From f4733e2ba65ee47542e855a52e06356b9b2b3d78 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Fri, 16 Oct 2026 00:08:04 +0200 Subject: [PATCH] Download assets from CompMetEng/toolbox-assets raven-data moved to CompMetEng/toolbox-assets. The baked registries, the manifest, the publishing and registry scripts and the docs point there; publish_to_raven_data.py is renamed publish_to_toolbox_assets.py. --- CONTRIBUTING.md | 2 +- data/manifest.example.json | 28 +++++++-------- data/manifest.json | 36 +++++++++---------- scripts/README.md | 10 +++--- scripts/build_binary_bundles.py | 2 +- scripts/build_transporter_data.py | 4 +-- scripts/make_registry_snippet.py | 4 +-- ...n_data.py => publish_to_toolbox_assets.py} | 10 +++--- src/raven_toolbox/binaries.py | 20 +++++------ src/raven_toolbox/data.py | 18 +++++----- .../localization/substrate_ontology.py | 4 +-- .../localization/transport_evidence.py | 2 +- src/raven_toolbox/manifest.py | 4 +-- tests/test_binaries.py | 4 +-- tests/test_scripts_registry.py | 6 ++-- 15 files changed, 77 insertions(+), 77 deletions(-) rename scripts/{publish_to_raven_data.py => publish_to_toolbox_assets.py} (93%) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 6097bb64..3a4486ae 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -256,7 +256,7 @@ hand, so the checksums come from the same helper `ensure_binary` verifies with: ```bash python scripts/make_registry_snippet.py binary --bundle blast --version 2.17.0 \ --provides blastp makeblastdb --dir zips \ - --base-url https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0 + --base-url https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0 ``` Adding a new tool needs no new provisioning code: a bundle entry with the right diff --git a/data/manifest.example.json b/data/manifest.example.json index 1c3bb871..2a075d19 100644 --- a/data/manifest.example.json +++ b/data/manifest.example.json @@ -6,25 +6,25 @@ "version": "kegg118", "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/SysBioChalmers/raven-data/releases/tag/kegg118", + "source": "https://github.com/CompMetEng/toolbox-assets/releases/tag/kegg118", "files": { "kegg118_core.tar.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_core.tar.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_core.tar.gz", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "kegg118_eukaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "kegg118_prokaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "kegg118_taxonomy.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_taxonomy.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_taxonomy.gz", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 } @@ -40,17 +40,17 @@ ], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 } @@ -65,17 +65,17 @@ ], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 } @@ -90,17 +90,17 @@ ], "platforms": { "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", "sha256": "0000000000000000000000000000000000000000000000000000000000000000", "bytes": 0 } diff --git a/data/manifest.json b/data/manifest.json index 5c2739b9..b8759a35 100644 --- a/data/manifest.json +++ b/data/manifest.json @@ -6,25 +6,25 @@ "version": "kegg118", "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/SysBioChalmers/raven-data/releases/tag/kegg118", + "source": "https://github.com/CompMetEng/toolbox-assets/releases/tag/kegg118", "files": { "kegg118_core.tar.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_core.tar.