Merge pull request #189 from Sahil-u07/fix-exception-handling-and-logging

Add CLI for concore (#183)

Author: pradeeban

README.md

@@ -28,6 +28,35 @@ Please follow the [ReadTheDocs](https://control-core.readthedocs.io/en/latest/in
 
 Installation instructions for concore can be found [here](https://control-core.readthedocs.io/en/latest/installation.html). Usage instructions can be found [here](https://control-core.readthedocs.io/en/latest/usage.html).
 
+## Command-Line Interface (CLI)
+
+_concore_ now includes a command-line interface for easier workflow management. Install it with:
+
+```bash
+pip install -e .
+```
+
+Quick start with the CLI:
+
+```bash
+# Create a new project
+concore init my-project
+
+# Validate your workflow
+concore validate workflow.graphml
+
+# Run your workflow
+concore run workflow.graphml --auto-build
+
+# Monitor running processes
+concore status
+
+# Stop all processes
+concore stop
+```
+
+For detailed CLI documentation, see [concore_cli/README.md](concore_cli/README.md).
+
 For a detailed and more scientific documentation, please read our extensive [open-access research paper on CONTROL-CORE](https://doi.org/10.1109/ACCESS.2022.3161471). This paper has a complete discussion on the CONTROL-CORE architecture and deployment, together with the commands to execute the studies in different programming languages and programming environments (Ubuntu, Windows, MacOS, Docker, and distributed execution).
 
 

concore_cli/README.md

@@ -0,0 +1,180 @@
+# Concore CLI
+
+A command-line interface for managing concore neuromodulation workflows.
+
+## Installation
+
+```bash
+pip install -e .
+```
+
+## Quick Start
+
+```bash
+# Create a new project
+concore init my-project
+
+# Navigate to your project
+cd my-project
+
+# Validate your workflow
+concore validate workflow.graphml
+
+# Run your workflow
+concore run workflow.graphml
+
+# Check running processes
+concore status
+
+# Stop all processes
+concore stop
+```
+
+## Commands
+
+### `concore init <name>`
+
+Creates a new concore project with a basic structure.
+
+**Options:**
+- `--template` - Template type to use (default: basic)
+
+**Example:**
+```bash
+concore init my-workflow
+```
+
+Creates:
+```
+my-workflow/
+├── workflow.graphml    # Sample workflow definition
+├── src/
+│   └── script.py      # Sample processing script
+└── README.md          # Project documentation
+```
+
+### `concore run <workflow_file>`
+
+Generates and optionally builds a workflow from a GraphML file.
+
+**Options:**
+- `-s, --source <dir>` - Source directory (default: src)
+- `-o, --output <dir>` - Output directory (default: out)
+- `-t, --type <type>` - Execution type: windows, posix, or docker (default: windows)
+- `--auto-build` - Automatically run build script after generation
+
+**Example:**
+```bash
+concore run workflow.graphml --source ./src --output ./build --auto-build
+```
+
+### `concore validate <workflow_file>`
+
+Validates a GraphML workflow file before running.
+
+Checks:
+- Valid XML structure
+- GraphML format compliance
+- Node and edge definitions
+- File references and naming conventions
+- ZMQ vs file-based communication
+
+**Example:**
+```bash
+concore validate workflow.graphml
+```
+
+### `concore status`
+
+Shows all currently running concore processes with details:
+- Process ID (PID)
+- Process name
+- Uptime
+- Memory usage
+- Command
+
+**Example:**
+```bash
+concore status
+```
+
+### `concore stop`
+
+Stops all running concore processes. Prompts for confirmation before proceeding.
+
+**Example:**
+```bash
+concore stop
+```
+
+## Development Workflow
+
+1. **Create a new project**
+   ```bash
+   concore init my-neuro-study
+   cd my-neuro-study
+   ```
+
+2. **Edit your workflow**
+   - Open `workflow.graphml` in yEd or similar GraphML editor
+   - Add nodes for your processing steps
+   - Connect nodes with edges to define data flow
+
+3. **Add processing scripts**
+   - Place your Python/C++/MATLAB/Verilog files in the `src/` directory
+   - Reference them in your workflow nodes
+
+4. **Validate before running**
+   ```bash
+   concore validate workflow.graphml
+   ```
+
+5. **Generate and run**
+   ```bash
+   concore run workflow.graphml --auto-build
+   cd out
+   ./run.bat  # or ./run on Linux/Mac
+   ```
+
+6. **Monitor execution**
+   ```bash
+   concore status
+   ```
+
+7. **Stop when done**
+   ```bash
+   concore stop
+   ```
+
+## Workflow File Format
+
+Nodes should follow the format: `ID:filename.ext`
+
+Example:
+```
+N1:controller.py
+N2:processor.cpp
+M1:analyzer.m
+```
+
+Supported file types:
+- `.py` - Python
+- `.cpp` - C++
+- `.m` - MATLAB/Octave
+- `.v` - Verilog
+- `.java` - Java
+
+## Troubleshooting
+
+**Issue: "Output directory already exists"**
+- Remove the existing output directory or choose a different name
+- Use `concore stop` to terminate any running processes first
+
+**Issue: Validation fails**
+- Check that your GraphML file is properly formatted
+- Ensure all nodes have labels in the format `ID:filename.ext`
+- Verify that edge connections reference valid nodes
+
+**Issue: Processes won't stop**
+- Try running `concore stop` with administrator/sudo privileges
+- Manually kill processes using Task Manager (Windows) or `kill` command (Linux/Mac)

