Merge branch 'main' into main

Author: MartinBaGar

docs/examples/examples.yml

@@ -1,3 +1,8 @@
+- title: EvolutionaryScale.ai
+  description: Images and videos created for the EvolutionScale.ai landing page
+  path: https://www.evolutionaryscale.ai/
+  image: https://imgur.com/2zXf8ng.png
+
 - title:  Your Operating System ｜Eukaryotic Transcription 
   author: Clockwork
   description: 🧬How does your DNA actually become who you are? Let's go on the incredible journey it takes to transcribe your DNA into mRNA.

docs/generate.py

@@ -1,13 +1,14 @@
-import bpy
 import pathlib
 
-import molecularnodes as mn
+import bpy
 import nodepad
 
+import molecularnodes as mn
+
 DOCS_FOLDER = pathlib.Path(__file__).resolve().parent
 
 # load the data file which contains all of the nodes to build docs for
-bpy.ops.wm.open_mainfile(filepath=mn.utils.MN_DATA_FILE)
+bpy.ops.wm.open_mainfile(filepath=str(mn.assets.MN_DATA_FILE))
 
 
 header = """---
@@ -56,14 +57,14 @@
     file.write(
         "### Residue Names\n\n" "| Name | Integer |\n" "|----------:|:------------|\n"
     )
-    for name, res in mn.data.residues.items():
+    for name, res in mn.assets.data.residues.items():
         file.write(f"| {name} | `{res['res_name_num']}::Int` |\n")
     file.write("\n")
     file.write("\n")
 
     file.write(
         "### Atom Names\n\n" "| Name | Integer |\n" "|----------:|:------------|\n"
     )
-    for name, value in mn.data.atom_names.items():
+    for name, value in mn.assets.data.atom_names.items():
         file.write(f"| {name} | `{value}::Int` |\n")
     file.write("\n")

molecularnodes/__init__.py

@@ -1,6 +1,7 @@
-from .addon import register, unregister
+from . import assets, blender, color, session, ui
+from .assets import template
 from .entities import fetch, parse
-from . import color, blender
+from .ui.addon import register, unregister
 
 try:
     from .scene import Canvas

molecularnodes/assets/__init__.py

@@ -0,0 +1,8 @@
+from pathlib import Path
+
+from .template import install, uninstall
+from . import data
+
+ASSET_DIR = Path(__file__).resolve().parent
+ADDON_DIR = ASSET_DIR.parent
+MN_DATA_FILE = ASSET_DIR / "MN_data_file_4.2.blend"

molecularnodes/data.py renamed to molecularnodes/assets/data.py

@@ -0,0 +1,42 @@
+import shutil
+from pathlib import Path
+import bpy
+
+
+SUBFOLDER = "Molecular Nodes"
+
+
+def is_installed():
+    base_path = Path(
+        bpy.utils.user_resource(
+            "SCRIPTS", path=str(Path("startup") / "bl_app_templates_user"), create=False
+        )
+    )
+    molecular_nodes_path = base_path / "Molecular Nodes"
+    return molecular_nodes_path.exists()
+
+
+def install():
+    base_path = Path(
+        bpy.utils.user_resource(
+            "SCRIPTS", path=str(Path("startup") / "bl_app_templates_user"), create=True
+        )
+    )
+
+    base_path.mkdir(parents=True, exist_ok=True)
+    path_app_templates = base_path / SUBFOLDER
+    path_app_templates.mkdir(parents=True, exist_ok=True)
+    startup_file = Path(__file__).parent / "template/startup.blend"
+    shutil.copy(startup_file, path_app_templates)
+    bpy.utils.refresh_script_paths()
+
+
+def uninstall():
+    for folder in bpy.utils.app_template_paths():
+        path = Path(folder).absolute() / SUBFOLDER
+        if "Molecular Nodes" not in str(path):
+            continue
+
+        if path.exists():
+            shutil.rmtree(path)
+    bpy.utils.refresh_script_paths()

molecularnodes/assets/template.py

@@ -1,6 +1,6 @@
 from bpy.types import Material
 from databpy.material import append_from_blend
-from ..utils import MN_DATA_FILE
+from ..assets import MN_DATA_FILE
 
 MATERIAL_NAMES = [
     "MN Default",
@@ -13,7 +13,7 @@
 
 def append(name: str) -> Material:
     "Append a material from the MN_DATA_FILE."
-    return append_from_blend(name, MN_DATA_FILE)
+    return append_from_blend(name, str(MN_DATA_FILE))
 
 
 def add_all_materials() -> None:

molecularnodes/blender/material.py

@@ -13,7 +13,7 @@
 )
 
 from .. import color, utils
-from ..utils import MN_DATA_FILE
+from ..assets import MN_DATA_FILE
 from . import material, mesh
 
 NODE_WIDTH = 180
@@ -214,8 +214,8 @@ def swap(node: bpy.types.GeometryNode, tree: str | bpy.types.GeometryNodeTree) -
 
 def append(name: str, link: bool = False) -> bpy.types.GeometryNodeTree:
     "Append a GN node from the MN data file"
-    GN_TREES_PATH = os.path.join(MN_DATA_FILE, "NodeTree")
-    return append_from_blend(name, filepath=GN_TREES_PATH, link=link)
+    GN_TREES_PATH = MN_DATA_FILE / "NodeTree"
+    return append_from_blend(name, filepath=str(GN_TREES_PATH), link=link)
 
 
 def MN_micrograph_material():
@@ -360,7 +360,7 @@ def create_starting_node_tree(
     coll_frames: bpy.types.Collection | None = None,
     style: str = "spheres",
     name: str | None = None,
-    color: str = "common",
+    color: str | None = "common",
     material: str = "MN Default",
     is_modifier: bool = True,
 ):

molecularnodes/blender/nodes.py

@@ -1,13 +1,11 @@
 from . import molecule, trajectory, interaction
 from .base import EntityType, MolecularEntity
-from .density import MN_OT_Import_Map
 from .ensemble import CellPack, Ensemble, StarFile
-from .ensemble.ui import MN_OT_Import_Cell_Pack, MN_OT_Import_Star_File
 from .molecule import BCIF, CIF, PDB, SDF, Molecule
 from .molecule.pdb import PDB
 from .molecule.pdbx import BCIF, CIF
 from .molecule.sdf import SDF
-from .molecule.ui import fetch, load_local, parse
+from .molecule.io import fetch, load_local, parse
 from .trajectory import OXDNA, Trajectory
 from .trajectory.dna import MN_OT_Import_OxDNA_Trajectory
 
@@ -21,4 +19,4 @@
     + trajectory.CLASSES
     + molecule.CLASSES
     + interaction.CLASSES
-)
+)

molecularnodes/entities/__init__.py

@@ -1,3 +1,3 @@
-from .ui import MN_OT_Import_Map, load
+from .io import load
 from .mrc import MRC
 from .base import Density