Merge branch 'main' into docs-example-listing

.github/workflows/test-addon.yml

@@ -13,7 +13,7 @@ jobs:
             max-parallel: 4
             fail-fast: false
             matrix:
-              blender-version: ["4.2"]
+              version: ["4.2", "4.3"]
               os: [ubuntu-latest, macos-14, windows-latest]
         steps:
             - uses: actions/checkout@v4
@@ -32,7 +32,7 @@ jobs:
               if: matrix.os == 'ubuntu-latest'
               run: |
                 if [[ ! -f ./blender.tar.xz ]]; then
-                  wget -nv https://download.blender.org/release/Blender4.2/blender-4.2.0-linux-x64.tar.xz -O ./blender.tar.xz
+                  wget -nv https://download.blender.org/release/Blender${{ matrix.version }}/blender-${{ matrix.version }}.0-linux-x64.tar.xz -O ./blender.tar.xz
                 fi
                 mkdir -p ./blender
                 ls -lrta
@@ -45,33 +45,33 @@ jobs:
             - name: Test in Blender MacOS ARM
               if: matrix.os == 'macos-14'
               run: |
-                curl -L -o blender.dmg https://download.blender.org/release/Blender4.2/blender-4.2.0-macos-arm64.dmg
+                curl -L -o blender.dmg https://download.blender.org/release/Blender${{ matrix.version }}/blender-${{ matrix.version }}.0-macos-arm64.dmg
                 hdiutil attach blender.dmg
                 cp -R /Volumes/Blender/Blender.app /Applications/
                 hdiutil detach /Volumes/Blender
                 /Applications/Blender.app/Contents/MacOS/Blender --version
                 /Applications/Blender.app/Contents/MacOS/Blender -b --python tests/install.py
                 /Applications/Blender.app/Contents/MacOS/Blender -b --python tests/run.py -- -v tests/
-            
+                        
             - name: Test in Blender Windows
               if: matrix.os == 'windows-latest'
               shell: pwsh
               run: |
-                Invoke-WebRequest -Uri "https://download.blender.org/release/Blender4.2/blender-4.2.0-windows-x64.zip" -OutFile "blender.zip"
+                Invoke-WebRequest -Uri "https://download.blender.org/release/Blender${{ matrix.version }}/blender-${{ matrix.version }}.0-windows-x64.zip" -OutFile "blender.zip"
                 Expand-Archive -Path "blender.zip" -DestinationPath "blender"
-                .\blender\blender-4.2.0-windows-x64\blender.exe --version
-                .\blender\blender-4.2.0-windows-x64\blender.exe -b --python tests/install.py
-                .\blender\blender-4.2.0-windows-x64\blender.exe -b --python tests/run.py -- -v tests/
-
+                $blenderPath = Get-ChildItem -Path "blender" -Directory | Select-Object -First 1
+                .\blender\blender-${{ matrix.version }}.0-windows-x64\blender.exe --version
+                .\blender\blender-${{ matrix.version }}.0-windows-x64\blender.exe -b --python tests/install.py
+                .\blender\blender-${{ matrix.version }}.0-windows-x64\blender.exe -b --python tests/run.py -- -v tests/
     
             - name: Expose coverage as a CI download 
               uses: actions/upload-artifact@v4
-              if: matrix.os == 'ubuntu-latest'
+              if: matrix.os == 'ubuntu-latest' && matrix.version == '4.2'
               with:
                 name: coverage.xml
                 path: coverage.xml
 
             - name: Upload coverage reports to Codecov
               if: matrix.os == 'ubuntu-latest'
               uses: codecov/codecov-action@v3
-
+

molecularnodes/__init__.py

@@ -13,7 +13,8 @@
 
 import bpy
 from bpy.app.handlers import frame_change_post, load_post, save_post
-
+from bpy.props import PointerProperty, CollectionProperty
+from .handlers import update_trajectories
 from . import entities, operators, props, session, ui
 from .utils import add_current_module_to_path
 from .ui import pref
@@ -24,8 +25,8 @@
     ui.CLASSES
     + operators.CLASSES
     + entities.CLASSES
+    + props.CLASSES
     + [
-        props.MolecularNodesObjectProperties,
         MN_PT_Scene,
     ]
     + pref.CLASSES
@@ -56,14 +57,13 @@ def register():
 
