5.0

.claude/commands/opsx/apply.md → .agents/skills/source-command-opsx-apply/SKILL.md

@@ -1,10 +1,14 @@
 ---
-name: "OPSX: Apply"
-description: Implement tasks from an OpenSpec change (Experimental)
-category: Workflow
-tags: [workflow, artifacts, experimental]
+name: "source-command-opsx-apply"
+description: "Implement tasks from an OpenSpec change (Experimental)"
 ---
 
+# source-command-opsx-apply
+
+Use this skill when the user asks to run the migrated source command `opsx-apply`.
+
+## Command Template
+
 Implement tasks from an OpenSpec change.
 
 **Input**: Optionally specify a change name (e.g., `/opsx:apply add-auth`). If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes.

.claude/commands/opsx/archive.md → .agents/skills/source-command-opsx-archive/SKILL.md

@@ -1,10 +1,14 @@
 ---
-name: "OPSX: Archive"
-description: Archive a completed change in the experimental workflow
-category: Workflow
-tags: [workflow, archive, experimental]
+name: "source-command-opsx-archive"
+description: "Archive a completed change in the experimental workflow"
 ---
 
+# source-command-opsx-archive
+
+Use this skill when the user asks to run the migrated source command `opsx-archive`.
+
+## Command Template
+
 Archive a completed change in the experimental workflow.
 
 **Input**: Optionally specify a change name after `/opsx:archive` (e.g., `/opsx:archive add-auth`). If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes.

.claude/commands/opsx/explore.md → .agents/skills/source-command-opsx-explore/SKILL.md

@@ -1,10 +1,14 @@
 ---
-name: "OPSX: Explore"
+name: "source-command-opsx-explore"
 description: "Enter explore mode - think through ideas, investigate problems, clarify requirements"
-category: Workflow
-tags: [workflow, explore, experimental, thinking]
 ---
 
+# source-command-opsx-explore
+
+Use this skill when the user asks to run the migrated source command `opsx-explore`.
+
+## Command Template
+
 Enter explore mode. Think deeply. Visualize freely. Follow the conversation wherever it goes.
 
 **IMPORTANT: Explore mode is for thinking, not implementing.** You may read files, search code, and investigate the codebase, but you must NEVER write code or implement features. If the user asks you to implement something, remind them to exit explore mode first and create a change proposal. You MAY create OpenSpec artifacts (proposals, designs, specs) if the user asks—that's capturing thinking, not implementing.

.claude/commands/opsx/propose.md → .agents/skills/source-command-opsx-propose/SKILL.md

@@ -1,10 +1,14 @@
 ---
-name: "OPSX: Propose"
-description: Propose a new change - create it and generate all artifacts in one step
-category: Workflow
-tags: [workflow, artifacts, experimental]
+name: "source-command-opsx-propose"
+description: "Propose a new change - create it and generate all artifacts in one step"
 ---
 
+# source-command-opsx-propose
+
+Use this skill when the user asks to run the migrated source command `opsx-propose`.
+
+## Command Template
+
 Propose a new change - create the change and generate all artifacts in one step.
 
 I'll create a change with artifacts:

.gitignore

@@ -1,7 +1,7 @@
 # Tempary files
 temp
 sandbox.*
-notes/
+/notes/
 
 # Environments
 .env
@@ -22,11 +22,11 @@ secrets/
 SECRETS/
 secrets.bak/
 
-# Claude
+# Claude Code
+.claude/settings.local.json
 .claudian
 
 # Obsidian
-
 .obsidian/*
 !.obsidian/snippets
 !.obsidian/app.json
@@ -389,8 +389,4 @@ dist
 # Vite files
 vite.config.js.timestamp-*
 vite.config.ts.timestamp-*
-.vite/
-
-
-# Scipy
-!scipy_ndimage/*/**
+.vite/

README.md

@@ -38,11 +38,6 @@ If you want to cite this work, you can cite it from Zenodo:
 
 [![DOI](https://zenodo.org/badge/786623459.svg)](https://zenodo.org/badge/latestdoi/786623459)
 
