Imported from zerostwo/shennong (inst/codex/project-template/AGENTS.md). Install upstream with npx skills add zerostwo/shennong --skill project-template. Copyright stays with the author.

{{project_name}} Analysis Governance

This repository is a formal bioinformatics analysis project initialized from the Shennong package template. The agent must treat this repository as a governed analysis project, not as an ad hoc scratch directory.

Operating Priorities

1. Preserve reproducibility, traceability, and auditability.
2. Keep raw inputs immutable and derived artifacts attributable to a run.
3. Prefer formal scripts and recorded runs over notebook-only work.
4. Persist durable project knowledge so future sessions can reuse it safely.
5. Keep outputs organized so another analyst can re-run and review the work.

Hard Constraints

• The agent must read the required governance files before starting formal work.
• The agent must use the directory conventions defined in docs/standards/BioinformaticsAnalysisConventions.md.
• The agent must record durable project decisions in memory/Decisions.md.
• The agent must record current work state in memory/Status.md.
• The agent must update memory/Plan.md when scope or sequencing changes.
• The agent must update memory/Prompt.md when the durable operating context changes.
• The agent must record durable environment details such as executable paths, reference locations, and reusable environment names in config/default.yaml and, when they become project assumptions, in memory/Decisions.md.
• The agent must use skills/ for standard operating procedures inside this initialized project.
• If Shennong usage tracking is enabled, place its local SQLite database below ignored runs/, select development/production/test/benchmark mode explicitly, and never commit or upload the raw SQLite activity log. Enable before caching Shennong function references; the current namespace-binding tracker does not intercept references saved earlier. Remote DBI delivery must retain the local outbox and requires explicit versioned research consent and a sanitized flush.

The Agent Must Always Do

• Read governance in the required order before formal analysis work.
• Keep source data, derived data, runs, and exported results separated.
• Use explicit names, run identifiers, and dated artifacts.
• Promote reusable outputs only through documented promotion rules.
• Capture enough context so a later session can continue without guesswork.

The Agent Must Never Do

• Must not overwrite data/raw/ source files.
• Must not place formal outputs in ambiguous locations such as the repository root.
• Must not use ambiguous names such as final, final2, new, or test.
• Must not treat notebook output as the only record of formal analysis work.
• Must not silently change directory conventions or project rules.

Reading Priority Order

1. AGENTS.md
2. docs/standards/BioinformaticsAnalysisConventions.md
3. memory/Decisions.md
4. memory/Plan.md
5. memory/Status.md
6. memory/Prompt.md

Pointers

• Standards: docs/standards/BioinformaticsAnalysisConventions.md
• Memory: memory/
• Project skills: skills/
• Package usage skills can be installed separately from Shennong with sn_install_codex_skill(type = "package_skills") when API-level guidance is needed.
• An MCP-capable agent can use sn_get_mcp_server_config() to discover installed methods, exact function help, and workflow guides through Shennong's read-only stdio server. Keep analysis execution in explicit project scripts.
• Use sn_enable_usage_tracking() only for an explicitly requested local timing/usage audit; summarize optimization targets with sn_summarize_usage() and disable the tracker at the end of the session. For managed remote research, use sn_create_usage_store(), sn_confirm_usage_consent(), and sn_flush_usage_tracking(); do not place database credentials in project files or distribute them to desktop users.

Do / Do Not

Do:

• use explicit run IDs
• keep scripts stage-oriented
• persist durable knowledge after using it successfully

Do not:

• hide important paths only in transient chat
• export unchecked intermediates as final results
• invent new conventions without recording them