paper-repo-extract

To extract a standalone reproducibility repository from a monorepo for a journal submission, run the skill with a specific paper identifier to generate a separate directory containing all necessary code and data. This ensures the paper's assets are fully prepared for submission with a Zenodo DOI citation.

Extracting a paper repository for journal submission creates a standalone directory, rewrites internal imports to resolve external dependencies, and generates synthetic data. This process ensures the extracted code and data are fully reproducible and ready for archival.

Yes, you need Python and the giotto-tda library installed in your environment to run the repository extraction process. These dependencies are required to execute the scripts and handle the topological data analysis components referenced in the paper.

To prepare a paper with identifier P01-B for standalone repository extraction, execute the skill command targeting that specific identifier. The system will automatically handle directory creation, import rewriting, and synthetic data generation for the P01-B paper assets.

Yes, the repository extraction process requires explicit user confirmation before performing high-impact operations. This safety mechanism ensures you maintain control over critical steps like directory creation, import rewriting, and synthetic data generation during the extraction.

The automated import rewriting for reproducibility repositories focuses on adjusting internal monorepo references to work in a standalone context. While it handles directory creation and synthetic data generation, complex custom import structures may require manual verification to ensure full journal submission compliance.