more refactoring

molecularnodes/blender/__init__.py

@@ -1,19 +1 @@
-from pathlib import Path
-from typing import Union
-import bpy
-
-
-def path_resolve(path: Union[str, Path]) -> Path:
-    if isinstance(path, str):
-        return Path(bpy.path.abspath(path))
-    elif isinstance(path, Path):
-        return Path(bpy.path.abspath(str(path)))
-    else:
-        raise ValueError(f"Unable to resolve path: {path}")
-
-
-def active_object(context: bpy.types.Context = None) -> bpy.types.Object:
-    if context is None:
-        return bpy.context.active_object
-
-    return context.active_object
+from .utils import path_resolve

molecularnodes/blender/databpy/attribute.py → molecularnodes/blender/bpyd/attribute.py

@@ -1,11 +1,26 @@
 from dataclasses import dataclass
 from enum import Enum
 from typing import Type
-from .utils import evaluate_object
-
 import bpy
 import numpy as np
 
+from pathlib import Path
+
+
+def evaluate_object(obj: bpy.types.Object):
+    "Return an object which has the modifiers evaluated."
+    obj.update_tag()
+    return obj.evaluated_get(bpy.context.evaluated_depsgraph_get())
+
+
+def path_resolve(path: str | Path) -> Path:
+    if isinstance(path, str):
+        return Path(bpy.path.abspath(path))
+    elif isinstance(path, Path):
+        return Path(bpy.path.abspath(str(path)))
+    else:
+        raise ValueError(f"Unable to resolve path: {path}")
+
 
 @dataclass
 class AttributeTypeInfo:
@@ -161,6 +176,21 @@ def dtype(self) -> Type:
     def n_values(self) -> int:
         return np.prod(self.shape, dtype=int)
 
+    @classmethod
+    def from_object(
+        cls,
+        obj: bpy.types.Object,
+        name: str,
+        atype: AttributeType,
+        domain: DomainType,
+    ):
+        att = obj.data.get(name)
+        if att is None:
+            att = obj.data.attributes.new(
+                name=name, type=atype.value.type_name, domain=domain.value.name
+            )
+        return Attribute(att)
+
     def from_array(self, array: np.ndarray) -> None:
         """
         Set the attribute data from a numpy array
@@ -250,7 +280,7 @@ def store_named_attribute(
         )
 
     # the 'foreach_set' requires a 1D array, regardless of the shape of the attribute
-    # it also requires the order to be 'c' or blender might crash!!
+    # so we have to flatten it first
     attribute.data.foreach_set(atype.value.value_name, data.reshape(-1))
 
     # The updating of data doesn't work 100% of the time (see:

molecularnodes/blender/databpy/object.py → molecularnodes/blender/bpyd/object.py

@@ -1,7 +1,8 @@
 import bpy
 import numpy as np
-from typing import Union, Optional
+from typing import Optional
 from .attribute import (
+    evaluate_object,
     AttributeTypes,
     AttributeType,
     Domains,
@@ -124,25 +125,22 @@ def create_object(
     return obj
 
 
+def active_object(context: bpy.types.Context = None) -> bpy.types.Object:
+    if context is None:
+        return bpy.context.active_object
+
+    return context.active_object
+
+
 class BlenderObject:
     """
     A convenience class for working with Blender objects
     """
 
-    def __init__(self, object: bpy.types.Object | None):
-        self._object = object
-
-    def store_named_attribute(
-        self,
-        data: np.ndarray,
-        name: str,
-        atype: str | AttributeType | None = None,
-        domain: str | DomainType = Domains.POINT,
-    ) -> None:
-        attribute.store_named_attribute(
-            self.object, data=data, name=name, atype=atype, domain=domain
-        )
-        return self
+    def __init__(self, obj: bpy.types.Object | None):
+        if not isinstance(obj, bpy.types.Object):
+            raise ValueError(f"{obj} must be a Blender object of type bpy.types.Object")
+        self._object = obj
 
     @property
     def object(self) -> bpy.types.Object:
@@ -157,6 +155,39 @@ def object(self) -> bpy.types.Object:
     def object(self, value: bpy.types.Object) -> None:
         self._object = value
 