     save_post.append(session._pickle)
     load_post.append(session._load)
-    frame_change_post.append(entities.trajectory.handlers.update_trajectories)
+    frame_change_post.append(update_trajectories)
 
     bpy.types.Scene.MNSession = session.MNSession()
-    bpy.types.Object.mn = bpy.props.PointerProperty(
-        type=props.MolecularNodesObjectProperties
-    )
-    bpy.types.Object.mn_trajectory_selections = bpy.props.CollectionProperty(
-        type=entities.trajectory.selections.TrajectorySelectionItem
+    bpy.types.Object.mn = PointerProperty(type=props.MolecularNodesObjectProperties)
+    bpy.types.Scene.mn = PointerProperty(type=props.MolecularNodesSceneProperties)
+    bpy.types.Object.mn_trajectory_selections = CollectionProperty(
+        type=entities.trajectory.props.TrajectorySelectionItem
     )
 
 
@@ -81,7 +81,8 @@ def unregister():
 
     save_post.remove(session._pickle)
     load_post.remove(session._load)
-    frame_change_post.remove(entities.trajectory.handlers.update_trajectories)
+    frame_change_post.remove(update_trajectories)
     del bpy.types.Scene.MNSession
+    del bpy.types.Scene.mn
     del bpy.types.Object.mn
     del bpy.types.Object.mn_trajectory_selections

molecularnodes/blender/nodes.py

@@ -92,7 +92,7 @@ def set_selection(group, node, selection):
 
 
 def create_debug_group(name="MolecularNodesDebugGroup"):
-    group = new_group(name=name, fallback=False)
+    group = new_tree(name=name, fallback=False)
     info = group.nodes.new("GeometryNodeObjectInfo")
     group.links.new(info.outputs["Geometry"], group.nodes["Group Output"].inputs[0])
     return group
@@ -231,7 +231,9 @@ def MN_micrograph_material():
     return bpy.data.materials[mat_name]
 
 
-def new_group(name="Geometry Nodes", geometry=True, fallback=True):
+def new_tree(
+    name: str = "Geometry Nodes", geometry: bool = True, fallback: bool = True
+) -> bpy.types.GeometryNodeTree:
     group = bpy.data.node_groups.get(name)
     # if the group already exists, return it and don't create a new one
     if group and fallback:
@@ -307,7 +309,7 @@ def create_starting_nodes_starfile(object, n_images=1):
     node_name = f"MN_starfile_{object.name}"
 
     # create a new GN node group, specific to this particular molecule
-    group = new_group(node_name)
+    group = new_tree(node_name)
     node_mod.node_group = group
     link = group.links.new
 
@@ -327,7 +329,7 @@ def create_starting_nodes_density(object, threshold=0.8, style="density_surface"
     node_name = f"MN_density_{object.name}"
 
     # create a new GN node group, specific to this particular molecule
-    group = new_group(node_name, fallback=False)
+    group = new_tree(node_name, fallback=False)
     link = group.links.new
     mod.node_group = group
 
@@ -345,7 +347,12 @@ def create_starting_nodes_density(object, threshold=0.8, style="density_surface"
 
 
 def create_starting_node_tree(
-    object, coll_frames=None, style="spheres", name=None, color="common"
+    object: bpy.types.Object,
+    coll_frames: bpy.types.Collection | None = None,
+    style: str = "spheres",
+    name: str = None,
+    color: str = "common",
+    is_modifier: bool = True,
 ):
     """
     Create a starting node tree for the inputted object.
@@ -375,37 +382,36 @@ def create_starting_node_tree(
 
     # create a new GN node group, specific to this particular molecule
     mod = get_mod(object)
-    group = new_group(name)
-    link = group.links.new
-    mod.node_group = group
+    tree = new_tree(name)
+    tree.is_modifier = is_modifier
+    link = tree.links.new
+    mod.node_group = tree
 
     # move the input and output nodes for the group
-    node_input = get_input(group)
-    node_output = get_output(group)
+    node_input = get_input(tree)
+    node_output = get_output(tree)
     node_input.location = [0, 0]
     node_output.location = [700, 0]
 
-    node_style = add_custom(group, styles_mapping[style], [450, 0])
+    node_style = add_custom(tree, styles_mapping[style], [450, 0])
     link(node_style.outputs[0], node_output.inputs[0])
     link(node_input.outputs[0], node_style.inputs[0])
 
