chore(release): prepare v1.4.9 (#569)

Author: Hello-QM

.github/release-notes/v1.4.9.md

@@ -0,0 +1,131 @@
+## CatGo 1.4.9
+
+CatGo 1.4.9 makes large trajectory work fast and editable across the web app,
+desktop app, VS Code, and Antigravity. It also adds physics-aware verification
+for CatBot numerical results, per-pane structure-toolbar customization, and a
+periodic-aware JavaScript bond fallback for frontend-only sessions.
+
+### Highlights
+
+- **Fast trajectories on every CatGo surface** — indexed structure-only
+  streaming avoids eagerly loading full multi-frame files and keeps the same
+  trajectory behavior across browser, desktop, VS Code, and Antigravity.
+- **Edits remain valid across changing frame topologies** — add or remove atoms,
+  continue playback, save the edited trajectory as extXYZ, or export every
+  selected frame as a separate POSCAR.
+- **CatBot checks the physics, not only process exit codes** — `catgo_verify`
+  records provenance and applies workflow-consistency and scientific gates
+  before numerical results can be trusted or submitted onward.
+- **A structure toolbar that fits each pane** — collapse it, choose individual
+  tools, restore defaults, and retain open tool panels even when their buttons
+  are hidden.
+
+### Added
+
+#### Cross-platform trajectory workflow
+
+- Added indexed readers and frame streaming for supported text, compressed,
+  ASE, HDF5, and JSON trajectory families without making the UI parse every
+  frame up front.
+- Added a structure-only default path for responsive initial loading while
+  frame metadata and plot data remain lazy.
+- Added variable-topology edit tracking so each frame can carry its actual atom
+  count after atoms are added or deleted.
+- Added edited extXYZ saving and per-frame POSCAR export from the trajectory
+  export panel.
+
+#### Physics verification
+
+- Added provenance and verifiability checks for claimed numerical quantities;
+  absent or empty evidence cannot silently certify a result.
+- Added targeted gates for common silent-failure classes, including inconsistent
+  reference energies, stale convergence claims, invalid vibrational data,
+  scheduler/result disagreement, and implausible electrochemical outputs.
+- Added cross-step workflow checks and verification coverage accounting. An
+  empty all-skipped verification does not clear an unverified session.
+- Added submission enforcement so numerical tools mark a session unverified and
+  HPC submission remains blocked until a real verification gate has run.
+
+#### Structure tools
+
+- Added per-pane toolbar collapse and per-tool visibility with persisted
+  preferences, legacy-key migration, responsive settings, capability filtering,
+  accessibility labels, bilingual strings, and one-click default restoration.
+
+### Fixed
+
+#### Trajectory editing and interaction
+
+- Fixed playback after atom deletion or insertion and invalid frame payloads
+  caused by assuming that every frame has the original atom count.
+- Fixed atom and bond picking in trajectory views, ordered three-atom angle
+  measurement, and pointer cleanup that could rotate the whole structure after
+  an atom selection.
+- Fixed stale topology and bond caches after editing, including transitions
+  between frames with different atom counts.
+- Improved analytic bond joins and paused-frame supersampling while retaining
+  native-device-pixel-ratio rendering during playback.
+
+#### Periodic bond fallback
+
+- Made the JavaScript bond path periodic-boundary aware for orthogonal and
+  skewed cells, including self-image bonds and parity with the WASM cutoff and
+  atomic-radius rules.
+- Prevented frontend-only or temporarily unavailable-backend sessions from
+  caching non-periodic bond results for periodic structures.
+
+#### Documentation
+
+- Corrected the canonical CatGo acknowledgement URL to
+  `https://app.catgo-ucsd.org` throughout active documentation and release
+  metadata.
+
+### Upgrade notes
+
+- No project, structure-file, or workflow-data migration is required.
+- Existing toolbar preferences migrate automatically; use **Restore defaults**
+  in toolbar settings if you want the new standard layout.
+- Edited variable-topology trajectories should be saved as extXYZ. POSCAR export
+  writes one independent structure file per frame.
+- CatBot sessions that produce numerical scientific results may now require a
+  successful `catgo_verify` run before HPC submission. This is an intentional
+  safety gate, not a job failure.
+
+### Included pull requests
+
+- [#566](https://github.com/Hello-QM/catgo-LRG/pull/566) — Correct the CatGo
+  citation URL.
+- [#567](https://github.com/Hello-QM/catgo-LRG/pull/567) — Stream trajectories
+  across platforms and harden editing, export, interaction, and rendering.
+- [#546](https://github.com/Hello-QM/catgo-LRG/pull/546) — Add the CatBot
+  physics-verification layer and guarded submission flow.
+- [#568](https://github.com/Hello-QM/catgo-LRG/pull/568) — Add the collapsible,
+  customizable structure toolbar and periodic-aware JavaScript bond fallback.
+
+### Downloads
+
+- **Windows** — `.msi` or `-setup.exe`
+- **macOS** — `.dmg` for Apple Silicon
+- **Linux** — `.deb` or `.rpm`
+- **Android** — `CatGo-v*-android-universal.apk`
+- **iOS** — [TestFlight beta](https://testflight.apple.com/join/FdHup5Hz)
+
+### License and citation
+
+CatGo 1.4.9 distributions use **AGPL-3.0-or-later**.
+
+If CatGo contributes to your work, please include this acknowledgement and the
+preferred citation:
+
+> This work used CatGo (https://app.catgo-ucsd.org).
+
+Please cite DOI
+[`10.26434/chemrxiv.15002984/v1`](https://doi.org/10.26434/chemrxiv.15002984/v1).
+This request is not an additional condition of the AGPL license. Third-party
+materials retain their own terms.
+
+Historical AGPL grants remain in effect.
+
+See the
+[CHANGELOG](https://github.com/Hello-QM/catgo-LRG/blob/main/CHANGELOG.md)
+for the complete release history.

