GitHub Actions: Let's turn ruff green again

.github/workflows/python-package.yml

@@ -1,7 +1,7 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will install Python dependencies, run tests, and lint with a variety of Python versions
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
-name: PACKMAN Contineous Integration 
+name: PACKMAN Continuous Integration 
 
 on:
   push:
@@ -13,20 +13,20 @@ jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - run: pip install --user ruff
-    - run: ruff --exit-zero --line-length=1100 --target-version=py37 --statistics . | sort -k 2
-    - run: ruff --ignore=E402,E701,E722,E741,F401,F403,F841
-                --format=github --line-length=1100 --target-version=py37 .
+    - run: ruff --exit-zero --line-length=320 --target-version=py38 --statistics . | sort -k 2
+    - run: ruff --ignore=E402,E501,E701,E722,E741,F401,F403,F841
+                --output-format=github --target-version=py38 .
 
   build:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:

packman/molecule/atom.py

@@ -201,7 +201,7 @@ def get_bond(self,atom2):
         """
         if(type(atom2) == type(self)):
             None
-        elif(type(atom2) ==int):
+        elif(isinstance(atom2, int)):
             Model = self.get_parent().get_parent().get_parent()
             atom2 = Model.get_atom(atom2)
         else:

packman/molecule/model.py

@@ -320,15 +320,15 @@ def get_torsion(self, bond, neighbor1=None, neighbor2=None, radians=True):
             logging.error('neighbour2 not selected. Options available for neighbour2: ' + ', '.join( [str(i) for i in self.__ModelGraph[atom2.get_id()] if i != atom1.get_id() ]  ) )
             return None
 
-        if(type(neighbor1)==int):
+        if(isinstance(neighbor1, int)):
             neighbor1 = self.__AllAtoms[neighbor1]
         elif(type(neighbor1)==type(atom1)):
             None
         else:
             logging.error('neighbour1 should either be an integer or a packman.molecule.Atom object.')
             return None
 
-        if(type(neighbor2)==int):
+        if(isinstance(neighbor2, int)):
             neighbor2 = self.__AllAtoms[neighbor2]
         elif(type(neighbor2)==type(atom2)):
             None
@@ -448,15 +448,15 @@ def set_torsion(self, bond, theta, neighbor1=None, neighbor2=None, radians=True)
             logging.error('neighbour2 not selected. Options available for neighbour2: ' + ', '.join( [str(i) for i in self.__ModelGraph[atom2.get_id()] if i != atom1.get_id() ]  ) )
             return None
 
-        if(type(neighbor1)==int):
+        if(isinstance(neighbor1, int)):
             neighbor1 = self.__AllAtoms[neighbor1]
         elif(type(neighbor1)==type(atom1)):
             None
         else:
             logging.error('neighbour1 should either be an integer or a packman.molecule.Atom object.')
             return None
 
-        if(type(neighbor2)==int):
+        if(isinstance(neighbor2, int)):
             neighbor2 = self.__AllAtoms[neighbor2]
         elif(type(neighbor2)==type(atom2)):
             None
@@ -718,4 +718,4 @@ def check_clashes(self,distance=0.77):
         from scipy.spatial import KDTree
         all_atoms=[i for i in self.get_atoms()]
         T=KDTree([i.get_location() for i in all_atoms])
-        return len(T.query_pairs(distance))
+        return len(T.query_pairs(distance))