Reformat code using the new black

MDANSE/Src/MDANSE/Framework/Configurators/IConfigurator.py

@@ -112,9 +112,11 @@ def __init__(self, name, **kwargs):
 
         self._label = kwargs.get(
             "label",
-            self.__class__._label
-            if hasattr(self.__class__, "_label")
-            else " ".join(name.split("_")).strip(),
+            (
+                self.__class__._label
+                if hasattr(self.__class__, "_label")
+                else " ".join(name.split("_")).strip()
+            ),
         )
 
         self._widget = kwargs.get("widget", self.__class__)

MDANSE/Src/MDANSE/Framework/QVectors/SphericalLatticeQVectors.py

@@ -49,8 +49,7 @@ def _generate(self):
         )
 
         hklMax = (
-            np.ceil([qMax / np.sqrt(np.sum(v**2)) for v in self._inverseUnitCell.T])
-            + 1
+            np.ceil([qMax / np.sqrt(np.sum(v**2)) for v in self._inverseUnitCell.T]) + 1
         )
 
         vects = np.mgrid[

MDANSE/Src/MDANSE/IO/FortranFormat.py

@@ -61,7 +61,6 @@
 # which can be accessed as text or as a list of items.
 #
 class FortranLine:
-
     """Fortran-style record in formatted files
 
     FortranLine objects represent the content of one record of a
@@ -244,7 +243,6 @@ def _output(self):
 # little error checking.
 #
 class FortranFormat:
-
     """
     Parsed Fortran-style format string
 

MDANSE/Src/MDANSE/IO/PDB.py

@@ -100,7 +100,6 @@ def cmp(a, b):
 # for everything.
 #
 class PDBFile:
-
     """
     X{PDB} file with access at the record level
 
@@ -551,7 +550,6 @@ def __del__(self):
 # Representation of objects.
 #
 class PDBAtom:
-
     """
     Atom in a PDB structure
     """
@@ -638,7 +636,6 @@ def writeToFile(self, file):
 
 
 class PDBHetAtom(PDBAtom):
-
     """
     HetAtom in a PDB structure
 
@@ -651,7 +648,6 @@ def type(self):
 
 
 class PDBGroup:
-
     """
     Atom group (residue or molecule) in a PDB file
 
@@ -771,7 +767,6 @@ def writeToFile(self, file):
 
 
 class PDBMolecule(PDBGroup):
-
     """
     Molecule in a PDB file
 
@@ -789,7 +784,6 @@ class PDBResidue(PDBGroup):
 
 
 class PDBAminoAcidResidue(PDBResidue):
-
     """
     Amino acid residue in a PDB file
     """
@@ -850,7 +844,6 @@ def writeToFile(self, file):
 
 
 class PDBNucleotideResidue(PDBResidue):
-
     """
     Nucleotide residue in a PDB file
     """
@@ -922,7 +915,6 @@ def writeToFile(self, file):
 
 
 class PDBChain:
-
     """Chain of PDB residues
 
     This is an abstract base class. Instances can be created using
@@ -1035,7 +1027,6 @@ def writeToFile(self, file):
 
 
 class PDBPeptideChain(PDBChain):
-
     """
     Peptide chain in a PDB file
     """
@@ -1056,7 +1047,6 @@ def isCompatible(self, chain_data, residue_data):
 
 
 class PDBNucleotideChain(PDBChain):
-
     """
     Nucleotide chain in a PDB file
     """
@@ -1105,7 +1095,6 @@ def isCompatible(self, chain_data, residue_data):
 # Residue number class for dealing with insertion codes
 #
 class ResidueNumber:
-
     """
     PDB residue number
 
@@ -1145,7 +1134,6 @@ def __str__(self):
 # The configuration class.
 #
 class Structure:
-
     """
     A high-level representation of the contents of a PDB file
 

MDANSE/Src/MDANSE/IO/TextFile.py

@@ -25,7 +25,6 @@
 
 
 class TextFile:
-
     """
     Text files with line iteration and transparent compression
 

MDANSE/Src/MDANSE/Mathematics/LinearAlgebra.py

@@ -6,7 +6,6 @@ def cmp(a, b):
 
 
 class Vector:
-
     """Vector in 3D space
 
     Constructor:
@@ -228,7 +227,6 @@ def angle(self, other):
 
 
 class Quaternion:
-
     """
     Quaternion (hypercomplex number)
 
@@ -387,7 +385,6 @@ def asRotation(self):
 
 
 class Tensor:
-
     """Tensor in 3D space
 
     Tensors support the usual arithmetic operations

MDANSE/Src/MDANSE/Mathematics/Transformation.py

@@ -32,7 +32,6 @@
 # Abstract base classes
 #
 class Transformation:
-
     """
     Linear coordinate transformation.
 
