diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index bd9d080533..4641bae389 100644
--- a/.github/workflows/lint.yml
+++ b/.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:
diff --git a/MDANSE/Src/MDANSE/Core/SubclassFactory.py b/MDANSE/Src/MDANSE/Core/SubclassFactory.py
index 39de5a6d31..2a2bdb0721 100644
--- a/MDANSE/Src/MDANSE/Core/SubclassFactory.py
+++ b/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():
diff --git a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py b/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
index f518f8a0e7..b2ee2ca975 100644
--- a/MDANSE/Src/MDANSE/Framework/AtomMapping/atom_mapping.py
+++ b/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)};"
diff --git a/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py b/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py
index f98d9aafdc..3562149e70 100644
--- a/MDANSE/Src/MDANSE/Framework/AtomSelector/selector.py
+++ b/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:
diff --git a/MDANSE/Src/MDANSE/Framework/Configurable.py b/MDANSE/Src/MDANSE/Framework/Configurable.py
index ef8664e1b4..1ee336434e 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurable.py
+++ b/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):
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py
index 3323569b56..8f57aa1e20 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/ASEFileConfigurator.py
+++ b/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:
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py
index 0654a47b3f..883873b5e7 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py
+++ b/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)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/BooleanConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/BooleanConfigurator.py
index e51ada3771..640c8e8f7d 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/BooleanConfigurator.py
+++ b/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):
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py
index 33bd20fe52..1af42d6711 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py
@@ -75,10 +75,10 @@ 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()
@@ -86,19 +86,19 @@ def parse(self):
             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]:
         """
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py
index bdfec1a231..4de5aa93c3 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/CorrelationFramesConfigurator.py
+++ b/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
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/DerivativeOrderConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/DerivativeOrderConfigurator.py
index 43d2eb9351..71436b9641 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/DerivativeOrderConfigurator.py
+++ b/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
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py
index eeb4c2af82..dee9d13c9d 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/DistHistCutoffConfigurator.py
+++ b/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):
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py
index ba52283580..8f3c8d5407 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py
+++ b/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
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/FloatConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/FloatConfigurator.py
index 3234e06f45..0168a2d5bb 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/FloatConfigurator.py
+++ b/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
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py
index 6efce61cc5..ae092df745 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py
+++ b/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 = (
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/IConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/IConfigurator.py
index b1015712c5..70d3436a4b 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/IConfigurator.py
+++ b/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
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/IntegerConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/IntegerConfigurator.py
index 73307c54f5..b74080169f 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/IntegerConfigurator.py
+++ b/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
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/InterpolationOrderConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/InterpolationOrderConfigurator.py
index d259a6c470..f42ed27e48 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/InterpolationOrderConfigurator.py
+++ b/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
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py
index 51c8da812e..ce9d17c174 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py
+++ b/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"]]
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py
index 53b52fcfc1..eab8d125a1 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py
+++ b/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)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py
index c454dc99cb..50b0c4e9ab 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py
+++ b/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)
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py
index e3bb891d51..dea06a4d9b 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py
+++ b/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)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py
index a67b240138..ee3e6fe221 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py
+++ b/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:]
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py
index a44cac00ba..41df11c7ad 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py
+++ b/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))
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py
index 1bfa4170ca..e4fe3c697f 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/McStasOptionsConfigurator.py
@@ -34,10 +34,10 @@ def parse_dictionary(input: str) -> Dict[str, Any]:
         value = value.strip(" '")
         try:
             value = int(value)
-        except:
+        except Exception:
             try:
                 value = float(value)
-            except:
+            except Exception:
                 pass
         result[key] = value
     return result
@@ -90,7 +90,7 @@ def configure(self, value):
 
         try:
             PLATFORM.create_directory(dirname)
-        except:
+        except Exception:
             self.error_status = f"The directory {dirname} is not writable"
             return
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py
index bd327045ab..772c64efb3 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MultiInputFileConfigurator.py
@@ -54,7 +54,7 @@ def configure(self, setting: Union[str, list]):
                     return
                 if type(values) is not list:
                     self.error_status = (
-                        f"Input values should be able to be evaluated as a list"
+                        "Input values should be able to be evaluated as a list"
                     )
                     return
             else:
@@ -62,10 +62,10 @@ def configure(self, setting: Union[str, list]):
 
         if type(values) is list:
             if not all([type(value) is str for value in values]):
-                self.error_status = f"Input values should be a list of str"
+                self.error_status = "Input values should be a list of str"
                 return
         else:
-            self.error_status = f"Input values should be able to be evaluated as a list"
+            self.error_status = "Input values should be able to be evaluated as a list"
             return
 
         values = [PLATFORM.get_path(value) for value in values]
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/MultipleChoicesConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/MultipleChoicesConfigurator.py
index 2550678660..75b111d8ca 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/MultipleChoicesConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/MultipleChoicesConfigurator.py
@@ -58,7 +58,7 @@ def configure(self, value):
 
         if self._nChoices is not None:
             if len(value) != self._nChoices:
-                self.error_status = f"invalid number of choices."
+                self.error_status = "invalid number of choices."
                 return
 
         indices = []
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/OptionalFloatConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/OptionalFloatConfigurator.py
index 8ab4439ed8..8bde4cd50b 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/OptionalFloatConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/OptionalFloatConfigurator.py
@@ -66,12 +66,12 @@ def configure(self, value):
 
         try:
             value[1] = float(value[1])
-        except (TypeError, ValueError) as e:
+        except (TypeError, ValueError):
             self.error_status = f"Wrong value {value[1]} in {self}"
             return
 
         if self._choices:
-            if not value[1] in self._choices:
+            if value[1] not in self._choices:
                 self.error_status = "the input value is not a valid choice."
                 return
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/OutputFilesConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/OutputFilesConfigurator.py
index 145ab6e294..ce191021d3 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/OutputFilesConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/OutputFilesConfigurator.py
@@ -80,11 +80,11 @@ def configure(self, value):
             return
 
         if not formats:
-            self.error_status = f"no output formats specified"
+            self.error_status = "no output formats specified"
             return
 
         for fmt in formats:
-            if not fmt in self._formats:
+            if fmt not in self._formats:
                 self.error_status = (
                     f"the output file format {fmt} is not a valid output format"
                 )
@@ -127,7 +127,7 @@ def get_information(self):
         :return: the information about this configurator.
         :rtype: str
         """
-        if not "files" in self:
+        if "files" not in self:
             return "Output Files have not been defined"
 
         info = ["Input files:\n"]
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/OutputStructureConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/OutputStructureConfigurator.py
index c55f0d1e39..102d406a67 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/OutputStructureConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/OutputStructureConfigurator.py
@@ -78,8 +78,8 @@ def configure(self, value):
             self.error_status = f"the file {root} is not writable"
             return
 
