feat: complete daemon integration testing and troubleshooting

- Fix daemon executable path from apt-ostree.py to apt-ostree
- Resolve daemon package installation with --break-system-packages flag
- Fix test script path calculations for proper apt-layer.sh location
- Identify and document import conflicts between local and system dbus modules
- Complete test infrastructure and automation for daemon + D-Bus integration
- Update changelog and TODO to reflect current status and remaining work
- All daemon integration foundation complete, ready for import conflict resolution

apt-layer.sh

@@ -6,7 +6,7 @@
 # DO NOT modify this file directly as it will be overwritten                                                 #
 #                                                                                                              #
 # apt-layer Tool                                                                                 #
-# Generated on: 2025-07-15 17:15:04                                                                 #
+# Generated on: 2025-07-15 17:57:47                                                                 #
 #                                                                                                              #
 ################################################################################################################
 
@@ -7123,7 +7123,7 @@ APT_OSTREE_DBUS_PATH="/org/debian/aptostree1/Sysroot"
 APT_OSTREE_DBUS_INTERFACE="org.debian.aptostree1.Sysroot"
 
 # Daemon executable path
-APT_OSTREE_DAEMON_PATH="/usr/local/bin/apt-ostree.py"
+APT_OSTREE_DAEMON_PATH="/usr/local/bin/apt-ostree"
 APT_OSTREE_DAEMON_SERVICE="apt-ostree.service"
 
 # Check if daemon is available and running

src/apt-layer/CHANGELOG.md

@@ -1647,7 +1647,15 @@ This project is part of the Particle-OS system tools and follows the same licens
 ### Changed
 - Updated compile.sh to include new scriptlet and ensure correct build order
 - Improved main dispatch and help text for daemon commands
+- Fixed daemon executable path from `/usr/local/bin/apt-ostree.py` to `/usr/local/bin/apt-ostree`
 
 ### Fixed
 - Path and invocation issues for test scripts and daemon lifecycle
-- D-Bus communication reliability and timeout handling
+- D-Bus communication reliability and timeout handling
+- Daemon package installation with `--break-system-packages` flag for externally managed environments
+- Test script path calculations for proper apt-layer.sh location
+
+### Technical Notes
+- Identified and documented import conflicts between local `dbus` module and system `dbus` module
+- Daemon package successfully installed but requires import conflict resolution for full functionality
+- Test infrastructure complete and ready for use once daemon import issues are resolved

src/apt-layer/scriptlets/20-daemon-integration.sh

@@ -10,7 +10,7 @@ APT_OSTREE_DBUS_PATH="/org/debian/aptostree1/Sysroot"
 APT_OSTREE_DBUS_INTERFACE="org.debian.aptostree1.Sysroot"
 
 # Daemon executable path
-APT_OSTREE_DAEMON_PATH="/usr/local/bin/apt-ostree.py"
+APT_OSTREE_DAEMON_PATH="/usr/local/bin/apt-ostree"
 APT_OSTREE_DAEMON_SERVICE="apt-ostree.service"
 
 # Check if daemon is available and running

src/apt-layer/test-scripts/test-daemon-integration.sh

@@ -13,9 +13,9 @@ NC='\033[0m' # No Color
 
 # Test configuration
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-PROJECT_ROOT="$(dirname "$SCRIPT_DIR")/.."
+PROJECT_ROOT="$(dirname "$(dirname "$(dirname "$SCRIPT_DIR")")")"
 APT_LAYER_PATH="$PROJECT_ROOT/apt-layer.sh"
-APT_OSTREE_DAEMON_PATH="/usr/local/bin/apt-ostree.py"
+APT_OSTREE_DAEMON_PATH="/usr/local/bin/apt-ostree"
 DBUS_NAME="org.debian.aptostree1"
 DBUS_PATH="/org/debian/aptostree1"
 

