From 5f1e12f55cba038f0dcd9d13bd0d66d29bc17706 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Tue, 3 Nov 2026 09:33:05 +0100 Subject: [PATCH] Update the KEGG assets to kegg120 The manifest and the baked registry list the kegg120 release of toolbox-assets: the core bundle, the taxonomy and the prokaryotic and eukaryotic HMM libraries. --- CHANGELOG.md | 6 ++++++ data/manifest.json | 38 +++++++++++++++++++------------------- src/raven_toolbox/data.py | 26 +++++++++++++------------- 3 files changed, 38 insertions(+), 32 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c57f863..22bc0d8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## Unreleased + +### Data + +* The KEGG assets are the `kegg120` release of `toolbox-assets` (was: `kegg118`): the reference model and tables, the taxonomy and the profile HMM libraries of 4246 prokaryotic and 2724 eukaryotic KOs. The baked registry and `data/manifest.json` list them. + ## 3.0.0b2 — 2026-11-01 Second beta toward 3.0. The main changes are RAVEN-format model export, SuppOrth homology input, and a closer match to RAVEN in homology, gap-filling, curation tables and `ftinit`. diff --git a/data/manifest.json b/data/manifest.json index b8759a3..261f1bb 100644 --- a/data/manifest.json +++ b/data/manifest.json @@ -1,32 +1,32 @@ { "manifest_version": 1, - "generated": "2026-06-16", + "generated": "2026-11-03", "data": { "kegg": { - "version": "kegg118", + "version": "kegg120", "description": "KEGG reference model + KO/reaction tables (core bundle), taxonomy, and prokaryote/eukaryote HMM libraries for getKEGGModelForOrganism.", "license": "Derived from the KEGG database; redistributed with permission from KEGG.", - "source": "https://github.com/CompMetEng/toolbox-assets/releases/tag/kegg118", + "source": "https://github.com/CompMetEng/toolbox-assets/releases/tag/kegg120", "files": { - "kegg118_core.tar.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_core.tar.gz", - "sha256": "520ba8bb09d6ca479ca1ab84ea70bf7c1d7f82d8f6406b717cee293b7c8609ca", - "bytes": 49049340 + "kegg120_core.tar.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_core.tar.gz", + "sha256": "d988ba2901e12ab3ddf7e1b6dfcdd0336475a8d6050102af5409762c5129d27d", + "bytes": 50543551 }, - "kegg118_eukaryotes.hmm.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", - "sha256": "05999a38f3a1a5186d19d4e415f5029c33af56a08edb75190bd98ea19437765a", - "bytes": 135087358 + "kegg120_eukaryotes.hmm.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_eukaryotes.hmm.gz", + "sha256": "aa8293ca155221148cb5afe86d6598cec0f8643aa274f1e2bc2b85435ef7669d", + "bytes": 139852556 }, - "kegg118_prokaryotes.hmm.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", - "sha256": "ff9f25389e4c9c1cd58c13ee8d48d68a23152d04761d2e5875a9b5de8051b7b4", - "bytes": 154511741 + "kegg120_prokaryotes.hmm.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_prokaryotes.hmm.gz", + "sha256": "f0f37c14678da9b48c3f065b97d05294a2fe010266cf1310ec8f1b5520a0ec80", + "bytes": 159123618 }, - "kegg118_taxonomy.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_taxonomy.gz", - "sha256": "5499c9537ac2697592dd1b484f309027509472e25a9d39d925dc581b9eef46e2", - "bytes": 228754 + "kegg120_taxonomy.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_taxonomy.gz", + "sha256": "bde8266dcebdfb22229255211f5ec73a91196e5d4f11cac5684c8e7b1001fd67", + "bytes": 230357 } } }, diff --git a/src/raven_toolbox/data.py b/src/raven_toolbox/data.py index ca8c2fe..dda722b 100644 --- a/src/raven_toolbox/data.py +++ b/src/raven_toolbox/data.py @@ -34,23 +34,23 @@ # manifest with `python scripts/make_registry_snippet.py sync` (never hand-edit). _DATA_REGISTRY: dict = { "kegg": { - "version": "kegg118", + "version": "kegg120", "files": { - "kegg118_core.tar.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_core.tar.gz", - "sha256": "520ba8bb09d6ca479ca1ab84ea70bf7c1d7f82d8f6406b717cee293b7c8609ca", + "kegg120_core.tar.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_core.tar.gz", + "sha256": "d988ba2901e12ab3ddf7e1b6dfcdd0336475a8d6050102af5409762c5129d27d", }, - "kegg118_eukaryotes.hmm.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", - "sha256": "05999a38f3a1a5186d19d4e415f5029c33af56a08edb75190bd98ea19437765a", + "kegg120_eukaryotes.hmm.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_eukaryotes.hmm.gz", + "sha256": "aa8293ca155221148cb5afe86d6598cec0f8643aa274f1e2bc2b85435ef7669d", }, - "kegg118_prokaryotes.hmm.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", - "sha256": "ff9f25389e4c9c1cd58c13ee8d48d68a23152d04761d2e5875a9b5de8051b7b4", + "kegg120_prokaryotes.hmm.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_prokaryotes.hmm.gz", + "sha256": "f0f37c14678da9b48c3f065b97d05294a2fe010266cf1310ec8f1b5520a0ec80", }, - "kegg118_taxonomy.gz": { - "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_taxonomy.gz", - "sha256": "5499c9537ac2697592dd1b484f309027509472e25a9d39d925dc581b9eef46e2", + "kegg120_taxonomy.gz": { + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg120/kegg120_taxonomy.gz", + "sha256": "bde8266dcebdfb22229255211f5ec73a91196e5d4f11cac5684c8e7b1001fd67", }, }, },