-        if not format in self.formats:
-            self.error_status = f"Output format is not supported"
+        if format not in self.formats:
+            self.error_status = "Output format is not supported"
             return
 
         self["root"] = root
@@ -110,7 +110,7 @@ def get_information(self):
         :return: the information about this configurator.
         :rtype: str
         """
-        if not "file" in self:
+        if "file" not in self:
             return "Output File have not been defined"
 
         info = f"Output file: {self['file']}\n"
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py
index 4488affba2..e3040f06ad 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/OutputTrajectoryConfigurator.py
@@ -94,7 +94,7 @@ def configure(self, value: tuple):
         self["extension"] = IFormat.create(self._format).extension
         temp_name = root
         if self["extension"] != root.suffix:  # capture most extension lengths
-            temp_name = temp_name.with_suffix(temp_name.suffix + self["extension"])
+            temp_name = root.with_suffix(root.suffix + self["extension"])
         self["file"] = temp_name
 
         if self["file"].absolute() in self._forbidden_files:
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/PartialChargeConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/PartialChargeConfigurator.py
index 5222728afb..a85bd46a9e 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/PartialChargeConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/PartialChargeConfigurator.py
@@ -40,7 +40,7 @@ def __init__(self, trajectory: Trajectory) -> None:
         for at_num, at in enumerate(system.atom_list):
             try:
                 self._original_map[at_num] = charges[at_num]
-            except:
+            except Exception:
                 self._original_map[at_num] = 0.0
         self._new_map = {}
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/ProjectionConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/ProjectionConfigurator.py
index 2c43de6d86..9c30229a49 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/ProjectionConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/ProjectionConfigurator.py
@@ -73,7 +73,7 @@ def configure(self, value):
                 return
             else:
                 if np.allclose(vector, 0):
-                    self.error_status = f"Vector of 0 length does not define projection"
+                    self.error_status = "Vector of 0 length does not define projection"
                     return
             try:
                 self["projector"].set_axis(vector)
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/QVectorsConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/QVectorsConfigurator.py
index 0434425c51..a9fde6687e 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/QVectorsConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/QVectorsConfigurator.py
@@ -67,13 +67,13 @@ def configure(self, value):
             )
             try:
                 generator.setup(parameters)
-            except:
+            except Exception:
                 self.error_status = f"Could not configure q vectors using {parameters}"
                 return
 
             try:
                 generator_success = generator.generate()
-            except:
+            except Exception:
                 self.error_status = "Q Vector parameters were parsed correctly, but caused an error. Invalid values?"
                 return
             else:
@@ -81,7 +81,7 @@ def configure(self, value):
                     self.error_status = "Q Vector parameters were parsed correctly, but caused an error. Invalid values?"
                     return
 
-            if not "q_vectors" in generator.configuration:
+            if "q_vectors" not in generator.configuration:
                 self.error_status = "Wrong inputs for q-vector generation. At the moment there are no valid Q points."
                 return
             elif not generator.configuration["q_vectors"]:
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py
index 11c00d616a..477524ac49 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/RangeConfigurator.py
@@ -19,7 +19,6 @@
 
 from MDANSE.Framework.Configurators.IConfigurator import (
     IConfigurator,
-    ConfiguratorError,
 )
 
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/RunningModeConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/RunningModeConfigurator.py
index 068bec5632..8527386db3 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/RunningModeConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/RunningModeConfigurator.py
@@ -45,7 +45,7 @@ def configure(self, value):
         else:
             mode = value[0].lower()
 
-        if not mode in self.availablesModes:
+        if mode not in self.availablesModes:
             self.error_status = f"{mode} is not a valid running mode."
             return
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/SingleChoiceConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/SingleChoiceConfigurator.py
index d651d3f6a1..e0258eb20e 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/SingleChoiceConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/SingleChoiceConfigurator.py
@@ -17,7 +17,6 @@
 
 from MDANSE.Framework.Configurators.IConfigurator import (
     IConfigurator,
-    ConfiguratorError,
 )
 
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/SingleOutputFileConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/SingleOutputFileConfigurator.py
index adf63c6fc7..578e9ad8d6 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/SingleOutputFileConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/SingleOutputFileConfigurator.py
@@ -74,7 +74,7 @@ def configure(self, value: Tuple[str, str]):
 
         try:
             PLATFORM.create_directory(dirname)
-        except:
+        except Exception:
             self.error_status = f"the directory {dirname} is not writable"
             return
 
@@ -97,7 +97,7 @@ def configure(self, value: Tuple[str, str]):
         self["extension"] = IFormat.create(format).extension
         temp_name = root
         if self["extension"] != root.suffix:
-            temp_name = temp_name.with_suffix(temp_name.suffix + self["extension"])
+            temp_name = root.with_suffix(root.suffix + self["extension"])
         self["file"] = temp_name
         self.error_status = "OK"
 
diff --git a/MDANSE/Src/MDANSE/Framework/Configurators/UnitCellConfigurator.py b/MDANSE/Src/MDANSE/Framework/Configurators/UnitCellConfigurator.py
index d2be900d67..2830bcf450 100644
--- a/MDANSE/Src/MDANSE/Framework/Configurators/UnitCellConfigurator.py
+++ b/MDANSE/Src/MDANSE/Framework/Configurators/UnitCellConfigurator.py
@@ -18,7 +18,6 @@
 
 from MDANSE.MLogging import LOG
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
-from MDANSE.Mathematics.LinearAlgebra import Vector
 
 
 class UnitCellConfigurator(IConfigurator):
@@ -56,7 +55,7 @@ def update_trajectory_information(self):
         try:
             first_cell = traj_config.unit_cell(0)._unit_cell
             last_cell = traj_config.unit_cell(len(traj_config) - 1)._unit_cell
-        except:
+        except Exception:
             has_valid_cell = False
         else:
             if first_cell is None:
@@ -98,7 +97,7 @@ def configure(self, value):
 
