Merge first Release

.github/workflows/release.yml

@@ -0,0 +1,120 @@
+name: Release Build
+
+on:
+  push:
+    branches:
+      - releases
+    tags:
+      - 'v*'
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-release:
+    runs-on: macos-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Configure Git for private repos
+        run: |
+          git config --global url."https://x-access-token:${{ secrets.PRIVATE_REPO_TOKEN }}@github.com/".insteadOf "https://github.com/"
+
+      - name: Install dependencies
+        env:
+          GIT_CREDENTIALS: ${{ secrets.PRIVATE_REPO_TOKEN }}
+        run: |
+          uv sync
+
+      - name: Build .app bundle
+        run: make build
+
+      - name: Get version from tag or commit
+        id: get_version
+        run: |
+          if [[ $GITHUB_REF == refs/tags/* ]]; then
+            VERSION=${GITHUB_REF#refs/tags/}
+          else
+            VERSION="v$(date +'%Y.%m.%d')-$(git rev-parse --short HEAD)"
+          fi
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "Building version: $VERSION"
+
+      - name: Create DMG
+        run: |
+          # Create a simple DMG for easier distribution
+          mkdir -p dmg_contents
+          cp -R dist/VoxKit.app dmg_contents/
+          hdiutil create -volname "VoxKit" -srcfolder dmg_contents -ov -format UDZO VoxKit.dmg
+        continue-on-error: true
+
+      - name: Zip .app for release
+        run: |
+          cd dist
+          zip -r VoxKit.app.zip VoxKit.app
+          cd ..
+
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ steps.get_version.outputs.version }}
+          release_name: VoxKit ${{ steps.get_version.outputs.version }} (macOS)
+          body: |
+            **VoxKit Release ${{ steps.get_version.outputs.version }}**
+
+            🍎 **Platform:** macOS (Apple Silicon & Intel)
+
+            Automated build from releases branch.
+
+            ## Installation
+            1. Download VoxKit-macOS.app.zip
+            2. Unzip the file
+            3. Move VoxKit.app to your Applications folder
+            4. Right-click and select "Open" the first time (macOS security)
+
+            ## System Requirements
+            - macOS 10.13 or later
+            - Works on both Intel and Apple Silicon Macs
+
+            ## Changes
+            - Built from commit: ${{ github.sha }}
+
+          draft: false
+          prerelease: false
+
+      - name: Upload .app.zip to Release
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./dist/VoxKit.app.zip
+          asset_name: VoxKit-macOS.app.zip
+          asset_content_type: application/zip
+
+      - name: Upload DMG to Release (if created)
+        if: success()
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./VoxKit.dmg
+          asset_name: VoxKit-macOS.dmg
+          asset_content_type: application/x-apple-diskimage
+        continue-on-error: true

.github/workflows/sync-docs.yml

@@ -0,0 +1,39 @@
+# name: Sync Docs Artifact
+
+# on:
+#   push:
+#     branches:
+#       - main
+
+# jobs:
+#   sync-docs:
+#     runs-on: ubuntu-latest
+
+#     steps:
+#       - name: Checkout code
+#         uses: actions/checkout@v4
+
+#       - name: Install uv
+#         uses: astral-sh/setup-uv@v1
+
+#       - name: Set up Python
+#         run: uv python install 3.11
+
+#       - name: Install dependencies
+#         run: |
+#           uv pip install pdoc
+#           uv pip install ".[docs]"
+
+#       - name: Generate HTML docs
+#         run: |
+#           mkdir -p docs
+#           pdoc voxkit --output-dir docs --search --math --mermaid
+
+#       - name: Upload docs artifact
+#         uses: actions/upload-artifact@v4
+#         with:
+#           name: pdoc-html
+#           path: docs/
+#           retention-days: 30
+
+#     #   - name: Send docs to Vercel

.gitignore

@@ -59,4 +59,4 @@ computed_likelihoods/
 
 # OS files
 .DS_Store
-Thumbs.db
+Thumbs.db

.pre-commit-config.yaml

@@ -1,2 +1,19 @@
-# TODO add hooks for pre-commit -> ruff, run tests, pii-check? security-check?
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.1
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
 
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.0
+    hooks:
+      - id: mypy
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml

