algal-bio

Imported from 0thernet/algal-bio (AGENTS.md). Install upstream with npx skills add 0thernet/algal-bio. Copyright stays with the author.

Algal Bio

This repository owns biology protocols, analyses, and research records. Algal Lab owns experimental registration and evidence contracts; ALGAL owns bounded runtime effects; Sponge is an optional source and review interface. Public fixtures must work without a sibling checkout, account, API key, or paid inference.

• Preserve historical scripts, data, results, and all 289 native ALGAL receipts. tests/fixtures/legacy/manifest.json records their baseline hashes. A deliberate historical correction requires review and an explanation; never regenerate the manifest to conceal a changed or missing artifact.
• Keep evidence integrity, deterministic replay, fresh computation, computational association, novelty review, and experimental biology as separate claims.
• Register predictions and controls before observations; freeze selection before evaluator access. Retain failures, exclusions, and negative findings. Synthetic fixtures establish software behavior, not biological discoveries or agent merit.
• Model output is untrusted data. Proposed code gains no execution authority until admitted. Keep holdout data and evaluator credentials outside investigator mounts.
• Live inference and compute default to disabled. Admit them only with a verified account, exact model/provider configuration, current prices, resource limits, and an explicitly funded campaign envelope. Never infer a budget from a proposal.
• Do not add credentials, private collaborator data, restricted full text, transient runs, or personal filesystem paths. Large public data stays external with hashes. Publication artifacts need their own explicit reviewed rights/evidence manifest.
• Keep Python and Bun dependencies locked; use immutable qualified Algal Lab/ALGAL identities. The old native CLI is a separate, currently unqualified toolchain.
• Add Python tests under tests/ as test_*.py, and Bun tests as *.test.ts. make check discovers both. Tests must be deterministic and credential-free; network-dependent scientific work belongs to an explicitly configured campaign.
• Implementers run focused checks and report commands/results. The integrator owns the final make check, make reproduce-fixture, and clean-checkout reproduction. Follow any host scheduling requirement before broad or heavyweight validation.
• Deliver through a feature branch and PR, independent review, and required checks. Do not force-push or change unrelated work. Routine delivery is authorized by the user's standing instructions after applicable gates pass.

Layout

• campaigns/, datasets/manifests/, schemas/: registered designs and contracts.
• src/bio_lab/, orchestrator/: domain instrument and bounded campaign control.
• scripts/, tests/: portable verification and offline fixtures.
• docs/, reports/: method, evidence limits, and reviewed public results.
• Root legacy scripts, facts/, rules/, out/, codebase/, .algal*: retained historical work; see docs/legacy-evidence.md before attempting reproduction.