Refactor entrypoints and initialization throughout

main.py

@@ -12,8 +12,10 @@
 from voxkit.config.app_config import AppConfig, get_app_config, get_profile_config_path
 from voxkit.config.logging_config import setup_logging
 
-# Disable Qt emoji support to prevent crashes in frozen builds
-
+# Minimal early config so frozen-env messages below are emitted before
+# setup_logging() runs in main(); setup_logging() will reconfigure handlers.
+logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(name)s: %(message)s")
+log = logging.getLogger("voxkit.main")
 
 # CRITICAL: Must be at the top for frozen apps using multiprocessing
 if __name__ == "__main__":
@@ -55,10 +57,10 @@
     if conda_bin:
         existing_path = os.environ.get('PATH', '/usr/bin:/bin:/usr/sbin:/sbin')
         minimal_env['PATH'] = f"{conda_bin}:{existing_path}"
-        print(f"[FROZEN] Added conda to PATH: {conda_bin}")
+        log.info("[FROZEN] Added conda to PATH: %s", conda_bin)
     else:
         minimal_env['PATH'] = os.environ.get('PATH', '/usr/bin:/bin:/usr/sbin:/sbin')
-        print("[FROZEN] Warning: conda not found in standard locations. MFA alignment may fail.")
+        log.warning("[FROZEN] conda not found in standard locations. MFA alignment may fail.")
 
     # PyInstaller-specific: Add Qt plugin paths
     if getattr(sys, '_MEIPASS', None):
@@ -67,30 +69,26 @@
         if os.path.exists(qt_plugins):
             minimal_env['QT_PLUGIN_PATH'] = qt_plugins
             minimal_env['QT_QPA_PLATFORM_PLUGIN_PATH'] = os.path.join(qt_plugins, 'platforms')
-        
+
         # Additional Qt environment for frozen apps
         minimal_env['QT_AUTO_SCREEN_SCALE_FACTOR'] = '1'
         minimal_env['QT_LOGGING_RULES'] = '*.debug=false;qt.qpa.*=false'
-        
-        print(f"[FROZEN] Qt plugins directory: {qt_plugins}")
-        print(f"[FROZEN] Bundle directory: {bundle_dir}")
+
+        log.info("[FROZEN] Qt plugins directory: %s", qt_plugins)
+        log.info("[FROZEN] Bundle directory: %s", bundle_dir)
 
     # IMPORTANT: Don't clear os.environ - preserve system environment
     # Just add/override our minimal required variables
     for key, value in minimal_env.items():
         if value:
             os.environ[key] = value
-
-    print("[FROZEN] Environment configured for frozen app")
-
 
+    log.info("[FROZEN] Environment configured for frozen app")
 
 from PyQt6.QtWidgets import QApplication
 from voxkit.config import STARTUP_SCRIPT
-from voxkit.gui import AlignmentGUI
+from voxkit.gui import VoxKitGUI
 from voxkit.gui.workers.startup import execute_startup_script
-from pathlib import Path
-
 
 def main():
     # Initialize logging as early as possible so startup work is captured.
@@ -108,7 +106,6 @@ def main():
     from voxkit.gui.components.log_handler import get_gui_log_handler
     get_gui_log_handler()
 
-    log = logging.getLogger("voxkit.main")
     log.info("VoxKit starting (frozen=%s)", bool(getattr(sys, "frozen", False)))
 
     app = QApplication(sys.argv)
@@ -128,14 +125,13 @@ def main():
         app_config = AppConfig.from_yaml(profile_path / "app_info.yaml")
         pipeline_config = PipelineConfig.from_yaml(profile_path / "pipeline_definitions.yaml")
 