Makefile

@@ -1 +1,90 @@
-# TODO : Make commands for build - dev - watch - test - lint - format - typecheck
+.PHONY: help watch build clean
+.DEFAULT_GOAL := help
+
+# Colors for output
+BLUE := \033[36m
+GREEN := \033[32m
+YELLOW := \033[33m
+RED := \033[31m
+RESET := \033[0m
+
+help:
+	@echo "$(BLUE)VoxKit - Dev Commands$(RESET)"
+	@echo "======================================"
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "$(GREEN)%-15s$(RESET) %s\n", $$1, $$2}'
+
+watch: ## Watch for file changes and restart dev server (requires entr)
+	@if command -v entr >/dev/null 2>&1; then \
+		echo "$(BLUE)Watching for changes... Press Ctrl+C to stop$(RESET)"; \
+		find src/ -name "*.py" | entr -r uv run main.py; \
+	else \
+		echo "$(RED)entr not installed. Install with: brew install entr$(RESET)"; \
+		echo "$(YELLOW)Falling back to single run...$(RESET)"; \
+		uv run main.py; \
+	fi
+
+build: clean ## Build standalone executable for current platform
+	@echo "$(BLUE)Building VoxKit for macOS...$(RESET)"
+	uv run --group installation python build.py build --entry main.py --name VoxKit --windowed
+
+build-info: ## Show information about the built app
+	@echo "$(BLUE)Checking build output...$(RESET)"
+	@if [ -d "dist/VoxKit" ]; then \
+		echo "$(GREEN)Found: dist/VoxKit/$(RESET)"; \
+		ls -lh dist/VoxKit/; \
+		echo ""; \
+		echo "$(BLUE)Checking executable...$(RESET)"; \
+		file dist/VoxKit/VoxKit; \
+		echo ""; \
+		echo "$(BLUE)Checking library dependencies...$(RESET)"; \
+		otool -L dist/VoxKit/VoxKit | head -10; \
+	else \
+		echo "$(RED)dist/VoxKit not found. Run 'make build' first.$(RESET)"; \
+	fi
+
+run-app: ## Run the built app from terminal (shows errors)
+	@echo "$(BLUE)Running VoxKit from terminal...$(RESET)"
+	@if [ -f "/Users/beckettfrey/Repos/waisman/PyPLLR_GUI/dist/VoxKit/VoxKit" ]; then \
+		/Users/beckettfrey/Repos/waisman/PyPLLR_GUI/dist/VoxKit/VoxKit; \
+	else \
+		echo "$(RED)dist/VoxKit/VoxKit not found. Run 'make build' first.$(RESET)"; \
+	fi
+
+open-app: ## Open the app bundle with macOS (background)
+	@echo "$(BLUE)Opening VoxKit.app...$(RESET)"
+	@if [ -d "dist/VoxKit" ]; then \
+		open dist/VoxKit; \
+	else \
+		echo "$(RED)dist/VoxKit not found. Run 'make build' first.$(RESET)"; \
+	fi
+
+clean: ## Clean build artifacts
+	@echo "$(BLUE)Cleaning build artifacts...$(RESET)"
+	@rm -rf build/ dist/ *.spec
+	@find . -type d -name "__pycache__" -exec rm -rf {} + 2>/dev/null || true
+	@find . -type f -name "*.pyc" -delete 2>/dev/null || true
+	@echo "$(GREEN)Cleanup completed$(RESET)"
+
+format: ## Format code with Ruff
+	@echo "$(BLUE)Formatting code with Ruff...$(RESET)"
+	uv run --only-group dev ruff format .
+
+format-check: ## Check code formatting with Ruff
+	@echo "$(BLUE)Checking code formatting with Ruff...$(RESET)"
+	uv run --only-group dev ruff format --check .
+
+lint: ## Lint code with Ruff
+	@echo "$(BLUE)Linting with Ruff...$(RESET)"
+	uv run --only-group dev ruff check --fix .
+
+lint-check: ## Check linting with Ruff
+	@echo "$(BLUE)Checking linting with Ruff...$(RESET)"
+	uv run --only-group dev ruff check .
+
+mypy-check: ## Run mypy for type checking
+	@echo "$(BLUE)Running mypy for type checking...$(RESET)"
+	uv run --only-group dev mypy .
+
+fresh-slate: ## Remove virtual environment and lock file
+	@echo "$(BLUE)Removing virtual environment and lock file...$(RESET)"
+	@read -p "Are you sure you want to proceed? [y/N] " confirm && [ $${confirm} = "y" ] || [ $${confirm} = "Y" ] && rm -rf uv.lock .venv || echo "Aborted."

README.md

@@ -1,5 +1,10 @@
 # TODO : Update README
 
+[![Release](https://img.shields.io/github/v/release/BrainBehaviorAnalyticsLab/PyPLLR_GUI?label=Latest%20Release)](https://github.com/BrainBehaviorAnalyticsLab/PyPLLR_GUI/releases/latest)
+[![Downloads](https://img.shields.io/github/downloads/BrainBehaviorAnalyticsLab/PyPLLR_GUI/total)](https://github.com/BrainBehaviorAnalyticsLab/PyPLLR_GUI/releases)
+[![Project Management](https://img.shields.io/badge/Project-Jira%20Board-0052CC?logo=jira)](https://voxkit.atlassian.net/jira/software/projects/VOX/boards/2/)
+
+
 A modern PyQt6-based graphical user interface for phonetic alignment and PLLR (Phoneme-Level Likelihood Ratios) score extraction. This application provides an intuitive workflow for researchers working with speech data.
 
 ## Features

_frozen_patch.py

@@ -0,0 +1,33 @@
+"""
+Runtime patch to disable problematic inspect operations in frozen apps
+"""
+import sys
+
+if getattr(sys, 'frozen', False):
+    # We're running in a PyInstaller bundle
+    import inspect
+
+    # Patch inspect.getsource to return empty string instead of raising
+    _original_getsource = inspect.getsource
+
+    def _patched_getsource(object):
+        try:
+            return _original_getsource(object)
+        except (OSError, TypeError):
+            # Return a dummy source code
+            return "# Source code not available in frozen application\npass\n"
+
+    inspect.getsource = _patched_getsource
+
+    # Patch getsourcelines similarly
+    _original_getsourcelines = inspect.getsourcelines
+
+    def _patched_getsourcelines(object):
+        try:
+            return _original_getsourcelines(object)
+        except (OSError, TypeError):
+            return (["# Source code not available\n", "pass\n"], 0)
+
+    inspect.getsourcelines = _patched_getsourcelines
+
+    print("[PATCH] Disabled source code inspection for frozen app")