Upgrade to koza 2.x and restore kgx RDF output#9
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kevinschaper wants to merge 6 commits intomainfrom
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- Migrate transform.yaml config for koza 2.2.0 (remove deprecated name fields, fix header_mode, add header_prefix, fix data path) - Fix sibling module import in transform.py for koza 2.x loader - Fix download command in justfile (koza download -> downloader) - Add kgx dependency and RDF generation step to postprocess - Include .nt.gz files in release artifacts - Update all dependencies to latest versions Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The downloader CLI is provided by kghub-downloader, which was missing from project dependencies (only available globally on dev machines). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
Changes
pyproject.toml— new hatchling build system, added kgx dependencyjustfile— full pipeline with download, transform, postprocess (taxon split + RDF)src/transform.yaml— koza 2.x config (removed deprecated fields, fixed paths/headers)src/transform.py— fixed module import for koza 2.x loader.github/workflows/release.yaml— includes.nt.gzin release artifactsuv.lock— new lockfileTest plan
just runcompletes successfully (2.7M nodes, 113 taxa, 119M RDF output)uv run pytestpasses🤖 Generated with Claude Code