initial cli files, core and solvents

mdmix/cli/__init__.py

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+from cli.base import app, DisplayUtils
+from cli.project_plugin import ProjectPlugin
+from cli.solvent_plugin import SolventPlugin
+
+# Register plugins
+project_plugin = ProjectPlugin()
+project_plugin.attach_to_main(app)
+
+solvent_plugin = SolventPlugin()
+solvent_plugin.attach_to_main(app)
+
+__all__ = ['app', 'DisplayUtils', 'project_plugin', 'solvent_plugin']

mdmix/cli/base.py

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+
+import typer
+from typing import Optional, List
+from pathlib import Path
+from rich.console import Console
+from rich.table import Table
+from rich.panel import Panel
+from rich import print as rprint
+import logging
+from abc import ABC, abstractmethod
+
+# Initialize console for rich output
+console = Console()
+
+# Base CLI app
+app = typer.Typer(
+    name="pymdmix3",
+    help="PyMDMix3 - Advanced Molecular Dynamics Mixed Solvent Simulations",
+    rich_markup_mode="rich"
+)
+
+
+class CLIPlugin(ABC):
+    """Base class for CLI plugins"""
+
+    def __init__(self, name: str, help_text: str):
+        self.name = name
+        self.help_text = help_text
+        self.app = typer.Typer(help=help_text)
+
+    @abstractmethod
+    def register_commands(self):
+        """Register plugin commands"""
+        pass
+
+    def attach_to_main(self, main_app: typer.Typer):
+        """Attach plugin to main app"""
+        self.register_commands()
+        main_app.add_typer(self.app, name=self.name)
+
+
+class DisplayUtils:
+    """Utilities for rich console output"""
+
+    @staticmethod
+    def show_header(title: str, subtitle: str = ""):
+        """Display a styled header"""
+        if subtitle:
+            content = f"[bold cyan]{title}[/bold cyan]\n[dim]{subtitle}[/dim]"
+        else:
+            content = f"[bold cyan]{title}[/bold cyan]"
+        console.print(Panel(content, expand=False))
+
+    @staticmethod
+    def show_error(message: str):
+        """Display error message"""
+        console.print(f"[bold red]Error:[/bold red] {message}")
+
+    @staticmethod
+    def show_success(message: str):
+        """Display success message"""
+        console.print(f"[bold green]Success:[/bold green] {message}")
+
+    @staticmethod
+    def show_warning(message: str):
+        """Display warning message"""
+        console.print(f"[bold yellow]Warning:[/bold yellow] {message}")
+
+    @staticmethod
+    def show_info(message: str):
+        """Display info message"""
+        console.print(f"[bold blue]Info:[/bold blue] {message}")
+
+    @staticmethod
+    def create_table(title: str, columns: List[str]) -> Table:
+        """Create a styled table"""
+        table = Table(title=title, show_header=True, header_style="bold magenta")
+        for col in columns:
+            table.add_column(col)
+        return table
+
+
+# Logging configuration
+def setup_logging(verbose: bool = False):
+    """Setup logging configuration"""
+    level = logging.DEBUG if verbose else logging.INFO
+    logging.basicConfig(
+        level=level,
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+        datefmt='%Y-%m-%d %H:%M:%S'
+    )
+
+
+# Main app callbacks
+@app.callback()
+def main_callback(
+    verbose: bool = typer.Option(False, "--verbose", "-v", help="Enable verbose output"),
+    version: bool = typer.Option(False, "--version", help="Show version")
+):
+    """
+    PyMDMix3 - Advanced Molecular Dynamics Mixed Solvent Simulations
+
+    A modern Python implementation for mixed-solvent MD simulations.
+    """
+    if version:
+        from .. import __version__
+        console.print(f"PyMDMix3 version {__version__}")
+        raise typer.Exit()
+
+    setup_logging(verbose)
+
+
+# Main command
+@app.command()
+def info():
+    """Show PyMDMix3 information and status"""
+    from .. import __version__, __description__
+
+    DisplayUtils.show_header("PyMDMix3", __description__)
+
+    info_table = Table(show_header=False, box=None)
+    info_table.add_column("Property", style="cyan")
+    info_table.add_column("Value", style="white")
+
+    info_table.add_row("Version", __version__)
+    info_table.add_row("Python", "3.8+")
+    info_table.add_row("License", "GPL-3.0")
+
+    console.print(info_table)
+    console.print("\nUse [bold]pymdmix3 --help[/bold] to see available commands.")

mdmix/cli/main.py

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+
+from cli.base import app
+
+def main():
+    """Main entry point for PyMDMix3 CLI"""
+    app()
+
+if __name__ == "__main__":
+    main()