src/apt-ostree.py/python/apt_ostree.egg-info/PKG-INFO

@@ -0,0 +1,365 @@
+Metadata-Version: 2.2
+Name: apt-ostree
+Version: 0.1.0
+Summary: Atomic package management system for Debian/Ubuntu inspired by rpm-ostree
+Home-page: https://github.com/particle-os/apt-ostree
+Author: Particle-OS Team
+Author-email: team@particle-os.org
+Project-URL: Bug Reports, https://github.com/particle-os/apt-ostree/issues
+Project-URL: Source, https://github.com/particle-os/apt-ostree
+Project-URL: Documentation, https://github.com/particle-os/apt-ostree/docs
+Keywords: debian ubuntu package management atomic ostree
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: System Administrators
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: System :: Systems Administration
+Classifier: Topic :: System :: Operating System
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: PyGObject>=3.40.0
+Requires-Dist: python-apt>=2.0.0
+Requires-Dist: dbus-python>=1.2.0
+Requires-Dist: PyYAML>=6.0.0
+Requires-Dist: ostree>=0.1.1
+Requires-Dist: psutil>=5.8.0
+Requires-Dist: structlog>=21.0.0
+Requires-Dist: systemd-python>=234
+Requires-Dist: pytest>=6.0.0
+Requires-Dist: pytest-asyncio>=0.18.0
+Requires-Dist: pytest-cov>=3.0.0
+Requires-Dist: black>=22.0.0
+Requires-Dist: flake8>=4.0.0
+Requires-Dist: mypy>=0.950
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# apt-ostree Python Daemon
+
+This is the Python implementation of the apt-ostree daemon, providing atomic package management for Debian/Ubuntu systems inspired by rpm-ostree.
+
+## Overview
+
+The apt-ostree daemon provides:
+- **D-Bus API**: Clean interface for package management operations
+- **OSTree Integration**: Atomic filesystem management using OSTree
+- **APT Integration**: Native Debian package management
+- **Transaction Management**: Atomic operations with rollback capabilities
+- **Security**: PolicyKit integration and AppArmor support
+- **Concurrent Operations**: Multiple simultaneous transactions
+
+## Architecture
+
+```
+apt-ostree.py/
+├── apt_ostree.py              # Main daemon entry point
+├── core/                      # Core daemon components
+│   ├── daemon.py             # Main daemon class
+│   ├── transaction.py        # Transaction management
+│   ├── client_manager.py     # D-Bus client tracking
+│   └── sysroot.py            # OSTree sysroot management
+├── dbus/                      # D-Bus interface components
+│   └── interface.py          # D-Bus API implementation
+├── utils/                     # Utility components
+│   ├── config.py             # Configuration management
+│   ├── logging.py            # Structured logging
+│   └── security.py           # Security utilities
+├── tests/                     # Test suite
+│   └── test_basic.py         # Basic functionality tests
+├── requirements.txt           # Python dependencies
+├── setup.py                   # Package setup
+└── README.md                  # This file
+```
+
+## Installation
+
+### Prerequisites
+
+- Python 3.8 or higher
+- OSTree development libraries
+- D-Bus development libraries
+- PolicyKit development libraries
+
+### System Dependencies
+
+```bash
+# Ubuntu/Debian
+sudo apt-get install \
+    python3-dev \
+    python3-gi \
+    python3-gi-cairo \
+    gir1.2-ostree-1.0 \
+    libostree-dev \
+    libdbus-1-dev \
+    libpolkit-gobject-1-dev \
+    apparmor-utils
+
+# Build dependencies
+sudo apt-get install \
+    build-essential \
+    pkg-config \
+    libglib2.0-dev \
+    libgirepository1.0-dev
+```
+
+### Python Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/particle-os/apt-ostree.git
+cd apt-ostree/src/apt-ostree.py/python
+
+# Install Python dependencies
+pip install -r requirements.txt
+
+# Install the package
+pip install -e .
+```
+
+## Configuration
+
+The daemon uses YAML configuration files. Default configuration is loaded from `/etc/apt-ostree/config.yaml`.
+
+### Example Configuration
+
+```yaml
+daemon:
+  dbus:
+    bus_name: "org.debian.aptostree1"
+    object_path: "/org/debian/aptostree1"
+  
+  concurrency:
+    max_workers: 3
+    transaction_timeout: 300
+    
+  logging:
+    level: "INFO"
+    format: "json"
+    file: "/var/log/apt-ostree/daemon.log"
+
+sysroot:
+  path: "/"
+  repo_path: "/var/lib/ostree/repo"
+
+shell_integration:
+  script_path: "/usr/local/bin/apt-layer.sh"
+  timeout:
+    install: 300
+    remove: 300
+    composefs: 600
+
+security:
+  polkit_required: true
+  apparmor_profile: "/etc/apparmor.d/apt-ostree"
+```
+
+## Usage
+
+### Running the Daemon
+
+```bash
+# Run as root (required for system operations)
+sudo python3 -m apt_ostree
+
+# Or install and run as service
+sudo apt-ostree
+```
+
+### D-Bus API
+
+The daemon provides a D-Bus API at `org.debian.aptostree1`.
+
+#### Example: Install Packages
+
+```python
+import dbus
+
+# Connect to system bus
+bus = dbus.SystemBus()
+
+# Get daemon interface
+daemon = bus.get_object(
+    'org.debian.aptostree1',
+    '/org/debian/aptostree1/Sysroot'
+)
+
+# Install packages
+result = daemon.InstallPackages(['firefox', 'thunderbird'], False)
+print(f"Install result: {result}")
+```
+
+#### Example: System Upgrade
+
+```python
+# Upgrade system
+result = daemon.Upgrade({})
+print(f"Upgrade result: {result}")
+```
+
+### Command Line Interface
+
+```bash
+# Install packages
+apt-ostree install firefox thunderbird
+
+# Remove packages
+apt-ostree remove firefox
+
+# System upgrade
+apt-ostree upgrade
+
+# System rollback
+apt-ostree rollback
+
+# Check status
+apt-ostree status
+```
+
+## Development
+
+### Running Tests
+
+```bash
+# Run all tests
+python -m pytest tests/
+
+# Run specific test
+python -m pytest tests/test_basic.py::TestConfigManager::test_default_config
+
+# Run with coverage
+python -m pytest --cov=apt_ostree tests/
+```
+
+### Code Formatting
+
+```bash
+# Format code
+black .
+
+# Lint code
+flake8 .
+
+# Type checking
+mypy .
+```
+
+### Development Setup
+
+```bash
+# Install development dependencies
+pip install -r requirements.txt
+pip install pytest pytest-cov black flake8 mypy
+
+# Setup pre-commit hooks
+pre-commit install
+```
+
+## D-Bus Interface
+
+### Sysroot Interface
+
+- `RegisterClient(options)` - Register client for monitoring
+- `UnregisterClient(options)` - Unregister client
+- `Reload()` - Reload sysroot state
+- `ReloadConfig()` - Reload configuration
+- `GetStatus()` - Get daemon status
+- `GetOS()` - Get list of OS instances
+
+### OS Interface
+
+- `Deploy(revision, options)` - Deploy specific revision
+- `Upgrade(options)` - Upgrade to latest version
+- `Rollback(options)` - Rollback to previous deployment
+- `PkgChange(packages_added, packages_removed, options)` - Add/remove packages
+- `Rebase(refspec, options)` - Switch to different base OS
+- `GetDeployments()` - Get list of deployments
+- `GetBootedDeployment()` - Get currently booted deployment
+
+### Transaction Interface
+
+- `Start()` - Start the transaction
+- `Cancel()` - Cancel the transaction
+- `Title` (property) - Transaction title
+- `InitiatingClientDescription` (property) - Client description
+
+## Security
+
+### PolicyKit Integration
+
+The daemon uses PolicyKit for authorization. Required actions:
+
+- `org.debian.aptostree.package.install` - Install packages
+- `org.debian.aptostree.package.remove` - Remove packages
+- `org.debian.aptostree.system.upgrade` - System upgrade
+- `org.debian.aptostree.system.rollback` - System rollback
+- `org.debian.aptostree.deploy` - Deploy operations
+- `org.debian.aptostree.rebase` - Rebase operations
+
+### AppArmor Support
+
+The daemon includes AppArmor profile support for enhanced security.
+
+## Logging
+
+The daemon uses structured logging with JSON format by default.
+
+### Log Levels
+
+- `DEBUG` - Detailed debug information
+- `INFO` - General information
+- `WARNING` - Warning messages
+- `ERROR` - Error messages
+
+### Log Files
+
+- Console output: Human-readable format
+- File output: JSON format for machine processing
+- Systemd journal: Integration with systemd logging
+
+## Integration
+
+### Systemd Integration
+
+The daemon integrates with systemd for service management and status reporting.
+
+### OSTree Integration
+
+Direct integration with libostree for filesystem management and atomic operations.
+
+### APT Integration
+
+Native integration with python-apt for Debian package management.
+
+## Contributing
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Add tests for new functionality
+5. Ensure all tests pass
+6. Submit a pull request
+
+## License
+
+This project is licensed under the MIT License - see the LICENSE file for details.
+
+## Support
+
+For support and questions:
+- GitHub Issues: https://github.com/particle-os/apt-ostree/issues
+- Documentation: https://github.com/particle-os/apt-ostree/docs
+- Wiki: https://github.com/particle-os/apt-ostree/wiki 

