From 82084a209936c980163937a1c326b3f2435ccfe7 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Tue, 3 Nov 2026 21:11:49 +0100 Subject: [PATCH 1/2] Read the manifest-v5 snapshot manifest-v5 lists kegg120, the transporter assets and the BRENDA files. --- CHANGELOG.md | 2 +- src/installation/fetchToolboxAsset.m | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a26fcd31..d38bf942 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ ### Data -* The KEGG assets are the `kegg120` release of `toolbox-assets` (was: `kegg118`), and `fetchToolboxAsset` reads the manifest `manifest-v4`. +* The KEGG assets are the `kegg120` release of `toolbox-assets` (was: `kegg118`), and `fetchToolboxAsset` reads the manifest `manifest-v5`. ## 3.0.0b2 — 2026-11-01 diff --git a/src/installation/fetchToolboxAsset.m b/src/installation/fetchToolboxAsset.m index ea550544..e545435d 100644 --- a/src/installation/fetchToolboxAsset.m +++ b/src/installation/fetchToolboxAsset.m @@ -9,7 +9,7 @@ % supplies the release tag and the asset name. % % A download is checked against the SHA-256 checksum that the -% toolbox-assets manifest (release manifest-v4) lists for it. A file whose +% toolbox-assets manifest (release manifest-v5) lists for it. A file whose % checksum differs is deleted and an error is raised. An asset that the % manifest does not list, or a manifest that cannot be read, gives a % warning and the file is kept unchecked. @@ -75,7 +75,7 @@ sha=''; if isempty(manifest) try - manifest=webread('https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v4/manifest.json', ... + manifest=webread('https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v5/manifest.json', ... weboptions('ContentType','json','Timeout',30)); catch ME warning('RAVEN:fetchToolboxAsset:manifest','Cannot read the toolbox-assets manifest: %s',ME.message); From c542ca6ab50b827b048a856605db9dbb1a02b116 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Tue, 3 Nov 2026 21:24:01 +0100 Subject: [PATCH 2/2] Remove the em dashes from the changelog The version headings give the date in parentheses, and the entries use the punctuation of the sentence. --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d38bf942..f20651e1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ * The KEGG assets are the `kegg120` release of `toolbox-assets` (was: `kegg118`), and `fetchToolboxAsset` reads the manifest `manifest-v5`. -## 3.0.0b2 — 2026-11-01 +## 3.0.0b2 (2026-11-01) Second beta toward 3.0. Changes below are relative to 3.0.0b1. @@ -151,7 +151,7 @@ Second beta toward 3.0. Changes below are relative to 3.0.0b1. * Help blocks of 176 files are rewritten in impersonal, present-tense wording with British spelling; the code is unchanged. Statements that differed from the code are corrected, for example `simplifyModel` `deleteDuplicates` (first occurrence kept), `removeBadRxns` `refModel`, `replaceMets` outputs, `getMinNrFluxes` `params`, `checkRaven` `developMode` and the `downloadRavenBinaries` offline bundle. `reverseRxns` has the RAVEN 3 help structure. -## 3.0.0b1 — 2026-09-07 +## 3.0.0b1 (2026-09-07) First beta toward 3.0. Changes below are relative to RAVEN 2.9.3. The last 2.x release is 2.11.4: a reorganized codebase, fewer toolbox dependencies, hardened I/O and MILP algorithms, plus