Add ruff as lintr and code formatter

.github/workflows/ruff.yml

@@ -0,0 +1,8 @@
+name: Ruff
+on: [ push, pull_request ]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

build.py

@@ -5,19 +5,23 @@
 # zips up the template file
 def zip_template():
     # Define the directory and zip file paths
-    dir_path = 'molecularnodes/assets/template/Molecular Nodes'
-    zip_file_path = 'molecularnodes/assets/template/Molecular Nodes.zip'
+    dir_path = "molecularnodes/assets/template/Molecular Nodes"
+    zip_file_path = "molecularnodes/assets/template/Molecular Nodes.zip"
 
     # Create a ZipFile object in write mode
-    with zipfile.ZipFile(zip_file_path, 'w', zipfile.ZIP_DEFLATED) as zipf:
+    with zipfile.ZipFile(zip_file_path, "w", zipfile.ZIP_DEFLATED) as zipf:
         # Walk the directory tree and add files to the zip file
         for root, dirs, files in os.walk(dir_path):
             for file in files:
                 # Get the path of the file
                 file_path = os.path.join(root, file)
                 # Add the file to the zip file
-                zipf.write(file_path, arcname=os.path.relpath(
-                    file_path, start='molecularnodes/assets/template/'))
+                zipf.write(
+                    file_path,
+                    arcname=os.path.relpath(
+                        file_path, start="molecularnodes/assets/template/"
+                    ),
+                )
 
 
 if __name__ == "__main__":

molecularnodes/blender/bones.py

@@ -11,7 +11,7 @@ def clear_armature(object):
             object.modifiers.remove(mod)
 
 
-def add_bones(object, name='armature'):
+def add_bones(object, name="armature"):
     # creates bones and assigns correct weights
 
     clear_armature(object)
@@ -20,27 +20,25 @@ def add_bones(object, name='armature'):
 
     armature = create_bones(bone_positions, chain_ids)
     for i in range(bone_weights.shape[1]):
-        group = object.vertex_groups.new(name=f'mn_armature_{i}')
+        group = object.vertex_groups.new(name=f"mn_armature_{i}")
         vertex_indices = np.where(bone_weights[:, i] == 1)[0]
-        group.add(vertex_indices.tolist(), 1, 'ADD')
+        group.add(vertex_indices.tolist(), 1, "ADD")
 
     object.select_set(True)
     armature.select_set(True)
     bpy.context.view_layer.objects.active = armature
-    bpy.ops.object.parent_set(type='ARMATURE')
+    bpy.ops.object.parent_set(type="ARMATURE")
 
     bpy.context.view_layer.objects.active = object
-    bpy.ops.object.modifier_move_to_index(
-        'EXEC_DEFAULT', modifier="Armature", index=0)
+    bpy.ops.object.modifier_move_to_index("EXEC_DEFAULT", modifier="Armature", index=0)
 
     return armature
 
 
 def get_bone_positions(object):
-
     positions, atom_name, chain_id, res_id, sec_struct = [
         obj.get_attribute(object, att)
-        for att in ['position', 'atom_name', 'chain_id', 'res_id', 'sec_struct']
+        for att in ["position", "atom_name", "chain_id", "res_id", "sec_struct"]
     ]
 
     is_alpha_carbon = atom_name == 2
@@ -59,17 +57,16 @@ def get_bone_positions(object):
 
 
 def get_bone_weights(object):
-    print('hello world')
-
+    print("hello world")
 
-def create_bones(positions, chain_ids, name='armature'):
 
-    bpy.ops.object.add(type='ARMATURE', enter_editmode=True)
+def create_bones(positions, chain_ids, name="armature"):
+    bpy.ops.object.add(type="ARMATURE", enter_editmode=True)
     object = bpy.context.active_object
     object.name = name
     coll.armature().objects.link(object)
     armature = object.data
-    armature.name = f'{name}_frame'
+    armature.name = f"{name}_frame"
     arm_name = armature.name
     bones = []
     # add bones
@@ -96,7 +93,7 @@ def create_bones(positions, chain_ids, name='armature'):
         armature.edit_bones.active = armature.edit_bones[bone_a]
         for bone in [bone_a, bone_b]:
             armature.edit_bones[bone].select = True
-        bpy.ops.armature.parent_set(type='CONNECTED')
+        bpy.ops.armature.parent_set(type="CONNECTED")
         for bone in [bone_a, bone_b]:
             armature.edit_bones[bone].select = False
     bpy.ops.object.editmode_toggle()
@@ -105,12 +102,14 @@ def create_bones(positions, chain_ids, name='armature'):
 
