Add ruff

.github/workflows/lint.yml

@@ -16,6 +16,15 @@ jobs:
           options: "--check --verbose"
           src: "MDANSE/Src"
 
+  lint_check_ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+        with:
+          src: "./MDANSE/Src"
+          args: "check"
+
   lint-mdanse-gui:
     runs-on: ubuntu-latest
     steps:

MDANSE/Src/MDANSE/Core/SubclassFactory.py

@@ -90,7 +90,7 @@ def recursive_keys(parent_class: type) -> list:
     """
     try:
         results = parent_class.subclasses()
-    except:
+    except Exception:
         return []
     else:
         for child in parent_class.subclasses():
@@ -117,7 +117,7 @@ def recursive_dict(parent_class: type) -> dict:
             ckey: parent_class._registered_subclasses[ckey]
             for ckey in parent_class.subclasses()
         }
-    except:
+    except Exception:
         return {}
     else:
         for child in parent_class.subclasses():

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

@@ -37,7 +37,7 @@ def __init__(self, atm_label: str, **kwargs):
         # methods as of writing e.g. re.sub
         translation = str.maketrans("", "", ";=")
         self.atm_label = atm_label.translate(translation)
-        self.grp_label = f""
+        self.grp_label = ""
         if kwargs:
             for k, v in kwargs.items():
                 self.grp_label += f"{k}={str(v).translate(translation)};"

MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py

@@ -13,15 +13,31 @@
 #    You should have received a copy of the GNU General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
-import json
 import copy
+import json
 from typing import Union
+
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
 from MDANSE.MolecularDynamics.Trajectory import Trajectory
 from MDANSE.Framework.AtomSelector.all_selector import select_all
-from MDANSE.Framework.AtomSelector.atom_selectors import *
-from MDANSE.Framework.AtomSelector.group_selectors import *
-from MDANSE.Framework.AtomSelector.molecule_selectors import *
+from MDANSE.Framework.AtomSelector.atom_selectors import (
+    select_atom_fullname,
+    select_atom_name,
+    select_dummy,
+    select_element,
+    select_hs_on_element,
+    select_hs_on_heteroatom,
+    select_index,
+)
+from MDANSE.Framework.AtomSelector.group_selectors import (
+    select_hydroxy,
+    select_methyl,
+    select_phosphate,
+    select_primary_amine,
+    select_sulphate,
+    select_thiol,
+)
+from MDANSE.Framework.AtomSelector.molecule_selectors import select_water
 
 
 class Selector:

MDANSE/Src/MDANSE/Framework/Configurable.py

@@ -93,7 +93,7 @@ def build_configuration(self):
                     typ, name, configurable=self, **kwds
                 )
             # Any kind of error has to be caught
-            except:
+            except Exception:
                 raise ConfigurationError(f"Could not set {name!r} configuration item")
 
     def set_settings(self, settings):

MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py

@@ -31,7 +31,7 @@ def parse(self):
 
         try:
             self._input = ASETrajectory(self["filename"])
-        except:
+        except Exception:
             self._input = iread(self["filename"], index="[:]")
             first_frame = read(self["filename"], index=0)
         else:

MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py

@@ -70,7 +70,7 @@ def configure(self, values):
         if file_format == "guess":
             file_format = None
 
-        if file_format is not None and not file_format in self._allowed_formats:
+        if file_format is not None and file_format not in self._allowed_formats:
             LOG.error(f"WRONG FORMAT in {self._name}")
             self.error_status = f"The ASE file format {file_format} is not supported"
             return
@@ -99,7 +99,7 @@ def get_information(self):
         :rtype: str
         """
         try:
-            val = self["value"]
+            self["value"]
         except KeyError:
             result = f"No VALUE in {self._name}"
             LOG.error(result)

MDANSE/Src/MDANSE/Framework/Configurators/BooleanConfigurator.py

@@ -32,13 +32,11 @@ class BooleanConfigurator(IConfigurator):
         "yes": True,
         "y": True,
         "1": True,
-        1: True,
         False: False,
         "false": False,
         "no": False,
         "n": False,
         "0": False,
-        0: False,
     }
 
     def configure(self, value):

MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py

@@ -75,30 +75,30 @@ def parse(self):
 
         with open(self._filename, "r") as source_file:
             lines = []
-            for l in source_file.readlines():
-                l = l.strip()
-                if l:
-                    lines.append(l)
+            for line in source_file.readlines():
+                line = line.strip()
+                if line:
+                    lines.append(line)
 
         for i, line in enumerate(lines):
             toks = line.split()
 
             if "xlo" in line and "xhi" in line:
                 try:
                     x_inputs = [float(x) for x in toks[0:3]]
-                except:
+                except Exception:
                     xspan = float(toks[1]) - float(toks[0])
                     self["unit_cell"][0, 0] = xspan
             elif "ylo" in line and "yhi" in line:
                 try:
                     y_inputs = [float(x) for x in toks[0:3]]
-                except:
+                except Exception:
                     yspan = float(toks[1]) - float(toks[0])
                     self["unit_cell"][1, 1] = yspan
             elif "zlo" in line and "zhi" in line:
                 try:
                     z_inputs = [float(x) for x in toks[0:3]]
-                except:
+                except Exception:
                     zspan = float(toks[1]) - float(toks[0])
                     self["unit_cell"][2, 2] = zspan
 
@@ -142,7 +142,7 @@ def parse(self):
                 self["bonds"] = np.array(self["bonds"], dtype=np.int32)
 
             if re.match("^\s*Atoms\s*$", line.split("#")[0]):
-                if not "#" in line:
+                if "#" not in line:
                     num_of_columns = len(lines[i + 2].split())
                     if num_of_columns <= 5:
                         type_index = 1
@@ -184,8 +184,8 @@ def parse(self):
                 self["unit_cell"] = parse_unit_cell(
                     np.concatenate([x_inputs, y_inputs, z_inputs])
                 )
-            except:
-                LOG.error(f"LAMMPS ConfigFileConfigurator failed to find a unit cell")
+            except Exception:
+                LOG.error("LAMMPS ConfigFileConfigurator failed to find a unit cell")
 
     def atom_labels(self) -> Iterable[AtomLabel]:
         """

MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py

@@ -42,16 +42,16 @@ def configure(self, value: tuple[int, int, int, int]):
 
         if c_frames > self["n_frames"]:
             self.error_status = (
-                f"Number of frames used for the correlation "
-                f"greater than the total number of frames of "
-                f"the trajectory."
+                "Number of frames used for the correlation "
+                "greater than the total number of frames of "
+                "the trajectory."
             )
             return
 
         if c_frames < 2:
             self.error_status = (
-                f"Number of frames used for the correlation "
-                f"should be greater then zero."
+                "Number of frames used for the correlation "
+                "should be greater then zero."
             )
             return
 

MDANSE/Src/MDANSE/Framework/Configurators/DerivativeOrderConfigurator.py

@@ -43,7 +43,7 @@ def configure(self, value: Optional[int]) -> None:
         """
         frames_configurator = self._configurable[self._dependencies["frames"]]
         if not frames_configurator._valid:
-            self.error_status = f"Frames configurator is not valid."
+            self.error_status = "Frames configurator is not valid."
             return
 
         self._original_input = value
@@ -54,8 +54,8 @@ def configure(self, value: Optional[int]) -> None:
 
         if value <= 0 or value > 5:
             self.error_status = (
-                f"Use an interpolation order less than or equal to zero or "
-                f"greater than 5 is not implemented."
+                "Use an interpolation order less than or equal to zero or "
+                "greater than 5 is not implemented."
             )
             return
 

MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py

@@ -44,7 +44,7 @@ def get_largest_cutoff(self) -> float:
                     for frame in range(len(traj_config))
                 ]
             )
-        except:
+        except Exception:
             return np.linalg.norm(traj_config.min_span)
         else:
             if np.allclose(trajectory_array, 0.0):

MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py

@@ -42,7 +42,7 @@ def configure(self, filepath: str) -> None:
 
         self.labels = self.unique_labels()
         if len(self.labels) == 0:
-            self.error_status = f"Unable to generate atom labels"
+            self.error_status = "Unable to generate atom labels"
             return
 
     @abstractmethod

MDANSE/Src/MDANSE/Framework/Configurators/FloatConfigurator.py

@@ -60,12 +60,12 @@ def configure(self, value):
 
         try:
             value = float(value)
-        except (TypeError, ValueError) as e:
+        except (TypeError, ValueError):
             self.error_status = f"Wrong value {value} in {self}"
             return
 
         if self._choices:
-            if not value in self._choices:
+            if value not in self._choices:
                 self.error_status = "the input value is not a valid choice."
                 return
 

MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py

@@ -76,7 +76,7 @@ def configure(self, value):
                 self[v] = self["instance"][v][:]
                 try:
                     self._units[v] = self["instance"][v].attrs["units"]
-                except:
+                except Exception:
                     self._units[v] = "unitless"
             else:
                 self.error_status = (

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

@@ -294,7 +294,7 @@ def check_dependencies(self, configured=None):
         :rtype: bool
         """
 
