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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Development Environment Setup

Python Environment

This project uses Python 3.6.9+ with virtual environments. Install dependencies:

# Create virtual environment
mkdir ~/venv
cd ~/venv
python3 -m venv neurolibre
source ~/venv/neurolibre/bin/activate

# Install dependencies
pip3 install --upgrade pip
pip3 install -r api/requirements.txt

Environment Configuration

Copy the appropriate environment template and configure:

# For preview server
cp api/env_templates/env.preview.template api/.env

# For preprint server  
cp api/env_templates/env.preprint.template api/.env

Architecture Overview

Server Types

The system operates two distinct server environments:

  1. Preview Server (neurolibre_preview_api.py) - Handles preview & screening tasks prior to submission
  2. Preprint Server (neurolibre_preprint_api.py) - Handles publishing tasks after technical screening

Core Components

Flask Application Structure

  • Common API (neurolibre_common_api.py) - Shared functionality between servers
  • Server-specific APIs - Preview and preprint specific endpoints
  • Configuration - YAML-based config in api/config/ directory
    • common.yaml - Shared configuration
    • preview.yaml - Preview server specific
    • preprint.yaml - Preprint server specific

Key Technologies

  • Flask - Web framework with API blueprints
  • Gunicorn - WSGI application server
  • Celery - Asynchronous task queue with Redis backend
  • NGINX - Reverse proxy and static file serving
  • Docker - Containerization for reproducible environments

Task Management

Celery handles asynchronous operations:

  • Book building (JupyterBook/MyST)
  • Data synchronization between servers
  • Zenodo archival processes
  • Binder image builds

Development Commands

Running the Application

# Activate environment
source ~/venv/neurolibre/bin/activate

# Preview server (development)
python api/neurolibre_preview_api.py

# Preprint server (development)  
python api/neurolibre_preprint_api.py

Celery Worker

# Start Celery worker
source ~/venv/neurolibre/bin/activate
cd api/
celery -A neurolibre_celery_tasks worker --loglevel=info

Production Deployment

The application runs as systemd services:

  • neurolibre-preview.service - Preview server
  • neurolibre-preprint.service - Preprint server
  • Celery workers for async tasks

Key Directories

  • api/ - Main application code
    • config/ - YAML configuration files
    • templates/ - HTML templates
    • env_templates/ - Environment file templates
  • nginx/ - NGINX configuration templates
  • systemd/ - Service configuration files
  • fail2ban/ - Security configuration

Configuration Notes

Server Domains

  • Preview: preview.neurolibre.org
  • Preprint: preprint.neurolibre.org
  • Both use same domain (neurolibre.org) with different subdomains

Data Paths

  • Root data path: /DATA (shared between servers)
  • Book artifacts: /DATA/book-artifacts
  • MyST sources: /DATA/myst
  • Logs: /DATA/logs

GitHub Integration

  • Uses GitHub API for repository management
  • Forked repositories go to roboneurolibre organization
  • Review issues tracked in neurolibre/neurolibre-reviews

Security Features

  • HTTP Basic Authentication for API endpoints
  • SSL/TLS with Cloudflare integration
  • fail2ban for brute-force protection
  • Separate preview/production environments

Monitoring

  • NewRelic integration for infrastructure monitoring
  • NGINX status monitoring
  • Celery task monitoring
  • Comprehensive logging with journalctl