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TST: test_streamplot_2D faster #4221

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merged 2 commits into from
Aug 10, 2023
Merged

TST: test_streamplot_2D faster #4221

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373e861
TST: test_streamplot_2D faster
tylerjereddy Aug 1, 2023
4a6fbdf
TST: PR 4221 revisions
tylerjereddy Aug 3, 2023
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22 changes: 5 additions & 17 deletions testsuite/MDAnalysisTests/visualization/test_streamlines.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ def membrane_xtc(tmpdir_factory, univ):
z_delta += 0.02
return str(tmp_xtc)

def test_streamplot_2D(membrane_xtc, univ, tmpdir):
def test_streamplot_2D(membrane_xtc, univ):
# simple roundtrip test to ensure that
# a plot is generated by the 2D streamplot
# code
Expand All @@ -67,22 +67,10 @@ def test_streamplot_2D(membrane_xtc, univ, tmpdir):
ymax=univ.atoms.positions[...,1].max(),
maximum_delta_magnitude=2.0,
num_cores=1)
x = np.linspace(univ.atoms.positions[...,0].min(),
univ.atoms.positions[...,0].max(),
5)
y = np.linspace(univ.atoms.positions[...,1].min(),
univ.atoms.positions[...,1].max(),
5)
speed = np.sqrt(u1*u1 + v1*v1)
fig = plt.figure()
ax = fig.add_subplot(111, aspect='equal')
ax.streamplot(x, y, u1, v1, density=(10,10), color=speed, linewidth=3*speed/speed.max(),
cmap=plt.cm.viridis)
plot_outpath = os.path.join(str(tmpdir), 'testing_streamline.png')
fig.savefig(plot_outpath, dpi=300)

with open(plot_outpath, 'rb'):
pass
assert u1.shape == (5, 5)
assert v1.shape == (5, 5)
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maybe spot checking values here might make sense--to be fair, we weren't doing that before either though

assert_allclose(avg, 0.965194167)
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Are these single value checks? If so could we use pytest.approx instead (it is much faster last I checked)?

assert_allclose(std, 4.444808820e-06)


def test_streamplot_2D_zero_return(membrane_xtc, univ, tmpdir):
Expand Down