Download assets from CompMetEng/toolbox-assets

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

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
         }

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
         }

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`

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 <base>/<bundle>-<version>/<asset>",
     )
     args = p.parse_args(argv)

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-<date>`` release, then run
-``make_registry_snippet.py`` + ``publish_to_raven_data.py`` per
+Produces four toolbox-assets artefacts (host them under a ``transporters-<date>`` 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

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/<tag>`` asset prefix
+``https://github.com/CompMetEng/toolbox-assets/releases/download/<tag>`` 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:

scripts/publish_to_raven_data.py → 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 <bundle>-<version> 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