-    window = AlignmentGUI(pipeline_config=pipeline_config, app_config=app_config)
+    window = VoxKitGUI(pipeline_config=pipeline_config, app_config=app_config)
     window.show()
     log.info("Main window shown, entering Qt event loop")
     sys.exit(app.exec())
 
 
 if __name__ == "__main__":
     # Prevent multiprocessing from spawning new app windows in frozen builds
-    multiprocessing.freeze_support()
     multiprocessing.set_start_method('spawn', force=True)
     main()

src/voxkit/__init__.py

@@ -1,20 +1,17 @@
-"""VoxKit - Speech Analysis and Forced Alignment Toolkit.
-
-A desktop application bridging AI/ML research and clinical speech-language
-pathology. Provides accessible interfaces to forced alignment engines and
-flexible dataset analysis tools.
+"""Modules for VoxKit; Provides accessible interfaces to forced alignment engines and
+flexible dataset analysis and management tools.
 
 Subpackages
 -----------
-- **engines**: Speech toolkit backends (MFA, Faster-Whisper)
+- **engines**: Speech toolkit backends (MFA, W2TG. FasterWhisper, etc.)
 - **analyzers**: Dataset metadata extraction
 - **storage**: Persistence for datasets, models, and alignments
 - **gui**: PyQt6 desktop interface
 - **config**: Application and pipeline configuration
 """
 
-__version__ = "0.1.0"
-__author__ = "Beckett Frey @beckettfrey.com"
+__version__ = "0.4.0"
+__author__ = "Beckett Frey - code@beckettfrey.com"
 
 # Import subpackages for pdoc discoverability (not re-exported in __all__)
 from . import analyzers, config, engines, gui, storage

src/voxkit/analyzers/__init__.py

@@ -1,19 +1,16 @@
-"""VoxKit Analyzers Module.
-
-Analyzers observe datasets and link metadata in flexible, abstract ways. They
-extract structured information at registration time, producing CSV summaries
+"""Analyzers observe datasets and link metadata. They
+extract structured information at registration time (ingestion), producing CSV summaries
 that can be visualized within VoxKit without rescanning the filesystem.
 
 API
 ---
 - **AnalyzerManager.list_analyzers**: List registered analyzer IDs
 - **AnalyzerManager.get_analyzer**: Retrieve analyzer instance by ID
 - **AnalyzerManager.get_analyzers**: Get all registered analyzers
-- **DatasetAnalyzer**: Abstract base class for all analyzers
 
 Available Analyzers
 -------------------
-**DefaultAnalyzer** (``default_analyzer.py``)
+**DefaultAnalyzer**
     Extracts speaker count and audio file counts per speaker directory.
     Includes a bar chart visualization for quick dataset overview.
 
@@ -28,7 +25,7 @@
 
 Notes
 -----
-- Analyzers run during dataset registration
+- Analyzers run during dataset registration (ingestion)
 - Each analyzer's ``name`` property serves as its unique identifier
 - Output is a list of dicts where keys become CSV column headers
 - Custom visualizations can be provided via the ``visualize`` method
@@ -78,7 +75,4 @@ def get_analyzer(self, analyzer_id: str) -> DatasetAnalyzer:
 
 __all__ = [
     "ManageAnalyzers",
-    "AnalyzerManager",
-    "DatasetAnalyzer",
-    "DefaultAnalyzer",
 ]

src/voxkit/config/__init__.py

@@ -1,6 +1,15 @@
-"""VoxKit configuration module.
+"""This module provides access to configurable info about the application.
 
-This module provides access to application and pipeline configurations.
+Configurations
+--------------
+- App config: application metadata and provenance (``app_config``).
+- Pipeline config: pipeline steps and UI wiring (``pipeline_config``).
+- Startup config: launch-time constants and defaults (``startup_config``).
+- Logging config: rotating file logger setup (``logging_config``).
+
+Only ``app_config`` and ``pipeline_config`` are dynamic post-build; they are
+loaded from YAML files under the active profile and can change without a
+rebuild. ``startup_config`` and ``logging_config`` are baked in at build time.
 