     # if requested, setup the nodes for generating colors in the node tree
     if color is not None:
         if color == "common":
-            node_color_set = add_custom(group, "Set Color", [200, 0])
-            node_color_common = add_custom(group, "Color Common", [-50, -150])
-            node_random_color = add_custom(
-                group, "Color Attribute Random", [-300, -150]
-            )
+            node_color_set = add_custom(tree, "Set Color", [200, 0])
+            node_color_common = add_custom(tree, "Color Common", [-50, -150])
+            node_random_color = add_custom(tree, "Color Attribute Random", [-300, -150])
 
             link(node_input.outputs["Geometry"], node_color_set.inputs[0])
             link(node_random_color.outputs["Color"], node_color_common.inputs["Carbon"])
             link(node_color_common.outputs[0], node_color_set.inputs["Color"])
             link(node_color_set.outputs[0], node_style.inputs[0])
             to_animate = node_color_set
         elif color.lower() == "plddt":
-            node_color_set = add_custom(group, "Set Color", [200, 0])
-            node_color_plddt = add_custom(group, "Color pLDDT", [-50, -150])
+            node_color_set = add_custom(tree, "Set Color", [200, 0])
+            node_color_plddt = add_custom(tree, "Color pLDDT", [-50, -150])
 
             link(node_input.outputs["Geometry"], node_color_set.inputs["Atoms"])
             link(node_color_plddt.outputs[0], node_color_set.inputs["Color"])
@@ -420,8 +426,8 @@ def create_starting_node_tree(
         node_output.location = [1100, 0]
         node_style.location = [800, 0]
 
-        node_animate_frames = add_custom(group, "Animate Frames", [500, 0])
-        node_animate = add_custom(group, "Animate Value", [500, -300])
+        node_animate_frames = add_custom(tree, "Animate Frames", [500, 0])
+        node_animate = add_custom(tree, "Animate Value", [500, -300])
 
         node_animate_frames.inputs["Frames"].default_value = coll_frames
         node_animate.inputs["Value Max"].default_value = len(coll_frames.objects) - 1
@@ -451,7 +457,7 @@ def split_geometry_to_instances(name, iter_list=("A", "B", "C"), attribute="chai
     define how many times to create the required nodes.
 
     """
-    group = new_group(name)
+    group = new_tree(name)
     node_input = get_input(group)
     node_output = get_output(group)
 
@@ -515,7 +521,7 @@ def create_assembly_node_tree(
     if existing_node_tree:
         return existing_node_tree
 
-    tree: bpy.types.NodeTree = new_group(name=node_group_name)
+    tree: bpy.types.NodeTree = new_tree(name=node_group_name)
     link = tree.links.new
 
     node_split = add_custom(tree, "Split to Centred Instances", [-150, 0])
@@ -683,7 +689,7 @@ def custom_iswitch(
         return tree
 
     socket_type = socket_types[dtype]
-    tree = new_group(name, geometry=False, fallback=False)
+    tree = new_tree(name, geometry=False, fallback=False)
 
     # try creating the node group, otherwise on fail cleanup the created group and
     # report the error

molecularnodes/blender_manifest.toml

@@ -1,7 +1,7 @@
 schema_version = "1.0.0"
 