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_core.tar.gz", "sha256": "520ba8bb09d6ca479ca1ab84ea70bf7c1d7f82d8f6406b717cee293b7c8609ca", "bytes": 49049340 }, "kegg118_eukaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", "sha256": "05999a38f3a1a5186d19d4e415f5029c33af56a08edb75190bd98ea19437765a", "bytes": 135087358 }, "kegg118_prokaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", "sha256": "ff9f25389e4c9c1cd58c13ee8d48d68a23152d04761d2e5875a9b5de8051b7b4", "bytes": 154511741 }, "kegg118_taxonomy.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_taxonomy.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_taxonomy.gz", "sha256": "5499c9537ac2697592dd1b484f309027509472e25a9d39d925dc581b9eef46e2", "bytes": 228754 } @@ -36,22 +36,22 @@ "source": "Pfam/InterPro HMMs + TCDB sequences", "files": { "tcdb.dmnd": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/tcdb.dmnd", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/tcdb.dmnd", "sha256": "ae8db23287ef415cad8a3004134b0d94024230f82afb5eb00a45941f8b8c04e6", "bytes": 13813605 }, "transporter_pfam.hmm": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/transporter_pfam.hmm", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/transporter_pfam.hmm", "sha256": "0c44e7bfc1390a08c914915a87b9b85398528be5db4294f91c33387c46c48f19", "bytes": 3524685 }, "tcdb_substrates.tsv": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/tcdb_substrates.tsv", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/tcdb_substrates.tsv", "sha256": "f85f7b866b325d1e221089ccb5fd7a0491d1c26f8282c9ebb7c2d11bf3f1e79c", "bytes": 219635 }, "chebi_relations.tsv.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/chebi_relations.tsv.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/chebi_relations.tsv.gz", "sha256": "b6910bf9c7a405e4f1fc112030123dd79c982112b8f460cebefd9235c621d192", "bytes": 1231364 } @@ -67,17 +67,17 @@ ], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", "sha256": "c887deae9f3ac85bb5a0bbbf9af254d00f3bebf9764304a9582db39e1c843085", "bytes": 25262842 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", "sha256": "f1ff0b9e718fbb252d240e31e4f85f842f6ef8e99a0e97bf5f66390295c795da", "bytes": 35244129 }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", "sha256": "b80d6ee1c1f85b8c18ae009e7d2ee844738d1a17338928570f5113ecd16e8326", "bytes": 13016674 } @@ -92,17 +92,17 @@ ], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", "sha256": "6e432f8b205fb14c355c330cd4d802acb7decaaf17cfbe90573c614b6dc976c8", "bytes": 8968841 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", "sha256": "3f929c151b8d8061391d73510b2011e9c8820fa5e2b6b9ae142c3b4dfccced5d", "bytes": 6476740 }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", "sha256": "daabab3d6072f4a37e701a5e02944f0fbcf8791ae5daa125fb7b5daed4a9be6d", "bytes": 3341980 } @@ -117,17 +117,17 @@ ], "platforms": { "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", "sha256": "19ce00c5dcdead0cdcb1f89cfafac299521afa79296e9a671baf73a64b7385eb", "bytes": 1802736 }, "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", "sha256": "d60e6b4bead44cf6d0cbd5711f9bda4a11cf72d7db07545ee0a43160b60b9fac", "bytes": 215961 }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", "sha256": "89596237e4a6a325a5f8526983696a1197e6970b1352db81a9817a165cd62f82", "bytes": 339284 } diff --git a/scripts/README.md b/scripts/README.md index 6cb8fc58..78b24a65 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -27,15 +27,15 @@ provenance. See [maintaining_binaries.md](https://github.com/SysBioChalmers/rave python scripts/build_binary_bundles.py # -> dist/binaries/*.zip (+ checksums, PROVENANCE) ``` -## `publish_to_raven_data.py` +## `publish_to_toolbox_assets.py` -Upload release assets to the [`raven-data`](https://github.com/SysBioChalmers/raven-data) +Upload release assets to the [`toolbox-assets`](https://github.com/CompMetEng/toolbox-assets) repo