Run ruff format

.github/workflows/lint.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: psf/black@stable
+      - uses: astral-sh/ruff-action@v3
         with:
-          options: "--check --verbose"
-          src: "MDANSE_GUI/Src"
+          src: "./MDANSE/Src"
+          args: "format --check"
 
   lint_check_ruff:
     runs-on: ubuntu-latest

MDANSE/Doc/conf_api.py

@@ -24,7 +24,7 @@
 # License along with this library; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
-""" 
+"""
 Created on Mar 30, 2015
 
 @author: Gael Goret and Eric C. Pellegrini

MDANSE/Doc/conf_help.py

@@ -24,7 +24,7 @@
 # License along with this library; if not, write to the Free Software
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
-""" 
+"""
 Created on Mar 30, 2015
 
 @author: Gael Goret and Eric C. Pellegrini

MDANSE/Src/MDANSE/Chemistry/ChemicalSystem.py

@@ -28,7 +28,6 @@
 
 
 class ChemicalSystem:
-
     def __init__(self, name: str = "", trajectory=None):
         """
 
@@ -80,9 +79,7 @@ def add_atom(self, atm_num: int) -> int:
     def add_bonds(self, pair_list: List[Tuple[int]]):
         self._bonds += list(pair_list)
         for pair in pair_list:
-            self.rdkit_mol.AddBond(
-                int(pair[0]), int(pair[1]), Chem.rdchem.BondType.UNSPECIFIED
-            )
+            self.rdkit_mol.AddBond(int(pair[0]), int(pair[1]), Chem.rdchem.BondType.UNSPECIFIED)
 
     def add_labels(self, label_dict: Dict[str, List[int]]):
         for key, item in label_dict.items():
@@ -98,9 +95,7 @@ def add_clusters(self, group_list: List[List[int]]):
                 continue
             atom_list = [self._atom_types[index] for index in group]
             unique_atoms, counts = np.unique(atom_list, return_counts=True)
-            name = "_".join(
-                [str(unique_atoms[n]) + str(counts[n]) for n in range(len(counts))]
-            )
+            name = "_".join([str(unique_atoms[n]) + str(counts[n]) for n in range(len(counts))])
             if name not in self._clusters:
                 self._clusters[name] = [sorted_group]
             else:
@@ -122,9 +117,7 @@ def has_substructure_match(self, smarts: str) -> bool:
         """
         return self.rdkit_mol.HasSubstructMatch(Chem.MolFromSmarts(smarts))
 
-    def get_substructure_matches(
-        self, smarts: str, maxmatches: int = 1000000
-    ) -> set[int]:
+    def get_substructure_matches(self, smarts: str, maxmatches: int = 1000000) -> set[int]:
         """Get the indices which match the smarts string. Note that
         the default bond type in MDANSE is
         Chem.rdchem.BondType.UNSPECIFIED.

MDANSE/Src/MDANSE/Chemistry/Databases.py

@@ -244,9 +244,7 @@ def add_atom(self, atom: str) -> None:
         """
 
         if atom in self._data:
-            raise AtomsDatabaseError(
-                "The atom {} is already stored in the database".format(atom)
-            )
+            raise AtomsDatabaseError("The atom {} is already stored in the database".format(atom))
 
         self._data[atom] = {}
 
@@ -304,9 +302,7 @@ def get_isotopes(self, atom: str) -> list[str]:
         # The isotopes are searched according to |symbol| property
         symbol = self._data[atom]["symbol"]
 
-        return [
-            iname for iname, props in self._data.items() if props["symbol"] == symbol
-        ]
+        return [iname for iname, props in self._data.items() if props["symbol"] == symbol]
 
     @property
     def properties(self) -> list[str]:
@@ -338,8 +334,7 @@ def get_property(self, pname: str) -> dict[str, Union[str, int, float, list]]:
         ptype = AtomsDatabase._TYPES[self._properties[pname]]
 
         return {
-            element: properties.get(pname, ptype())
-            for element, properties in self._data.items()
+            element: properties.get(pname, ptype()) for element, properties in self._data.items()
         }
 
     def get_value(self, atom: str, pname: str) -> Union[str, int, float, list]:
@@ -400,9 +395,7 @@ def get_values_for_multiple_atoms(
         values = {name: self._data[name][prop] for name in unique_atoms}
         return [values[atom] for atom in atoms]
 
-    def set_value(
-        self, atom: str, pname: str, value: Union[str, int, float, list]
-    ) -> None:
+    def set_value(self, atom: str, pname: str, value: Union[str, int, float, list]) -> None:
         """
         Set the given property of the given atom to the given value.
 
