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Concore CLI

A command-line interface for managing concore neuromodulation workflows.

Installation

pip install -e .

Quick Start

# Create a new project
concore init my-project

# Navigate to your project
cd my-project

# Validate your workflow
concore validate workflow.graphml

# Build your workflow
concore build 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:

concore init my-workflow

Creates:

my-workflow/
├── workflow.graphml    # Sample workflow definition
├── src/
│   └── script.py      # Sample processing script
└── README.md          # Project documentation

concore build <workflow_file>

Compiles a concore workflow GraphML file into executable scripts (POSIX, Windows, or Docker).

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
  • --compose - Generate docker-compose.yml (only valid with --type docker)

Example:

concore build workflow.graphml --source ./src --output ./build --auto-build

Docker compose example:

concore build workflow.graphml --source ./src --output ./out --type docker --compose
cd out
docker compose up

concore validate <workflow_file>

Validates a GraphML workflow file before running.

Options:

  • -s, --source <dir> - Source directory to verify file references exist

Checks:

  • Valid XML structure
  • GraphML format compliance
  • Node and edge definitions
  • File references and naming conventions
  • Source file existence (when --source provided)
  • ZMQ port conflicts and reserved ports
  • Circular dependencies (warns for control loops)
  • Edge connectivity

Options:

  • -s, --source <dir> - Source directory (default: src)

Example:

concore validate workflow.graphml
concore validate workflow.graphml --source ./src

concore status

Shows all currently running concore processes with details:

  • Process ID (PID)
  • Process name
  • Uptime
  • Memory usage
  • Command

Example:

concore status

concore stop

Stops all running concore processes. Prompts for confirmation before proceeding.

Example:

concore stop

Development Workflow

  1. Create a new project

    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

    concore validate workflow.graphml

  5. Generate and run

    concore build workflow.graphml --auto-build
cd out
./run.bat  # or ./run on Linux/Mac

  6. Monitor execution

    concore status

  7. Stop when done

    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)