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Update test_density.py
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Added  client_DensityAnalysis to tests
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@talagayev
talagayev authored Oct 8, 2024
1 parent 3731096 commit 129cf62
Showing 1 changed file with 109 additions and 51 deletions.
160 changes: 109 additions & 51 deletions testsuite/MDAnalysisTests/analysis/test_density.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,12 +230,20 @@ def universe(self):


class TestDensityAnalysis(DensityParameters):
def check_DensityAnalysis(self, ag, ref_meandensity,
tmpdir, runargs=None, **kwargs):
def check_DensityAnalysis(
self,
ag,
ref_meandensity,
tmpdir,
client_DensityAnalysis,
runargs=None,
**kwargs
):
runargs = runargs if runargs else {}
with tmpdir.as_cwd():
D = density.DensityAnalysis(
ag, delta=self.delta, **kwargs).run(**runargs)
D = density.DensityAnalysis(ag, delta=self.delta, **kwargs).run(
**runargs, **client_DensityAnalysis
)
assert_almost_equal(D.results.density.grid.mean(), ref_meandensity,
err_msg="mean density does not match")
D.results.density.export(self.outfile)
Expand All @@ -247,125 +255,174 @@ def check_DensityAnalysis(self, ag, ref_meandensity,
)

@pytest.mark.parametrize("mode", ("static", "dynamic"))
def test_run(self, mode, universe, tmpdir):
def test_run(self, mode, universe, tmpdir, client_DensityAnalysis):
updating = (mode == "dynamic")
self.check_DensityAnalysis(
universe.select_atoms(self.selections[mode], updating=updating),
self.references[mode]['meandensity'],
tmpdir=tmpdir
tmpdir=tmpdir,
client_DensityAnalysis=client_DensityAnalysis,
)

def test_sliced(self, universe, tmpdir):
def test_sliced(self, universe, tmpdir, client_DensityAnalysis):
self.check_DensityAnalysis(
universe.select_atoms(self.selections['static']),
self.references['static_sliced']['meandensity'],
tmpdir=tmpdir,
client_DensityAnalysis=client_DensityAnalysis,
runargs=dict(start=1, stop=-1, step=2),
)

def test_userdefn_eqbox(self, universe, tmpdir):
def test_userdefn_eqbox(self, universe, tmpdir, client_DensityAnalysis):
with warnings.catch_warnings():
# Do not need to see UserWarning that box is too small
warnings.simplefilter("ignore")
self.check_DensityAnalysis(
universe.select_atoms(self.selections['static']),
self.references['static_defined']['meandensity'],
tmpdir=tmpdir,
client_DensityAnalysis=client_DensityAnalysis,
gridcenter=self.gridcenters['static_defined'],
xdim=10.0,
ydim=10.0,
zdim=10.0,
)

def test_userdefn_neqbox(self, universe, tmpdir):
def test_userdefn_neqbox(self, universe, tmpdir, client_DensityAnalysis):
self.check_DensityAnalysis(
universe.select_atoms(self.selections['static']),
self.references['static_defined_unequal']['meandensity'],
tmpdir=tmpdir,
client_DensityAnalysis=client_DensityAnalysis,
gridcenter=self.gridcenters['static_defined'],
xdim=10.0,
ydim=15.0,
zdim=20.0,
)

def test_userdefn_boxshape(self, universe):
def test_userdefn_boxshape(self, universe, client_DensityAnalysis):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=1.0, xdim=8.0, ydim=12.0, zdim=17.0,
gridcenter=self.gridcenters['static_defined']).run()
universe.select_atoms(self.selections["static"]),
delta=1.0,
xdim=8.0,
ydim=12.0,
zdim=17.0,
gridcenter=self.gridcenters["static_defined"],
).run(**client_DensityAnalysis)
assert D.results.density.grid.shape == (8, 12, 17)

def test_warn_userdefn_padding(self, universe):
def test_warn_userdefn_padding(self, universe, client_DensityAnalysis):
regex = (r"Box padding \(currently set at 1\.0\) is not used "
r"in user defined grids\.")
with pytest.warns(UserWarning, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim=100.0, ydim=100.0, zdim=100.0, padding=1.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)

def test_warn_userdefn_smallgrid(self, universe):
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim=100.0,
ydim=100.0,
zdim=100.0,
padding=1.0,
gridcenter=self.gridcenters["static_defined"],
).run(step=5, **client_DensityAnalysis)

def test_warn_userdefn_smallgrid(self, universe, client_DensityAnalysis):
regex = ("Atom selection does not fit grid --- "
"you may want to define a larger box")
with pytest.warns(UserWarning, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim=1.0, ydim=2.0, zdim=2.0, padding=0.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)

