AIPOCH Open-Science v1.0.7

AIPOCH Open-Science v1.0.7

Pi joins as a fifth agent framework, references add straight from DOI or arXiv links, reading agents annotate linked PDFs, scanned PDFs become readable with optional OCR in nine languages, and Windows notebooks, OpenCode sessions, and proxied full-text downloads 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.

v1.0.7 follows v1.0.6 with an agents-and-literature release. Alongside Claude Code, OpenCode, Codex, and CodeBuddy, sessions can now run with the Pi agent, including onboarding, settings, connection validation, and subscription sign-in where available. The literature library gains three additions: Add from DOI or link resolves a bare DOI, a DOI resolver link, or an arXiv abstract/PDF URL into a ready-to-save reference; reading agents can list, locate, and create notes and marks on linked PDFs so requests like "mark this paragraph and summarize why it matters" persist as real annotations; and OCR becomes an on-demand component with downloadable recognition data for nine languages, making scanned pages searchable in reading with per-page coverage indicators. The research-case marketplace becomes searchable from Home and the conversation workspace, with category tabs, keyword search, and browsing state preserved between visits.

✨ Highlights

• Pi joins as a fifth agent framework. Alongside Claude Code, OpenCode, Codex, and CodeBuddy, you can now run sessions with the Pi agent, including onboarding, settings, connection validation, and subscription sign-in where available. (#3921)
• Add references straight from a DOI or arXiv link. The literature library gains an Add from DOI or link entry: paste a bare DOI, a DOI resolver link, or an arXiv abstract/PDF URL, review the resolved metadata, and save it as a reference without preparing an import file. (#3990)
• Agents annotate PDFs while you read. Reading agents can now list, locate, and create notes and marks in the literature library's existing Notes & Annotations for linked PDFs, so requests like "mark this paragraph and summarize why it matters" persist as real annotations. (#3981)
• Scanned PDFs become readable with optional OCR and nine language packs. OCR is now an on-demand component rather than bundled payload, with downloadable recognition data for English, Simplified and Traditional Chinese, German, Spanish, French, Japanese, Korean, and Russian — text from scanned pages appears in literature reading, with coverage indicators per page. (#3973, #4000)

🚀 New Features

• The Sharing marketplace for research cases becomes searchable from Home and the conversation workspace: category tabs, keyword search, direct downloads from case details, and your filters and scroll position survive moving between the marketplace and a project. (#3996)

🔧 Improvements

• Settings now describes each scientific connector individually — Europe PMC, Research Datasets, ChEA3, bioDBnet, and CTD — instead of sharing one generic summary. (#3993)
• Composer failure notices are unified into one consistent surface: provider, environment, input, session, and internal failures each present a clear recovery action instead of competing error formats. (#3989)
• Publishing or restoring an artifact always brings its latest published version forward, and the provenance panel explains version relationships more clearly. (#3783)
• OCR language selection stays responsive while saving, and local model cards present status and actions more consistently. (#4017)

🐛 Bug Fixes

• Windows notebooks prepare their shell runtime before first use again, restoring PowerShell access on fresh backends. (#4011)
• OpenCode sessions no longer terminate when compaction streams emit nonstandard message identities. (#3998)
• Asking a follow-up question while a background task is settling no longer discards the new run. (#3997)
• Full-text downloads work on hosts using Fake-IP DNS modes such as Mihomo or Clash, deferring resolution to the configured proxy when every local answer is a placeholder. (#3977)
• Pi tool activity renders with the shared Skill, Notebook, and literature presentation instead of generic input/output labels. (#4016)
• A stalled OCR component download no longer blocks ordinary PDF reads past the existing deadline. (#4019)

📦 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 v1.0.6, plus the Pi agent framework, Add from DOI or link and agent PDF annotations in the literature library, optional OCR with nine language packs, a searchable research-case marketplace, per-connector descriptions, unified composer failure notices, latest-published artifact versions with clearer provenance, 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 downloaded, and coverage indicators show which pages still lack text.
• 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, @LJLJ111, @roxi3906, @justemu, @yishu-ziyu and everyone in Discord, X, and Discussions.

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Full Changelog: https://github.com/aipoch/open-science/commits/v1.0.7