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Merged
edkerk merged 1 commit into from
Nov 3, 2026
Merged

Update the KEGG assets to kegg120 #196

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6 changes: 6 additions & 0 deletions CHANGELOG.md
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@@ -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`.
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38 changes: 19 additions & 19 deletions data/manifest.json
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@@ -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
}
}
},
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26 changes: 13 additions & 13 deletions src/raven_toolbox/data.py
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Expand Up @@ -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",
},
},
},
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