feat: Phase I I9 public-good contribution guide -- institutions can now formally contribute

Makefile

@@ -1,4 +1,4 @@
-.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check
+.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -824,3 +824,8 @@ license-check:
 artifact-compat-check:
 	.venv/bin/openamp-foundry artifact-compat-check
 	@echo "Artifact compatibility check complete."
+
+contribution-check:
+	.venv/bin/openamp-foundry contribution-check \
+		--intake-json '{"institution_name":"Example University","contact_email":"research@example.edu","contribution_type":"dataset_donation","proposed_scope":"Curated AMP dataset 500 sequences","human_review_required":false,"dry_lab_only":true,"data_license":"CC-BY-4.0","dataset_description":"AMP sequences with MIC data","record_count":500}'
+	@echo "Contribution intake check complete."

docs/community/PUBLIC_GOOD_CONTRIBUTION_GUIDE.md

@@ -0,0 +1,174 @@
+# Public-Good Contribution Guide
+
+## Purpose
+
+OpenAMP Foundry is an open-source, dry-lab infrastructure for antimicrobial
+peptide candidate selection. Its mission is to make candidate selection more
+reproducible, safer to audit, and harder to fool.
+
+**Public-good contributions** are contributions that advance this mission
+without proprietary gatekeeping, private benefit, or biological harm. They
+are reviewed, attributed, and released under open terms so that the whole
+research community benefits.
+
+Institutional contributions are how universities, research hospitals,
+nonprofits, government labs, and open-source bioinformatics projects turn
+computational outputs into shared evidence. This guide tells you how.
+
+---
+
+## Who can contribute
+
+- **Universities** and academic research groups
+- **Research hospitals** and clinical research organisations
+- **Nonprofit** research institutes and foundations
+- **Government laboratories** and public-health agencies
+- **Open-source bioinformatics projects** publishing under OSI-approved
+  licenses
+
+Commercial entities are welcome to contribute through other channels
+(see [GOVERNANCE.md](../../GOVERNANCE.md)). This guide is scoped to
+public-good institutional contributors.
+
+---
+
+## Contribution types
+
+| Type | What it is | Minimum requirements | Review class |
+|------|-----------|---------------------|-------------|
+| `wet_lab_validation` | Experimental MIC / hemolysis data for nominated dry-lab candidates | institution_name, contact_email, candidate_ids, assay_type, data_license | D (human review mandatory) |
+| `dataset_donation` | Curated AMP or non-AMP datasets with full provenance | institution_name, contact_email, dataset_description, data_license, record_count | B |
+| `compute_sponsorship` | HPC time or GPU credits for simulation runs | institution_name, contact_email, compute_hours, platform | B |
+| `expert_review` | Structured peer review of evidence packets | institution_name, contact_email, reviewer_expertise, scope | D (human review recommended) |
+| `governance_participation` | Serving on advisory or review panels | institution_name, contact_email, role, availability | A |
+| `algorithm_contribution` | New scoring or simulation modules with tests | institution_name, contact_email, algorithm_description, has_tests, data_license | B |
+
+### Review classes
+
+- **A** — Low risk. Governance roles and administrative contributions.
+  Fast-track review.
+- **B** — Moderate risk. Datasets, algorithms, and compute sponsorships
+  require verification of claims, licensing, and reproducibility.
+- **C** — Reserved for future use.
+- **D** — High risk. Wet-lab validation and expert review require
+  mandatory human review before acceptance into the pipeline.
+
+---
+
+## How to initiate
+
+1. **Open a GitHub issue** at
+   [github.com/anomalyco/openamp-foundry/issues](https://github.com/anomalyco/openamp-foundry/issues).
+2. **Apply the label** `institutional-contribution`.
+3. **Include:**
+   - Institution name
+   - Contact email
+   - Contribution type (from the table above)
+   - Proposed scope (what you want to do or provide)
+   - Any relevant links (preprints, repositories, data sources)