@@ -70,7 +69,6 @@ def inverse(self):
 # Rigid body transformations
 #
 class RigidBodyTransformation(Transformation):
-
     """
     Combination of translations and rotations
     """
@@ -110,7 +108,6 @@ def screwMotion(self):
 # Pure translation
 #
 class Translation(RigidBodyTransformation):
-
     """
     Translational transformation
     """
@@ -167,7 +164,6 @@ def screwMotion(self):
 # Pure rotation
 #
 class Rotation(RigidBodyTransformation):
-
     """
     Rotational transformation
     """
@@ -383,7 +379,6 @@ def screwMotion(self):
 # Combined translation and rotation
 #
 class RotationTranslation(RigidBodyTransformation):
-
     """
     Combined translational and rotational transformation.
 
@@ -448,7 +443,6 @@ def screwMotion(self):
 # Scaling
 #
 class Scaling(Transformation):
-
     """
     Scaling
     """
@@ -524,7 +518,6 @@ def inverse(self):
 # General linear transformation
 #
 class LinearTransformation(Transformation):
-
     """
     General linear transformation.
 

MDANSE/Tests/UnitTests/test_databases.py

@@ -161,9 +161,10 @@ def test_add_atom_existing_atom(self):
             ATOMS_DATABASE.add_atom("H")
 
     def test_add_atom_valid(self):
-        with patch("json.dump") as m, patch(
-            "MDANSE.Chemistry.Databases.AtomsDatabase.save"
-        ) as n:
+        with (
+            patch("json.dump") as m,
+            patch("MDANSE.Chemistry.Databases.AtomsDatabase.save") as n,
+        ):
             ATOMS_DATABASE.add_atom("new_atom")
             self.assertDictEqual({}, ATOMS_DATABASE["new_atom"])
             assert not m.called
@@ -334,9 +335,10 @@ def test__reset(self):
         self.assertDictEqual({}, ATOMS_DATABASE._properties)
 
     def test_save(self):
-        with patch("builtins.open", new_callable=mock_open) as op, patch(
-            "json.dump"
-        ) as dump:
+        with (
+            patch("builtins.open", new_callable=mock_open) as op,
+            patch("json.dump") as dump,
+        ):
             ATOMS_DATABASE.save()
             op.assert_called_with(ATOMS_DATABASE._USER_DATABASE, "w")
             dump.assert_called_with(
@@ -383,9 +385,12 @@ def test__load_default_database(self):
             self.assertDictEqual(self.data, MOLECULES_DATABASE._data)
 
     def test__load_user_database(self):
-        with patch(
-            "builtins.open", new_callable=mock_open, read_data=json.dumps(self.data)
-        ) as m, patch("os.path.exists", spec=True):
+        with (
+            patch(
+                "builtins.open", new_callable=mock_open, read_data=json.dumps(self.data)
+            ) as m,
+            patch("os.path.exists", spec=True),
+        ):
             MOLECULES_DATABASE._load("user.json", "default.json")
             m.assert_called_with("user.json", "r")
             self.assertDictEqual(self.data, MOLECULES_DATABASE._data)
@@ -410,9 +415,10 @@ def test_add_molecule_existing_molecule(self):
             MOLECULES_DATABASE.add_molecule("WAT")
 
     def test_add_molecule_valid(self):
-        with patch("json.dump") as m, patch(
-            "MDANSE.Chemistry.Databases.MoleculesDatabase.save"
-        ) as n:
+        with (
+            patch("json.dump") as m,
+            patch("MDANSE.Chemistry.Databases.MoleculesDatabase.save") as n,
+        ):
             MOLECULES_DATABASE.add_molecule("new_molecule")
             self.assertDictEqual(
                 {"alternatives": [], "atoms": {}}, MOLECULES_DATABASE["new_molecule"]
@@ -438,9 +444,10 @@ def test__reset(self):
         self.assertDictEqual({}, MOLECULES_DATABASE._data)
 
     def test_save(self):
-        with patch("builtins.open", new_callable=mock_open) as op, patch(
-            "json.dump"
-        ) as dump:
+        with (
+            patch("builtins.open", new_callable=mock_open) as op,
+            patch("json.dump") as dump,
+        ):
             MOLECULES_DATABASE.save()
             op.assert_called_with(MOLECULES_DATABASE._USER_DATABASE, "w")
             dump.assert_called_with(self.data, ANY)
@@ -489,9 +496,12 @@ def test__load_default_database(self):
             )
 