src/apt-ostree.py/python/apt_ostree.egg-info/SOURCES.txt

@@ -0,0 +1,20 @@
+README.md
+setup.py
+apt_ostree.egg-info/PKG-INFO
+apt_ostree.egg-info/SOURCES.txt
+apt_ostree.egg-info/dependency_links.txt
+apt_ostree.egg-info/entry_points.txt
+apt_ostree.egg-info/requires.txt
+apt_ostree.egg-info/top_level.txt
+core/__init__.py
+core/client_manager.py
+core/daemon.py
+core/sysroot.py
+core/transaction.py
+dbus/__init__.py
+dbus/interface.py
+tests/test_basic.py
+utils/__init__.py
+utils/config.py
+utils/logging.py
+utils/security.py

src/apt-ostree.py/python/apt_ostree.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

src/apt-ostree.py/python/apt_ostree.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+apt-ostree = apt_ostree:main

src/apt-ostree.py/python/apt_ostree.egg-info/requires.txt

@@ -0,0 +1,14 @@
+PyGObject>=3.40.0
+PyYAML>=6.0.0
+black>=22.0.0
+dbus-python>=1.2.0
+flake8>=4.0.0
+mypy>=0.950
+ostree>=0.1.1
+psutil>=5.8.0
+pytest-asyncio>=0.18.0
+pytest-cov>=3.0.0
+pytest>=6.0.0
+python-apt>=2.0.0
+structlog>=21.0.0
+systemd-python>=234

src/apt-ostree.py/python/apt_ostree.egg-info/top_level.txt

@@ -0,0 +1,3 @@
+core
+dbus
+utils