Pytest Style: test_modelling.py#1468
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orbeckst
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orbeckst
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lgtm ... but perhaps @jbarnoud or @kain88-de should have a quick look, too.
| @@ -266,9 +264,9 @@ def test_merge_with_topology_from_different_universes(self): | |||
| assert_(not hasattr(u3.atoms, 'dihedrals') or len(u3.atoms.bonds) == 0) | |||
| assert_(not hasattr(u3.atoms, 'impropers') or len(u3.atoms.bonds) == 0) | |||
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these asserts should be replaced
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all of them in the whole file.
| a = AtomGroup([], u) | ||
| b = AtomGroup([], u) | ||
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| assert_raises(ValueError, Merge, a, b) |
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please use with pytest.raises
| @@ -215,30 +213,30 @@ def test_empty_ValueError(self): | |||
| def test_nonsense_TypeError(self): | |||
| assert_raises(TypeError, Merge, ['1', 2]) | |||
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| def test_merge_same_universe(self): | ||
| u1, _, _ = self.universes | ||
| def test_merge_same_universe(self, universes): |
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only use u1 as a fixture here
| return [u1, u2, u3] | ||
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| def test_merge(self, universes, tmpdir): | ||
| u1, u2, u3 = universes |
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please use the fixtures explicit instead of the universes collection
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| @staticmethod | ||
| @pytest.fixture() | ||
| def u1(): |
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Since we're at it, could you rename u1, u2, and u3 to u_protein, u_ligand, and u_water, respectively. The current names are not informative, and there is no way anybody will remember which of u2 and u3 has the ligand.
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| def test_residue_references(self): | ||
| u1, u2, u3 = self.universes | ||
| def test_residue_references(self, universes): |
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This test does not use u3. Pass u1 and u2 explicitly.
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| def test_segment_references(self): | ||
| u1, u2, u3 = self.universes | ||
| def test_segment_references(self, universes): |
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Same as above. Pass u1 and u2 only.
| del self.u2 | ||
| @staticmethod | ||
| @pytest.fixture() | ||
| def u2(): |
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This is the same as TestCaping.u2. You can move TestCaping.u1, TestCaping.u2, and TestCaping.u3 in the module scope instead of the scope of the scope of the TestCaping class. Then you can use the same fixture thoughout the file and we know they correspind to the same things. Do not forget the renaming I asked above, though.
| def test_merge_with_topology_from_different_universes(self): | ||
| u3 = MDAnalysis.Merge(self.u.atoms[:110], self.u2.atoms) | ||
| def test_merge_with_topology_from_different_universes(self, u, u2): | ||
| u3 = MDAnalysis.Merge(u.atoms[:110], u2.atoms) |
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If u1 and u2 are moved and renamed, this cannot remain u3. Maybe u_merge?
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I think I haven't understood what you said here. Can you confirm the change I've done is the one you wanted.
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This variable was named u3 because the function was already using self.u and self.u2. Beside the fact that u3 is a terrible name for a variable in general, there is no u2 any more as one could expect from the name u3.
This variable cannot keep be called u3. I suggest renaming it u_merge. u2 in the test above and the test bellow could be renamed u_merge as well. This name makes it clear that they point to the universe produced by the merge.
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| @staticmethod | ||
| @pytest.fixture() | ||
| def universes(u1, u2, u3): |
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As @kain88-de suggests, you should use the individual fixtures explicitly. You can remove this one.
| from MDAnalysisTests import parser_not_found, tempdir | ||
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| from numpy.testing import (TestCase, dec, assert_equal, assert_raises, assert_, | ||
| from numpy.testing import (assert_equal, assert_raises, assert_, |
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Did you remove all assert_raises and assert_ from this file. Then they shouldn't be imported anymore
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There is still #1468 (comment) to address, then it should be good to go. |
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@jbarnoud Is it okay now? |
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