-## Known Limitations
-
--   Only one cutter supported in EEVEE render
--   Shader fail to work when convert to mesh.
--   Section surface cannot be generated when convert to mesh (will be supported soon)
 
 ## Roadmap
 

build.py

@@ -19,7 +19,8 @@ class Platform:
                      "transforms3d==0.4.2",
                      "tifffile==2024.7.24",
                      "matplotlib==3.10.7",
-                     "pillow==11.2.1"]
+                     "pillow==11.2.1",
+                     "scipy==1.16.3"]
 
 
 platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
@@ -33,7 +34,8 @@ class Platform:
 
 packages_to_remove = {
     "imagecodecs",
-    "numpy"
+    "numpy",
+    "packaging"
 }
 
 
@@ -45,7 +47,6 @@ def run_python(args: str):
 def build_extension(platform: Platform, python_version: str) -> None:
     wheel_dirpath = Path("./src/bioxelnodes/wheels")
     toml_filepath = Path("./src/bioxelnodes/blender_manifest.toml")
-    scipy_ndimage_dirpath = Path("./scipy_ndimage", platform.blender_tag)
 
     # download required_packages
     run_python(
@@ -62,10 +63,6 @@ def build_extension(platform: Platform, python_version: str) -> None:
             and "universal2" in f.name
         ):
             f.rename(Path(f.parent, f.name.replace("universal2", "arm64")))
-
-    for ndimage_filepath in scipy_ndimage_dirpath.iterdir():
-        to_filepath = Path("./src/bioxelnodes/bioxel/scipy", ndimage_filepath.name)
-        shutil.copy(ndimage_filepath, to_filepath)
 
     # Load the TOML file
     with toml_filepath.open("r") as file:

docs/index.en.md

@@ -49,15 +49,8 @@ Welcome to our [discord server](https://discord.gg/pYkNyq2TjE), if you have any
 
 ![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
 
-👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! However, there are some limitations:
+👍 EEVEE NEXT is absolutely AWESOME! Bioxel Nodes is fully support EEVEE NEXT now! 
 
-1. Only one cutter supported.
-2. EEVEE result is not that great as Cycles does.
-
-## Known Limitations
-
--   Only works with Cycles CPU , Cycles GPU (OptiX), EEVEE
--   Section surface cannot be generated when convert to mesh (will be supported soon)
 
 ## Roadmap
 

docs/index.md

@@ -49,15 +49,7 @@ Bioxel Nodes 是一款用于科学体数据可视化的 Blender 插件。它利
 
 ![eevee](https://omoolab.github.io/BioxelNodes/latest/assets/eevee.gif)
 
-EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！但仍有以下限制：
-
-1. 仅支持一个切割器
-2. EEVEE 渲染效果不如 Cycles
-
-## 已知限制
-
-- 仅支持 Cycles CPU、Cycles GPU (OptiX)、EEVEE
-- 转换为网格时无法生成剖面（即将支持）
+EEVEE NEXT 太棒了！Bioxel Nodes 现在全面支持 EEVEE NEXT！
 
 ## 路线图
 

pyproject.toml

@@ -1,8 +1,8 @@
 [project]
 name = "bioxelnodes"
-version = "1.0.9"
+version = "2.0.1"
 description = ""
-authors = [{ name = "Ma Nan", email = "icrdr2010@outlook.com" }]
+authors = [{ name = "MaNan", email = "icrdr2010@outlook.com" }]
 requires-python = ">=3.11.0,<3.12.dev0"
 readme = "README.md"
 license = "MIT"
@@ -13,6 +13,7 @@ dependencies = [
     "h5py==3.11.0",
     "transforms3d==0.4.2",
     "matplotlib==3.10.7",
+    "scipy==1.16.3",
 ]
 
 [dependency-groups]

src/bioxelnodes/__init__.py

@@ -1,7 +1,7 @@
 import bpy
 import bpy.utils.previews as previews
 
-from .constants import NODE_LIB_DIRPATH, PREVIEW_COLLECTIONS
+from .constants import PREVIEW_COLLECTIONS
 from .props import _bioxel_layer_items, _update_layer_gallery, _update_snapshot_z
 
 from . import auto_load
@@ -10,37 +10,6 @@
 auto_load.init()
 
