From 43f61536f16c953686057e1a4b38053efafcd696 Mon Sep 17 00:00:00 2001 From: Maciej Bartkowiak Date: Mon, 18 Mar 2024 10:57:47 +0000 Subject: [PATCH] Correct formatting using black --- .../Src/MDANSE/Framework/Formats/MDAFormat.py | 2 +- .../Tests/UnitTests/Analysis/test_dynamics.py | 37 ++++++----- .../Tests/UnitTests/Analysis/test_infrared.py | 37 ++++++----- .../Tests/UnitTests/Analysis/test_mcstas.py | 35 +++++----- .../UnitTests/Analysis/test_scattering.py | 66 +++++++++++-------- .../UnitTests/Analysis/test_structure.py | 35 +++++----- .../UnitTests/Analysis/test_trajectory.py | 45 +++++++------ .../AtomSelector/test_atom_selectors.py | 2 +- .../Tests/UnitTests/test_chemical_entity.py | 21 +++++- MDANSE/Tests/UnitTests/test_documentation.py | 1 - 10 files changed, 164 insertions(+), 117 deletions(-) diff --git a/MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py b/MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py index 3e854cb610..6fb7a418b0 100644 --- a/MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py +++ b/MDANSE/Src/MDANSE/Framework/Formats/MDAFormat.py @@ -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: diff --git a/MDANSE/Tests/UnitTests/Analysis/test_dynamics.py b/MDANSE/Tests/UnitTests/Analysis/test_dynamics.py index 839721a839..a6b12586df 100644 --- a/MDANSE/Tests/UnitTests/Analysis/test_dynamics.py +++ b/MDANSE/Tests/UnitTests/Analysis/test_dynamics.py @@ -50,6 +50,7 @@ def test_vacf(trajectory, interp_order, normalise): assert path.isfile(temp_name + ".mda") os.remove(temp_name + ".mda") + ################################################################ # Job parameters # ################################################################ @@ -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", [ @@ -88,7 +93,7 @@ def parameters(): "MeanSquareDisplacement", "VelocityAutoCorrelationFunction", # "OrderParameter", - "PositionAutoCorrelationFunction" + "PositionAutoCorrelationFunction", ], ) def test_dynamics_analysis(parameters, job_type): diff --git a/MDANSE/Tests/UnitTests/Analysis/test_infrared.py b/MDANSE/Tests/UnitTests/Analysis/test_infrared.py index 663a17e89c..1508c2adce 100644 --- a/MDANSE/Tests/UnitTests/Analysis/test_infrared.py +++ b/MDANSE/Tests/UnitTests/Analysis/test_infrared.py @@ -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: diff --git a/MDANSE/Tests/UnitTests/Analysis/test_mcstas.py b/MDANSE/Tests/UnitTests/Analysis/test_mcstas.py index abf953f712..412ecaa270 100644 --- a/MDANSE/Tests/UnitTests/Analysis/test_mcstas.py +++ b/MDANSE/Tests/UnitTests/Analysis/test_mcstas.py @@ -17,6 +17,7 @@ "short_trajectory_after_changes.mdt", ) + ################################################################ # Job parameters # ################################################################ @@ -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: diff --git a/MDANSE/Tests/UnitTests/Analysis/test_scattering.py b/MDANSE/Tests/UnitTests/Analysis/test_scattering.py index e6555fdbf4..4881951037 100644 --- a/MDANSE/Tests/UnitTests/Analysis/test_scattering.py +++ b/MDANSE/Tests/UnitTests/Analysis/test_scattering.py @@ -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() @@ -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" @@ -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() @@ -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" @@ -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 = {} @@ -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): @@ -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") diff --git a/MDANSE/Tests/UnitTests/Analysis/test_structure.py b/MDANSE/Tests/UnitTests/Analysis/test_structure.py index 58bb38df8f..db5920d10f 100644 --- a/MDANSE/Tests/UnitTests/Analysis/test_structure.py +++ b/MDANSE/Tests/UnitTests/Analysis/test_structure.py @@ -17,6 +17,7 @@ "short_trajectory_after_changes.mdt", ) + ################################################################ # Job parameters # ################################################################ @@ -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", [ diff --git a/MDANSE/Tests/UnitTests/Analysis/test_trajectory.py