@@ -425,9 +418,7 @@ def set_value(
             )
 
         try:
-            self._data[atom][pname] = AtomsDatabase._TYPES[self._properties[pname]](
-                value
-            )
+            self._data[atom][pname] = AtomsDatabase._TYPES[self._properties[pname]](value)
         except ValueError:
             raise AtomsDatabaseError(
                 "Can not coerce {} to {} type".format(value, self._properties[pname])
@@ -482,9 +473,7 @@ def info(self, atom: str) -> str:
 
         # The values for all element's properties
         for pname in sorted(self._properties):
-            info.append(
-                " {0:<20}{1:>50}".format(pname, str(self._data[atom].get(pname, None)))
-            )
+            info.append(" {0:<20}{1:>50}".format(pname, str(self._data[atom].get(pname, None))))
 
         info.append(delimiter)
         info = "\n".join(info)
@@ -564,11 +553,7 @@ def numeric_properties(self) -> list[str]:
         :return: the name of the numeric properties stored in the atoms database
         :rtype: list
         """
-        return [
-            pname
-            for pname, prop in self._properties.items()
-            if prop in ["int", "float"]
-        ]
+        return [pname for pname, prop in self._properties.items() if prop in ["int", "float"]]
 
     def _reset(self) -> None:
         """

MDANSE/Src/MDANSE/Core/Platform.py

@@ -433,9 +433,7 @@ def etime_to_ctime(self, etime):
 
         days, hours, minutes, seconds = etime[-4:]
 
-        etime = datetime.timedelta(
-            days=days, hours=hours, minutes=minutes, seconds=seconds
-        )
+        etime = datetime.timedelta(days=days, hours=hours, minutes=minutes, seconds=seconds)
 
         return (datetime.datetime.today() - etime).strftime("%d-%m-%Y %H:%M:%S")
 
@@ -457,9 +455,7 @@ def get_processes_info(self):
         procs = [p.split() for p in procs if p]
 
         # A mapping between the active processes pid and their corresponding exectuable.
-        procs = dict(
-            [(int(p[0].strip()), self.etime_to_ctime(p[1].strip())) for p in procs]
-        )
+        procs = dict([(int(p[0].strip()), self.etime_to_ctime(p[1].strip())) for p in procs])
 
         return procs
 

MDANSE/Src/MDANSE/Core/Singleton.py

@@ -28,8 +28,6 @@ def __call__(self, *args, **kwargs):
         """
 
         if self.__name__ not in self.__instances:
-            self.__instances[self.__name__] = super(Singleton, self).__call__(
-                *args, **kwargs
-            )
+            self.__instances[self.__name__] = super(Singleton, self).__call__(*args, **kwargs)
 
         return self.__instances[self.__name__]

MDANSE/Src/MDANSE/Core/SubclassFactory.py

@@ -70,9 +70,7 @@ def recursive_search(parent_class: type, name: str):
         return return_type
     else:
         for child in parent_class._registered_subclasses.keys():
-            return_type = recursive_search(
-                parent_class._registered_subclasses[child], name
-            )
+            return_type = recursive_search(parent_class._registered_subclasses[child], name)
             if return_type is not None:
                 return return_type
 
@@ -114,8 +112,7 @@ def recursive_dict(parent_class: type) -> dict:
     """
     try:
         results = {
-            ckey: parent_class._registered_subclasses[ckey]
-            for ckey in parent_class.subclasses()
+            ckey: parent_class._registered_subclasses[ckey] for ckey in parent_class.subclasses()
         }
     except Exception:
         return {}

MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py

@@ -21,7 +21,6 @@
 
 
 class AtomLabel:
-
     def __init__(self, atm_label: str, **kwargs):
         """Creates an atom label object which is used for atom mapping
         and atom type guessing.
@@ -171,9 +170,7 @@ def guess_element(atm_label: str, mass: Union[float, int, None] = None) -> str:
     raise AttributeError(f"Unable to guess: {atm_label}")
 
 
-def get_element_from_mapping(
-    mapping: dict[str, dict[str, str]], label: str, **kwargs
-) -> str:
+def get_element_from_mapping(mapping: dict[str, dict[str, str]], label: str, **kwargs) -> str:
     """Determine the symbol of the element from the atom label and
     the information from the kwargs.
 
