add-growth-conditions: batch sweep runner + skill batch section#202
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Extends the add-growth-conditions skill (v1.0.0 -> v1.1.0) with a deterministic sweep-prep runner so a whole-KB growth-conditions pass starts from ready source bundles instead of each extraction agent re-fetching. - scripts/growth_conditions_sweep.py: enumerate records lacking growth_media AND cultivation_setup; resolve each record's primary (most-cited) reference; fetch the Europe PMC abstract; run the legal full-text access ladder (reuses scripts/fulltext_access.py). Writes per-record staging bundles + an INDEX.md progress report bucketing OA_FULLTEXT / ABSTRACT_ONLY / NO_REFERENCE. Never edits kb/ — extraction + YAML writes stay the agent's job. - skill.md: rewrote the "whole KB (sweep)" section around the runner + INDEX report; flagged the most-cited-ref-may-be-a-review pitfall (bundle lists every cited ref by frequency so agents can pick the community's methods paper). - reports/growth_conditions_sweep/.gitignore: per-record bundles are regenerable; track only INDEX.md. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Extends the
add-growth-conditionsskill (per the request to add a batch sweep runner) so a whole-KB growth-conditions pass starts from ready source bundles instead of each extraction agent re-fetching.What
scripts/growth_conditions_sweep.py— deterministic prep runner:--listthe records lacking bothgrowth_mediaandcultivation_setup--prep(live fetch): resolve each record's primary (most-cited) reference, fetch the Europe PMC abstract, and run the legal full-text access ladder (reusesscripts/fulltext_access.py: Europe PMC OA → Unpaywall → CORE → author-request draft).INDEX.mdprogress report bucketing each asOA_FULLTEXT/ABSTRACT_ONLY/NO_REFERENCE. Never editskb/— extraction + YAML writes stay the agent's job, so a curator reviews the prep first.skill.md(v1.0.0 → v1.1.0): rewrote the whole-KB sweep section around the runner + INDEX report; flagged that the most-cited ref is sometimes a review, so the bundle lists every cited ref by frequency for the agent to pick the community's methods paper.Current KB landscape (from a live
--prep)45 records lack any conditions block: 24 OA full text, 21 abstract-only (paywalled), 0 without a citable reference.
Lint-clean (black + ruff). The data enrichment from running the sweep lands in a separate follow-up PR.
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