with `gh`, idempotently (immutable per-version tags; skips assets already present). ```bash -python scripts/publish_to_raven_data.py binaries --dir dist/binaries -python scripts/publish_to_raven_data.py release --tag kegg118 --dir artefacts -python scripts/publish_to_raven_data.py --dry-run release --tag manifest-v1 data/manifest.json +python scripts/publish_to_toolbox_assets.py binaries --dir dist/binaries +python scripts/publish_to_toolbox_assets.py release --tag kegg118 --dir artefacts +python scripts/publish_to_toolbox_assets.py --dry-run release --tag manifest-v1 data/manifest.json ``` ## `build_kegg_artefacts.py` diff --git a/scripts/build_binary_bundles.py b/scripts/build_binary_bundles.py index 6eaabffb..b8733817 100644 --- a/scripts/build_binary_bundles.py +++ b/scripts/build_binary_bundles.py @@ -155,7 +155,7 @@ def main(argv: list[str] | None = None) -> None: p.add_argument("--out", type=Path, default=Path("dist/binaries"), help="output folder") p.add_argument( "--base-url", - default="https://github.com/SysBioChalmers/raven-toolbox/releases/download", + default="https://github.com/CompMetEng/toolbox-assets/releases/download", help="release-download base; the snippet URLs become /-/", ) args = p.parse_args(argv) diff --git a/scripts/build_transporter_data.py b/scripts/build_transporter_data.py index 47777cf2..dd172dd2 100644 --- a/scripts/build_transporter_data.py +++ b/scripts/build_transporter_data.py @@ -1,8 +1,8 @@ #!/usr/bin/env python3 """Build the transporter reference databases for evidence-aware transport scoring. -Produces four raven-data artefacts (host them under a ``transporters-`` release, then run -``make_registry_snippet.py`` + ``publish_to_raven_data.py`` per +Produces four toolbox-assets artefacts (host them under a ``transporters-`` release, then run +``make_registry_snippet.py`` + ``publish_to_toolbox_assets.py`` per https://github.com/SysBioChalmers/raven-gecko-parity/blob/main/docs/artefact_hosting.md): * ``transporter_pfam.hmm`` — the HMMER database of the transporter Pfam families in diff --git a/scripts/make_registry_snippet.py b/scripts/make_registry_snippet.py index df5c341a..da2d22e7 100644 --- a/scripts/make_registry_snippet.py +++ b/scripts/make_registry_snippet.py @@ -8,7 +8,7 @@ Examples -------- Pass ``--tag`` (the GitHub release tag the assets were uploaded to); the script builds the -``https://github.com/SysBioChalmers/raven-toolbox/releases/download/`` asset prefix +``https://github.com/CompMetEng/toolbox-assets/releases/download/`` asset prefix itself, so you never hand it a full URL (and can't fumble the ``releases/download`` path). Data artefacts (KEGG reference model + tables + HMM libraries) for one release:: @@ -46,7 +46,7 @@ from raven_toolbox.binaries import _sha256 #: Default GitHub repository whose release assets the registry/manifest point at. -DEFAULT_REPO = "SysBioChalmers/raven-toolbox" +DEFAULT_REPO = "CompMetEng/toolbox-assets" def release_base_url(tag: str, repo: str = DEFAULT_REPO) -> str: diff --git a/scripts/publish_to_raven_data.py b/scripts/publish_to_toolbox_assets.py similarity index 93% rename from scripts/publish_to_raven_data.py rename to scripts/publish_to_toolbox_assets.py index a8262e50..0085d798 100644 --- a/scripts/publish_to_raven_data.py +++ b/scripts/publish_to_toolbox_assets.py @@ -1,5 +1,5 @@ #!