Fix Qt Platform Initialization for WSL2

.gitconfig

@@ -0,0 +1,2 @@
+[core]
+    hooksPath = hooks

.github/workflows/integration-tests.yml

@@ -46,14 +46,25 @@ on:
         options:
         - cpu-only
         - full-coverage
+      dependency_source:
+        description: 'Dependency source for external modules'
+        required: true
+        default: 'submodules'
+        type: choice
+        options:
+        - submodules
+        - pypi
+
+env:
+  OPENHCS_CI_DEP_SOURCE: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.dependency_source || 'submodules' }}
 
 jobs:
   # Group 1: Python version boundary testing (6 jobs)
   # Test oldest (3.11) and newest (3.13) Python on all 3 OSes
   # Python 3.14 excluded: no pre-built NumPy wheels yet (builds from source stall on Windows)
   python-boundary-tests:
     runs-on: ${{ matrix.os }}
-    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
@@ -64,12 +75,30 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          # ubuntu-latest (23.10+) no longer provides libgl1-mesa-glx; use libgl1.
+          # PyQt6 requires libEGL.so.1 (EGL) and libGL.so.1 (OpenGL).
+          sudo apt-get install -y libgl1
+          sudo apt-get install -y libegl1 || sudo apt-get install -y libegl1-mesa
+          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 xvfb
+
+      - name: Install local external modules (submodule mode)
+        if: env.OPENHCS_CI_DEP_SOURCE == 'submodules'
+        run: |
+          python -m pip install --upgrade pip
+          python -c "import subprocess,sys;mods=['external/ObjectState','external/python-introspect','external/metaclass-registry','external/arraybridge','external/pycodify','external/PolyStore','external/pyqt-reactive','external/zmqruntime'];[subprocess.check_call([sys.executable,'-m','pip','install','-e',m]) for m in mods]"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -145,7 +174,7 @@ jobs:
   # Test all backend/microscope combinations on all 3 OSes with Python 3.12
   backend-microscope-tests:
     runs-on: ${{ matrix.os }}
-    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
@@ -156,12 +185,30 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Setup Python 3.12
         uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          # ubuntu-latest (23.10+) no longer provides libgl1-mesa-glx; use libgl1.
+          # PyQt6 requires libEGL.so.1 (EGL) and libGL.so.1 (OpenGL).
+          sudo apt-get install -y libgl1
+          sudo apt-get install -y libegl1 || sudo apt-get install -y libegl1-mesa
+          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 xvfb
+
+      - name: Install local external modules (submodule mode)
+        if: env.OPENHCS_CI_DEP_SOURCE == 'submodules'
+        run: |
+          python -m pip install --upgrade pip
+          python -c "import subprocess,sys;mods=['external/ObjectState','external/python-introspect','external/metaclass-registry','external/arraybridge','external/pycodify','external/PolyStore','external/pyqt-reactive','external/zmqruntime'];[subprocess.check_call([sys.executable,'-m','pip','install','-e',m]) for m in mods]"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -239,7 +286,7 @@ jobs:
   # See: https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/tag/20240202
   omero-tests-linux:
     runs-on: ubuntu-latest
-    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
@@ -253,12 +300,29 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Install system dependencies (Linux)
+        run: |
+          sudo apt-get update
+          # ubuntu-latest (23.10+) no longer provides libgl1-mesa-glx; use libgl1.
+          # PyQt6 requires libEGL.so.1 (EGL) and libGL.so.1 (OpenGL).
+          sudo apt-get install -y libgl1
+          sudo apt-get install -y libegl1 || sudo apt-get install -y libegl1-mesa
+          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 xvfb
+
+      - name: Install local external modules (submodule mode)
+        if: env.OPENHCS_CI_DEP_SOURCE == 'submodules'
+        run: |
+          python -m pip install --upgrade pip
+          python -c "import subprocess,sys;mods=['external/ObjectState','external/python-introspect','external/metaclass-registry','external/arraybridge','external/pycodify','external/PolyStore','external/pyqt-reactive','external/zmqruntime'];[subprocess.check_call([sys.executable,'-m','pip','install','-e',m]) for m in mods]"
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
@@ -299,11 +363,13 @@ jobs:
   # Code quality checks (linting, formatting, type checking)
   code-quality:
     runs-on: ubuntu-latest
-    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -333,7 +399,7 @@ jobs:
   # Test PyPI-style installation across Python versions and OSes (6 jobs)
   pypi-installation-test:
     runs-on: ${{ matrix.os }}
-    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    if: github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'
     strategy:
       fail-fast: false
       matrix:
@@ -343,6 +409,8 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Setup Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
@@ -401,17 +469,27 @@ jobs:
   # Run integration tests against wheel installation
   wheel-integration-test:
     runs-on: ubuntu-latest
-    if: github.event_name == 'push' || github.event_name == 'pull_request' || startsWith(github.ref, 'refs/tags/v')
+    if: github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' || startsWith(github.ref, 'refs/tags/v')
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          submodules: ${{ env.OPENHCS_CI_DEP_SOURCE == 'submodules' && 'recursive' || 'false' }}
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
+      - name: Install system dependencies (Linux)
+        run: |
+          sudo apt-get update
+          # PyQt6 requires libEGL.so.1 (EGL) and libGL.so.1 (OpenGL).
+          sudo apt-get install -y libgl1
+          sudo apt-get install -y libegl1 || sudo apt-get install -y libegl1-mesa
+          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 xvfb
+
       - name: Build wheel
         run: |
           python -m pip install --upgrade pip build
@@ -435,4 +513,3 @@ jobs:
           name: coverage-wheel-integration
           path: .coverage.wheel
           retention-days: 1
-