+    def store_named_attribute(
+        self,
+        data: np.ndarray,
+        name: str,
+        atype: str | AttributeType | None = None,
+        domain: str | DomainType = Domains.POINT,
+    ) -> None:
+        """
+        Parameters
+        ----------
+        data : np.ndarray
+            The data to be stored as an attribute.
+        name : str
+            The name for the attribute. Will overwrite an already existing attribute.
+        atype : str or AttributeType or None, optional
+            The attribute type to store the data as. Either string or selection from the
+            AttributeTypes enum. None will attempt to infer the attribute type from the
+            input array.
+        domain : str or DomainType, optional
+            The domain to store the attribute on. Defaults to Domains.POINT.
+
+        Returns
+        -------
+        self
+        """
+        attribute.store_named_attribute(
+            self.object, data=data, name=name, atype=atype, domain=domain
+        )
+        return self
+
+    def evaluate(self):
+        return BlenderObject(evaluate_object(self.object))
+
     def named_attribute(self, name: str, evaluate: bool = False) -> np.ndarray:
         return attribute.named_attribute(self.object, name=name, evaluate=evaluate)
 
@@ -203,3 +234,6 @@ def selected_positions(self, mask: Optional[np.ndarray] = None) -> np.ndarray:
             return self.position[np.logical_and(self.selected, mask)]
 
         return self.position[self.selected]
+
+    def __len__(self) -> int:
+        return len(self.object.data.vertices)

molecularnodes/blender/mesh.py

@@ -1,19 +1,9 @@
-from typing import Optional
-
 import bpy
 import numpy as np
 
 from . import coll, nodes
-from .databpy.attribute import (
-    Attribute,
-    AttributeMismatchError,
-    AttributeTypes,
-    guess_atype_from_array,
-    store_named_attribute,
-    named_attribute,
-)
-from .databpy.object import ObjectTracker, create_object
-from .databpy.utils import evaluate_object
+from .bpyd.attribute import AttributeTypes, evaluate_object
+from .bpyd.object import ObjectTracker, create_object, BlenderObject
 
 
 def centre(position: np.ndarray):
@@ -95,7 +85,7 @@ def create_data_object(array, collection=None, name="DataObject", world_scale=0.
     if not collection:
         collection = coll.data()
 
-    obj = create_object(locations, collection=collection, name=name)
+    bob = BlenderObject(create_object(locations, collection=collection, name=name))
 
     attributes = [
         ("rotation", AttributeTypes.QUATERNION),
@@ -114,6 +104,6 @@ def create_data_object(array, collection=None, name="DataObject", world_scale=0.
         if np.issubdtype(data.dtype, str):
             data = np.unique(data, return_inverse=True)[1]
 
-        store_named_attribute(obj=obj, data=data, name=column, atype=type)
+        bob.store_named_attribute(data=data, name=column, atype=type)
 
-    return obj
+    return bob.object

molecularnodes/blender/nodes.py

@@ -13,6 +13,7 @@
 
 from .. import color, utils
 from . import mesh
+from . import bpyd
 import re
 
 NODE_WIDTH = 180
@@ -725,7 +726,7 @@ def create_assembly_node_tree(
             "name": "assembly_id",
             "type": "NodeSocketInt",
             "min": 1,
-            "max": max(mesh.named_attribute(data_object, "assembly_id")),
+            "max": max(bpyd.named_attribute(data_object, "assembly_id")),
             "default": 1,
         },
     )

molecularnodes/blender/utils.py

@@ -0,0 +1,11 @@
+import bpy
+from pathlib import Path
+
+
+def path_resolve(path: str | Path) -> Path:
+    if isinstance(path, str):
+        return Path(bpy.path.abspath(path))
+    elif isinstance(path, Path):
+        return Path(bpy.path.abspath(str(path)))
+    else:
+        raise ValueError(f"Unable to resolve path: {path}")