/usr/bin/env python -"""Publish release assets to the raven-data repo with the GitHub CLI (``gh``). +"""Publish release assets to the toolbox-assets repo with the GitHub CLI (``gh``). Maintainer-side. Creates per-artefact, **immutable** release tags and uploads the assets to them — idempotently: an existing tag is reused and only *missing* assets @@ -10,11 +10,11 @@ Subcommands:: # one release tag from explicit files or a whole directory - publish_to_raven_data.py release --tag kegg118 --dir C:/Work/GitHub/kegg118 - publish_to_raven_data.py release --tag manifest-v1 data/manifest.json + publish_to_toolbox_assets.py release --tag kegg118 --dir C:/Work/GitHub/kegg118 + publish_to_toolbox_assets.py release --tag manifest-v1 data/manifest.json # every binary ZIP in a dir, auto-grouped into - tags - publish_to_raven_data.py binaries --dir dist/binaries + publish_to_toolbox_assets.py binaries --dir dist/binaries Add ``--dry-run`` to print the ``gh`` calls without executing them. """ @@ -26,7 +26,7 @@ import subprocess from pathlib import Path -DEFAULT_REPO = "SysBioChalmers/raven-data" +DEFAULT_REPO = "CompMetEng/toolbox-assets" # Metadata sidecars produced by the build scripts — never uploaded as assets. _SKIP = {"checksums.txt", "PROVENANCE.txt", "manifest_binaries.json"} _BUNDLE_RE = re.compile(r"^([a-z0-9]+)-(\d+\.\d+(?:\.\d+)?)-") # blast-2.17.0-linux-x86_64.zip diff --git a/src/raven_toolbox/binaries.py b/src/raven_toolbox/binaries.py index 24a0c8b6..a1e3d2ad 100644 --- a/src/raven_toolbox/binaries.py +++ b/src/raven_toolbox/binaries.py @@ -22,7 +22,7 @@ from pathlib import Path from urllib.request import urlopen -# Registry of bundled binaries, hosted as release assets in the raven-data repo. +# Registry of bundled binaries, hosted as release assets in the toolbox-assets repo. # Keyed by *bundle*; one bundle can provide several executables (e.g. "blast" -> # blastp + makeblastdb). Baked snapshot of data/manifest.json's `binaries` block — # regenerate from the manifest with `python scripts/make_registry_snippet.py sync` @@ -34,15 +34,15 @@ "provides": ["blastp", "makeblastdb"], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-linux-x86_64.zip", "sha256": "c887deae9f3ac85bb5a0bbbf9af254d00f3bebf9764304a9582db39e1c843085", }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-macos-arm64.zip", "sha256": "f1ff0b9e718fbb252d240e31e4f85f842f6ef8e99a0e97bf5f66390295c795da", }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/blast-2.17.0/blast-2.17.0-windows-x86_64.zip", "sha256": "b80d6ee1c1f85b8c18ae009e7d2ee844738d1a17338928570f5113ecd16e8326", }, }, @@ -52,15 +52,15 @@ "provides": ["diamond"], "platforms": { "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-linux-x86_64.zip", "sha256": "6e432f8b205fb14c355c330cd4d802acb7decaaf17cfbe90573c614b6dc976c8", }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-macos-arm64.zip", "sha256": "3f929c151b8d8061391d73510b2011e9c8820fa5e2b6b9ae142c3b4dfccced5d", }, "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/diamond-2.1.17/diamond-2.1.17-windows-x86_64.zip", "sha256": "daabab3d6072f4a37e701a5e02944f0fbcf8791ae5daa125fb7b5daed4a9be6d", }, }, @@ -70,15 +70,15 @@ "provides": ["hmmsearch"], "platforms": { "windows-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.3.2/hmmer-3.3.2-windows-x86_64.zip", "sha256": "19ce00c5dcdead0cdcb1f89cfafac299521afa79296e9a671baf73a64b7385eb", }, "linux-x86_64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-linux-x86_64.zip", "sha256": "d60e6b4bead44cf6d0cbd5711f9bda4a11cf72d7db07545ee0a43160b60b9fac", }, "macos-arm64": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/hmmer-3.4.0/hmmer-3.4.0-macos-arm64.zip", "sha256": "89596237e4a6a325a5f8526983696a1197e6970b1352db81a9817a165cd62f82", }, }, diff --git a/src/raven_toolbox/data.py b/src/raven_toolbox/data.py index 6b4ea5cd..5c3a4fbd 100644 --- a/src/raven_toolbox/data.py +++ b/src/raven_toolbox/data.py @@ -30,26 +30,26 @@ # dataset -> {"version": str, "files": {filename: {"url": str, "sha256": str}}} # Baked snapshot of data/manifest.json (the cross-language source of truth). Assets -# are hosted in the raven-data repo's releases. Regenerate this block from the +# are hosted in the toolbox-assets repo's releases. Regenerate this block from the # manifest with `python scripts/make_registry_snippet.py sync` (never hand-edit). _DATA_REGISTRY: dict = { "kegg": { "version": "kegg118", "files": { "kegg118_core.tar.