 id = "molecularnodes"
-version = "4.2.8"
+version = "4.2.9"
 name = "Molecular Nodes"
 tagline = "A toolbox for molecular import and animation in Blender"
 maintainer = "Brady Johnston<[email protected]>"
@@ -35,16 +35,16 @@ wheels = [
 	"./wheels/biotite-0.41.2-cp311-cp311-macosx_11_0_arm64.whl",
 	"./wheels/biotite-0.41.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
 	"./wheels/biotite-0.41.2-cp311-cp311-win_amd64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-macosx_10_9_x86_64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/contourpy-1.3.0-cp311-cp311-win_amd64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-macosx_10_9_x86_64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-macosx_11_0_arm64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/contourpy-1.3.1-cp311-cp311-win_amd64.whl",
 	"./wheels/cycler-0.12.1-py3-none-any.whl",
 	"./wheels/fasteners-0.19-py3-none-any.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-macosx_10_9_universal2.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/fonttools-4.54.1-cp311-cp311-win_amd64.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-macosx_10_9_universal2.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-macosx_10_9_x86_64.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/fonttools-4.55.0-cp311-cp311-win_amd64.whl",
 	"./wheels/joblib-1.4.2-py3-none-any.whl",
 	"./wheels/kiwisolver-1.4.7-cp311-cp311-macosx_10_9_x86_64.whl",
 	"./wheels/kiwisolver-1.4.7-cp311-cp311-macosx_11_0_arm64.whl",
@@ -62,7 +62,7 @@ wheels = [
 	"./wheels/msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
 	"./wheels/msgpack-1.1.0-cp311-cp311-win_amd64.whl",
 	"./wheels/networkx-3.4.2-py3-none-any.whl",
-	"./wheels/packaging-24.1-py3-none-any.whl",
+	"./wheels/packaging-24.2-py3-none-any.whl",
 	"./wheels/pandas-2.2.3-cp311-cp311-macosx_10_9_x86_64.whl",
 	"./wheels/pandas-2.2.3-cp311-cp311-macosx_11_0_arm64.whl",
 	"./wheels/pandas-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
@@ -81,7 +81,7 @@ wheels = [
 	"./wheels/six-1.16.0-py2.py3-none-any.whl",
 	"./wheels/starfile-0.5.6-py3-none-any.whl",
 	"./wheels/threadpoolctl-3.5.0-py3-none-any.whl",
-	"./wheels/tqdm-4.66.6-py3-none-any.whl",
+	"./wheels/tqdm-4.67.1-py3-none-any.whl",
 	"./wheels/typing_extensions-4.12.2-py3-none-any.whl",
 	"./wheels/tzdata-2024.2-py2.py3-none-any.whl",
 ]

molecularnodes/bpyd/object.py

@@ -428,14 +428,14 @@ def list_attributes(
             A list of attribute names if the molecule object exists, None otherwise.
         """
         if evaluate:
-            strings = list(self.evaluate().attributes.keys())
+            strings = list(self.evaluate().object.data.attributes.keys())
         else:
-            strings = list(self.object.attributes.keys())
+            strings = list(self.object.data.attributes.keys())
 
         if not drop_hidden:
             return strings
         else:
-            return filter(lambda x: not x.startswith("."), strings)
+            return [x for x in strings if not x.startswith(".")]
 
     def __len__(self) -> int:
         """

molecularnodes/entities/ensemble/cellpack.py

@@ -97,7 +97,7 @@ def _create_data_object(self, name="DataObject"):
     def _setup_node_tree(self, name="CellPack", fraction=1.0, as_points=False):
         mod = bl.nodes.get_mod(self.data_object)
 
-        group = bl.nodes.new_group(name=f"MN_ensemble_{name}", fallback=False)
+        group = bl.nodes.new_tree(name=f"MN_ensemble_{name}", fallback=False)
         mod.node_group = group
 
         node_pack = bl.nodes.add_custom(group, "Ensemble Instance", location=[-100, 0])

molecularnodes/entities/ensemble/cif.py

@@ -30,16 +30,15 @@ def _get_structure(self, extra_fields: str = None, sec_struct=True, bonds=True):
         # which can be extracted with the get_component()
         try:
             array = pdbx.get_structure(self.file, extra_fields=extra_fields)
-            try:
-                array.set_annotation(
-                    "sec_struct", _get_secondary_structure(array, self.file)
-                )
-            except KeyError:
-                warnings.warn("No secondary structure information.")
-            try:
-                array.set_annotation("entity_id", _get_entity_id(array, self.file))
-            except KeyError:
-                warnings.warn("Non entity_id information.")
+            annotations = {
+                "sec_struct": _get_secondary_structure,
+                "entity_id": _get_entity_id,
+            }
+            for key, func in annotations.items():
+                try:
+                    array.set_annotation(key, func(array, self.file))
+                except KeyError:
+                    pass
 
         except InvalidFileError:
             array = pdbx.get_component(self.file)

molecularnodes/entities/molecule/molecule.py

@@ -137,6 +137,10 @@ def n_models(self):
         else:
             return self.array.shape[0]
 
+    @property
+    def tree(self) -> bpy.types.GeometryNodeTree:
+        return self.object.modifiers["MolecularNodes"].node_group
+
     @property
     def chain_ids(self) -> Optional[list]:
         """