biopython Audit report.

Warnings

• Dependency or permission surface needs review
• Permission surface may require sandboxing
• SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.
• The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.
• The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved.
• Permission surface needs review: secrets or environment access, shell or command execution
• Dependency/runtime risk: command execution surface, credential or environment access
• Permission surface: secrets or environment access, shell or command execution

Method

This report combines public metadata, AI review output, repository freshness, install readiness, OpenAgentSkill events, quality scoring, trust checks, and the agent safety gate. It is not a full source-code security review.