b/MDANSE/Tests/UnitTests/Analysis/test_trajectory.py index 1c7cec8d8d..3b21af07db 100644 --- a/MDANSE/Tests/UnitTests/Analysis/test_trajectory.py +++ b/MDANSE/Tests/UnitTests/Analysis/test_trajectory.py @@ -17,6 +17,7 @@ "short_trajectory_after_changes.mdt", ) + ################################################################ # Job parameters # ################################################################ @@ -27,23 +28,26 @@ 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 @@ -51,7 +55,7 @@ def parameters(): def test_RigidBodyTrajectory(parameters): """We ignore the failure to merge other changes.""" temp_name = tempfile.mktemp() - parameters["output_file"] = (temp_name, 64, 'gzip') + parameters["output_file"] = (temp_name, 64, "gzip") job = IJob.create("RigidBodyTrajectory") job.run(parameters, status=True) assert path.exists(temp_name + ".mdt") @@ -63,7 +67,7 @@ def test_RigidBodyTrajectory(parameters): def test_GlobalMotionFilteredTrajectory(parameters): """We ignore the failure here to merge other changes.""" temp_name = tempfile.mktemp() - parameters["output_file"] = (temp_name, 64, 'gzip') + parameters["output_file"] = (temp_name, 64, "gzip") job = IJob.create("GlobalMotionFilteredTrajectory") job.run(parameters, status=True) assert path.exists(temp_name + ".mdt") @@ -73,7 +77,7 @@ def test_GlobalMotionFilteredTrajectory(parameters): def test_CroppedTrajectory(parameters): temp_name = tempfile.mktemp() - parameters["output_file"] = (temp_name, 64, 'gzip') + parameters["output_file"] = (temp_name, 64, "gzip") job = IJob.create("CroppedTrajectory") job.run(parameters, status=True) assert path.exists(temp_name + ".mdt") @@ -86,7 +90,7 @@ def test_CenterOfMassesTrajectory(parameters): """This will need to detect molecules before it can find the centre of each one of them.""" temp_name = tempfile.mktemp() - parameters["output_file"] = (temp_name, 64, 'gzip') + parameters["output_file"] = (temp_name, 64, "gzip") job = IJob.create("CenterOfMassesTrajectory") job.run(parameters, status=True) assert path.exists(temp_name + ".mdt") @@ -96,10 +100,9 @@ def test_CenterOfMassesTrajectory(parameters): def test_UnfoldedTrajectory(parameters): temp_name = tempfile.mktemp() - parameters["output_file"] = (temp_name, 64, 'gzip') + parameters["output_file"] = (temp_name, 64, "gzip") job = IJob.create("UnfoldedTrajectory") job.run(parameters, status=True) assert path.exists(temp_name + ".mdt") assert path.isfile(temp_name + ".mdt") os.remove(temp_name + ".mdt") - diff --git a/MDANSE/Tests/UnitTests/AtomSelector/test_atom_selectors.py b/MDANSE/Tests/UnitTests/AtomSelector/test_atom_selectors.py index 3c019910b4..f5047c2fb6 100644 --- a/MDANSE/Tests/UnitTests/AtomSelector/test_atom_selectors.py +++ b/MDANSE/Tests/UnitTests/AtomSelector/test_atom_selectors.py @@ -5,7 +5,7 @@ select_element, select_hs_on_heteroatom, select_hs_on_element, - select_dummy + select_dummy, ) diff --git a/MDANSE/Tests/UnitTests/test_chemical_entity.py b/MDANSE/Tests/UnitTests/test_chemical_entity.py index a6f521a404..5a5671371f 100644 --- a/MDANSE/Tests/UnitTests/test_chemical_entity.py +++ b/MDANSE/Tests/UnitTests/test_chemical_entity.py @@ -516,9 +516,24 @@ def test_build(self): ] ], "atoms": [ - [repr("O").encode("UTF-8"), repr("OW").encode("UTF-8"), "None", b"False"], - [repr("H").encode("UTF-8"), repr("HW2").encode("UTF-8"), "None", b"False"], - [repr("H").encode("UTF-8"), repr("HW1").encode("UTF-8"), "None", b"False"], + [ + repr("O").encode("UTF-8"), + repr("OW").encode("UTF-8"), + "None", + b"False", + ], + [ + repr("H").encode("UTF-8"), + repr("HW2").encode("UTF-8"), + "None", + b"False", + ], + [ + repr("H").encode("UTF-8"), + repr("HW1").encode("UTF-8"), + "None", + b"False", + ], ], } m = ce.Molecule.build(h5, [0, 1, 2], "WAT", "water") diff --git a/MDANSE/Tests/UnitTests/test_documentation.py b/MDANSE/Tests/UnitTests/test_documentation.py index ce49e6f866..d539acbca3 100644 --- a/MDANSE/Tests/UnitTests/test_documentation.py +++ b/MDANSE/Tests/UnitTests/test_documentation.py @@ -1,4 +1,3 @@ - import pytest from MDANSE.Framework.Jobs.IJob import IJob