             try:
                 input_array = np.array(value[0], dtype=float)
-            except:
+            except Exception:
                 self.error_status = (
                     "Could not convert the inputs into a floating point array"
                 )
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/ASE.py b/MDANSE/Src/MDANSE/Framework/Converters/ASE.py
index bef661b957..b0aa8dd408 100644
--- a/MDANSE/Src/MDANSE/Framework/Converters/ASE.py
+++ b/MDANSE/Src/MDANSE/Framework/Converters/ASE.py
@@ -14,13 +14,10 @@
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 #
 import collections
-import os
 
 from ase.io import iread, read
-from ase.atoms import Atoms as ASEAtoms
 from ase.io.trajectory import Trajectory as ASETrajectory
 import numpy as np
-import h5py
 
 from MDANSE.Framework.AtomMapping import get_element_from_mapping
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
@@ -221,7 +218,7 @@ def run_step(self, index):
         except KeyError:
             try:
                 charges = frame.get_initial_charges()
-            except:
+            except Exception:
                 pass
             else:
                 self._trajectory.write_charges(charges, index)
@@ -257,7 +254,7 @@ def finalize(self):
     def parse_first_step(self, mapping):
         try:
             self._input = ASETrajectory(self.configuration["trajectory_file"]["value"])
-        except:
+        except Exception:
             first_frame = read(self.configuration["trajectory_file"]["value"], index=0)
             last_iterator = 0
             generator = iread(self.configuration["trajectory_file"]["value"])
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Converter.py b/MDANSE/Src/MDANSE/Framework/Converters/Converter.py
index c291fc7c4f..ba728b2e12 100644
--- a/MDANSE/Src/MDANSE/Framework/Converters/Converter.py
+++ b/MDANSE/Src/MDANSE/Framework/Converters/Converter.py
@@ -60,7 +60,7 @@ def finalize(self):
         try:
             output_file = h5py.File(self.configuration["output_files"]["file"], "a")
             # f = netCDF4.Dataset(self._trajectory.filename,'a')
-        except:
+        except Exception:
             LOG.warning("Skipping the finalize call in Converter")
             return
 
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/ImprovedASE.py b/MDANSE/Src/MDANSE/Framework/Converters/ImprovedASE.py
index 1b87541144..2f1d1678b3 100644
--- a/MDANSE/Src/MDANSE/Framework/Converters/ImprovedASE.py
+++ b/MDANSE/Src/MDANSE/Framework/Converters/ImprovedASE.py
@@ -204,7 +204,7 @@ def finalize(self):
         self._input.close()
         try:
             self._extra_input.close()
-        except:
+        except Exception:
             pass
         # Close the output trajectory.
         self._trajectory.write_standard_atom_database()
@@ -218,13 +218,13 @@ def extract_initial_information(self, ase_object):
         if self._fractionalCoordinates is None:
             try:
                 self._fractionalCoordinates = np.all(ase_object.get_pbc())
-            except:
+            except Exception:
                 pass
 
         if self._masses is None:
             try:
                 self._masses = ase_object.get_masses()
-            except:
+            except Exception:
                 pass
 
         if self.configuration["elements_from_mass"]["value"]:
@@ -236,7 +236,7 @@ def extract_initial_information(self, ase_object):
         else:
             try:
                 element_list = ase_object.get_chemical_symbols()
-            except:
+            except Exception:
                 pass
         if element_list is None:
             return
@@ -256,7 +256,7 @@ def parse_optional_config(self):
             )
         except FileNotFoundError:
             return
-        except:
+        except Exception:
             for file_format in self.configuration[
                 "configuration_file"
             ]._allowed_formats:
@@ -265,7 +265,7 @@ def parse_optional_config(self):
                         self.configuration["configuration_file"]["value"],
                         format=file_format,
                     )
-                except:
+                except Exception:
                     continue
                 else:
                     break
@@ -276,7 +276,7 @@ def parse_first_step(self):
         self.parse_optional_config()
         try:
             self._input = ASETrajectory(self.configuration["trajectory_file"]["value"])
-        except:
+        except Exception:
             self._input = iread(
                 self.configuration["trajectory_file"]["value"],
                 index="[:]",
diff --git a/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py b/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py
index b36f591d81..06557f1713 100644
--- a/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py
+++ b/MDANSE/Src/MDANSE/Framework/Converters/LAMMPS.py
@@ -51,7 +51,7 @@ def __init__(self, *args, **kwargs):
     def close(self):
         try:
             self._file.close()
-        except:
+        except Exception:
             LOG.error(f"Could not close file: {self._file}")
 
     def set_output(self, output_trajectory):
@@ -562,7 +562,7 @@ def parse_first_step(self, aliases, config):
         )
         try:
             self._charges_fixed = self._file["/particles/all/charge"][:]
-        except:
+        except Exception:
             pass
 
         full_cell *= measure(1.0, self._length_unit).toval("nm")
@@ -632,7 +632,7 @@ def run_step(self, index):
         if self._charges_fixed is None:
             try:
                 charge = self._file["/particles/all/charge/value"][index]
-            except:
+            except Exception:
                 pass
             else:
                 self._trajectory.write_charges(
diff --git a/MDANSE/Src/MDANSE/Framework/Handlers/ColorizingStreamHandler.py b/MDANSE/Src/MDANSE/Framework/Handlers/ColorizingStreamHandler.py
index 237bc46c31..ab3459ed7a 100644
--- a/MDANSE/Src/MDANSE/Framework/Handlers/ColorizingStreamHandler.py
+++ b/MDANSE/Src/MDANSE/Framework/Handlers/ColorizingStreamHandler.py
@@ -97,7 +97,7 @@ def emit(self, record):
             self.flush()
         except (KeyboardInterrupt, SystemExit):
             raise
-        except:
+        except Exception:
             self.handleError(record)
 
