Skip to content

Commit

Permalink
Correct formatting using black
Browse files Browse the repository at this point in the history
  • Loading branch information
@MBartkowiakSTFC
MBartkowiakSTFC committed Mar 18, 2024
1 parent cf4a73b commit 43f6153
Show file tree
Hide file tree
Showing 10 changed files with 164 additions and 117 deletions.
2 changes: 1 addition & 1 deletion MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ class MDAFormat(IFormat):
def write(
cls,
filename: str,
data: dict[str, 'IOutputVariable'],
data: dict[str, "IOutputVariable"],
header: str = "",
extension: str = extensions[0],
) -> None:
Expand Down
37 changes: 21 additions & 16 deletions MDANSE/Tests/UnitTests/Analysis/test_dynamics.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ def test_vacf(trajectory, interp_order, normalise):
assert path.isfile(temp_name + ".mda")
os.remove(temp_name + ".mda")


################################################################
# Job parameters #
################################################################
Expand All @@ -60,25 +61,29 @@ def parameters():
# parameters['atom_transmutation'] = None
# parameters['frames'] = (0, 1000, 1)
parameters["trajectory"] = short_traj
parameters['running_mode'] = ('threadpool', 4)
parameters['q_vectors'] = ('SphericalLatticeQVectors',{
"seed": 0,
"shells": (0, 5.0, 0.5),
parameters["running_mode"] = ("threadpool", 4)
parameters["q_vectors"] = (
"SphericalLatticeQVectors",
{
"seed": 0,
"shells": (0, 5.0, 0.5),
"n_vectors": 100,
"width": 0.5,
})
parameters['q_values'] = (0.0, 10.0, 0.1)
parameters['r_values'] = (0.0, 10.0, 0.1)
parameters['per_axis'] = False
parameters['reference_direction'] = (0, 0, 1)
parameters['instrument_resolution'] = ('Gaussian', {'sigma' : 1.0, 'mu': 0.0})
parameters['interpolation_order'] = 3
parameters['projection'] = None
parameters['normalize'] = True
parameters['grouping_level'] = 'atom'
parameters['weights'] = 'equal'
},
)
parameters["q_values"] = (0.0, 10.0, 0.1)
parameters["r_values"] = (0.0, 10.0, 0.1)
parameters["per_axis"] = False
parameters["reference_direction"] = (0, 0, 1)
parameters["instrument_resolution"] = ("Gaussian", {"sigma": 1.0, "mu": 0.0})
parameters["interpolation_order"] = 3
parameters["projection"] = None
parameters["normalize"] = True
parameters["grouping_level"] = "atom"
parameters["weights"] = "equal"
return parameters


@pytest.mark.parametrize(
"job_type",
[
Expand All @@ -88,7 +93,7 @@ def parameters():
"MeanSquareDisplacement",
"VelocityAutoCorrelationFunction",
# "OrderParameter",
"PositionAutoCorrelationFunction"
"PositionAutoCorrelationFunction",
],
)
def test_dynamics_analysis(parameters, job_type):
Expand Down
37 changes: 21 additions & 16 deletions MDANSE/Tests/UnitTests/Analysis/test_infrared.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,35 +17,40 @@
"short_trajectory_after_changes.mdt",
)


################################################################
# Job parameters #
################################################################
@pytest.fixture(scope="function")
def parameters():
parameters = {}
parameters['atom_selection'] = '{"all": true}'
parameters["atom_selection"] = '{"all": true}'
# parameters['atom_transmutation'] = None
# parameters['frames'] = (0, 1000, 1)
parameters["trajectory"] = short_traj
parameters['running_mode'] = ('threadpool', 4)
parameters['q_vectors'] = ('SphericalLatticeQVectors',{
"seed": 0,
"shells": (0, 5.0, 0.5),
parameters["running_mode"] = ("threadpool", 4)
parameters["q_vectors"] = (
"SphericalLatticeQVectors",
{
"seed": 0,
"shells": (0, 5.0, 0.5),
"n_vectors": 100,
"width": 0.5,
})
parameters['q_values'] = (0.0, 10.0, 0.1)
parameters['r_values'] = (0.0, 10.0, 0.1)
parameters['per_axis'] = False
parameters['reference_direction'] = (0, 0, 1)
parameters['instrument_resolution'] = ('Gaussian', {'sigma' : 1.0, 'mu': 0.0})
parameters['interpolation_order'] = '3rd order'
parameters['projection'] = None
parameters['normalize'] = True
parameters['grouping_level'] = 'atom'
parameters['weights'] = 'equal'
},
)
parameters["q_values"] = (0.0, 10.0, 0.1)
parameters["r_values"] = (0.0, 10.0, 0.1)
parameters["per_axis"] = False
parameters["reference_direction"] = (0, 0, 1)
parameters["instrument_resolution"] = ("Gaussian", {"sigma": 1.0, "mu": 0.0})
parameters["interpolation_order"] = "3rd order"
parameters["projection"] = None
parameters["normalize"] = True
parameters["grouping_level"] = "atom"
parameters["weights"] = "equal"
return parameters


