edkerk · Oct 15, 2026
diff --git a/.github/scripts/assemble_offline_software.py b/.github/scripts/assemble_offline_software.py
@@ -1,14 +1,14 @@
 #!/usr/bin/env python
 """Populate RAVEN's software/ with every platform's external binaries.
 
-Downloads the per-platform binary ZIPs from raven-data and lays them out under
+Downloads the per-platform binary ZIPs from toolbox-assets and lays them out under
 ``<raven>/software/<tool>/`` using RAVEN's suffix scheme — bare name = Linux,
 ``.mac`` = macOS, ``.exe`` = Windows. With all platforms present in one tree, the
 whole RAVEN checkout can be zipped into a single **OS-independent** offline
 distribution (see the release-bundle workflow).
 
 Run from the RAVEN root, or pass ``--raven <dir>``. Requires network access to
-https://github.com/SysBioChalmers/raven-data .
+https://github.com/CompMetEng/toolbox-assets .
 """
 from __future__ import annotations
 
@@ -18,11 +18,11 @@
 import zipfile
 from pathlib import Path
 
-RAVEN_DATA = "https://github.com/SysBioChalmers/raven-data/releases/download"
-# raven-data platform key -> RAVEN binary suffix.
+TOOLBOX_ASSETS = "https://github.com/CompMetEng/toolbox-assets/releases/download"
+# toolbox-assets platform key -> RAVEN binary suffix.
 PLATFORMS = {"linux-x86_64": "", "macos-arm64": ".mac", "windows-x86_64": ".exe"}
 
-# (software subdir, raven-data bundle, {platform|"_": version}, {bare executable names})
+# (software subdir, toolbox-assets bundle, {platform|"_": version}, {bare executable names})
 CLI_TOOLS = [
     ("blast+",  "blast",   {"_": "2.17.0"},                          {"blastp", "makeblastdb"}),
     ("diamond", "diamond", {"_": "2.1.17"},                          {"diamond"}),
@@ -31,7 +31,7 @@
 
 
 def _fetch(url: str) -> bytes:
-    with urllib.request.urlopen(url, timeout=120) as resp:  # noqa: S310 (pinned raven-data URLs)
+    with urllib.request.urlopen(url, timeout=120) as resp:  # noqa: S310 (pinned toolbox-assets URLs)
         return resp.read()
 
 
@@ -60,7 +60,7 @@ def assemble(raven: Path) -> None:
             # macOS ships bare names; rename them to <name>.mac. Linux keeps bare names,
             # Windows already carries .exe — so only the macOS members need renaming.
             rename = {e: e + ".mac" for e in exes} if suffix == ".mac" else {}
-            _extract(_fetch(f"{RAVEN_DATA}/{bundle}-{version}/{asset}"), dest, rename)
+            _extract(_fetch(f"{TOOLBOX_ASSETS}/{bundle}-{version}/{asset}"), dest, rename)
 
 
 def main(argv: list[str] | None = None) -> None:

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -72,7 +72,7 @@ jobs:
 
   binary-tests:
     name: Binary download (${{ matrix.os }})
-    # Validate the on-demand fetch of the external binaries from raven-data on
+    # Validate the on-demand fetch of the external binaries from toolbox-assets on
     # Linux and macOS. Running the downloaded binaries also confirms the macOS
     # Gatekeeper quarantine is cleared so they can execute.
     strategy:

diff --git a/checkRaven.m b/checkRaven.m
@@ -251,13 +251,13 @@
     printOrange('    Skipping check of binary executables\n')
 else
     % The BLAST+/DIAMOND/HMMER binaries are downloaded on demand from
-    % raven-data; fetch any that are missing for this platform before
+    % toolbox-assets; fetch any that are missing for this platform before
     % checking. This doubles as the up-front "prefetch" for users who want
     % everything ready after installation.
     try
         downloadRavenBinaries({'blast+','diamond','hmmer'});
     catch ME
-        printOrange(['    Could not download binaries from raven-data: ' ME.message '\n' ...
+        printOrange(['    Could not download binaries from toolbox-assets: ' ME.message '\n' ...
             '    (offline? fetch the "*-binaries" RAVEN release for an offline install)\n']);
     end
     % Run each bundled binary with a version/help flag to confirm it
@@ -294,7 +294,7 @@ function testSolver(solver, model)
 function testBinary(ravenDir, tool, binName, versionArg)
 % Run a bundled binary with versionArg to confirm it executes; error if not.
 if ispc
-    binEnd = '.exe'; % native Windows builds (raven-data windows-x86_64 ZIPs)
+    binEnd = '.exe'; % native Windows builds (toolbox-assets windows-x86_64 ZIPs)
 elseif ismac
     binEnd = '.mac';
 else

