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Use a fixture for npz files in test_bat #2981

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merged 3 commits into from
Oct 14, 2020
Merged

Use a fixture for npz files in test_bat #2981

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a0cb72e
Use a ficture for npz files in test_bat
jbarnoud Oct 12, 2020
2f5345c
Remove unused import
jbarnoud Oct 12, 2020
cecfe06
Update Changelog
jbarnoud Oct 12, 2020
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2 changes: 2 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,8 @@ Fixes
Universe (PR #2893)
* ensure that unistd.h is included on macOS when compiling ENCORE's spe.c
(Issue #2934)
* Fix tests for analysis.bat that could fail when run in parallel and that
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I guess technically it should be newest first, but I've seen plenty of cases where we've not followed this so it's a bit late to be pedantic now 🤷‍♂️

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Oops... I have been doing it wrong for a while 😅

would create a test artifact (Issue #2979, PR #2981)

Enhancements
* Refactored analysis.helanal into analysis.helix_analysis
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19 changes: 12 additions & 7 deletions testsuite/MDAnalysisTests/analysis/test_bat.py
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Expand Up @@ -45,6 +45,14 @@ def bat(self, selected_residues):
R.run()
return R.bat

@pytest.fixture
def bat_npz(self, tmpdir, selected_residues):
filename = str(tmpdir / 'test_bat_IO.npy')
R = BAT(selected_residues)
R.run()
R.save(filename)
return filename

def test_bat_root_selection(self, selected_residues):
R = BAT(selected_residues)
assert_equal(R._root.indices, [8, 2, 1],
Expand Down Expand Up @@ -79,11 +87,8 @@ def test_bat_reconstruction(self, selected_residues, bat):
err_msg="error: Reconstructed Cartesian coordinates " + \
"don't match original")

def test_bat_IO(self, selected_residues, bat):
R = BAT(selected_residues)
R.run()
R.save('test_bat_IO.npy')
R2 = BAT(selected_residues, filename='test_bat_IO.npy')
def test_bat_IO(self, bat_npz, selected_residues, bat):
R2 = BAT(selected_residues, filename=bat_npz)
test_bat = R2.bat
assert_almost_equal(
bat,
Expand All @@ -107,8 +112,8 @@ def test_bat_disconnected_atom_group(self):
with pytest.raises(ValueError):
R = BAT(selected_residues)

def test_bat_incorrect_dims(self):
def test_bat_incorrect_dims(self, bat_npz):
u = mda.Universe(PSF, DCD)
selected_residues = u.select_atoms("resid 1-3")
with pytest.raises(ValueError):
R = BAT(selected_residues, filename='test_bat_IO.npy')
R = BAT(selected_residues, filename=bat_npz)