 
 class MN_MT_Add_Armature(bpy.types.Operator):
-    bl_idname = 'mn.add_armature'
-    bl_label = 'Add Armature'
-    bl_description = 'Automatically add armature for each amino acid of the structure   '
+    bl_idname = "mn.add_armature"
+    bl_label = "Add Armature"
+    bl_description = (
+        "Automatically add armature for each amino acid of the structure   "
+    )
 
     def execute(self, context):
         object = context.active_object
         add_bones(bpy.data.objects[object.name], name=object.name)
 
-        return {'FINISHED'}
+        return {"FINISHED"}

molecularnodes/blender/coll.py

@@ -4,17 +4,17 @@
 def mn():
     """Return the MolecularNodes Collection
 
-    The collection called 'MolecularNodes' inside the Blender scene is returned. If the 
+    The collection called 'MolecularNodes' inside the Blender scene is returned. If the
     collection does not exist first, it is created.
     """
-    coll = bpy.data.collections.get('MolecularNodes')
+    coll = bpy.data.collections.get("MolecularNodes")
     if not coll:
-        coll = bpy.data.collections.new('MolecularNodes')
+        coll = bpy.data.collections.new("MolecularNodes")
         bpy.context.scene.collection.children.link(coll)
     return coll
 
 
-def armature(name='MN_armature'):
+def armature(name="MN_armature"):
     coll = bpy.data.collections.get(name)
     if not coll:
         coll = bpy.data.collections.new(name)
@@ -23,8 +23,7 @@ def armature(name='MN_armature'):
 
 
 def data(suffix=""):
-    """A collection for storing MN related data objects.
-    """
+    """A collection for storing MN related data objects."""
     name = f"MN_data{suffix}"
 
     collection = bpy.data.collections.get(name)
@@ -33,7 +32,9 @@ def data(suffix=""):
         mn().children.link(collection)
 
         # disable the view of the data collection
-        bpy.context.view_layer.layer_collection.children['MolecularNodes'].children[name].exclude = True
+        bpy.context.view_layer.layer_collection.children["MolecularNodes"].children[
+            name
+        ].exclude = True
     return collection
 
 
@@ -42,7 +43,7 @@ def frames(name="", parent=None, suffix="_frames"):
 
     Args:
         name (str, optional): Name of the collection for the frames. Defaults to "".
-        parent (_type_, optional): A blender collection which will become the parent 
+        parent (_type_, optional): A blender collection which will become the parent
         collection. Defaults to the MolecularNodes collection if None.
     """
     coll_frames = bpy.data.collections.new(name + suffix)

molecularnodes/blender/node.py

@@ -1,14 +1,10 @@
 from abc import ABCMeta
-from typing import Optional, Any
-import warnings
-import time
 import numpy as np
 import bpy
 
 
 class Node(metaclass=ABCMeta):
     def __init__(self, node: bpy.types.Node, chain=[]):
-
         self.node = node
         self.group = node.id_data
         self.chain = chain
@@ -20,18 +16,15 @@ def location(self):
     def new(self, name):
         "Add a new node to the node group."
         try:
-            return self.group.nodes.new(f'GeometryNode{name}')
+            return self.group.nodes.new(f"GeometryNode{name}")
         except RuntimeError:
-            return self.group.nodes.new(f'ShaderNode{name}')
+            return self.group.nodes.new(f"ShaderNode{name}")
 
     def link(self, name, linkto=0, linkfrom=0):
         "Create a new node along in the chain and create a link to it. Return the new node."
         new_node = self.new(name)
         new_node.location = self.location + np.array((200, 0))
 
-        self.group.links.new(
-            self.node.outputs[linkfrom],
-            new_node.inputs[linkto]
-        )
+        self.group.links.new(self.node.outputs[linkfrom], new_node.inputs[linkto])
 
         return Node(new_node, chain=self.chain + [self])