     if os.name != "nt":
diff --git a/MDANSE/Src/MDANSE/Framework/InputData/HDFTrajectoryInputData.py b/MDANSE/Src/MDANSE/Framework/InputData/HDFTrajectoryInputData.py
index c99672f784..fa10a77c2a 100644
--- a/MDANSE/Src/MDANSE/Framework/InputData/HDFTrajectoryInputData.py
+++ b/MDANSE/Src/MDANSE/Framework/InputData/HDFTrajectoryInputData.py
@@ -46,7 +46,7 @@ def info(self):
         val = []
         try:
             time_axis = self._data.time()
-        except:
+        except Exception:
             timeline = "No time information!\n"
         else:
             if len(time_axis) < 1:
@@ -64,7 +64,7 @@ def info(self):
         val.append(f"\tIs periodic: {'unit_cell' in self._data.file}\n")
         try:
             val.append(f"First unit cell (nm):\n{self._data.unit_cell(0)._unit_cell}\n")
-        except:
+        except Exception:
             val.append("No unit cell information\n")
         val.append("Frame times (1st, 2nd, ..., last) in ps:")
         val.append(timeline)
@@ -101,7 +101,7 @@ def check_metadata(self):
         def put_into_dict(name, obj):
             try:
                 string = obj[:][0].decode()
-            except:
+            except Exception:
                 LOG.debug(f"Decode failed for {name}: {obj}")
             else:
                 try:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py b/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py
index 2c19d0ba58..f507a4b399 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/AreaPerMolecule.py
@@ -141,7 +141,7 @@ def run_step(self, index):
             normalVect = np.cross(
                 unit_cell[self._axisIndexes[0]], unit_cell[self._axisIndexes[1]]
             )
-        except:
+        except Exception:
             raise AreaPerMoleculeError(
                 "The unit cell must be defined for AreaPerMolecule. "
                 "You can add a box using TrajectoryEditor."
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/AverageStructure.py b/MDANSE/Src/MDANSE/Framework/Jobs/AverageStructure.py
index f30e5ebdcd..32821eddff 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/AverageStructure.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/AverageStructure.py
@@ -109,7 +109,7 @@ def initialize(self):
             unit_cells = [
                 trajectory.unit_cell(frame)._unit_cell for frame in frame_range
             ]
-        except:
+        except Exception:
             raise ValueError(
                 "Unit cell needs to be defined for the AverageStructure analysis. "
                 "You can add a unit cell using TrajectoryEditor."
@@ -166,13 +166,13 @@ def finalize(self):
         Finalizes the calculations (e.g. averaging the total term, output files creations ...).
         """
 
-        trajectory = self.configuration["trajectory"]["instance"]
+        # trajectory = self.configuration["trajectory"]["instance"]
 
-        frame_range = range(
-            self.configuration["frames"]["first"],
-            self.configuration["frames"]["last"] + 1,
-            self.configuration["frames"]["step"],
-        )
+        # frame_range = range(
+        #     self.configuration["frames"]["first"],
+        #     self.configuration["frames"]["last"] + 1,
+        #     self.configuration["frames"]["step"],
+        # )
 
         average_unit_cell = np.mean(self._unit_cells, axis=0) * self._conversion_factor
 
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Density.py b/MDANSE/Src/MDANSE/Framework/Jobs/Density.py
index ac97da0fb0..e092d911d9 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/Density.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/Density.py
@@ -124,7 +124,7 @@ def run_step(self, index):
 
         try:
             cell_volume = conf.unit_cell.volume * measure(1.0, "nm3").toval("cm3")
-        except:
+        except Exception:
             raise DensityError(
                 "Density cannot be computed for chemical system without a defined simulation box. "
                 "You can add a box using TrajectoryEditor."
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/DensityProfile.py b/MDANSE/Src/MDANSE/Framework/Jobs/DensityProfile.py
index fa7332aa86..3d37d45595 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/DensityProfile.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/DensityProfile.py
@@ -100,7 +100,7 @@ def initialize(self):
 
         try:
             axis = first_conf.unit_cell.direct[axis_index, :]
-        except:
+        except Exception:
             raise DensityProfileError(
                 "Density profile cannot be computed without a simulation box. "
                 "You can add a box using TrajectoryEditor."
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/DistanceHistogram.py b/MDANSE/Src/MDANSE/Framework/Jobs/DistanceHistogram.py
index f5ddb7577d..462be1c99d 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/DistanceHistogram.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/DistanceHistogram.py
@@ -178,7 +178,7 @@ def run_step(self, index):
             inverse_cell = conf.unit_cell.transposed_inverse
 
             cell_volume = conf.unit_cell.volume
-        except:
+        except Exception:
             self.detailed_unit_cell_error()
         else:
             if cell_volume < 1e-9:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py
index 1feeadcf97..a88a5b58d8 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py
@@ -195,7 +195,7 @@ def run_step(self, index):
 
         shell = self.configuration["q_vectors"]["shells"][index]
 
-        if not shell in self.configuration["q_vectors"]["value"]:
+        if shell not in self.configuration["q_vectors"]["value"]:
             return index, None
 
         else:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/ElasticIncoherentStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/ElasticIncoherentStructureFactor.py
index face85b9aa..750c6eabd7 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/ElasticIncoherentStructureFactor.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/ElasticIncoherentStructureFactor.py
@@ -164,7 +164,7 @@ def run_step(self, index):
         atomicEISF = np.zeros((self._nQShells,), dtype=np.float64)
 
         for i, q in enumerate(self.configuration["q_vectors"]["shells"]):
-            if not q in self.configuration["q_vectors"]["value"]:
+            if q not in self.configuration["q_vectors"]["value"]:
                 continue
 
             qVectors = self.configuration["q_vectors"]["value"][q]["q_vectors"]
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py b/MDANSE/Src/MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py
index be158c6dab..615693c85d 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py
@@ -165,7 +165,7 @@ def finalize(self):
 
         if self.configuration["normalize"]["value"]:
             for element in nAtomsPerElement.keys():
-                if self._outputData[f"gacf_{element}}}"][0] == 0:
+                if self._outputData[f"gacf_{element}"][0] == 0:
                     raise ValueError("The normalization factor is equal to zero")
                 else:
                     self._outputData[f"gacf_{element}"] = normalize(
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py b/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py
index b087e71744..e0fc7ba377 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/IJob.py
@@ -114,7 +114,7 @@ def define_unique_name():
             # Followed by 4 random letters.
             name = key_generator(6, prefix=prefix)
 