@@ -202,9 +199,7 @@ def get_element_from_mapping(
     return element
 
 
-def fill_remaining_labels(
-    mapping: dict[str, dict[str, str]], labels: list[AtomLabel]
-) -> None:
+def fill_remaining_labels(mapping: dict[str, dict[str, str]], labels: list[AtomLabel]) -> None:
     """Given a list of labels fill the remaining labels in the mapping
     dictionary.
 

MDANSE/Src/MDANSE/Framework/AtomSelector/all_selector.py

@@ -17,9 +17,7 @@
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 
 
-def select_all(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_all(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects all atoms in the chemical system except for the dummy
     atoms.
 
@@ -45,10 +43,4 @@ def select_all(
         for atm in system._unique_elements:
             if trajectory.get_atom_property(atm, "dummy"):
                 dummy_list.append(atm)
-        return set(
-            [
-                index
-                for index in system._atom_indices
-                if atom_list[index] not in dummy_list
-            ]
-        )
+        return set([index for index in system._atom_indices if atom_list[index] not in dummy_list])

MDANSE/Src/MDANSE/Framework/AtomSelector/atom_selectors.py

@@ -55,9 +55,7 @@ def select_element(
         return system.get_substructure_matches(pattern)
 
 
-def select_dummy(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_dummy(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects all dummy atoms in the chemical system.
 
     Parameters
@@ -86,11 +84,7 @@ def select_dummy(
             if trajectory.get_atom_property(atm, "dummy"):
                 dummy_list.append(atm)
         return set(
-            [
-                index
-                for index, element in enumerate(system.atom_list)
-                if element in dummy_list
-            ]
+            [index for index, element in enumerate(system.atom_list) if element in dummy_list]
         )
 
 
@@ -119,9 +113,7 @@ def select_atom_name(
             return True
         return False
     else:
-        return set(
-            [index for index, element in enumerate(system.atom_list) if element == name]
-        )
+        return set([index for index, element in enumerate(system.atom_list) if element == name])
 
 
 def select_atom_fullname(
@@ -149,9 +141,7 @@ def select_atom_fullname(
             return True
         return False
     else:
-        return set(
-            [index for index, name in enumerate(system.name_list) if name == fullname]
-        )
+        return set([index for index, name in enumerate(system.name_list) if name == fullname])
 
 
 def select_hs_on_element(

MDANSE/Src/MDANSE/Framework/AtomSelector/group_selectors.py

@@ -52,9 +52,7 @@ def select_primary_amine(
         return system.get_substructure_matches(pattern)
 
 
-def select_hydroxy(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_hydroxy(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects the O and H atoms of all hydroxy groups including water.
 
     Parameters
@@ -77,9 +75,7 @@ def select_hydroxy(
         return system.get_substructure_matches(pattern)
 
 
-def select_methyl(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_methyl(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects the C and H atoms of all methyl groups.
 
     Parameters
@@ -102,9 +98,7 @@ def select_methyl(
         return system.get_substructure_matches(pattern)
 
 
-def select_phosphate(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_phosphate(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects the P and O atoms of all phosphate groups.
 
     Parameters
@@ -127,9 +121,7 @@ def select_phosphate(
         return system.get_substructure_matches(pattern)
 
 
-def select_sulphate(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_sulphate(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects the S and O atoms of all sulphate groups.
 
     Parameters
@@ -152,9 +144,7 @@ def select_sulphate(
         return system.get_substructure_matches(pattern)
 
 
-def select_thiol(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_thiol(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects the S and H atoms of all thiol groups.
 
     Parameters

MDANSE/Src/MDANSE/Framework/AtomSelector/molecule_selectors.py

@@ -22,9 +22,7 @@
 ]
 
 
-def select_water(
-    trajectory: Trajectory, check_exists: bool = False
-) -> Union[set[int], bool]:
+def select_water(trajectory: Trajectory, check_exists: bool = False) -> Union[set[int], bool]:
     """Selects the O and H atoms of all water molecules.
 
     Parameters