.github/workflows/publish.yml

@@ -41,4 +41,4 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
         run: |
           twine check dist/*
-          twine upload dist/*
+          twine upload dist/* --skip-existing

.gitignore

@@ -166,3 +166,4 @@ win_logs.txt
 # Chunkhound
 .chunkhound/
 docs/generated_md/
+.grepai/

.gitmodules

@@ -5,7 +5,7 @@
 [submodule "external/python-introspect"]
 	path = external/python-introspect
 	url = https://github.com/OpenHCSDev/python-introspect.git
-	branch = master
+	branch = main
 [submodule "external/arraybridge"]
 	path = external/arraybridge
 	url = https://github.com/OpenHCSDev/arraybridge.git

CHANGELOG.md

@@ -9,8 +9,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-#### LLM-Powered Code Generation
+#### Auto-Add Output Plate Feature
+- **Automatic output plate registration** - New `auto_add_output_plate_to_plate_manager` config option in GlobalPipelineConfig
+  - When enabled, successfully completed plate runs automatically add the computed output plate to Plate Manager
+  - Allows immediate visualization of processed results without manual plate addition
+  - Environment variable: `OPENHCS_AUTO_ADD_OUTPUT_PLATE`
+  - Accessible via Config Window under Pipeline Settings
+
+#### Compilation Architecture Improvements
+- **Remote compilation via ZMQ server** - Compilation now happens on the ZMQ execution server instead of locally
+  - New shared `ZMQClientService` for managing ZMQ client connections between compilation and execution
+  - `CompilationService` and `ZMQExecutionService` now share a single client service instance
+  - Improved consistency and resource management across compile/run workflows
+  - Requires ZMQ server to be running for compilation (same as execution)
+
+#### LLM-Powered Code Generation Improvements
 - **LLM Assist in Code Editor** - Added LLM-powered code generation directly into the OpenHCS code editor
+  - **Automatic array backend handling** - Generated functions no longer require manual backend conversions (`cp.asnumpy()`, `cle.pull()`)
+  - **Context-aware system prompts** - New `get_system_prompt(code_type)` method provides different prompts for pipeline vs function generation
+  - **Array format clarification** - Documentation now specifies (C, Y, X) a.k.a. (Z, Y, X) format for 3D arrays
+  - **Memory decorator awareness** - LLM understands `@numpy`, `@cupy`, `@pyclesperanto` decorators and their implications
   - New `LLMPipelineService` for communicating with local LLM endpoints (Ollama)
   - New `LLMChatPanel` widget with chat interface for natural language code generation
   - Integrated LLM panel into `QScintillaCodeEditorDialog` with toggle button

Makefile

@@ -0,0 +1,19 @@
+.PHONY: dev install-hooks help
+
+help: ## Show this help
+	@grep -E '^[a-zA-Z_-]+:.*?## ' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+dev: install-hooks ## Set up development environment (installs hooks and dependencies)
+	pip install -e ".[dev]"
+	@echo "✅ Development environment ready!"
+	@echo "Hooks are installed and will auto-update submodules on git operations."
+
+install-hooks: ## Install git hooks for submodule auto-update
+	@git config core.hooksPath hooks
+	@echo "✅ Git hooks installed"
+
+update-submodules: ## Manually update all submodules to latest
+	git submodule update --remote
+
+status: ## Show submodule status
+	git submodule status