-        if configured == None:
+        if configured is None:
             names = [str(key) for key in self._configurable._configuration.keys()]
             configured = [
                 name

MDANSE/Src/MDANSE/Framework/Configurators/IntegerConfigurator.py

@@ -17,7 +17,6 @@
 
 from MDANSE.Framework.Configurators.IConfigurator import (
     IConfigurator,
-    ConfiguratorError,
 )
 
 
@@ -72,7 +71,7 @@ def configure(self, value):
             return
 
         if self._choices:
-            if not value in self._choices:
+            if value not in self._choices:
                 self.error_status = "the input value is not a valid choice."
                 return
 

MDANSE/Src/MDANSE/Framework/Configurators/InterpolationOrderConfigurator.py

@@ -20,11 +20,11 @@ class InterpolationOrderConfigurator(IntegerConfigurator):
     """
     This configurator allows to input the interpolation order to be applied when deriving velocities from atomic coordinates.
 
-    The allowed value are *'no interpolation'*,*'1st order'*,*'2nd order'*,*'3rd order'*,*'4th order'* or *'5th order'*, the 
+    The allowed value are *'no interpolation'*,*'1st order'*,*'2nd order'*,*'3rd order'*,*'4th order'* or *'5th order'*, the
     former one will not interpolate the velocities from atomic coordinates but will directly use the velocities stored in the trajectory file.
-    
+
     :attention: it is of paramount importance for the trajectory to be sampled with a very low time \
-    step to get accurate velocities interpolated from atomic coordinates. 
+    step to get accurate velocities interpolated from atomic coordinates.
 
     :note: this configurator depends on 'trajectory' configurator to be configured.
     """
@@ -50,7 +50,7 @@ def configure(self, value):
         """
         frames_configurator = self._configurable[self._dependencies["frames"]]
         if not frames_configurator._valid:
-            self.error_status = f"Frames configurator is not valid."
+            self.error_status = "Frames configurator is not valid."
             return
 
         self._original_input = value
@@ -62,15 +62,15 @@ def configure(self, value):
         if value == 0:
             trajConfig = self._configurable[self._dependencies["trajectory"]]
 
-            if not "velocities" in trajConfig["instance"].variables():
-                self.error_status = f"the trajectory does not contain any velocities. Use an interpolation order higher than 0"
+            if "velocities" not in trajConfig["instance"].variables():
+                self.error_status = "the trajectory does not contain any velocities. Use an interpolation order higher than 0"
                 return
 
             self["variable"] = "velocities"
 
         elif value > 5:
             self.error_status = (
-                f"Use an interpolation order greater than 5 is not implemented."
+                "Use an interpolation order greater than 5 is not implemented."
             )
             return
 

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py

@@ -47,7 +47,7 @@ def configure(self, setting: tuple[Union[str, list], str]):
             if format in mda._READERS.keys():
                 self["format"] = format
             else:
-                self.error_status = f"MDAnalysis coordinate file format not recognised."
+                self.error_status = "MDAnalysis coordinate file format not recognised."
                 return
 
         topology_configurator = self._configurable[self._dependencies["input_file"]]

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py

@@ -60,7 +60,7 @@ def configure(self, value):
                     )
                     return
             else:
-                self.error_status = f"Unable to determine a time step from MDAnalysis"
+                self.error_status = "Unable to determine a time step from MDAnalysis"
                 return
 
         super().configure(value)

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py

@@ -39,7 +39,7 @@ def configure(self, setting: str) -> None:
             if format in mda._PARSERS.keys():
                 self["format"] = format
             else:
-                self.error_status = f"MDAnalysis topology file format not recognised."
+                self.error_status = "MDAnalysis topology file format not recognised."
                 return
         super().configure(filepath)
 

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py

@@ -52,7 +52,7 @@ def configure(self, value):
                     )
                     return
             else:
-                self.error_status = f"Unable to determine a time step from MDTraj"
+                self.error_status = "Unable to determine a time step from MDTraj"
                 return
 
         super().configure(value)

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py

@@ -62,7 +62,7 @@ def configure(self, value: Optional[str]):
 
             self.labels = self.unique_labels()
             if len(self.labels) == 0:
-                self.error_status = f"Unable to generate atom labels"
+                self.error_status = "Unable to generate atom labels"
 
         else:
             extension = "".join(Path(value).suffixes)[1:]

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py

@@ -27,7 +27,7 @@ def configure(self, value):
 
         extensions = {"".join(Path(value).suffixes)[1:] for value in self["values"]}
         if len(extensions) != 1:
-            self.error_status = f"Files should be of a single format."
+            self.error_status = "Files should be of a single format."
             return
         self.extension = next(iter(extensions))