aipoch/open-science: v0.31.0

Abstract

✨ Highlights Fork a session into a new writable copy. A local or imported session can be forked with its complete research history — conversation branches, Notebook records, artifact versions, literature, annotations, and private bookmarks all receive fresh identities. The source session is never altered, and imported sessions stay read-only. (#2719) One product name: Open-Science. The app now presents itself consistently as Open-Science across the interface, CLI, and packaging. Existing installations keep their current names and locations — research data, credentials, and settings are preserved untouched. (#2567) Session plans survive context reconstruction. After the agent rebuilds its context, the active Session Plan is recovered with its identity, revision, and pending approvals, and plan tools stay available in the conversation. (#2661) Provider connections are validated before they stick. Provider edits are tested and saved only when the connection succeeds; when a saved provider is rejected at runtime, its availability updates instead of silently failing. (#2746) 🚀 New Features A session information card in the conversation header shows the session's number, title, description, source session, timestamps, and message and artifact counts, with a pin control that keeps long titles compact. (#2764) Credential prompts for OpenAlex and NCBI link directly to the official API key pages. (#2761) gnomAD variant lookups can optionally include population-level allele frequencies and genotype counts. (#2741) Sessions branched into a new chat show a "continued from" divider anchored to their source turn. (#2747) Settings unifies panel titles, section headings, save feedback, and control alignment across all panels. (#2739) ⚠️ Breaking Changes Expanded STRING networks now report the complete returned graph in nodes: added neighbors carry is_query=false, and n_nodes no longer equals the number of input proteins. Notebook scripts that treated nodes as input mappings must filter is_query. (#2737) 🐛 Bug Fixes Notebook and compute — Windows R runs in standard mode without protected-mode setup (#2708); artifact execution logs no longer show false environment-evidence gaps (#2720); per-run lock diagnostics are preserved for reproducibility checks (#2738). Agent runtime — Codex conversations stay usable when switching reasoning effort (#2724); stalled stop, resume, and queued follow-up commands settle reliably (#2745); cancelled network approvals are retired instead of lingering as dead cards (#2744). Sessions and permissions — session-plan step progress stays visible while permission updates arrive (#2759); permission completion reconciles with concurrent turns and duplicate send retries no longer append undispatched messages (#2743); permission changes are allowed before branch history replay (#2736); fork dividers anchor to the copied turn (#2733); unpublished artifact heads survive forking without blocking startup (#2730). Connectors — UniProt secondary accessions resolve to their current primary entries (#2762); Ensembl resolves FlyBase, WormBase, and yeast identifiers before symbol fallback and preserves sequence-request errors (#2715, #2752); cBioPortal mutation frequencies count gene-profiled samples (#2721); clinical-trial eligibility filters respect age and sex boundaries (#2734); molecule rendering preserves molfile headers and rejects empty structures (#2751). Interface and storage — the active custom model synchronizes when its provider is saved (#2712); opening attachments preserves parent dialogs (#2735); dialog dismissal no longer flashes or resets content (#2723, #2742); transcript follow intent survives layout changes (#2732); storage cleanup and local imports are protected against symlinked directories and rewritten source files (#2711); specialist packages align import defaults and export controls (#2756); read-only OpenCode skills are cleaned up after delegation (#2716).