concore_cli/__init__.py

@@ -0,0 +1,3 @@
+from .cli import cli
+
+__all__ = ['cli']

concore_cli/cli.py

@@ -0,0 +1,78 @@
+import click
+from rich.console import Console
+from rich.table import Table
+from rich.panel import Panel
+from rich import print as rprint
+import sys
+import os
+from pathlib import Path
+
+from .commands.init import init_project
+from .commands.run import run_workflow
+from .commands.validate import validate_workflow
+from .commands.status import show_status
+from .commands.stop import stop_all
+
+console = Console()
+
+@click.group()
+@click.version_option(version='1.0.0', prog_name='concore')
+def cli():
+    pass
+
+@cli.command()
+@click.argument('name', required=True)
+@click.option('--template', default='basic', help='Template type to use')
+def init(name, template):
+    """Create a new concore project"""
+    try:
+        init_project(name, template, console)
+    except Exception as e:
+        console.print(f"[red]Error:[/red] {str(e)}")
+        sys.exit(1)
+
+@cli.command()
+@click.argument('workflow_file', type=click.Path(exists=True))
+@click.option('--source', '-s', default='src', help='Source directory')
+@click.option('--output', '-o', default='out', help='Output directory')
+@click.option('--type', '-t', default='windows', type=click.Choice(['windows', 'posix', 'docker']), help='Execution type')
+@click.option('--auto-build', is_flag=True, help='Automatically run build after generation')
+def run(workflow_file, source, output, type, auto_build):
+    """Run a concore workflow"""
+    try:
+        run_workflow(workflow_file, source, output, type, auto_build, console)
+    except Exception as e:
+        console.print(f"[red]Error:[/red] {str(e)}")
+        sys.exit(1)
+
+@cli.command()
+@click.argument('workflow_file', type=click.Path(exists=True))
+def validate(workflow_file):
+    """Validate a workflow file"""
+    try:
+        validate_workflow(workflow_file, console)
+    except Exception as e:
+        console.print(f"[red]Error:[/red] {str(e)}")
+        sys.exit(1)
+
+@cli.command()
+def status():
+    """Show running concore processes"""
+    try:
+        show_status(console)
+    except Exception as e:
+        console.print(f"[red]Error:[/red] {str(e)}")
+        sys.exit(1)
+
+@cli.command()
+@click.confirmation_option(prompt='Stop all running concore processes?')
+def stop():
+    """Stop all running concore processes"""
+    try:
+        stop_all(console)
+    except Exception as e:
+        console.print(f"[red]Error:[/red] {str(e)}")
+        sys.exit(1)
+
+if __name__ == '__main__':
+    cli()

concore_cli/commands/__init__.py

@@ -0,0 +1,7 @@
+from .init import init_project
+from .run import run_workflow
+from .validate import validate_workflow
+from .status import show_status
+from .stop import stop_all
+
+__all__ = ['init_project', 'run_workflow', 'validate_workflow', 'show_status', 'stop_all']