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_core.tar.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_core.tar.gz", "sha256": "520ba8bb09d6ca479ca1ab84ea70bf7c1d7f82d8f6406b717cee293b7c8609ca", }, "kegg118_eukaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_eukaryotes.hmm.gz", "sha256": "05999a38f3a1a5186d19d4e415f5029c33af56a08edb75190bd98ea19437765a", }, "kegg118_prokaryotes.hmm.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_prokaryotes.hmm.gz", "sha256": "ff9f25389e4c9c1cd58c13ee8d48d68a23152d04761d2e5875a9b5de8051b7b4", }, "kegg118_taxonomy.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/kegg118_taxonomy.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/kegg118/kegg118_taxonomy.gz", "sha256": "5499c9537ac2697592dd1b484f309027509472e25a9d39d925dc581b9eef46e2", }, }, @@ -58,19 +58,19 @@ "version": "transporters-2026-07-01", "files": { "tcdb.dmnd": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/tcdb.dmnd", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/tcdb.dmnd", "sha256": "ae8db23287ef415cad8a3004134b0d94024230f82afb5eb00a45941f8b8c04e6", }, "transporter_pfam.hmm": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/transporter_pfam.hmm", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/transporter_pfam.hmm", "sha256": "0c44e7bfc1390a08c914915a87b9b85398528be5db4294f91c33387c46c48f19", }, "tcdb_substrates.tsv": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/tcdb_substrates.tsv", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/tcdb_substrates.tsv", "sha256": "f85f7b866b325d1e221089ccb5fd7a0491d1c26f8282c9ebb7c2d11bf3f1e79c", }, "chebi_relations.tsv.gz": { - "url": "https://github.com/SysBioChalmers/raven-data/releases/download/transporters-2026-07-01/chebi_relations.tsv.gz", + "url": "https://github.com/CompMetEng/toolbox-assets/releases/download/transporters-2026-07-01/chebi_relations.tsv.gz", "sha256": "b6910bf9c7a405e4f1fc112030123dd79c982112b8f460cebefd9235c621d192", }, }, diff --git a/src/raven_toolbox/localization/substrate_ontology.py b/src/raven_toolbox/localization/substrate_ontology.py index 340b6c7a..5c49f029 100644 --- a/src/raven_toolbox/localization/substrate_ontology.py +++ b/src/raven_toolbox/localization/substrate_ontology.py @@ -1,6 +1,6 @@ """ChEBI-ontology substrate matching — the substrate-specific layer of evidence-aware transport scoring. -Two curated raven-data artefacts underlie this (built by ``scripts/build_transporter_data.py``): +Two curated toolbox-assets artefacts underlie this (built by ``scripts/build_transporter_data.py``): * ``tcdb_substrates.tsv`` — TCDB's curated ``TC-ID -> substrate ChEBI(s)`` table; * ``chebi_relations.tsv.gz`` — the ChEBI ``is_a`` graph plus the protonation/tautomer bridges. @@ -77,7 +77,7 @@ def load( substrates_path: str | Path | None = None, ) -> SubstrateOntology: """Build a :class:`SubstrateOntology` from the ChEBI relations graph and the TCDB substrate - table, auto-downloading/caching each (the packaged raven-data artefacts) when its path is + table, auto-downloading/caching each (the packaged toolbox-assets artefacts) when its path is left as ``None``.""" relations_path = (relations_path if relations_path is not None else ensure_data_file("transporters", "chebi_relations.tsv.gz")) diff --git