def test_ValueError_userdefn_gridcenter_shape(self, universe):
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim=1.0,
ydim=2.0,
zdim=2.0,
padding=0.0,
gridcenter=self.gridcenters["static_defined"],
).run(step=5, **client_DensityAnalysis)

def test_ValueError_userdefn_gridcenter_shape(
self, universe, client_DensityAnalysis
):
# Test len(gridcenter) != 3
with pytest.raises(ValueError, match="Gridcenter must be a 3D coordinate"):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim=10.0, ydim=10.0, zdim=10.0,
gridcenter=self.gridcenters['error1']).run(step=5)
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters["error1"],
).run(step=5, **client_DensityAnalysis)

def test_ValueError_userdefn_gridcenter_type(self, universe):
def test_ValueError_userdefn_gridcenter_type(
self, universe, client_DensityAnalysis
):
# Test gridcenter includes non-numeric strings
with pytest.raises(ValueError, match="Gridcenter must be a 3D coordinate"):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim=10.0, ydim=10.0, zdim=10.0,
gridcenter=self.gridcenters['error2']).run(step=5)
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters["error2"],
).run(step=5, **client_DensityAnalysis)

def test_ValueError_userdefn_gridcenter_missing(self, universe):
def test_ValueError_userdefn_gridcenter_missing(
self, universe, client_DensityAnalysis
):
# Test no gridcenter provided when grid dimensions are given
regex = ("Gridcenter or grid dimensions are not provided")
with pytest.raises(ValueError, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim=10.0, ydim=10.0, zdim=10.0).run(step=5)
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim=10.0,
ydim=10.0,
zdim=10.0,
).run(step=5, **client_DensityAnalysis)

def test_ValueError_userdefn_xdim_type(self, universe):
def test_ValueError_userdefn_xdim_type(self, universe, client_DensityAnalysis):
# Test xdim != int or float
with pytest.raises(ValueError, match="xdim, ydim, and zdim must be numbers"):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim="MDAnalysis", ydim=10.0, zdim=10.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim="MDAnalysis",
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters["static_defined"],
).run(step=5, **client_DensityAnalysis)

def test_ValueError_userdefn_xdim_nanvalue(self, universe):
def test_ValueError_userdefn_xdim_nanvalue(self, universe, client_DensityAnalysis):
# Test xdim set to NaN value
regex = ("Gridcenter or grid dimensions have NaN element")
with pytest.raises(ValueError, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']),
delta=self.delta, xdim=np.nan, ydim=10.0, zdim=10.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)
universe.select_atoms(self.selections["static"]),
delta=self.delta,
xdim=np.nan,
ydim=10.0,
zdim=10.0,
gridcenter=self.gridcenters["static_defined"],
).run(step=5, **client_DensityAnalysis)

def test_warn_noatomgroup(self, universe):
def test_warn_noatomgroup(self, universe, client_DensityAnalysis):
regex = ("No atoms in AtomGroup at input time frame. "
"This may be intended; please ensure that "
"your grid selection covers the atomic "
"positions you wish to capture.")
with pytest.warns(UserWarning, match=regex):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['none']),
delta=self.delta, xdim=1.0, ydim=2.0, zdim=2.0, padding=0.0,
gridcenter=self.gridcenters['static_defined']).run(step=5)

def test_ValueError_noatomgroup(self, universe):
universe.select_atoms(self.selections["none"]),
delta=self.delta,
xdim=1.0,
ydim=2.0,
zdim=2.0,
padding=0.0,
gridcenter=self.gridcenters["static_defined"],
).run(step=5, **client_DensityAnalysis)

def test_ValueError_noatomgroup(self, universe, client_DensityAnalysis):
with pytest.raises(ValueError, match="No atoms in AtomGroup at input"
" time frame. Grid for density"
" could not be automatically"
Expand All @@ -374,12 +431,13 @@ def test_ValueError_noatomgroup(self, universe):
" defined grid will "
"need to be provided instead."):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['none'])).run(step=5)
universe.select_atoms(self.selections["none"])
).run(step=5, **client_DensityAnalysis)

def test_warn_results_deprecated(self, universe):
def test_warn_results_deprecated(self, universe, client_DensityAnalysis):
D = density.DensityAnalysis(
universe.select_atoms(self.selections['static']))
D.run(stop=1)
D.run(stop=1, **client_DensityAnalysis)
wmsg = "The `density` attribute was deprecated in MDAnalysis 2.0.0"
with pytest.warns(DeprecationWarning, match=wmsg):
assert_equal(D.density.grid, D.results.density.grid)
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