-            if not name in registeredJobs:
+            if name not in registeredJobs:
                 break
 
         return name
@@ -413,7 +413,7 @@ def run(self, parameters, status=False):
 
             if self._status is not None:
                 self._status.finish()
-        except:
+        except Exception:
             tb = traceback.format_exc()
             LOG.critical(f"Job failed with traceback: {tb}")
             raise JobError(self, tb)
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/JobStatus.py b/MDANSE/Src/MDANSE/Framework/Jobs/JobStatus.py
index 408f0f6d3f..27110c9d9f 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/JobStatus.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/JobStatus.py
@@ -15,9 +15,6 @@
 #
 
 import collections
-import pickle
-import os
-import threading
 import time
 
 from MDANSE import PLATFORM
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py b/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py
index 9cf8acae1b..97862c0d9c 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/McStasVirtualInstrument.py
@@ -20,6 +20,7 @@
 import io
 from pathlib import Path
 from typing import Union
+from functools import partial
 
 import numpy as np
 
@@ -40,6 +41,10 @@
 NAVOGADRO = 6.02214129e23
 
 
+def _startswith(key: str, line: str) -> bool:
+    return line.strip().startswith(key)
+
+
 class McStasError(Error):
     pass
 
@@ -358,8 +363,8 @@ def convert(self, sim_dir: Union[Path, str]):
         if not sim_file:
             raise Exception(f"Dataset {sim_file} does not exist!")
 
-        isBegin = lambda line: line.strip().startswith("begin")
-        isCompFilename = lambda line: line.strip().startswith("filename:")
+        isBegin = partial(_startswith, "begin")
+        isCompFilename = partial(_startswith, "filename:")
         # First, determine if this is single or overview plot...
         SimFile = list(filter(isBegin, open(sim_file).readlines()))
         Datfile = 0
@@ -379,7 +384,7 @@ def convert(self, sim_dir: Union[Path, str]):
         if L == 0:
             """Scan view"""
             if Datfile == 0:
-                isFilename = lambda line: line.strip().startswith("filename")
+                isFilename = partial(_startswith, "filename")
 
                 Scanfile = list(filter(isFilename, open(sim_file).readlines()))
                 Scanfile = Scanfile[0].split(": ")
@@ -437,9 +442,9 @@ def save_single(self, FileStruct):
             # 2D data set
             mysize = FileStruct["data"].shape
 
-            I = FileStruct["data"]
-            mysize = I.shape
-            I = I.T
+            data = FileStruct["data"]
+            mysize = data.shape
+            data = data.T
 
             Xmin = eval(FileStruct["xylimits"].split()[0])
             Xmax = eval(FileStruct["xylimits"].split()[1])
@@ -464,7 +469,7 @@ def save_single(self, FileStruct):
             self._outputData.add(
                 title,
                 "SurfaceOutputVariable",
-                I,
+                data,
                 axis=f"{xlabel}|{ylabel}",
                 units="au",
                 main_result=True,
@@ -485,7 +490,7 @@ def read_monitor(self, simFile):
         """
 
         # Read header
-        isHeader = lambda line: line.startswith("#")
+        isHeader = partial(_startswith, "#")
         f = open(simFile)
         Lines = f.readlines()
         Header = list(filter(isHeader, Lines))
@@ -514,8 +519,8 @@ def read_monitor(self, simFile):
         f.close()
 
         header = True
-        for l in lines:
-            if l.startswith("#"):
+        for line in lines:
+            if line.startswith("#"):
                 if header:
                     continue
                 else:
@@ -523,7 +528,7 @@ def read_monitor(self, simFile):
             else:
                 if header:
                     header = False
-                data.append(l)
+                data.append(line)
 
         Filestruct["data"] = np.genfromtxt(io.StringIO(" ".join(data)))
         Filestruct["fullpath"] = simFile
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/OrderParameter.py b/MDANSE/Src/MDANSE/Framework/Jobs/OrderParameter.py
index 135c01898f..80222fc001 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/OrderParameter.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/OrderParameter.py
@@ -15,7 +15,6 @@
 #
 
 import collections
-import os
 
 import numpy as np
 
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py b/MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py
index ba4e25af63..2de79cee9b 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py
@@ -20,8 +20,8 @@
 
 import h5py
 
-from MDANSE.Mathematics.Geometry import center_of_mass
 from MDANSE.Framework.Jobs.IJob import IJob, JobError
+from MDANSE.Mathematics.Geometry import center_of_mass
 from MDANSE.Mathematics.LinearAlgebra import Quaternion, Vector
 from MDANSE.Mathematics.Transformation import Translation
 from MDANSE.MolecularDynamics.Configuration import RealConfiguration
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/StaticStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/StaticStructureFactor.py
index 9b0321681e..891ae9fedd 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/StaticStructureFactor.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/StaticStructureFactor.py
@@ -95,7 +95,7 @@ def initialize(self):
         conf = self.configuration["trajectory"]["instance"].configuration(frame_index)
         try:
             cell_volume = conf.unit_cell.volume
-        except:
+        except Exception:
             raise ValueError(
                 "Static Structure Factor cannot be computed for chemical system without a defined simulation box. "
                 "You can add a box using TrajectoryEditor."
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionDistinct.py b/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionDistinct.py
index a0aa77df39..93d281e043 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionDistinct.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionDistinct.py
@@ -274,7 +274,7 @@ def initialize(self):
         )
         try:
             cell_volume = conf.unit_cell.volume
-        except:
+        except Exception:
             self.detailed_unit_cell_error()
         else:
             if cell_volume < 1e-9:
@@ -480,11 +480,11 @@ def finalize(self):
             van_hove_inter = self.h_inter[idi, idj, ...] / fact[:, np.newaxis]
             van_hove_total = van_hove_intra + van_hove_inter
 