a/src/raven_toolbox/localization/transport_evidence.py b/src/raven_toolbox/localization/transport_evidence.py index a844bcd3..cc0b154a 100644 --- a/src/raven_toolbox/localization/transport_evidence.py +++ b/src/raven_toolbox/localization/transport_evidence.py @@ -308,7 +308,7 @@ def annotate_proteome( Scans the proteome FASTA (headers = gene ids, as written by :func:`prepare_deeploc_input`) against the transporter Pfam HMM database (``hmmsearch --cut_ga``) and the TCDB DIAMOND database - (``diamond blastp``); both databases auto-download from raven-data if not supplied. Pfam families + (``diamond blastp``); both databases auto-download from toolbox-assets if not supplied. Pfam families and TCDB TC-families map to coarse substrate classes via :mod:`raven_toolbox.localization.transporter_tables`, and each gene's TCDB TC-IDs map to their curated **substrate ChEBIs** (``substrates``: a ``tcdb_substrates.tsv`` path, or ``False`` to skip diff --git a/src/raven_toolbox/manifest.py b/src/raven_toolbox/manifest.py index 7eb00869..3db9adbd 100644 --- a/src/raven_toolbox/manifest.py +++ b/src/raven_toolbox/manifest.py @@ -1,4 +1,4 @@ -"""Load a raven-data manifest into the runtime resolver registries. +"""Load a toolbox-assets manifest into the runtime resolver registries. A *manifest* is the single, language-agnostic source of truth for every downloadable artefact (KEGG tables / HMMs, …) and external-binary bundle (BLAST / DIAMOND / HMMER). @@ -15,7 +15,7 @@ Usage:: from raven_toolbox import manifest - manifest.load_into_registries("https://github.com/SysBioChalmers/raven-data/releases/download/manifest-v1/manifest.json") + manifest.load_into_registries("https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v1/manifest.json") or set ``RAVEN_PYTHON_MANIFEST`` (a path or URL) and the resolvers load it lazily on first use:: diff --git a/tests/test_binaries.py b/tests/test_binaries.py index 39d88fda..fae05aee 100644 --- a/tests/test_binaries.py +++ b/tests/test_binaries.py @@ -35,7 +35,7 @@ def test_resolve_unresolvable_raises(monkeypatch): binaries.resolve_binary("mafft") -def test_default_registry_urls_point_at_raven_data(): +def test_default_registry_urls_point_at_toolbox_assets(): # Guard against a straggler/old host slipping into the baked registries. from raven_toolbox import data as data_mod @@ -44,7 +44,7 @@ def test_default_registry_urls_point_at_raven_data(): f["url"] for d in data_mod._DATA_REGISTRY.values() for f in d["files"].values() ] assert urls, "registries should not be empty" - assert all("/SysBioChalmers/raven-data/releases/download/" in u for u in urls), urls + assert all("/CompMetEng/toolbox-assets/releases/download/" in u for u in urls), urls # --------------------------------------------------------------------------- # diff --git a/tests/test_scripts_registry.py b/tests/test_scripts_registry.py index 12130e10..c78c2b32 100644 --- a/tests/test_scripts_registry.py +++ b/tests/test_scripts_registry.py @@ -56,12 +56,12 @@ def test_release_base_url_builds_releases_download_prefix(): # Default repo + an arbitrary tag → the canonical GitHub release-asset prefix. assert ( mrs.release_base_url("v0.3.0") - == "https://github.com/SysBioChalmers/raven-toolbox/releases/download/v0.3.0" + == "https://github.com/CompMetEng/toolbox-assets/releases/download/v0.3.0" ) # --repo override is honoured; the fixed "releases/download" path is always present. assert ( - mrs.release_base_url("blast-2.16.0", repo="ORG/raven-data") - == "https://github.com/ORG/raven-data/releases/download/blast-2.16.0" + mrs.release_base_url("blast-2.16.0", repo="ORG/toolbox-assets") + == "https://github.com/ORG/toolbox-assets/releases/download/blast-2.16.0" )