@pytest.mark.xfail(reason="see docstring")
def test_infrared_analysis(parameters):
"""It is a known problem, and will have to be fixed:
Expand Down
35 changes: 20 additions & 15 deletions MDANSE/Tests/UnitTests/Analysis/test_mcstas.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
"short_trajectory_after_changes.mdt",
)


################################################################
# Job parameters #
################################################################
Expand All @@ -27,25 +28,29 @@ def parameters():
# parameters['atom_transmutation'] = None
# parameters['frames'] = (0, 1000, 1)
parameters["trajectory"] = short_traj
parameters['running_mode'] = ('threadpool', 4)
parameters['q_vectors'] = ('SphericalLatticeQVectors',{
"seed": 0,
"shells": (0, 5.0, 0.5),
parameters["running_mode"] = ("threadpool", 4)
parameters["q_vectors"] = (
"SphericalLatticeQVectors",
{
"seed": 0,
"shells": (0, 5.0, 0.5),
"n_vectors": 100,
"width": 0.5,
})
parameters['q_values'] = (0.0, 10.0, 0.1)
parameters['r_values'] = (0.0, 10.0, 0.1)
parameters['per_axis'] = False
parameters['reference_direction'] = (0, 0, 1)
parameters['instrument_resolution'] = ('Gaussian', {'sigma' : 1.0, 'mu': 0.0})
parameters['interpolation_order'] = '3rd order'
parameters['projection'] = None
parameters['normalize'] = True
parameters['grouping_level'] = 'atom'
parameters['weights'] = 'equal'
},
)
parameters["q_values"] = (0.0, 10.0, 0.1)
parameters["r_values"] = (0.0, 10.0, 0.1)
parameters["per_axis"] = False
parameters["reference_direction"] = (0, 0, 1)
parameters["instrument_resolution"] = ("Gaussian", {"sigma": 1.0, "mu": 0.0})
parameters["interpolation_order"] = "3rd order"
parameters["projection"] = None
parameters["normalize"] = True
parameters["grouping_level"] = "atom"
parameters["weights"] = "equal"
return parameters


@pytest.mark.xfail(reason="see docstring")
def test_mcstas(parameters):
"""This test will be difficult to run:
Expand Down
66 changes: 38 additions & 28 deletions MDANSE/Tests/UnitTests/Analysis/test_scattering.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ def qvector_spherical_lattice(trajectory):
{"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
)


@pytest.fixture(scope="function")
def dcsf():
temp_name = tempfile.mktemp()
Expand All @@ -40,8 +41,10 @@ def dcsf():
parameters["frames"] = (0, 10, 1)
parameters["instrument_resolution"] = ("Ideal", {})
parameters["output_files"] = (temp_name, ("MDAFormat",))
parameters["q_vectors"] = ("SphericalLatticeQVectors",
{"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0})
parameters["q_vectors"] = (
"SphericalLatticeQVectors",
{"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
)
parameters["running_mode"] = ("monoprocessor",)
parameters["trajectory"] = short_traj
parameters["weights"] = "b_coherent"
Expand All @@ -50,6 +53,7 @@ def dcsf():
yield temp_name + ".mda"
os.remove(temp_name + ".mda")


@pytest.fixture(scope="function")
def disf():
temp_name = tempfile.mktemp()
Expand All @@ -59,8 +63,10 @@ def disf():
parameters["frames"] = (0, 10, 1)
parameters["instrument_resolution"] = ("Ideal", {})
parameters["output_files"] = (temp_name, ("MDAFormat",))
parameters["q_vectors"] = ("SphericalLatticeQVectors",
{"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0})
parameters["q_vectors"] = (
"SphericalLatticeQVectors",
{"seed": 0, "shells": (5.0, 36, 10.0), "n_vectors": 10, "width": 9.0},
)
parameters["running_mode"] = ("monoprocessor",)
parameters["trajectory"] = short_traj
parameters["weights"] = "b_incoherent2"
Expand All @@ -69,6 +75,7 @@ def disf():
yield temp_name + ".mda"
os.remove(temp_name + ".mda")


def test_dcsf(trajectory, qvector_spherical_lattice):
temp_name = tempfile.mktemp()
parameters = {}
Expand Down Expand Up @@ -143,41 +150,44 @@ def test_gdisf(trajectory):
assert path.isfile(temp_name + ".mda")
os.remove(temp_name + ".mda")