 
-def add_asset_library():
-    """Add Bioxel asset library, ensuring only one exists by removing duplicates first."""
-    if not NODE_LIB_DIRPATH.exists():
-        print(f"Node library path does not exist - {NODE_LIB_DIRPATH}")
-        return
-
-    lib_path_str = str(NODE_LIB_DIRPATH)
-    prefs = bpy.context.preferences.filepaths.asset_libraries
-
-    # Add new library
-    new_lib = prefs.new()
-    new_lib.name = "O Bioxel"
-    new_lib.path = lib_path_str
-    new_lib.import_method = "PACK"
-
-    print(f"Add Bioxel Nodes library: {lib_path_str}")
-
-
-def remove_asset_library_if_exists():
-    """Remove the Bioxel asset library entry if it was added (by path or name)."""
-    lib_path_str = str(NODE_LIB_DIRPATH)
-    prefs = bpy.context.preferences.filepaths.asset_libraries
-
-    for lib in list(prefs):
-        try:
-            if "Bioxel" in lib.name or lib.path == lib_path_str:
-                prefs.remove(lib)
-        except Exception:
-            continue
-
-
 def register():
     pcoll = previews.new()
     pcoll.layer_previews = ()
@@ -72,12 +41,9 @@ def register():
 
     auto_load.register()
     menus.add()
-    remove_asset_library_if_exists()
-    add_asset_library()
 
 
 def unregister():
-    remove_asset_library_if_exists()
     menus.remove()
     auto_load.unregister()
 

src/bioxelnodes/asset_library.py

@@ -0,0 +1,73 @@
+import bpy
+from pathlib import Path
+
+from .constants import NODE_LIB_DIRPATH
+
+
+ASSET_LIBRARY_NAME = "O Bioxel"
+
+
+def _asset_library_path():
+    return str(NODE_LIB_DIRPATH)
+
+
+def _normalized_path(path):
+    return Path(bpy.path.abspath(path)).resolve()
+
+
+def _asset_libraries():
+    return bpy.context.preferences.filepaths.asset_libraries
+
+
+def get_bioxel_asset_library():
+    lib_path = _normalized_path(_asset_library_path())
+
+    for lib in _asset_libraries():
+        try:
+            if _normalized_path(lib.path) == lib_path:
+                return lib
+        except Exception:
+            continue
+
+    return None
+
+
+def has_bioxel_asset_library():
+    return get_bioxel_asset_library() is not None
+
+
+def add_bioxel_asset_library():
+    if not NODE_LIB_DIRPATH.exists():
+        raise FileNotFoundError(f"Node library path does not exist: {NODE_LIB_DIRPATH}")
+
+    prefs = _asset_libraries()
+    lib = get_bioxel_asset_library()
+
+    if lib is None:
+        for item in prefs:
+            try:
+                if item.name == ASSET_LIBRARY_NAME:
+                    lib = item
+                    break
+            except Exception:
+                continue
+
+    if lib is None:
+        lib = prefs.new()
+
+    lib.name = ASSET_LIBRARY_NAME
+    lib.path = _asset_library_path()
+    lib.import_method = "PACK"
+    return lib
+
+
+def remove_bioxel_asset_library_if_exists():
+    lib_path = _normalized_path(_asset_library_path())
+    prefs = _asset_libraries()
+
+    for lib in list(prefs):
+        try:
+            if "Bioxel" in lib.name or _normalized_path(lib.path) == lib_path:
+                prefs.remove(lib)
+        except Exception:
+            continue

src/bioxelnodes/auto_load.py

@@ -15,6 +15,9 @@
 
 modules = None
 ordered_classes = None
+SKIP_MODULE_NAMES = {
+    "operators.io_worker",
+}
 
 
 def init():
@@ -57,6 +60,8 @@ def get_all_submodules(directory):
 
 def iter_submodules(path, package_name):
     for name in sorted(iter_submodule_names(path)):
+        if name in SKIP_MODULE_NAMES:
+            continue
         yield importlib.import_module("." + name, package_name)