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Add CLI for concore (#183)
Features: - concore init: Create new project with templates - concore run: Execute workflows with auto-build option - concore validate: Check GraphML files before running - concore status: Show running processes with details - concore stop: Stop all concore processes safely Tech: - Built with Click and Rich for beautiful output - Cross-platform support (Windows, Linux, macOS) - All 9 tests passing Closes #183
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‎README.md‎

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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).
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## Command-Line Interface (CLI)
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_concore_ now includes a command-line interface for easier workflow management. Install it with:
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```bash
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pip install -e .
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```
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Quick start with the CLI:
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```bash
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# Create a new project
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concore init my-project
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# Validate your workflow
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concore validate workflow.graphml
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# Run your workflow
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concore run workflow.graphml --auto-build
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# Monitor running processes
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concore status
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# Stop all processes
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concore stop
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```
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For detailed CLI documentation, see [concore_cli/README.md](concore_cli/README.md).
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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).
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‎concore_cli/README.md‎

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

‎concore_cli/__init__.py‎

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from .cli import cli
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__all__ = ['cli']

‎concore_cli/cli.py‎

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

‎concore_cli/commands/__init__.py‎

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from .init import init_project
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from .run import run_workflow
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from .validate import validate_workflow
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from .status import show_status
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from .stop import stop_all
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__all__ = ['init_project', 'run_workflow', 'validate_workflow', 'show_status', 'stop_all']

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