@pytest.mark.xfail(reason="see docstring")
def test_ndtsf(disf, dcsf, qvector_spherical_lattice):
"""A known problem that will have to be fixed."""
temp_name = tempfile.mktemp()
parameters = {}
parameters['atom_selection'] = None
parameters['atom_transmutation'] = None
parameters['frames'] = (0, 10, 1)
parameters['disf_input_file'] = disf
parameters['dcsf_input_file'] = dcsf
parameters["atom_selection"] = None
parameters["atom_transmutation"] = None
parameters["frames"] = (0, 10, 1)
parameters["disf_input_file"] = disf
parameters["dcsf_input_file"] = dcsf
parameters["q_vectors"] = qvector_spherical_lattice
parameters['running_mode'] = ('monoprocessor',)
parameters['trajectory'] = short_traj
parameters["running_mode"] = ("monoprocessor",)
parameters["trajectory"] = short_traj
parameters["output_files"] = (temp_name, ("MDAFormat",))
parameters['weights'] = 'b_incoherent2'
parameters["weights"] = "b_incoherent2"
ndtsf = IJob.create("NeutronDynamicTotalStructureFactor")
ndtsf.run(parameters,status=True)
assert path.exists(temp_name + '.mda')
assert path.isfile(temp_name + '.mda')
os.remove(temp_name + '.mda')
ndtsf.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")
os.remove(temp_name + ".mda")


@pytest.mark.xfail(reason="see docstring")
def test_ssfsf(disf):
"""Also fails at the moment. Must be fixed soon"""
temp_name = tempfile.mktemp()
parameters = {}
parameters['sample_inc'] = disf
parameters['running_mode'] = ('monoprocessor',)
parameters["sample_inc"] = disf
parameters["running_mode"] = ("monoprocessor",)
parameters["instrument_resolution"] = ("Ideal", {})
parameters["output_files"] = (temp_name, ("MDAFormat",))
ndtsf = IJob.create("StructureFactorFromScatteringFunction")
ndtsf.run(parameters,status=True)
assert path.exists(temp_name + '.mda')
assert path.isfile(temp_name + '.mda')
os.remove(temp_name + '.mda')
ndtsf.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")
os.remove(temp_name + ".mda")


@pytest.mark.xfail(reason="see docstring")
def test_ccf(qvector_spherical_lattice):
Expand All @@ -189,15 +199,15 @@ def test_ccf(qvector_spherical_lattice):
parameters["atom_transmutation"] = None
parameters["frames"] = (0, 10, 1)
parameters["instrument_resolution"] = ("Ideal", {})
parameters['interpolation_order'] = 3
parameters['interpolation_mode'] = 'automatic'
parameters["interpolation_order"] = 3
parameters["interpolation_mode"] = "automatic"
parameters["output_files"] = (temp_name, ("MDAFormat",))
parameters["q_vectors"] = qvector_spherical_lattice
parameters["running_mode"] = ("monoprocessor",)
parameters["trajectory"] = short_traj
parameters["weights"] = "b_coherent"
ndtsf = IJob.create("CurrentCorrelationFunction")
ndtsf.run(parameters,status=True)
assert path.exists(temp_name + '.mda')
assert path.isfile(temp_name + '.mda')
os.remove(temp_name + '.mda')
ndtsf.run(parameters, status=True)
assert path.exists(temp_name + ".mda")
assert path.isfile(temp_name + ".mda")
os.remove(temp_name + ".mda")
35 changes: 20 additions & 15 deletions MDANSE/Tests/UnitTests/Analysis/test_structure.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
"short_trajectory_after_changes.mdt",
)


################################################################
# Job parameters #
################################################################
Expand All @@ -27,25 +28,29 @@ def parameters():
# parameters['atom_transmutation'] = None
# parameters['frames'] = (0, 1000, 1)
parameters["trajectory"] = short_traj
parameters['running_mode'] = ('threadpool', 4)
parameters['q_vectors'] = ('SphericalLatticeQVectors',{
"seed": 0,
"shells": (0, 5.0, 0.5),
parameters["running_mode"] = ("threadpool", 4)
parameters["q_vectors"] = (
"SphericalLatticeQVectors",
{
"seed": 0,
"shells": (0, 5.0, 0.5),
"n_vectors": 100,
"width": 0.5,
})
parameters['q_values'] = (0.0, 10.0, 0.1)
parameters['r_values'] = (0.0, 10.0, 0.1)
parameters['per_axis'] = False
parameters['reference_direction'] = (0, 0, 1)
parameters['instrument_resolution'] = ('Gaussian', {'sigma' : 1.0, 'mu': 0.0})
parameters['interpolation_order'] = '3rd order'
parameters['projection'] = None
parameters['normalize'] = True
parameters['grouping_level'] = 'atom'
parameters['weights'] = 'equal'
},
)
parameters["q_values"] = (0.0, 10.0, 0.1)
parameters["r_values"] = (0.0, 10.0, 0.1)
parameters["per_axis"] = False
parameters["reference_direction"] = (0, 0, 1)
parameters["instrument_resolution"] = ("Gaussian", {"sigma": 1.0, "mu": 0.0})
parameters["interpolation_order"] = "3rd order"
parameters["projection"] = None
parameters["normalize"] = True
parameters["grouping_level"] = "atom"
parameters["weights"] = "equal"
return parameters


@pytest.mark.parametrize(
"job_type",
[
Expand Down
Loading

0 comments on commit 43f6153

Please sign in to comment.