Propose 36 literature-backed ENVIRONMENT + METABOLISM traits

[realmarcin]

Summary

Adds 39 PROPOSED candidate trait records (18 ENVIRONMENT + 21 METABOLISM) filling clear coverage gaps in two categories. Every PROPOSED record carries ≥2 distinct, verified literature citations (PMID/DOI), and that bar is enforced in CI.

Schema

• Add PROPOSED value to MappingStatusEnum.

Validation

• New scripts/audit_proposals.py: requires ≥2 distinct, well-formed citations per PROPOSED record (counted across definition_source ∪ evidence[].reference); wired into the qc justfile target and CI; emits reports/proposal_citation_audit.tsv.
• tests/test_audit_proposals.py locks the rule; tests/test_seed.py relaxed to allow traitmech: IDs and PROPOSED.

ENVIRONMENT (traitmech:000001–000018)

Pressure/piezophily, radiation (ionizing/UV), desiccation/xerophily, heavy-metal/metalloid tolerance (Cd/Zn/Co/Hg/As/Cu).

METABOLISM (traitmech:000019–000039)

Six autotrophic carbon-fixation pathways (+carbon_fixation head), product-specific fermentations, DNRA, dissimilatory iron reduction, manganese oxidation, anaerobic oxidation of methane, oxygenic/anoxygenic photosynthesis, proteorhodopsin phototrophy, plus intermediate axis classes (phototrophy, photosynthesis, dissimilatory_metal_reduction). DNRA/AOM/metal-reduction parent to the existing METPO:1000802 anaerobic respiration class.

Reports

reports/environment_trait_proposals.md, reports/metabolism_trait_proposals.md.

Verification

• just validate-strict → 0 errors over 396 files
• just qc / audit-proposals → 39/39 PROPOSED passing
• pytest → 70 passed
• minted IDs contiguous 000001–000039; all traitmech: parent refs resolve

🤖 Generated with Claude Code

[Copilot]

Pull request overview

Adds 39 PROPOSED candidate TraitRecord YAMLs (18 ENVIRONMENT + 21 METABOLISM) filling clear coverage gaps (pressure/piezophily, radiation, desiccation, heavy-metal tolerance, carbon-fixation pathways, product-specific fermentations, DNRA, AOM, metal redox, phototrophy/photosynthesis). Each record carries ≥2 distinct verified citations, with a new PROPOSED enum value and a new scripts/audit_proposals.py audit (wired into just qc / CI) enforcing the citation bar.

Changes:

• Schema: add PROPOSED value to MappingStatusEnum; relax tests/test_seed.py to accept traitmech: IDs and the new status.
• New scripts/audit_proposals.py + unit tests; audit-proposals justfile recipe added to the qc composite target.
• 39 candidate trait YAMLs under data/traits/{environment,metabolism}/ minted traitmech:000001–traitmech:000039, plus two narrative reports and a generated TSV audit report.

Reviewed changes

Copilot reviewed 47 out of 47 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/traitmech/schema/traitmech.yaml	Add PROPOSED mapping status with description referencing the citation audit.
scripts/audit_proposals.py	New citation-bar audit for PROPOSED records (≥2 distinct, well-formed citations).
tests/test_audit_proposals.py	Locks the audit rules (skip non-PROPOSED, dedupe, placeholders, malformed).
tests/test_seed.py	Accept traitmech: identifiers and PROPOSED status.
justfile	Add audit-proposals recipe and chain it into qc.
reports/proposal_citation_audit.tsv	Generated audit output (uses absolute filesystem paths — see comment).
reports/environment_trait_proposals.md, reports/metabolism_trait_proposals.md	Narrative justification + citation indexes for the two proposal cohorts.
data/traits/environment/*.yaml (18 files)	New PROPOSED ENVIRONMENT traits (pressure, radiation, desiccation, metal tolerance).
data/traits/metabolism/*.yaml (21 files)	New PROPOSED METABOLISM traits (carbon fixation pathways, fermentations, DNRA, AOM, metal redox, phototrophy).

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