diff --git a/docs/v3_review.md b/docs/v3_review.md
@@ -30,7 +30,7 @@ So the review does not repeat completed work. v3 already:
   and `combnk`.
 - Dropped the Statistics, Bioinformatics and Text Analytics toolbox dependencies.
 - Moved KEGG HMM libraries and external binaries out of git to on-demand fetch from the
-  `raven-data` release.
+  `toolbox-assets` release.
 - Reorganized the repo into functional folders; reformatted docstrings to NumPy style.
 - Added `progressReport`, `parseRAVENargs` (positional-or-named arguments), and a
   `matlab.unittest` suite.
@@ -147,7 +147,7 @@ Plus a standalone `mapIDsViaMNXref(type, ids, fromDB, toDB)` ID translator.
 1. Relocate to the develop3 layout (e.g. `reconstruction/metanetx/` or `annotation/metanetx/`),
    drop the duplicated `struct_conversion/*`, rebase on develop3's `convertMiriams`.
 2. **Delete the committed data**; host MNXref 4.5 (gzipped TSVs, and ideally a prebuilt `.mat`)
-   as a `raven-data` release asset and add a `downloadMNXref.m` modeled exactly on the
+   as a `toolbox-assets` release asset and add a `downloadMNXref.m` modeled exactly on the
    develop3 KEGG-HMM / `downloadRavenBinaries` on-demand pattern (sentinel-file check, cache
    under a gitignored dir).
 3. Update parsing to the documented **4.5** columns (header-driven `readtable`, handle the
@@ -379,6 +379,6 @@ tracked as a low-priority item in the Tier-3 table.
 2. **Where should new strain-design / community code that needs metaheuristics live**, given
    the dependency question — lean on the Global Optimization Toolbox (`gamultiobj`), or keep
    v3's "minimize toolbox dependencies" stance and ship a self-contained EA?
-4. **MNXref data hosting** — confirm the `raven-data` release is the right home for the MNXref
+4. **MNXref data hosting** — confirm the `toolbox-assets` release is the right home for the MNXref
    4.5 assets (mirroring KEGG HMMs/binaries), and whether to ship a prebuilt `.mat` (7 MB,
    fast) or only the gzipped TSVs (slower first build, always current).
diff --git a/installation/downloadRavenBinaries.m b/installation/downloadRavenBinaries.m
@@ -1,7 +1,7 @@
 function downloadRavenBinaries(tools)
 % downloadRavenBinaries
 %   Download RAVEN's external command-line binaries on demand from the
-%   raven-data repository into RAVEN's software/ directory. Only the binary
+%   toolbox-assets repository into RAVEN's software/ directory. Only the binary
 %   matching the current platform is fetched, and only when needed.
 %
 %   Input:
@@ -14,7 +14,7 @@ function downloadRavenBinaries(tools)
 %   unzip it into the RAVEN software/ directory instead.
 %
 %   The binaries are hosted as release assets in
-%   https://github.com/SysBioChalmers/raven-data.
+%   https://github.com/CompMetEng/toolbox-assets.
 %
 %   Usage: downloadRavenBinaries({'blast+','diamond'})
 %
@@ -29,7 +29,7 @@ function downloadRavenBinaries(tools)
 
 ravenDir = findRAVENroot();
 
-% raven-data platform key for the per-platform binary ZIPs.
+% toolbox-assets platform key for the per-platform binary ZIPs.
 if ispc
     plat = 'windows-x86_64';
 elseif ismac
@@ -78,11 +78,11 @@ function downloadRavenBinaries(tools)
         continue;   % already provisioned
     end
 
-    zipPath = fetchRavenDataAsset(fullfile(ravenDir,'software'),tag,asset);
+    zipPath = fetchToolboxAsset(fullfile(ravenDir,'software'),tag,asset);
     unzip(zipPath,destDir);
     delete(zipPath);
 
-    % macOS uses the .mac suffix throughout RAVEN, but the raven-data macOS ZIP
+    % macOS uses the .mac suffix throughout RAVEN, but the toolbox-assets macOS ZIP
     % ships bare names, so rename the extracted executables to match.
     if ismac
         for k = 1:numel(execs)