 Profile System
 --------------
@@ -19,6 +28,11 @@
     get_profile_config_path,
     resolve_config_file,
 )
+from voxkit.config.logging_config import (
+    LOG_FILE,
+    reset_logging,
+    setup_logging,
+)
 from voxkit.config.pipeline_config import (
     PipelineConfig,
     PipelineStep,
@@ -55,4 +69,8 @@
     "Defaults",
     "Mode",
     "STARTUP_SCRIPT",
+    # Logging config
+    "LOG_FILE",
+    "setup_logging",
+    "reset_logging",
 ]

src/voxkit/engines/__init__.py

@@ -1,30 +1,28 @@
-"""VoxKit Engines Module.
-
-Engines are speech toolkit backends that perform alignment, training, and
-transcription operations. Each engine provides one or more tools with
-configurable settings.
+"""Engines are speech toolkit backends. Each engine provides one or more tools
+where each tool is a unit of functionality (e.g. alignment, training, transcription).
 
 API
 ---
 - **EngineManager.list_engines**: List registered engine IDs
 - **EngineManager.get_engine**: Retrieve engine instance by ID
 - **EngineManager.get_tool_providers**: Get engines providing a specific tool type
-- **AlignmentEngine**: Abstract base class for all engines
-- **ToolType**: Literal type for tool categories ("train", "align", "transcribe")
+- **ToolType**: Literal type for compatible tool types
 
 Available Engines
 -----------------
-**MFAEngine** (``mfa_engine.py``)
+**MFAEngine**
     Montreal Forced Aligner integration. Provides alignment using pretrained
     acoustic models and training via model adaptation.
+    Tools: ``alignment``, ``training``
 
-**FasterWhisperEngine** (``faster_whisper_engine.py``)
-    Faster-Whisper integration for transcription. Produces .lab label files
-    from audio using CTranslate2 backend.
+**W2TGEngine**
+    Wav2TextGrid integration using Wav2Vec 2.0 models.
+    Tools: ``alignment``, ``training``
 
-**W2TGEngine** (``w2tg_engine.py``) [disabled]
-    Wav2TextGrid integration using Wav2Vec 2.0 models. Supports both
-    alignment and from-scratch training.
+**FasterWhisperEngine**
+    Faster-Whisper integration for transcription. Produces .lab transcript files
+    from audio using CTranslate2 backend.
+    Tools: ``transcription``
 
 Storage Structure
 -----------------
@@ -60,7 +58,7 @@ class EngineManager:
     """
     Manager class for registered engines.
 
-    Provides a unified interface to list and retrieve registered alignment engines.
+    Provides a unified interface to list and retrieve engines.
 
     Methods:
         list_engines(): Return a list of registered engine IDs.
@@ -99,11 +97,4 @@ def get_tool_providers(self, tool: ToolType) -> dict[str, AlignmentEngine]:
 faster_whisper = FasterWhisperEngine(id="FASTERWHISPERENGINE")
 engines = EngineManager({mfa.id: mfa, faster_whisper.id: faster_whisper, w2tg.id: w2tg})
 
-__all__ = [
-    "engines",
-    "EngineManager",
-    "AlignmentEngine",
-    "ToolType",
-    "MFAEngine",
-    "FasterWhisperEngine",
-]
+__all__ = ["engines", "ToolType"]

src/voxkit/gui/__init__.py

@@ -1,10 +1,9 @@
-"""VoxKit GUI Module.
-
-PyQt6-based graphical user interface for the VoxKit desktop application.
+"""PyQt6-based graphical user interface for interacting with datasets using tools.
+Designed for ease of use and extensibility.
 
 API
 ---
-- **AlignmentGUI**: Main application window with toolbar navigation
+- **VoxKitGUI**: Main application window with toolbar navigation
 
 Submodules
 ----------
@@ -167,13 +166,13 @@
     """
 
 
-class AlignmentGUI(QMainWindow):
+class VoxKitGUI(QMainWindow):
     def __init__(
         self,
         app_config: Optional[AppConfig] = None,
         pipeline_config: Optional[PipelineConfig] = None,
     ):
-        """Initialize the AlignmentGUI.
+        """Initialize the VoxKitGUI.
 