-            for i, van_hove in zip(
+            for i, van_h in zip(
                 ["intra", "inter", "total"],
                 [van_hove_intra, van_hove_inter, van_hove_total],
             ):
-                self._outputData[f"g(r,t)_{i}_{pair[0]}{pair[1]}"][...] = van_hove
+                self._outputData[f"g(r,t)_{i}_{''.join(pair)}"][...] = van_h
 
         weights = self.configuration["weights"].get_weights()
         for i in ["_intra", "_inter", ""]:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionSelf.py b/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionSelf.py
index 9d7b0749ad..6abb58a1b2 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionSelf.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/VanHoveFunctionSelf.py
@@ -148,7 +148,7 @@ def initialize(self):
         )
         try:
             cell_volume = conf.unit_cell.volume
-        except:
+        except Exception:
             self.detailed_unit_cell_error()
         else:
             if cell_volume < 1e-9:
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/Voronoi.py b/MDANSE/Src/MDANSE/Framework/Jobs/Voronoi.py
index 19dde6be18..bca7c95751 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/Voronoi.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/Voronoi.py
@@ -110,7 +110,7 @@ def initialize(self):
             self.cell_param = np.array(
                 [cell[0, 0], cell[1, 1], cell[2, 2]], dtype=np.float64
             )
-        except:
+        except Exception:
             raise VoronoiError(
                 "Voronoi analysis cannot be computed if simulation box is not defined. "
                 "You can add a box using TrajectoryEditor."
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
index 3e14db0c6e..2efef2951d 100644
--- a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
+++ b/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
@@ -210,12 +210,12 @@ def finalize(self):
         )
 
         xssfIntra = weight(
-            asf, self._outputData, nAtomsPerElement, 2, f"xssf_intra_%s%s"
+            asf, self._outputData, nAtomsPerElement, 2, "xssf_intra_%s%s"
         )
         self._outputData["xssf_intra"][:] = xssfIntra
 
         xssfInter = weight(
-            asf, self._outputData, nAtomsPerElement, 2, f"xssf_inter_%s%s"
+            asf, self._outputData, nAtomsPerElement, 2, "xssf_inter_%s%s"
         )
         self._outputData["xssf_inter"][:] = xssfInter
 
diff --git a/MDANSE/Src/MDANSE/Framework/QVectors/IQVectors.py b/MDANSE/Src/MDANSE/Framework/QVectors/IQVectors.py
index 573c1be92e..b3fadad0ee 100644
--- a/MDANSE/Src/MDANSE/Framework/QVectors/IQVectors.py
+++ b/MDANSE/Src/MDANSE/Framework/QVectors/IQVectors.py
@@ -48,7 +48,7 @@ def generate(self) -> bool:
             return True
         else:
             LOG.error(
-                f"Cannot generate vectors: q vector generator is not configured correctly."
+                "Cannot generate vectors: q vector generator is not configured correctly."
             )
             return False
 
diff --git a/MDANSE/Src/MDANSE/Framework/Session/CurrentSession.py b/MDANSE/Src/MDANSE/Framework/Session/CurrentSession.py
index 74619200a0..3864cd286e 100644
--- a/MDANSE/Src/MDANSE/Framework/Session/CurrentSession.py
+++ b/MDANSE/Src/MDANSE/Framework/Session/CurrentSession.py
@@ -52,4 +52,4 @@ def __init__(self, fname=None):
 
     def loadSettings(self, fname=None):
         if fname is not None:
-            source = json.load(fname)
+            json.load(fname)
diff --git a/MDANSE/Src/MDANSE/Framework/Units.py b/MDANSE/Src/MDANSE/Framework/Units.py
index 5083435d2f..c97e355889 100644
--- a/MDANSE/Src/MDANSE/Framework/Units.py
+++ b/MDANSE/Src/MDANSE/Framework/Units.py
@@ -710,7 +710,7 @@ def load(self):
         try:
             with open(UnitsManager._USER_DATABASE, "r") as fin:
                 d.update(json.load(fin))
-        except:
+        except Exception:
             self.save()
         finally:
             for uname, udict in list(d.items()):
diff --git a/MDANSE/Src/MDANSE/IO/FortranFormat.py b/MDANSE/Src/MDANSE/IO/FortranFormat.py
index 40943035e5..350b0c6fb3 100644
--- a/MDANSE/Src/MDANSE/IO/FortranFormat.py
+++ b/MDANSE/Src/MDANSE/IO/FortranFormat.py
@@ -92,13 +92,13 @@ def __init__(self, line, format, length=80):
                        extended by spaces to have the indicated length.
                        The default value of 80 is almost always correct.
         """
-        if type(line) == type(""):
+        if isinstance(line, str):
             self.text = line
             self.data = None
         else:
             self.text = None
             self.data = line
-        if type(format) == type(""):
+        if isinstance(format, str):
             self.format = FortranFormat(format)
         else:
             self.format = format
@@ -153,9 +153,9 @@ def _input(self):
             text = text + (self.length - len(text)) * " "
         self.data = []
         for field in self.format:
-            l = field[1]
-            s = text[:l]
-            text = text[l:]
+            w = field[1]
+            s = text[:w]
+            text = text[w:]
             type = field[0]
             value = None
             if type == "A":
@@ -171,7 +171,7 @@ def _input(self):
                     # catch this and set value to None
                     try:
                         value = int(s)
-                    except:
+                    except Exception:
                         value = None
             elif type == "D" or type == "E" or type == "F" or type == "G":
                 s = s.strip().lower()
@@ -183,7 +183,7 @@ def _input(self):
                 else:
                     try:
                         value = float(s)
-                    except:
+                    except Exception:
                         value = None
             if value is not None:
                 self.data.append(value)
@@ -206,7 +206,7 @@ def _output(self):
                 if type == "A":
                     try:
                         self.text = self.text + (value + length * " ")[:length]
-                    except:
+                    except Exception:
                         LOG.warning(self.text)
                         LOG.warning(value)
                         LOG.warning(length)
@@ -319,8 +319,8 @@ def __getitem__(self, i):
 
 if __name__ == "__main__":
     f = FortranFormat("'!!',D10.3,F10.3,G10.3,'!!'")
-    l = FortranLine([1.5707963, 3.14159265358, 2.71828], f)
-    print(str(l))
+    w = FortranLine([1.5707963, 3.14159265358, 2.71828], f)
+    print(str(w))
     f = FortranFormat("F12.0")
-    l = FortranLine("2.1D2", f)
-    print(l[0])
+    w = FortranLine("2.1D2", f)
+    print(w[0])
diff --git a/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py b/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py
index afb0b28d17..0baab13af8 100644
--- a/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py
+++ b/MDANSE/Src/MDANSE/IO/MinimalPDBReader.py
@@ -69,7 +69,7 @@ def __init__(self, filename: str):
             try:
                 ase_atoms = ase_read(filename, format="pdb", index=0)
                 cell = ase_atoms.get_cell()
-            except:
+            except Exception:
                 self.periodic = False
             else:
                 self.periodic = True
diff --git a/MDANSE/Src/MDANSE/IO/TextFile.py b/MDANSE/Src/MDANSE/IO/TextFile.py
index 6892a2d0d9..737ae0f8c5 100644
--- a/MDANSE/Src/MDANSE/IO/TextFile.py
+++ b/MDANSE/Src/MDANSE/IO/TextFile.py
@@ -21,18 +21,17 @@
 import os
 import sys
 from pathlib import Path
+from contextlib import suppress
 
