AIPOCH Open-Science v0.33.2

AIPOCH Open-Science v0.33.2

A trust-and-polish release: stable Windows installers are now code-signed, the protein-annotation connector gains STRING protein-protein interaction enrichment analysis, live-source browser previews persist between visits, and delegation keeps completed results through cleanup failures.

AIPOCH Open-Science is an open-source, local-first, model-agnostic AI research workbench for scientists and researchers. It enables reproducible, inspectable research across models with scientific AI agents, Python and R execution, scientific data connectors, and cross-platform support for macOS, Windows, and Linux.

v0.33.2 leads with trust: stable Windows installers are now code-signed, so first launch is a normal, warning-free experience with no SmartScreen "unrecognized app" prompt. On the science side, the protein-annotation connector gains STRING protein-protein interaction enrichment analysis — submit a gene list and retrieve enrichment scores plus the scored interaction network. Live-source browser previews move to a persistent partition, so sign-ins and preview state survive app restarts. Fixes keep completed delegation results across cleanup failures, refresh the Figure Composer delegation workflow, show file type icons in preview headers, tighten smart collection option spacing, isolate retained macOS cleanup obligations in the notebook runtime, and disable plugin and app discovery in the Codex backend. App downloads now link to the official download page, with download verification notes linked from there.

✨ Highlights

• Code-signed Windows installers. Stable Windows packages are now signed, so the SmartScreen "unrecognized app" warning no longer appears on first launch. (#2980)
• STRING protein-interaction enrichment. The protein-annotation connector gains a STRING PPI enrichment analysis that scores the functional associations among your gene list. (#2984)
• Persistent live-source previews. Browser previews of live sources now use a persistent session, so sign-ins and state survive app restarts. (#2824)

🚀 New Features

• Windows installers are code-signed — first launch is a normal, warning-free experience. (#2980)
• STRING PPI enrichment in the protein-annotation connector: submit a gene list and retrieve enrichment scores and the scored interaction network. (#2984)
• Live-source browser previews run in a persistent partition, keeping your session between visits and across restarts. (#2824)
• Library Auto permission mode interrupts less often, asking for approval only where it matters during routine work. (#2983)

🔧 Improvements

• App downloads now point to the official download page, with verification notes linked from there. (#2987)

🐛 Bug Fixes

• Delegation — completed results survive cleanup failures instead of being dropped (#2977); the Figure Composer delegation workflow is refreshed (#2981).
• Workspace — file type icons now appear in preview headers, matching the workspace lists (#2982); smart collection options get tighter, more consistent spacing (#2985).
• Notebook — retained macOS cleanup obligations are isolated so notebook work is not blocked by unrelated cleanup bookkeeping (#2919).
• Agent runtime — native Responses routing and teardown cancellation are preserved (#2972).
• Codex backend — plugin and app discovery is disabled, reducing unexpected background activity (#2979).

📦 Install

Requirements: macOS 12+ (Apple Silicon or Intel), Linux x64, or Windows 10/11 x64. On first run, the onboarding wizard checks the environment and can install and configure an app-managed agent runtime. Once installed, the app can update itself in place.

Download the appropriate package from the Assets section below, or from the official download page:

Platform	Package
macOS (Apple Silicon)	DMG for ARM64
macOS (Intel)	DMG for x64
Linux	AppImage or Debian package for x64
Windows	Code-signed installer for x64

macOS — first launch. Official release builds are Developer ID signed and notarized by Apple, so they open like other trusted applications. A locally built copy is notarized differently and may require approval through macOS Privacy & Security.

Windows — first launch. Official release builds are code-signed; Windows recognizes the publisher and no SmartScreen warning appears. Verify that the package came from the official release page before continuing.

Build from source instead:

npm install
npm run build:mac   # or: build:linux / build:win

🧭 What's in this release (maturity)

• ✅ Implemented: everything shipping in v0.33.1, plus: code-signed Windows installers; STRING protein-protein interaction enrichment in the protein-annotation connector; persistent live-source browser previews; delegation results preserved across cleanup failures; and the refreshed Figure Composer delegation workflow.
• 🚧 Partial: provider choice remains constrained by the active framework's endpoint compatibility; remote compute covers direct SSH and Slurm (cloud-GPU submission is not built yet); WSL2 Bash remains an opt-in Windows x64 preview; the skills commons ships marketplace discovery but not cross-machine forking or user-facing version pinning; reproducibility ships replayable per-version verification and RO-Crate packaging, while full-session replay and solver-exact equivalence remain open; conditional package restore is an exported script workflow; and review is opt-in and record-scoped.
• 🗺️ Roadmap: a unified model gateway, cross-machine skill forking and version pinning, cloud-GPU execution, stronger sandboxing and credential isolation, and collaborative research workflows.

🐢 Known Limitations

• Verification checks a captured version, not a whole session. Full-fidelity session replay and solver-exact equivalence guarantees remain open, and starting a check from the web client currently requires the desktop app.
• Sensitive package evidence is opt-in. Session diagnostics include sensitive package evidence only after explicit confirmation, and the export stays local until you share it.
• Imported .science sessions are read-only. They stay inspectable and referenceable, and forking them into a writable continuation remains available; execution and continuation remain disabled on the import itself.
• Bookmarks belong to a single session. They do not follow branch switches, join .science package exports, or sync across machines — forking copies them into the new session with fresh identities.
• PDF annotations are bound to the file version they annotate. Notes follow the file across projects and sessions where that version is shared, but they do not sync across machines.
• WSL2 Bash is a preview. It is opt-in on Windows x64 only; PowerShell remains the default shell runtime.
• Remote compute covers direct SSH and Slurm. Cloud-GPU submission is not built yet.
• Editable artifacts cover text formats. Binary formats stay read-only, and editing always publishes new versions.
• Network sandboxing covers the app's notebook and compute runtimes, not the whole system. On Windows, the boundary applies only after the sandbox's one-time administrator setup.
• Provider choice is per framework, not one unified gateway. The available protocol depends on the selected agent backend, and remote endpoints must use HTTPS.
• Code reconstruction is LLM-generated. It does not replace deterministic reproduction; replayable verification is the deterministic check.
• The reviewer is opt-in and record-scoped. It does not replace domain-specific validation of citations, units, statistics, or methods.
• No local GPU compute backend.
• No multi-user real-time collaboration.

🙏 Acknowledgements

Thanks to @ewen-poch, @wen2zhou, @nasus2002, @Ada.Liu, and everyone in Discord, X, and Discussions.

---

Full Changelog: https://github.com/aipoch/open-science/commits/v0.33.2