Research Publishing Agent Skill

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:

• 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

• 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

• 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 (not actual weights)
  results/             # Key result files referenced in paper

Step 3: Reproducibility Checklist

For each experiment in the paper:

• [ ] Configuration file exists and matches paper's hyperparameters
• [ ] Random seeds are set and documented
• [ ] Training command is documented end-to-end
• [ ] Evaluation command produces the reported numbers
• [ ] Data preprocessing steps are scripted (not manual)
• [ ] Hardware requirements are documented (GPU type, memory, time)
• [ ] Dependencies are version-pinned

Step 4: README Structure

A research README must include:

• Title + one-line description
• Paper link (arXiv, venue page)
• Visual (architecture diagram, key result figure, or demo GIF)
• Installation (step-by-step, tested on clean environment)
• Quick start (inference on a single example, < 5 commands)
• Training (full reproduction commands)
• Evaluation (reproduce paper numbers)
• Model zoo / checkpoints (download links with expected metrics)
• Citation (BibTeX block)

10. License

Step 5: Code Cleanup

Apply minimal, targeted cleanup:

• Remove debugging prints, commented-out code, scratch experiments
• Replace hardcoded paths with configurable paths (env vars or args)
• Add docstrings to public functions (not internal helpers)
• Ensure the main entry points are clearly documented
• Do NOT refactor working code for style — it adds risk for no benefit

Step 6: License Selection

Guide the user through license choice:

| License | Allows commercial use | Requires attribution | Copyleft |

|---------|----------------------|---------------------|----------|

| MIT | Yes | Yes | No |

| Apache 2.0 | Yes | Yes | No (patent grant) |

| GPL 3.0 | Yes | Yes | Yes (derivative works) |

| CC BY 4.0 | Yes | Yes | No (for non-code) |

| CC BY-NC 4.0 | No | Yes | No (for non-code) |

Default recommendation: MIT for code, CC BY 4.0 for datasets/models.

Step 7: Pre-Release Testing

Before publishing:

• Clone into a fresh directory
• Follow README installation steps exactly
• Run quick start commands
• Run evaluation to verify numbers match paper
• Check that no sensitive information is in git history

Output Format

Produce:

• Audit report: sensitive content found, dependency issues, dead code
• Action list: specific files to modify/remove/add
• README draft: following the structure above
• Reproducibility checklist: per-experiment verification status