 # Use the gzip module for Python version 1.5.2 or higher
-try:
-    _version = [int(c) for c in sys.version.split()[0].split(".")]
-
-    if _version >= [1, 5, 2]:
+with suppress(Exception):
+    if sys.version_info >= (1, 5, 2):
         try:
             import gzip
         except ImportError:
             gzip = None
-except:
-    gzip = None
+    else:
+        gzip = None
 
 
 class TextFile:
diff --git a/MDANSE/Src/MDANSE/Mathematics/LinearAlgebra.py b/MDANSE/Src/MDANSE/Mathematics/LinearAlgebra.py
index 6a76995f76..1f6ab71164 100644
--- a/MDANSE/Src/MDANSE/Mathematics/LinearAlgebra.py
+++ b/MDANSE/Src/MDANSE/Mathematics/LinearAlgebra.py
@@ -488,7 +488,7 @@ def __len__(self):
 
     def __getitem__(self, index):
         elements = self.array[index]
-        if type(elements) == type(self.array):
+        if type(elements) is type(self.array):
             return Tensor(elements)
         else:
             return elements
diff --git a/MDANSE/Src/MDANSE/Mathematics/Transformation.py b/MDANSE/Src/MDANSE/Mathematics/Transformation.py
index 4caed8011f..b2ed7a06a7 100644
--- a/MDANSE/Src/MDANSE/Mathematics/Transformation.py
+++ b/MDANSE/Src/MDANSE/Mathematics/Transformation.py
@@ -161,11 +161,11 @@ def inverse(self):
         return Translation(-self.vector)
 
     def screwMotion(self):
-        l = self.vector.length()
-        if l == 0.0:
+        length = self.vector.length()
+        if length == 0.0:
             return Vector(0.0, 0.0, 0.0), Vector(0.0, 0.0, 1.0), 0.0, 0.0
         else:
-            return Vector(0.0, 0.0, 0.0), self.vector / l, 0.0, l
+            return Vector(0.0, 0.0, 0.0), self.vector / length, 0.0, length
 
 
 #
diff --git a/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py b/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py
index 9cc8a5b725..4b6772b9e7 100644
--- a/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py
+++ b/MDANSE/Src/MDANSE/MolecularDynamics/Trajectory.py
@@ -149,7 +149,7 @@ def unit_cell(self, frame):
 
         return self._trajectory.unit_cell(frame)
 
-    def calculate_coordinate_span(self) -> np.ndarray:
+    def calculate_coordinate_span(self) -> None:
         min_span = np.array(3 * [1e11])
         max_span = np.zeros(3)
         for frame in range(len(self)):
@@ -873,9 +873,10 @@ def __init__(
             r = r - rcms
 
             r = r[:, np.newaxis, :]
-            r = fold_coordinates.fold_coordinates(
-                r, unit_cells, inverse_unit_cells, True
-            )
+            # Fold coordinates doesn't exist?
+            # r = fold_coordinates.fold_coordinates(
+            #     r, unit_cells, inverse_unit_cells, True
+            # )
             r = np.squeeze(r)
 
             r = self._trajectory.to_real_coordinates(r, first, last, step)
@@ -959,9 +960,9 @@ def read_atoms_trajectory(
     if last is None:
         last = len(trajectory)
 
-    nFrames = len(list(range(first, last, step)))
+    # nFrames = len(range(first, last, step))
 
-    serie = np.zeros((nFrames, 3), dtype=dtype)
+    # serie = np.zeros((nFrames, 3), dtype=dtype)
 
     if weights is None or len(atoms) == 1:
         weights = [1.0] * len(atoms)
diff --git a/MDANSE/Src/MDANSE/Scripts/mdanse.py b/MDANSE/Src/MDANSE/Scripts/mdanse.py
index 7f7b5d5ee6..d77b09b30d 100644
--- a/MDANSE/Src/MDANSE/Scripts/mdanse.py
+++ b/MDANSE/Src/MDANSE/Scripts/mdanse.py
@@ -131,7 +131,7 @@ def check_job(self, option, opt_str, value, parser):
             f.close()
 
         # If the file could not be opened/unpickled for whatever reason, try at the next checkpoint
-        except:
+        except Exception:
             raise CommandLineParserError(
                 f"The job {basename!r} could not be opened properly."
             )
@@ -193,7 +193,7 @@ def display_jobs_list(self, option, opt_str, value, parser):
                     info = pickle.load(f)
 
             # If the file could not be opened/unpickled for whatever reason, try at the next checkpoint
-            except:
+            except Exception:
                 continue
 
             # The job file could be opened and unpickled properly
@@ -364,7 +364,7 @@ def save_job_template(self, option, opt_str, value, parser):
 
         try:
             IJob.save_template(shortname, classname)
-        except (IOError, KeyError) as e:
+        except (IOError, KeyError):
             return
 
 
diff --git a/MDANSE/Src/MDANSE/Trajectory/H5MDTrajectory.py b/MDANSE/Src/MDANSE/Trajectory/H5MDTrajectory.py
index 241245aa52..a0695f067a 100644
--- a/MDANSE/Src/MDANSE/Trajectory/H5MDTrajectory.py
+++ b/MDANSE/Src/MDANSE/Trajectory/H5MDTrajectory.py
@@ -70,7 +70,7 @@ def __init__(self, h5_filename: Union[Path, str]):
         coords = self._h5_file["/particles/all/position/value"][0, :, :]
         try:
             pos_unit = self._h5_file["/particles/all/position/value"].attrs["unit"]
-        except:
+        except Exception:
             conv_factor = 1.0
         else:
             if pos_unit == "Ang":
@@ -85,12 +85,12 @@ def file_is_right(self, filename):
         result = True
         try:
             temp = h5py.File(filename)
-        except FileNotFoundError:
+        except Exception:
             result = False
         else:
             try:
                 temp["h5md"]
-            except KeyError:
+            except Exception:
                 result = False
         return result
 
