Publish kegg116 KEGG artefacts + phyl_dist (v0.1.0)#29
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First downloadable KEGG artefact set, wired into the runtime resolvers: - All artefacts are gzip and version-prefixed (kegg116_<name>.gz) so MATLAB and Windows read them with the built-in gunzip, no external tool. organism_gene_ko moves from xz to gzip for the same reason. - HMM libraries ship as one gzip concatenated flatfile per domain; ensure_kegg_hmm_library decompresses and hmmpresses on first use, ~10x smaller than the pressed index and portable across HMMER versions. - Add a version-prefix-tolerant artefact resolver (_resolve_artefact) used by the organism/sequence entry points; parse_kegg_dump and build_kegg_artefacts.py gain an opt-in --version. - Populate data/manifest.json and _DATA_REGISTRY with the kegg116 release assets (real SHA256 + bytes); refresh the maintainer docs and manifest example. - Bump version to 0.1.0 and update CHANGELOG. Add KEGG taxonomy artefact and phyl_dist (RAVEN getPhylDist port) Publish kegg116_taxonomy.gz and regenerate RAVEN's keggPhylDist from it, so GECKO's organism-distance kcat selection needs no MATLAB .mat file: - reconstruction.kegg.phyl_dist + PhylDist faithfully reproduce RAVEN getPhylDist's (asymmetric, occasionally negative) distance metric; parse_taxonomy_records exposes ids/names/lineages and reads .gz transparently. - data.ensure_kegg_taxonomy fetches the artefact; build_kegg_artefacts.py emits it. - Register kegg116_taxonomy.gz in data/manifest.json and _DATA_REGISTRY (8 files). - Tests for phyl_dist (hand-checked against RAVEN) and the taxonomy fetch; update migration/IMPROVEMENTS/maintainer docs and CHANGELOG. Bundle core KEGG artefacts into kegg116_core.tar.gz Combine the five core model files (reference model + KO/reaction/organism-gene/ rxn-flag tables) into one kegg116_core.tar.gz; HMM libraries and taxonomy stay separate. The release drops from 8 assets to 4. - ensure_kegg_data now fetches the single bundle, SHA-verifies it, and extracts the version-prefixed members into the cache once (safe extraction, matching download.py). - build_kegg_artefacts.py groups the core files into the bundle after the HMM step. - Regenerate data/manifest.json and _DATA_REGISTRY (4 entries); update manifest.example, tests (bundle fixture), and docs.
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See CHANGELOG 0.1.0.