed_typeerror(): + err = "No atoms found in obj argument" + with pytest.raises(TypeError, match=err): + c = ParmEdConverter() + c.convert("we still don't support emojis :(") From 8b715ee8098e2091444be17cf898b342e799a9d9 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 23 Apr 2021 15:05:26 -0700 Subject: [PATCH 2/4] emoji in py3? --- testsuite/MDAnalysisTests/coordinates/test_parmed.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_parmed.py b/testsuite/MDAnalysisTests/coordinates/test_parmed.py index 4c73f94518b..21b284787f9 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_parmed.py +++ b/testsuite/MDAnalysisTests/coordinates/test_parmed.py @@ -300,4 +300,4 @@ def test_incorrect_object_passed_typeerror(): err = "No atoms found in obj argument" with pytest.raises(TypeError, match=err): c = ParmEdConverter() - c.convert("we still don't support emojis :(") + c.convert("🐍") From 6fa0afc8149fedfe253cb84bcab45e1b5a5dfe7d Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 23 Apr 2021 15:06:27 -0700 Subject: [PATCH 3/4] rm timestep check --- package/MDAnalysis/coordinates/ParmEd.py | 6 +----- testsuite/MDAnalysisTests/coordinates/test_parmed.py | 9 --------- 2 files changed, 1 insertion(+), 14 deletions(-) diff --git a/package/MDAnalysis/coordinates/ParmEd.py b/package/MDAnalysis/coordinates/ParmEd.py index a02041fea8c..a714d5a0fcb 100644 --- a/package/MDAnalysis/coordinates/ParmEd.py +++ b/package/MDAnalysis/coordinates/ParmEd.py @@ -172,11 +172,7 @@ def convert(self, obj): # make sure to use atoms (Issue 46) ag_or_ts = obj.atoms except AttributeError: - if isinstance(obj, base.Timestep): - raise ValueError("Writing Timesteps to ParmEd " - "objects is not supported") - else: - raise TypeError("No atoms found in obj argument") from None + raise TypeError("No atoms found in obj argument") from None # Check for topology information missing_topology = [] diff --git a/testsuite/MDAnalysisTests/coordinates/test_parmed.py b/testsuite/MDAnalysisTests/coordinates/test_parmed.py index 21b284787f9..31821e602c7 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_parmed.py +++ b/testsuite/MDAnalysisTests/coordinates/test_parmed.py @@ -287,15 +287,6 @@ class TestParmEdConverterPDB(BaseTestParmEdConverter): def test_equivalent_coordinates(self, ref, output): assert_almost_equal(ref.coordinates, output.coordinates, decimal=3) - -def test_pass_ts_error(): - u = mda.Universe(PDB_small) - err = "Writing Timesteps to ParmEd objects is not supported" - with pytest.raises(ValueError, match=err): - c = ParmEdConverter() - c.convert(u.trajectory.ts) - - def test_incorrect_object_passed_typeerror(): err = "No atoms found in obj argument" with pytest.raises(TypeError, match=err): From a3d28d0d25169bcd36f1cf4042a9e60f53f83142 Mon Sep 17 00:00:00 2001 From: Lily Wang Date: Fri, 23 Apr 2021 15:45:48 -0700 Subject: [PATCH 4/4] Revert "emoji in py3?" This reverts commit 8b715ee8098e2091444be17cf898b342e799a9d9. --- testsuite/MDAnalysisTests/coordinates/test_parmed.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/testsuite/MDAnalysisTests/coordinates/test_parmed.py b/testsuite/MDAnalysisTests/coordinates/test_parmed.py index 31821e602c7..99c93ea4bb7 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_parmed.py +++ b/testsuite/MDAnalysisTests/coordinates/test_parmed.py @@ -291,4 +291,4 @@ def test_incorrect_object_passed_typeerror(): err = "No atoms found in obj argument" with pytest.raises(TypeError, match=err): c = ParmEdConverter() - c.convert("🐍") + c.convert("we still don't support emojis :(")