molecularnodes/blender_manifest.toml

@@ -35,17 +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/colorama-0.4.6-py2.py3-none-any.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/cycler-0.12.1-py3-none-any.whl",
 	"./wheels/fasteners-0.19-py3-none-any.whl",
-	"./wheels/fonttools-4.54.0-cp311-cp311-macosx_10_9_universal2.whl",
-	"./wheels/fonttools-4.54.0-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/fonttools-4.54.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/fonttools-4.54.0-cp311-cp311-win_amd64.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/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",
@@ -62,17 +61,17 @@ wheels = [
 	"./wheels/msgpack-1.1.0-cp311-cp311-macosx_11_0_arm64.whl",
 	"./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-3.3-py3-none-any.whl",
+	"./wheels/networkx-3.4.2-py3-none-any.whl",
 	"./wheels/packaging-24.1-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",
 	"./wheels/pandas-2.2.3-cp311-cp311-win_amd64.whl",
-	"./wheels/pillow-10.4.0-cp311-cp311-macosx_10_10_x86_64.whl",
-	"./wheels/pillow-10.4.0-cp311-cp311-macosx_11_0_arm64.whl",
-	"./wheels/pillow-10.4.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
-	"./wheels/pillow-10.4.0-cp311-cp311-win_amd64.whl",
-	"./wheels/pyparsing-3.1.4-py3-none-any.whl",
+	"./wheels/pillow-11.0.0-cp311-cp311-macosx_10_10_x86_64.whl",
+	"./wheels/pillow-11.0.0-cp311-cp311-macosx_11_0_arm64.whl",
+	"./wheels/pillow-11.0.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+	"./wheels/pillow-11.0.0-cp311-cp311-win_amd64.whl",
+	"./wheels/pyparsing-3.2.0-py3-none-any.whl",
 	"./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl",
 	"./wheels/pytz-2024.2-py2.py3-none-any.whl",
 	"./wheels/scipy-1.14.1-cp311-cp311-macosx_10_13_x86_64.whl",
@@ -82,7 +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-4.66.5-py3-none-any.whl",
+	"./wheels/tqdm-4.66.6-py3-none-any.whl",
 	"./wheels/typing_extensions-4.12.2-py3-none-any.whl",
 	"./wheels/tzdata-2024.2-py2.py3-none-any.whl",
 ]

molecularnodes/entities/ensemble/cellpack.py

@@ -8,7 +8,7 @@
 from .cif import OldCIF
 from ..molecule import molecule
 from ... import blender as bl
-from ...blender.databpy import store_named_attribute, AttributeTypes
+from ...blender.bpyd import store_named_attribute, AttributeTypes
 from ... import color
 
 

molecularnodes/entities/ensemble/star.py

@@ -7,7 +7,7 @@
 from PIL import Image
 
 from ... import blender as bl
-from ...blender.databpy import AttributeTypes, store_named_attribute, BlenderObject
+from ...blender.bpyd import AttributeTypes, store_named_attribute, BlenderObject
 from .ensemble import Ensemble
 
 

molecularnodes/entities/entity.py

@@ -2,7 +2,7 @@
 import bpy
 from uuid import uuid1
 from .. import blender as bl
-from ..blender.databpy import (
+from ..blender.bpyd import (
     AttributeTypes,
     BlenderObject,
 )

molecularnodes/entities/molecule/molecule.py

@@ -13,7 +13,7 @@
 
 from ... import blender as bl
 from ... import color, data, utils
-from ...blender.databpy import Domains, AttributeTypes, BlenderObject
+from ...blender.bpyd import Domains, AttributeTypes, BlenderObject
 from ..entity import MolecularEntity
 
 

molecularnodes/entities/trajectory/dna.py

@@ -2,7 +2,7 @@
 import bpy
 from ... import color
 from ...blender import mesh, coll, nodes
-from ...blender.databpy import store_named_attribute, AttributeTypes
+from ...blender.bpyd import store_named_attribute, AttributeTypes
 
 bpy.types.Scene.MN_import_oxdna_topology = bpy.props.StringProperty(
     name="Toplogy",

molecularnodes/entities/trajectory/trajectory.py

@@ -8,7 +8,7 @@
 from ... import data
 from ..entity import MolecularEntity
 from ...blender import coll, mesh, nodes, path_resolve
-from ...blender import databpy as db
+from ...blender import bpyd as db
 from ...utils import lerp, correct_periodic_positions
 from .selections import Selection, TrajectorySelectionItem