.github/workflows/tauri-build.yml

@@ -332,7 +332,7 @@ jobs:
             One window for the whole loop: **read almost any code's files → build & edit → run DFT / ML / MD → submit to HPC → analyse → publish.** Ships with the bundled backend server (MLP libraries excluded to keep the download lean).
 
             ### License and citation
-            CatGo 1.4.8 distributions use **AGPL-3.0-or-later**.
+            CatGo 1.4.9 distributions use **AGPL-3.0-or-later**.
 
             If CatGo contributes to your work, please include this acknowledgement and the preferred citation:
 
@@ -362,10 +362,10 @@ jobs:
             - **Analysis** — DOS / band / COHP, Brillouin zone, XRD, phase diagrams, Gibbs & volcano plots
             - Built-in xTB / EMT calculators · OPTIMADE & PubChem search · HD render & trajectory video export
 
-            ### New in 1.4.8
-            - **Consistent periodic structures in both rendering modes** — standard WebGL and Large System Performance Mode now share atom, bond, boundary, camera, and visual-state data.
-            - **Database search works again across the app and VS Code** — Materials Project, OPTIMADE, and PubChem now use current provider APIs, pagination, and extension-host routing.
-            - **Large System Performance Mode remains WebGPU-accelerated** — the shared rendering contract removes visual drift while retaining the fast path and live interaction updates.
+            ### New in 1.4.9
+            - **Large trajectories open and edit across every CatGo surface** — indexed structure-only streaming now covers the web app, desktop app, VS Code, and Antigravity, including variable-topology edits and per-frame POSCAR export.
+            - **CatBot verifies physics before numerical results are trusted** — provenance, workflow-consistency, and scientific gates catch silent failures and guard HPC submission.
+            - **Structure tools are customizable per pane** — collapse the toolbar, choose visible tools, and keep periodic bonds correct even when the frontend uses the JavaScript fallback.
 
             See the [CHANGELOG](https://github.com/${{ github.repository }}/blob/main/CHANGELOG.md) for the full list.
           releaseDraft: true
@@ -531,12 +531,18 @@ jobs:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: bash scripts/ensure-release-body.sh "$CATGO_RELEASE_TAG"
 
-      - name: Finalize canonical release body
+      - name: Finalize canonical v1.4.8 release body
         if: env.CATGO_RELEASE_TAG == 'v1.4.8'
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: bash scripts/ensure-release-body.sh "$CATGO_RELEASE_TAG"
 
+      - name: Finalize canonical release body
+        if: env.CATGO_RELEASE_TAG == 'v1.4.9'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: bash scripts/ensure-release-body.sh "$CATGO_RELEASE_TAG"
+
       - name: Upload canonical legal bundle to release
         if: runner.os == 'Linux' && env.CATGO_RELEASE_TAG != ''
         env:

CHANGELOG.md

@@ -2,6 +2,20 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.4.9] - 2026-08-01
+
+### Added
+
+- **Fast, cross-platform trajectory streaming and editing** — large and compressed trajectories open through indexed structure-only readers in the web app, desktop app, VS Code, and Antigravity; variable-topology frame edits remain playable and can be saved as extXYZ or exported as one POSCAR per frame.
+- **Physics verification for CatBot numerical results** — `catgo_verify` checks provenance and workflow consistency, applies targeted scientific gates to silent-failure classes, and prevents unverified numerical results from flowing directly into HPC submission.
+- **Per-pane customizable structure toolbar** — each structure pane can collapse its toolbar, choose visible tools, migrate existing preferences, restore defaults, and retain mounted tool panels while buttons are hidden.
+
+### Fixed
+
+- **Trajectory interaction and rendering** — atom and bond picking, ordered three-atom angle measurement, pointer gesture cleanup, edited-frame topology caches, variable atom counts, analytic bond joins, and paused-frame supersampling now behave consistently.
+- **Periodic bonds without backend or WASM** — the JavaScript fallback now handles periodic images, skewed cells, self-image bonds, and the same cutoffs as the WASM path, avoiding incorrect cached bond sets in frontend-only sessions.
+- **Canonical citation link** — documentation and release metadata consistently use `https://app.catgo-ucsd.org`.
+
 ## [1.4.8] - 2026-07-30
 