diff --git a/installation/fetchRavenDataAsset.m → installation/fetchToolboxAsset.m b/installation/fetchRavenDataAsset.m → installation/fetchToolboxAsset.m
@@ -1,9 +1,10 @@
-function localPath=fetchRavenDataAsset(destDir,releaseTag,assetName)
-% fetchRavenDataAsset  Download (if needed) a raven-data release asset.
+function localPath=fetchToolboxAsset(destDir,releaseTag,assetName)
+% fetchToolboxAsset  Download (if needed) a toolbox-assets release asset.
 %
-% Downloads assetName from the given raven-data release tag into destDir
+% Downloads assetName from the given release tag of
+% https://github.com/CompMetEng/toolbox-assets into destDir
 % and returns its local path. An already-downloaded copy is reused as-is.
-% Generic across raven-data's release families (KEGG artefacts, HMM
+% Generic across toolbox-assets' release families (KEGG artefacts, HMM
 % libraries, binaries, ...): nothing here is specific to any one of
 % them, so callers supply the release tag and asset name rather than
 % this function hardcoding either.
@@ -13,7 +14,7 @@
 % destDir : char
 %     directory to download into (created if it does not exist yet).
 % releaseTag : char
-%     the raven-data release tag, e.g. 'kegg118'.
+%     the toolbox-assets release tag, e.g. 'kegg118'.
 % assetName : char
 %     the release asset file name, e.g. 'kegg118_core.tar.gz'.
 %
@@ -31,7 +32,7 @@
 end
 fprintf(['Downloading ' assetName '... ']);
 try
-    websave(localPath,['https://github.com/SysBioChalmers/raven-data/releases/download/' releaseTag '/' assetName]);
+    websave(localPath,['https://github.com/CompMetEng/toolbox-assets/releases/download/' releaseTag '/' assetName]);
 catch ME
     if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError')
         error('Failed to download %s, the server returned a 404 error, try again later. If the problem persists please report it on the RAVEN GitHub Issues page: https://github.com/SysBioChalmers/RAVEN/issues',assetName)

diff --git a/reconstruction/kegg/KEGG_VERSION.md b/reconstruction/kegg/KEGG_VERSION.md
@@ -1,12 +1,12 @@
 kegg118
 
-This is the raven-data release tag that every KEGG-artefact download in
+This is the toolbox-assets release tag that every KEGG-artefact download in
 this folder reads from --- getModelFromKEGG's core reference-model/table
 bundle, and getKEGGModelForOrganism's HMM libraries. It is the single
 place this version is recorded; every function that downloads a KEGG
 artefact reads it from here via keggDataVersion.m, instead of
 hardcoding a "kegg###" string of its own. Bump this file, not the
-calling code, when raven-data publishes a new KEGG release.
+calling code, when toolbox-assets publishes a new KEGG release.
 
 The version is read as the file's first line; everything below this
 point is only for a human reader.
diff --git a/reconstruction/kegg/buildGlobalKEGGModel.m b/reconstruction/kegg/buildGlobalKEGGModel.m
@@ -1,7 +1,7 @@
 function [model,KOModel,isSpontaneous,isUndefinedStoich,isIncomplete,isGeneral]=buildGlobalKEGGModel(ravenPath)
 % buildGlobalKEGGModel  Download and assemble the global KEGG model.
 %
-% Fetches the raven-data <kegg version>_core.tar.gz bundle (the
+% Fetches the toolbox-assets <kegg version>_core.tar.gz bundle (the
 % gene-free reference model plus the ko_reaction / organism_gene_ko /
 % rxn_flags relational tables), then joins every organism's
 % genes onto the reference reactions through their shared KO ids. The
@@ -27,7 +27,7 @@
 
 kver=keggDataVersion();
 keggDir=fullfile(ravenPath,'reconstruction','kegg');
-archive=fetchRavenDataAsset(keggDir,kver,[kver '_core.tar.gz']);
+archive=fetchToolboxAsset(keggDir,kver,[kver '_core.tar.gz']);
 
 coreDir=fullfile(keggDir,[kver '_core']);
 if ~isfolder(coreDir)

diff --git a/reconstruction/kegg/getKEGGModelForOrganism.m b/reconstruction/kegg/getKEGGModelForOrganism.m
@@ -30,7 +30,7 @@
 %     and whether the HMMs were trained on pro- or eukaryotic sequences. The
 %     directory name matches the published HMM library it is paired with. The
 %     prebuilt concatenated KO HMM library (dataDir.hmm) is downloaded here
-%     from the corresponding raven-data release if not already present. This
+%     from the corresponding toolbox-assets release if not already present. This
 %     parameter should ALWAYS be provided.
 % outDir : char
 %     directory to save the results from the quering of the hidden Markov
@@ -197,8 +197,8 @@
 %pre-trained HMM set, compatible with the current RAVEN version. The
 %reconstruction uses the concatenated KO HMM library (a single
 %gzip-compressed flatfile, queried in one hmmsearch); if it is not already
-%present it is downloaded from the corresponding raven-data release
-%(https://github.com/SysBioChalmers/raven-data).
+%present it is downloaded from the corresponding toolbox-assets release
+%(https://github.com/CompMetEng/toolbox-assets).
 %Only needed for the protein-homology path (fastaFile supplied): the
 %annotation-only path never touches libraryFile, so skip the (100+ MB)
 %download/extraction entirely when there is no FASTA file to search.
@@ -219,7 +219,7 @@
         gunzip([libraryFile '.gz']);
         fprintf('COMPLETE\n');
     else
-        fetchRavenDataAsset(fileparts(libraryFile),kver,[hmmName '.hmm.gz']);
+        fetchToolboxAsset(fileparts(libraryFile),kver,[hmmName '.hmm.gz']);
         fprintf('Extracting the HMM library file... ');
         gunzip([libraryFile '.gz']);
         fprintf('COMPLETE\n');

