fix lint problems

molecularnodes/io/parse/mda.py

@@ -150,16 +150,18 @@ def bonds(self) -> List[List[int]]:
     def elements(self) -> List[str]:
         try:
             elements = self.ag.elements.tolist()
-        except:
+        except AttributeError:  # If 'elements' attribute doesn't exist
             try:
                 elements = [
                     x
                     if x in data.elements.keys()
                     else mda.topology.guessers.guess_atom_element(x)
                     for x in self.ag.atoms.names
                 ]
-
-            except:
+            except (
+                KeyError,
+                ValueError,
+            ):  # If 'x' is not in 'data.elements.keys()' or 'guess_atom_element(x)' fails
                 elements = ["X"] * self.ag.n_atoms
         return elements
 
@@ -671,7 +673,13 @@ def in_memory(
             if add_occupancy:
                 try:
                     obj.set_attribute(frame, "occupancy", ts.data["occupancy"])
-                except:
+                except KeyError:
+                    print("KeyError: 'occupancy' not found in ts.data")
+                    add_occupancy = False
+                except TypeError:
+                    print(
+                        "TypeError: ts.data is not a dictionary or similar mapping type"
+                    )
                     add_occupancy = False
 
         # disable the frames collection from the viewer

molecularnodes/io/parse/molecule.py

@@ -679,9 +679,11 @@ def att_sec_struct():
             )
             if verbose:
                 print(f'Added {att["name"]} after {time.process_time() - start} s')
-        except:
+        except (TypeError, KeyError) as e:
             if verbose:
-                warnings.warn(f"Unable to add attribute: {att['name']}")
+                warnings.warn(
+                    f"Unable to add attribute: {att['name']}. Error: {str(e)}"
+                )
                 print(
                     f'Failed adding {att["name"]} after {time.process_time() - start} s'
                 )

molecularnodes/ui/panel.py

@@ -119,7 +119,7 @@ def panel_object(layout, context):
     if mol_type == "md":
         layout.prop(object.mn, "subframes")
     if mol_type == "star":
-        layout.label(text=f"Ensemble")
+        layout.label(text="Ensemble")
         box = layout.box()
         ui_from_node(box, nodes.get_star_node(object))
         return

molecularnodes/utils.py

@@ -117,16 +117,32 @@ def _install_template(filepath, subfolder="", overwrite=True):
     if not os.path.isdir(path_app_templates):
         try:
             os.makedirs(path_app_templates, exist_ok=True)
-        except:
+        except PermissionError:
+            print(
+                "Permission denied: You do not have the necessary permissions to create the directory."
+            )
+            traceback.print_exc()
+        except OSError as e:
+            print(f"OS error: {e}")
             traceback.print_exc()
 
     app_templates_old = set(os.listdir(path_app_templates))
 
-    # check to see if the file is in compressed format (.zip)
     if zipfile.is_zipfile(filepath):
         try:
             file_to_extract = zipfile.ZipFile(filepath, "r")
-        except:
+        except FileNotFoundError:
+            print("File not found: The specified file does not exist.")
+            traceback.print_exc()
+            return {"CANCELLED"}
+        except PermissionError:
+            print(
+                "Permission denied: You do not have the necessary permissions to open the file."
+            )
+            traceback.print_exc()
+            return {"CANCELLED"}
+        except zipfile.BadZipFile:
+            print("Bad zip file: The file is not a zip file or it is corrupted.")
             traceback.print_exc()
             return {"CANCELLED"}
 
@@ -143,7 +159,14 @@ def _install_template(filepath, subfolder="", overwrite=True):
 
         try:  # extract the file to "bl_app_templates_user"
             file_to_extract.extractall(path_app_templates)
-        except:
+        except PermissionError:
+            print(
+                "Permission denied: You do not have the necessary permissions to write to the directory."
+            )
+            traceback.print_exc()
+            return {"CANCELLED"}
+        except OSError as e:
+            print(f"OS error: {e}")
             traceback.print_exc()
             return {"CANCELLED"}
 

tests/test_mda.py

@@ -47,7 +47,7 @@ def test_create_mda_session(self, mda_session):
 
     def reload_mda_session(self, mda_session):
         with pytest.warns(UserWarning, match="The existing mda session"):
-            mda_session_2 = mn.mda.create_session()
+            mn.mda.create_session()
 
     @pytest.mark.parametrize("in_memory", [False, True])
     def test_show_universe(
@@ -281,7 +281,7 @@ def test_create_mda_session(self, mda_session):
 
     def reload_mda_session(self, mda_session):
         with pytest.warns(UserWarning, match="The existing mda session"):
-            mda_session_2 = mn.mda.create_session()
+            mn.mda.create_session()
 
     def test_frame_mapping(self, mda_session, universe):
         remove_all_molecule_objects(mda_session)

tests/test_nodes.py

@@ -168,7 +168,6 @@ def test_color_entity(snapshot_custom: NumpySnapshotExtension):
 
 
 def get_links(sockets):
-    links = []
     for socket in sockets:
         for link in socket.links:
             yield link

tests/test_star.py

@@ -1,6 +1,7 @@
 import bpy
 import pytest
 import starfile
+import importlib
 from scipy.spatial.transform import Rotation as R
 
 import molecularnodes as mn
@@ -29,9 +30,7 @@ def test_starfile_attributes(type):
         ].to_numpy()
 
     # Calculate Scipy rotation from the euler angles
-    rot_from_euler = quats = R.from_euler(
-        seq="ZYZ", angles=euler_angles, degrees=True
-    ).inv()
+    rot_from_euler = R.from_euler(seq="ZYZ", angles=euler_angles, degrees=True).inv()
 
     # Activate the rotation debug mode in the nodetreee and get the quaternion attribute
     debugnode = mn.blender.nodes.star_node(ensemble.node_group).node_tree.nodes[
@@ -83,7 +82,9 @@ def test_micrograph_loading():
     assert ensemble.star_node.inputs["Micrograph"].default_value.name == "montage.tiff"
 
 
-@pytest.mark.skipif(SKIP, reason="Test may segfault on GHA")
+@pytest.mark.skipif(
+    importlib.util.find_spec("pyopenvdb"), reason="Test may segfault on GHA"
+)
 def test_rehydration(tmp_path):
     bpy.ops.wm.read_homefile()
     ensemble = mn.io.star.load(data_dir / "cistem.star")