     def test__load_user_database(self):
-        with patch(
-            "builtins.open", new_callable=mock_open, read_data=json.dumps(self.data)
-        ) as m, patch("os.path.exists", spec=True):
+        with (
+            patch(
+                "builtins.open", new_callable=mock_open, read_data=json.dumps(self.data)
+            ) as m,
+            patch("os.path.exists", spec=True),
+        ):
             NUCLEOTIDES_DATABASE._load("user.json", "default.json")
             m.assert_called_with("user.json", "r")
             self.assertDictEqual(self.data, NUCLEOTIDES_DATABASE._data)
@@ -521,9 +531,10 @@ def test_add_nucleotide_existing_nucleotide(self):
             NUCLEOTIDES_DATABASE.add_nucleotide("5T")
 
     def test_add_nucleotide_valid(self):
-        with patch("json.dump") as m, patch(
-            "MDANSE.Chemistry.Databases.NucleotidesDatabase.save"
-        ) as n:
+        with (
+            patch("json.dump") as m,
+            patch("MDANSE.Chemistry.Databases.NucleotidesDatabase.save") as n,
+        ):
             NUCLEOTIDES_DATABASE.add_nucleotide("new_nucleotide", True, True)
             self.assertDictEqual(
                 {
@@ -555,9 +566,10 @@ def test__reset(self):
         self.assertDictEqual({}, NUCLEOTIDES_DATABASE._data)
 
     def test_save(self):
-        with patch("builtins.open", new_callable=mock_open) as op, patch(
-            "json.dump"
-        ) as dump:
+        with (
+            patch("builtins.open", new_callable=mock_open) as op,
+            patch("json.dump") as dump,
+        ):
             NUCLEOTIDES_DATABASE.save()
             op.assert_called_with(NUCLEOTIDES_DATABASE._USER_DATABASE, "w")
             dump.assert_called_with(self.data, ANY)
@@ -612,9 +624,12 @@ def test__load_default_database(self):
             )
 
     def test__load_user_database(self):
-        with patch(
-            "builtins.open", new_callable=mock_open, read_data=json.dumps(self.data)
-        ) as m, patch("os.path.exists", spec=True):
+        with (
+            patch(
+                "builtins.open", new_callable=mock_open, read_data=json.dumps(self.data)
+            ) as m,
+            patch("os.path.exists", spec=True),
+        ):
             RESIDUES_DATABASE._load("user.json", "default.json")
             m.assert_called_with("user.json", "r")
             self.assertDictEqual(self.data, RESIDUES_DATABASE._data)
@@ -644,9 +659,10 @@ def test_add_residue_existing_nucleotide(self):
             RESIDUES_DATABASE.add_residue("G")
 
     def test_add_residue_valid(self):
-        with patch("json.dump") as m, patch(
-            "MDANSE.Chemistry.Databases.ResiduesDatabase.save"
-        ) as n:
+        with (
+            patch("json.dump") as m,
+            patch("MDANSE.Chemistry.Databases.ResiduesDatabase.save") as n,
+        ):
             RESIDUES_DATABASE.add_residue("new_residues", True, True)
             self.assertDictEqual(
                 {
@@ -678,9 +694,10 @@ def test__reset(self):
         self.assertDictEqual({}, RESIDUES_DATABASE._data)
 
     def test_save(self):
-        with patch("builtins.open", new_callable=mock_open) as op, patch(
-            "json.dump"
-        ) as dump:
+        with (
+            patch("builtins.open", new_callable=mock_open) as op,
+            patch("json.dump") as dump,
+        ):
             RESIDUES_DATABASE.save()
             op.assert_called_with(RESIDUES_DATABASE._USER_DATABASE, "w")
             dump.assert_called_with(self.data, ANY)

MDANSE_GUI/Src/MDANSE_GUI/GUI/JobControllerPanel.py

@@ -126,10 +126,9 @@ def update(self, init=False):
                 start = datetime.datetime.strptime(
                     self._runningJobs[job]["start"], "%d-%m-%Y %H:%M:%S"
                 )
-                self._runningJobs[job][
-                    "elapsed"
-                ] = "%02d:%02dh:%02dm:%02ds" % convert_duration(
-                    total_seconds(datetime.datetime.today() - start)
+                self._runningJobs[job]["elapsed"] = (
+                    "%02d:%02dh:%02dm:%02ds"
+                    % convert_duration(total_seconds(datetime.datetime.today() - start))
                 )
 
         # Loop over the job whose temporary files are still present