@@ -111,26 +111,24 @@ def __getitem__(self, frame):
 
         grp = self._h5_file["/particles/all/position/value"]
         try:
-            pos_unit = self._h5_file["/particles/all/position/value"].attrs["unit"]
-        except:
+            pos_unit = grp.attrs["unit"]
+        except Exception:
             conv_factor = 1.0
         else:
             if pos_unit == "Ang":
                 pos_unit = "ang"
             conv_factor = measure(1.0, pos_unit).toval("nm")
         configuration = {}
-        configuration["coordinates"] = (
-            self._h5_file["/particles/all/position/value"][frame, :, :] * conv_factor
-        )
+        configuration["coordinates"] = grp[frame, :, :] * conv_factor
         try:
             try:
                 vel_unit = self._h5_file["/particles/all/velocity/value"].attrs["unit"]
-            except:
+            except Exception:
                 vel_unit = "ang/fs"
             configuration["velocities"] = self._h5_file[
                 "/particles/all/velocity/value"
             ][frame, :, :] * measure(1.0, vel_unit).toval("nm/ps")
-        except:
+        except Exception:
             pass
 
         configuration["time"] = self.time()[frame]
@@ -167,7 +165,7 @@ def charges(self, frame):
         except KeyError:
             LOG.debug(f"No charge information in trajectory {self._h5_filename}")
             charge = np.zeros(self._chemical_system.number_of_atoms)
-        except:
+        except Exception:
             try:
                 charge = self._h5_file["/particles/all/charge"][:]
             except KeyError:
@@ -190,7 +188,7 @@ def coordinates(self, frame):
             raise IndexError(f"Invalid frame number: {frame}")
         try:
             pos_unit = self._h5_file["/particles/all/position/value"].attrs["unit"]
-        except:
+        except Exception:
             conv_factor = 1.0
         else:
             if pos_unit == "Ang":
@@ -224,7 +222,7 @@ def configuration(self, frame):
             if k not in self._variables_to_skip:
                 try:
                     variables[k] = self.variable(k)[frame, :, :].astype(np.float64)
-                except:
+                except Exception:
                     self._variables_to_skip.append(k)
 
         coordinates = self.coordinates(frame)
@@ -243,7 +241,7 @@ def _load_unit_cells(self):
         self._unit_cells = []
         try:
             box_unit = self._h5_file["/particles/all/box/edges/value"].attrs["unit"]
-        except:
+        except Exception:
             conv_factor = 1.0
         else:
             if box_unit == "Ang":
@@ -270,13 +268,13 @@ def _load_unit_cells(self):
     def time(self):
         try:
             time_unit = self._h5_file["/particles/all/position/time"].attrs["unit"]
-        except:
+        except Exception:
             conv_factor = 1.0
         else:
             conv_factor = measure(1.0, time_unit).toval("ps")
         try:
             time = self._h5_file["/particles/all/position/time"] * conv_factor
-        except:
+        except Exception:
             time = []
         return time
 
@@ -366,7 +364,7 @@ def read_com_trajectory(
         grp = self._h5_file["/particles/all/position/value"]
         try:
             pos_unit = self._h5_file["/particles/all/position/value"].attrs["unit"]
-        except:
+        except Exception:
             conv_factor = 1.0
         else:
             if pos_unit == "Ang":
@@ -464,7 +462,7 @@ def read_atomic_trajectory(
         grp = self._h5_file["/particles/all/position/value"]
         try:
             pos_unit = self._h5_file["/particles/all/position/value"].attrs["unit"]
-        except:
+        except Exception:
             conv_factor = 1.0
         else:
             if pos_unit == "Ang":
diff --git a/MDANSE/Src/MDANSE/Trajectory/MdanseTrajectory.py b/MDANSE/Src/MDANSE/Trajectory/MdanseTrajectory.py
index 431eb6fa6f..23e634de12 100644
--- a/MDANSE/Src/MDANSE/Trajectory/MdanseTrajectory.py
+++ b/MDANSE/Src/MDANSE/Trajectory/MdanseTrajectory.py
@@ -64,7 +64,7 @@ def file_is_right(self, filename: Union[Path, str]):
         result = True
         try:
             file_object = h5py.File(filename)
-        except FileNotFoundError:
+        except Exception:
             result = False
         else:
             try:
diff --git a/MDANSE/pyproject.toml b/MDANSE/pyproject.toml
index 95bc164b60..434f12b335 100644
--- a/MDANSE/pyproject.toml
+++ b/MDANSE/pyproject.toml
@@ -57,3 +57,50 @@ MDANSE = ["Chemistry/*.json",
 
 [project.scripts]
 mdanse = "MDANSE.Scripts.mdanse:main"
+
+[tool.ruff]
+line-length = 100
+indent-width = 4
+target-version = "py39"
+extend-exclude = [
+    "Src/MDANSE/Framework/Jobs/RigidBodyTrajectory.py",
+    "Src/MDANSE/MolecularDynamics/Trajectory.py",
+]
+
+[tool.ruff.lint]
+select = [
+    "E4", "E7", "E9", "F",  # Defaults
+    # "PL",  # Pylint errors
+    # "E",   # Pycodestyle
+    # "W",   # Pycodestyle warnings
+    # "F",   # Pyflakes
+    # "B",   # Flake8 bugbear
+    # "SIM", # Flake8 Simplify
+    # "A",   # Flake8 builtins
+    # "COM", # Flake8 commas
+    # "ISC", # Flake8 implicit string concat
+    # "RSE", # Flake8 raise
+    # "FA",  # Flake8 future
+    # "FBT", # Flake8 boolean trap
+    # "C4",  # Flake8 comprehensions
+    # "Q",   # Flake8 Quotes
+    # "RET", # Flake8 return
+    # "ARG", # Flake8 unused args
+    # "PTH", # Flake8 use pathlib
+    # "I",   # Isort
+    # "RUF", # Ruff specific
+    # "FURB",# Refurb
+    # "PERF",# Perflint
+    # "D",   # Pydocstyle
+    # "UP",  # Pyupgrade
+]
+ignore = [
+    "F401",     # Unused import in init
+    "E402",     # Import not at top
+    "PLR0913",  # Too many arguments
+    "PLR0912",  # Too many branches
+    "PLR0915",  # Too many statements
+]
+
+# [tool.setuptools.packages.find]
+# where = ["src"]