 ### Fixed

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 message: If CatGo contributes to your work, please acknowledge and cite it as described below. This request is not an additional condition of AGPL-3.0-or-later.
-version: 1.4.8
+version: 1.4.9
 title: CatGo
 license: AGPL-3.0-or-later
 license-url: https://github.com/Hello-QM/catgo-LRG/blob/main/license

extensions/rust-wasm/CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 message: If CatGo contributes to your work, please acknowledge and cite it as described below. This request is not an additional condition of AGPL-3.0-or-later.
-version: 1.4.8
+version: 1.4.9
 title: CatGo
 license: AGPL-3.0-or-later
 license-url: https://github.com/Hello-QM/catgo-LRG/blob/main/license

extensions/vscode/CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 message: If CatGo contributes to your work, please acknowledge and cite it as described below. This request is not an additional condition of AGPL-3.0-or-later.
-version: 1.4.8
+version: 1.4.9
 title: CatGo
 license: AGPL-3.0-or-later
 license-url: https://github.com/Hello-QM/catgo-LRG/blob/main/license

extensions/vscode/package.json

@@ -2,7 +2,7 @@
   "name": "catgo",
   "displayName": "CatGo",
   "description": "3D viewer for crystal structures, molecules and MD / optimization trajectories — reads the file formats of VASP, Quantum ESPRESSO, CP2K, ABACUS, ORCA, Gaussian, CASTEP, SIESTA, OpenMX, LAMMPS and ASE: POSCAR/CONTCAR · CIF · XYZ/extXYZ · mol2 · PDB · vasprun.xml · OUTCAR · XDATCAR · .traj · HDF5 · cube/CHGCAR isosurfaces. Cross-cell PBC bond rendering, moyo space-group + Wyckoff symmetry, trajectory scrubbing with energy/force overlays, themes that follow VS Code. Right-click → Render, or Ctrl/Cmd+Shift+V.",
-  "version": "1.4.8",
+  "version": "1.4.9",
   "license": "AGPL-3.0-or-later",
   "publisher": "Guangsheng",
   "icon": "icon.png",

package.json

@@ -4,7 +4,7 @@
   "homepage": "https://github.com/Hello-QM/catgo-LRG",
   "repository": "https://github.com/Hello-QM/catgo-LRG",
   "license": "AGPL-3.0-or-later",
-  "version": "1.4.8",
+  "version": "1.4.9",
   "type": "module",
   "packageManager": "pnpm@10.28.2",
   "bugs": "https://github.com/Hello-QM/catgo-LRG/issues",

scripts/__tests__/docs-citation-license.test.mjs

@@ -48,7 +48,7 @@ test('CITATION.cff carries the exact non-binding citation request', () => {
   assert.equal(message, CITATION_REQUEST)
   assert.match(cff, new RegExp(
     `^cff-version: 1\\.2\\.0\\nmessage: ${escapeRegExp(CITATION_REQUEST)}\\n` +
-    'version: 1\\.4\\.8\\ntitle: CatGo\\nlicense: AGPL-3\\.0-or-later\\n' +
+    'version: 1\\.4\\.9\\ntitle: CatGo\\nlicense: AGPL-3\\.0-or-later\\n' +
     'license-url: https://github\\.com/Hello-QM/catgo-LRG/blob/main/license$',
     'm',
   ))

scripts/__tests__/license-policy.test.mjs

@@ -155,6 +155,7 @@ const licenseClaimInventory = {
     '.github/release-notes/v1.4.6.md',
     '.github/release-notes/v1.4.7.md',
     '.github/release-notes/v1.4.8.md',
+    '.github/release-notes/v1.4.9.md',
     '.github/workflows/tauri-build.yml',
   ],
   historicalOnly: [
@@ -293,7 +294,7 @@ test('canonical citation file requests citation without adding an AGPL condition
   assert.equal(existsSync(resolve(ROOT, 'citation.cff')), false)
   const text = read('CITATION.cff')
   assert.match(text, /^cff-version: 1\.2\.0$/m)
-  assert.match(text, /^version: 1\.4\.8$/m)
+  assert.match(text, /^version: 1\.4\.9$/m)
   assert.match(text, /^license: AGPL-3\.0-or-later$/m)
   assert.match(text, /^license-url: https:\/\/github\.com\/Hello-QM\/catgo-LRG\/blob\/main\/license$/m)
   assert.match(text, /CatGo: Bridging CLI Coding Agents/)