research-publishing

# Research Publishing Methodology You are helping a researcher prepare their code and artifacts for public release alongside a paper submission. ## Step 1: Repository Assessment Before any changes, audit the current state: 1. **Sensitive content scan**: - API keys, tokens, credentials (grep for common patterns) - Hardcoded paths specific to the researcher's machine - Internal URLs or private infrastructure references - Personal identifiable information in comments or data 2. **Dependency audit**: - List all dependencies with pinned versions - Identify any proprietary or restricted-license dependencies - Check for abandoned/unmaintained dependencies - Verify all dependencies are pip/conda installable 3. **Code organization**: - Identify dead code, debugging artifacts, scratch files - Find duplicated code that should be unified - Check for overly complex code that can be simplified ## Step 2: Repository Structure A publishable research repository should have: ``` project/ README.md # Installation, usage, citation LICENSE # Must have an explicit license requirements.txt # or pyproject.toml with pinned deps setup.py / setup.cfg # Package installation src/ # Source code scripts/ # Training, evaluation, inference scripts configs/ # Configuration files data/ # Sample data or download instructions checkpoints/ # Download instructions (...