         Args:
             app_config: Application configuration. If None, loads default from config files.
@@ -186,7 +185,7 @@ def __init__(
         self.pipeline_config = pipeline_config or get_pipeline_config()
 
         logger.info(
-            "AlignmentGUI initialized: app=%s version=%s",
+            "VoxKitGUI initialized: app=%s version=%s",
             self.app_config.app_name,
             self.app_config.version,
         )
@@ -450,4 +449,4 @@ def _open_log_viewer(self) -> None:
             self._log_viewer.activateWindow()
 
 
-__all__ = ["AlignmentGUI"]
+__all__ = ["VoxKitGUI"]

src/voxkit/gui/components/__init__.py

@@ -1,6 +1,4 @@
-"""Components Module.
-
-Reusable PyQt6 widgets used throughout the VoxKit application.
+"""Reusable PyQt6 widgets taiored functionally and stylistically for the VoxKit application.
 
 API
 ---
@@ -10,6 +8,9 @@
 - **GripSplitter**: QSplitter with visible grip handle for intuitive resizing
 - **HuggingFaceButton**: Branded button with HuggingFace logo
 - **LoadingDialog**: Splash screen / loading dialog with animated spinner
+- **LogViewerDialog**: Dialog for viewing live application logs
+- **QObjectLogHandler**: Qt-aware logging handler that emits records as Qt signals
+- **get_gui_log_handler**: Accessor for the singleton GUI log handler
 - **ModelSelectionPanel**: Combined engine and model selection panel
 - **MultiColumnComboBox**: QComboBox with multi-column dropdown table display
 - **OverlayWidget**: Semi-transparent overlay for modal blur effects
@@ -29,6 +30,7 @@
 from .grip_splitter import GripSplitter
 from .huggingface_button import HuggingFaceButton
 from .loading_dialog import LoadingDialog
+from .log_handler import QObjectLogHandler, get_gui_log_handler
 from .log_viewer_dialog import LogViewerDialog
 from .model_selection_panel import ModelSelectionPanel
 from .overlay_effects import OverlayWidget
@@ -45,5 +47,7 @@
     "ModelSelectionPanel",
     "MultiColumnComboBox",
     "OverlayWidget",
+    "QObjectLogHandler",
     "ToggleSwitch",
+    "get_gui_log_handler",
 ]

src/voxkit/gui/components/animate_stack.py

@@ -1,11 +1,4 @@
-"""Animated Stack Module.
-
-QStackedWidget with smooth slide transition animations.
-
-API
----
-- **AnimatedStackedWidget**: Stacked widget with animated page transitions
-"""
+"""QStackedWidget with smooth slide transition animations."""
 
 from PyQt6.QtCore import QEasingCurve, QPoint, QPropertyAnimation
 from PyQt6.QtWidgets import QStackedWidget

src/voxkit/gui/components/column_dropdown.py

@@ -1,11 +1,4 @@
-"""Column Dropdown Module.
-
-QComboBox with multi-column table dropdown display.
-
-API
----
-- **MultiColumnComboBox**: ComboBox with tabular dropdown (single selection)
-"""
+"""QComboBox with multi-column table dropdown display."""
 
 import sys
 

src/voxkit/gui/components/csv_viewer_dialog.py

@@ -1,11 +1,4 @@
-"""CSV Viewer Dialog Module.
-
-Modal dialog for viewing CSV files in a formatted table.
-
-API
----
-- **CSVViewerDialog**: Dialog that displays CSV data with blur background effect
-"""
+"""Modal dialog for viewing CSV files in a formatted table."""
 
 import csv
 import os

src/voxkit/gui/components/dna_strand.py

@@ -1,11 +1,4 @@
-"""DNA Strand Widget Module.
-
-Decorative audio waveform visualization for the toolbar.
-
-API
----
-- **DNAStrandWidget**: Procedural audio waveform decoration (Wav2Vec homage)
-"""
+"""Decorative audio waveform visualization for the toolbar."""
 
 import math