diff --git a/reconstruction/kegg/getModelFromKEGG.m b/reconstruction/kegg/getModelFromKEGG.m
@@ -4,7 +4,7 @@
 % Loads the global KEGG reaction/gene model from keggModel.mat. On first
 % use --- when no keggModel.mat is present yet --- the underlying
 % artefacts (the gene-free reference model plus the KO/reaction/organism-
-% gene relational tables, published as a raven-data release) are
+% gene relational tables, published as a toolbox-assets release) are
 % downloaded and assembled instead, and the result is cached to
 % keggModel.mat so later calls load instantly. The first build can take
 % a while (the organism-gene table covers every KEGG organism) and needs

diff --git a/reconstruction/kegg/getPhylDist.m b/reconstruction/kegg/getPhylDist.m
@@ -2,7 +2,8 @@
 % getPhylDist  Load the pre-built KEGG phylogenetic distance matrix.
 %
 % Loads the pre-built phylogenetic distance matrix from keggPhylDist.mat.
-% The artefact is distributed as a raven-data release asset.
+% The matrix ships with RAVEN; it is derived from the KEGG taxonomy, which
+% is a toolbox-assets release asset.
 %
 % Name-Value Arguments
 % --------------------

diff --git a/reconstruction/kegg/keggDataVersion.m b/reconstruction/kegg/keggDataVersion.m
@@ -1,16 +1,16 @@
 function version=keggDataVersion()
-% keggDataVersion  The raven-data release tag for KEGG artefacts.
+% keggDataVersion  The toolbox-assets release tag for KEGG artefacts.
 %
 % Reads reconstruction/kegg/KEGG_VERSION.md --- the single place this
 % version is recorded --- so every function that downloads a KEGG
 % artefact (getModelFromKEGG, getKEGGModelForOrganism) stays in sync
-% when raven-data publishes a new KEGG release. The version is the
+% when toolbox-assets publishes a new KEGG release. The version is the
 % file's first line.
 %
 % Returns
 % -------
 % version : char
-%     the raven-data release tag, e.g. 'kegg118'.
+%     the toolbox-assets release tag, e.g. 'kegg118'.
 
 ravenPath=findRAVENroot();
 versionFile=fullfile(ravenPath,'reconstruction','kegg','KEGG_VERSION.md');

diff --git a/testing/function_tests/tBinaries.m b/testing/function_tests/tBinaries.m
@@ -1,13 +1,13 @@
 classdef tBinaries < matlab.unittest.TestCase
-% tBinaries  On-demand download of RAVEN's external binaries from raven-data.
+% tBinaries  On-demand download of RAVEN's external binaries from toolbox-assets.
 %
 %   Validates downloadRavenBinaries on the current platform: each tool is
 %   fetched into software/<tool>/, the executable is present, and (for the CLI
 %   tools) it actually runs. On macOS, running the downloaded binary also
 %   confirms the Gatekeeper quarantine attribute was cleared.
 %
 %   Exercised on Linux and macOS by the "binary-tests" CI job. Requires network
-%   access to https://github.com/SysBioChalmers/raven-data .
+%   access to https://github.com/CompMetEng/toolbox-assets .
 
     methods (Test)
         function blast(testCase)

diff --git a/testing/function_tests/tReconstruction.m b/testing/function_tests/tReconstruction.m
@@ -112,14 +112,14 @@ function getDiamondRunsWhenAvailable(testCase)
         end
 
         function getKEGGModelForOrganismNeedsData(testCase)
-            testCase.assumeFail('Requires keggModel.mat and an HMM library from raven-data.');
+            testCase.assumeFail('Requires keggModel.mat and an HMM library from toolbox-assets.');
         end
 
         function getModelFromKEGGNeedsData(testCase)
             matFile = fullfile(testCase.ravenRoot, 'reconstruction', 'kegg', 'keggModel.mat');
             testCase.assumeFalse(exist(matFile, 'file') == 2, ...
                 'keggModel.mat is present; skipping the build-from-artefacts path.');
-            testCase.assumeFail('Downloads and assembles the full KEGG artefact set from raven-data; not run automatically.');
+            testCase.assumeFail('Downloads and assembles the full KEGG artefact set from toolbox-assets; not run automatically.');
         end
 
         function buildGlobalGPRJoinsGenesThroughSharedKO(testCase)