Add OpenSpec skills for change management and exploration

- Implement openspec-apply-change skill for applying tasks from OpenSpec changes.
- Create openspec-archive-change skill for archiving completed changes.
- Introduce openspec-explore skill for exploring ideas and clarifying requirements.
- Add openspec-propose skill for proposing new changes with generated artifacts.
- Migrate source command skills: source-command-opsx-apply, source-command-opsx-archive, source-command-opsx-explore, and source-command-opsx-propose for improved command handling.

.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.

.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.

.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.

.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/

CLAUDE.md

@@ -1 +0,0 @@
-@AGENTS.md

build.py

@@ -19,7 +19,8 @@ required_packages = ["SimpleITK==2.5.5",
                      "transforms3d==0.4.2",
                      "tifffile==2024.7.24",
                      "matplotlib==3.10.7",
-                     "pillow==11.2.1"]
+                     "pillow==11.2.1",
+                     "scipy==1.17.1"]
 
 
 platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
@@ -33,7 +34,8 @@ platforms = {"windows-x64": Platform(pypi_suffix="win_amd64",
 
 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:

pyproject.toml

@@ -1,8 +1,8 @@
 [project]
 name = "bioxelnodes"
-version = "1.0.9"
+version = "2.0.0"
 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==1.17.1",
 ]
 
 [dependency-groups]

src/bioxelnodes/blender_manifest.toml

@@ -6,7 +6,7 @@ name = "Bioxel Nodes"
 tagline = "For scientific volumetric data visualization in Blender"
 maintainer = "Nan <icrdr2010@outlook.com>"
 type = "add-on"
-website = "https://omoolab.github.io/BioxelNodes/latest"
+website = "https://docs.omoolab.xyz/bioxelnodes/"
 
 tags = ["Geometry Nodes", "Render", "Import-Export"]
 blender_version_min = "5.0.0"
@@ -29,12 +29,13 @@ wheels = [
     "./wheels/matplotlib-3.10.7-cp311-cp311-win_amd64.whl",
     "./wheels/matplotlib-3.10.7-cp313-cp313-win_amd64.whl",
     "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl",
-    "./wheels/packaging-26.2-py3-none-any.whl",
     "./wheels/pillow-11.2.1-cp311-cp311-win_amd64.whl",
     "./wheels/pillow-11.2.1-cp313-cp313-win_amd64.whl",
     "./wheels/pyometiff-1.0.0-py3-none-any.whl",
     "./wheels/pyparsing-3.3.2-py3-none-any.whl",
     "./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl",
+    "./wheels/scipy-1.17.1-cp311-cp311-win_amd64.whl",
+    "./wheels/scipy-1.17.1-cp313-cp313-win_amd64.whl",
     "./wheels/simpleitk-2.5.5-cp311-abi3-win_amd64.whl",
     "./wheels/six-1.17.0-py2.py3-none-any.whl",
     "./wheels/tifffile-2024.7.24-py3-none-any.whl",

uv.lock

@@ -25,13 +25,14 @@ wheels = [
 
 [[package]]
 name = "bioxelnodes"
-version = "1.0.9"
+version = "2.0.0"
 source = { editable = "." }
 dependencies = [
     { name = "h5py" },
     { name = "matplotlib" },
     { name = "mrcfile" },
     { name = "pyometiff" },
+    { name = "scipy" },
     { name = "simpleitk" },
     { name = "transforms3d" },
 ]
@@ -59,6 +60,7 @@ requires-dist = [
     { name = "matplotlib", specifier = "==3.10.7" },
     { name = "mrcfile", specifier = "==1.5.1" },
     { name = "pyometiff", specifier = "==1.0.0" },
+    { name = "scipy", specifier = "==1.17.1" },
     { name = "simpleitk", specifier = "==2.3.1" },
     { name = "transforms3d", specifier = "==0.4.2" },
 ]
@@ -945,6 +947,27 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/f9/9b/335f9764261e915ed497fcdeb11df5dfd6f7bf257d4a6a2a686d80da4d54/requests-2.32.3-py3-none-any.whl", hash = "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6", size = 64928, upload-time = "2024-05-29T15:37:47.027Z" },
 ]
 
+[[package]]
+name = "scipy"
+version = "1.17.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "numpy" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/7a/97/5a3609c4f8d58b039179648e62dd220f89864f56f7357f5d4f45c29eb2cc/scipy-1.17.1.tar.gz", hash = "sha256:95d8e012d8cb8816c226aef832200b1d45109ed4464303e997c5b13122b297c0", size = 30573822, upload-time = "2026-02-23T00:26:24.851Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/df/75/b4ce781849931fef6fd529afa6b63711d5a733065722d0c3e2724af9e40a/scipy-1.17.1-cp311-cp311-macosx_10_14_x86_64.whl", hash = "sha256:1f95b894f13729334fb990162e911c9e5dc1ab390c58aa6cbecb389c5b5e28ec", size = 31613675, upload-time = "2026-02-23T00:16:00.13Z" },
+    { url = "https://files.pythonhosted.org/packages/f7/58/bccc2861b305abdd1b8663d6130c0b3d7cc22e8d86663edbc8401bfd40d4/scipy-1.17.1-cp311-cp311-macosx_12_0_arm64.whl", hash = "sha256:e18f12c6b0bc5a592ed23d3f7b891f68fd7f8241d69b7883769eb5d5dfb52696", size = 28162057, upload-time = "2026-02-23T00:16:09.456Z" },
+    { url = "https://files.pythonhosted.org/packages/6d/ee/18146b7757ed4976276b9c9819108adbc73c5aad636e5353e20746b73069/scipy-1.17.1-cp311-cp311-macosx_14_0_arm64.whl", hash = "sha256:a3472cfbca0a54177d0faa68f697d8ba4c80bbdc19908c3465556d9f7efce9ee", size = 20334032, upload-time = "2026-02-23T00:16:17.358Z" },
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+]
+
 [[package]]
 name = "setuptools"
 version = "72.1.0"