+
+You can use the `openamp-foundry contribution-check` CLI to validate your
+intake before submitting:
+
+```bash
+openamp-foundry contribution-check \
+  --intake-json '{"institution_name":"Example University","contact_email":"research@example.edu","contribution_type":"dataset_donation","proposed_scope":"Curated AMP dataset 500 sequences","human_review_required":false,"dry_lab_only":true,"data_license":"CC-BY-4.0","dataset_description":"AMP sequences with MIC data","record_count":500}'
+```
+
+---
+
+## What to expect
+
+### Review timeline
+
+| Review class | Target turnaround | Notes |
+|-------------|-------------------|-------|
+| A | 5 business days | Governance and administrative |
+| B | 10 business days | Datasets, algorithms, compute |
+| C | (reserved) | |
+| D | 15 business days | Wet-lab data, expert review |
+
+### Evidence standards
+
+- All contributions must include the minimum required fields listed above.
+- Datasets must include provenance: source, collection method, curation
+  steps, and any exclusion criteria.
+- Wet-lab data must follow the lab result schema
+  (`schemas/lab_result.schema.json`) and include positive and negative
+  controls.
+- Algorithm contributions must include tests and a data-license declaration
+  for any training or evaluation data.
+
+### Publication rights
+
+- Contributors retain ownership of their contributed data and methods.
+- By contributing, you grant the OpenAMP project a non-exclusive,
+  royalty-free license to use, reproduce, and redistribute the contribution
+  for public-good purposes under the license you specify.
+- You may publish your own results separately. We encourage preprints and
+  open-access publication.
+
+### Attribution
+
+- All accepted contributions are recorded in the project's contribution
+  registry (metadata: institution, contact, type, date, scope).
+- Dataset and algorithm contributions are cited in the relevant
+  documentation and benchmark cards.
+- Contributors are listed in the project's acknowledgements section
+  (unless they opt out).
+- We follow academic citation norms for published work incorporated into
+  the pipeline.
+
+---
+
+## Data governance
+
+All contributed data is subject to:
+
+- [`DATA_GOVERNANCE.md`](../trust/DATA_GOVERNANCE.md) — data handling,
+  retention, and access policies.
+- [`DATA_LICENSE_NOTICE.md`](../../DATA_LICENSE_NOTICE.md) — licensing terms
+  for all data in the repository.
+
+Key rules:
+
+- Every dataset must declare a license from the approved list (CC0-1.0,
+  CC-BY-4.0, CC-BY-SA-4.0, MIT, Apache-2.0, GPL-3.0, LGPL-2.1,
+  BSD-2-Clause, BSD-3-Clause, ODbL-1.0, PDDL-1.0) or be reviewed by
+  governance for restricted licenses (CC-BY-NC-4.0, custom, proprietary).
+- Blocked licenses (unknown, unlicensed, all-rights-reserved) are never
+  accepted.
+- Contributors must confirm they have the right to share the data under
+  the declared license.
+
+---
+
+## Safety constraints
+
+- **Human review is required** before any wet-lab data or dual-use-relevant
+  data enters the pipeline. This is enforced by the `human_review_required`
+  flag, which must be `True` for `wet_lab_validation` contributions.
+- **Dry-lab only.** Computational outputs are hypotheses and review aids.
+  They are not biological proof.
+- **No biological instructions.** Contributions must not contain detailed
+  experimental protocols, dual-use information, or instructions for
+  unsupervised biological work.
+- Contributors must follow
+  [`SAFETY.md`](../../SAFETY.md) and
+  [`RESPONSIBLE_USE.md`](../../RESPONSIBLE_USE.md).
+
+Contributions that violate these constraints will be rejected or sent back
+for revision.
+
+---
+
+## Contact
+
+- Governance: [`GOVERNANCE.md`](../../GOVERNANCE.md)
+- Responsible use: [`RESPONSIBLE_USE.md`](../../RESPONSIBLE_USE.md)
+- Safety: [`SAFETY.md`](../../SAFETY.md)
+- Data governance: [`DATA_GOVERNANCE.md`](../trust/DATA_GOVERNANCE.md)
+
+For questions, open a GitHub issue with the `institutional-contribution`
+label, or contact the maintainers through the repository's discussion
+board.