AIPOCH Open-Science v1.0.8

AIPOCH Open-Science v1.0.8

Settings reorganize into focused tabs, references import in batches from DOI, arXiv, or PubMed, literature gains AI study snapshots, finished sessions release their agent processes, and updates, downloads, PDFs, and connectors are fixed across platforms.

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.

v1.0.8 follows v1.0.7 with a polish-and-reliability release. General settings split into focused tabs, with Appearance and Notifications under System settings and General surfacing app information, diagnostics, and a direct manual-install help link. The literature library imports mixed identifier batches of up to 100 — DOI, arXiv ID, PMID, PMCID, or official article links — through the existing review and transactional save flow, and the literature detail view gains an AI snapshot card that summarizes a paper into research question, study population, methods, main findings, and limitations, labeled by whether it read the full text or the abstract. Across all five agent frameworks, completed sessions now release their provider and tool processes: shared reviewer runtimes, superseded handoff leases, and failed cleanup attempts are retired or retried until confirmed, so sequential sessions no longer accumulate memory.

✨ Highlights

• Settings are reorganized into focused tabs. General preferences split into dedicated tabs: Appearance and Notifications move under System settings, while General now shows app information, diagnostics, command-line tools, and help resources — including a direct link to the manual installation and update guide — without digging. (#4022)
• Import references in batches from DOI, arXiv, or PubMed. Add from DOI or link now accepts up to 100 mixed identifiers per import — DOI, arXiv ID, PMID, PMCID, or official article links — normalizing and deduplicating them before the usual review and transactional save. (#4039)
• AI study snapshots for literature. The literature detail view gains an AI snapshot card that summarizes a paper into five structured sections — research question, study population, methods, main findings, and limitations — generated with your configured main model from the full text or abstract, and labeled by which it used. (#4037)
• Finished sessions release their agent processes. Completed sessions across all five agent frameworks no longer accumulate provider and tool processes in memory: shared reviewer runtimes, superseded handoff leases, and failed cleanup attempts are all released or retried until confirmed, so long workdays with many sessions stay responsive. (#4046, #4054, #4061)

🚀 New Features

• Tencent TokenHub gains the Hy4 reasoning model and current DeepSeek V4.1 Flash routes with 1,000,000-token context windows, and image input for GLM-5.3-Flash, Kimi K3, and MiniMax M3. (#4060)

🔧 Improvements

• eQTL Catalogue queries work again after the upstream REST API was retired, using indexed files, and now validate that coordinates use the GRCh38 assembly instead of silently returning misleading matches. (#4036)
• PDF reading order and extraction are more reliable: automatic ordering uses positioned text evidence to tell prose columns from table rows, crop boundaries are verified against the native source, ambiguous table cells keep their original text with a reliability warning, and the Windows PDF worker no longer crashes during teardown. (#3994, #4056)
• Update dialogs now name the blocking process instead of printing full system paths, and desktop recovery failures retain their actual error evidence in diagnostic packages and logs instead of reporting only a generic failure. (#4047, #4045)
• Reproduction coverage for R analyses is more honest: scientific calls that can force arguments or dispatch methods now revoke stale file proofs, so downstream verification no longer overstates which files a result depended on. (#4052)

🐛 Bug Fixes

• macOS updates are no longer blocked by ordinary read-only file holders such as StoreKit agent, and Windows no longer misclassifies the application's own backend processes as foreign during update preparation. (#4028)
• Windows update inspection no longer reports unknown occupancy when system tools are missing from PATH or scans run long, and stale Notebook receipts no longer block recovery after process-ID reuse. (#4042)
• A saved download no longer ends with a permission error when the destination directory itself is not readable; the completed file stands. (#4053)
• Sandboxed notebook command-line tools fall back to the application's own Node runtime when the PATH version is too old to use the configured proxy, fixing network access inside the sandbox. (#4058)
• Windows protection checks no longer close a healthy shared gateway between probes and report a false runtime failure. (#4029)
• Searching again for a paper clears the previous "PDF could not be added" notice once the new search succeeds. (#4041)
• Pi now installs correctly in the packaged desktop app instead of failing while locating its bootstrap files. (#4027)
• The composer no longer shows a duplicate unavailable-model notice next to the model picker status. (#4051)
• An artifact download that finishes and then fails while releasing its capability no longer escapes as an unhandled error that can terminate the backend. (#4055)
• Markdown artifacts repair a stale provenance head left by older versions when opened, and the provenance panel now explains incomplete execution evidence explicitly. (#4021)

📦 Install

Desktop client. Requirements: macOS 12+ (Apple Silicon or Intel), Linux x64 or ARM64, 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 updates itself in place.

Download the appropriate package from the Assets section below, or from the official download page. On macOS, the desktop app is also installable via Homebrew: brew install --cask open-science.

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

Command line via Homebrew (macOS and Linux). The standalone CLI and local Web UI live in the official tap — bundled Node runtime, no separate Node.js needed, and upgrades through the normal brew flow:

brew install aipoch/tap/open-science
open-science start --no-open
open-science url

Command line via npm. With Node.js 22.13+, install the CLI (and Task SDK) globally; updates then follow your normal npm upgrade flow:

npm install --global @aipoch/open-science
open-science --help

Command line standalone (all platforms, no toolchain). The Assets below also include standalone CLI archives — macOS and Linux arm64/x64 tarballs and a Windows x64 zip — with a bundled Node runtime, so they install and run without Homebrew, npm, or a local Node.js. Linux packages additionally arrive as standalone .deb and .rpm installers.

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 v1.0.7, plus tabbed settings, batch identifier imports from DOI/arXiv/PubMed, AI study snapshots in the literature detail view, confirmed release of completed-session agent processes, refreshed Tencent TokenHub models, restored eQTL Catalogue access with assembly validation, and the fixes described above.
• 🚧 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, session replay, and RO-Crate packaging, while solver-exact equivalence remains open; 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

• Replay reproduces recorded steps, it does not re-execute them. Solver-exact equivalence guarantees remain open; replayable verification remains the deterministic check, and starting a check from the web client currently requires the desktop app.
• 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.
• 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.
• OCR recognition data downloads on demand. Scanned pages are recognized after the matching language pack is installed, and coverage indicators show which pages still lack text.
• AI study snapshots reflect the configured main model. They summarize the available text at generation time and are not a substitute for reading the paper.
• 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.
• 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, @nasus2002, @roxi3906, @daanveer-tech, @wen2zhou and everyone in Discord, X, and Discussions.

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Full Changelog: https://github.com/aipoch/open-science/commits/v1.0.8