v0.4.0

v0.4.0 - 2026-09-23

Focused on the research loop

Feynman now ships only what serves finding papers, reading them, synthesizing with verified citations, auditing papers against code, and planning replications. Removed:

• Science workbench: feynman serve and its --port, --no-open, --no-auth and --host flags, the local web app, its demo seed data, and the workbench-only Pi tools feynman_connector_tools, feynman_connector_call, feynman_workbench_context, and feynman_open_chemistry_sketcher. The molecule, genome, alignment, and structure viewer libraries are no longer installed with Feynman.
• Non-literature databases: feynman_science_database_search now covers OpenAlex, arXiv ID lookup, PubMed, Europe PMC (including open-access full-text sections), bioRxiv/medRxiv, and Crossref. Biomedical, chemistry, genomics, variant, omics, regulatory, clinical-trial, grants, protein and structure sources were removed, along with DataCite. The tool's prompt text went from about 17 KB to about 2 KB per session.
• Model endpoints: the NVIDIA BioNeMo feynman_model_endpoint_call tool.
• Skills: protein and bio model templates (AlphaFold2, OpenFold3, Boltz, Chai-1, ESMFold, ESM2, Evo 2, Borzoi, DiffDock, ProteinMPNN, LigandMPNN, SolubleMPNN, scGPT, scvi-tools, indication dossier), Modal/RunPod/SSH/model-endpoint compute templates, and the customize, self-awareness, product-self-knowledge, contributing, skill-creator, figure-composer, figure-style, and paper-narrative skills. /replicate and /autoresearch still offer Docker, Modal, and RunPod as execution choices.
• Commands: /commands and /capabilities. Use /help for the grouped command list and /tools for the tool list.
• Workflows: /watch and /jobs (and feynman watch / feynman jobs). Both depended on a schedule_prompt scheduler tool that Feynman does not ship, so they could only report scheduling as blocked.
• PaperRank and paper access: feynman rank (with --limit, --expand-citations, --full-text-top, --critique-top, --synthesize, --synthesis-top, --synthesis-model, --preference-file, --reproduction-notes, --source-fixture, --output-dir, --json) and feynman paper (--fetch-full-text). PaperRank seeded from an OpenAlex keyword search without an API key and missed seminal papers that a citation-sorted search finds; use /lit or /deepresearch, which search, rank, and read papers through the literature tools. For one paper's full text, ask the agent, which uses Europe PMC, PubMed, and fetch_content.
• arXiv topic search: the arxiv source of feynman_science_database_search now only looks up papers by arXiv ID (bare IDs, URLs, or arxiv_get_papers:). arxiv_search: and free-text queries were removed because arXiv's lexical API ranked concept queries poorly (0 of 9 seminal papers in the search benchmark); search topics with semanticscholar or openalex instead.
• Removed commands exit with a pointer: feynman serve, watch, jobs, rank, and paper now print that the command was removed after 0.3.49 and exit with status 1 instead of starting a chat with that word as the prompt.
• Local state: Feynman no longer creates ~/.feynman/active-org.json or ~/.feynman/orgs/. Existing workbench data in those folders is left in place; delete it if you no longer need it.

Everything removed is preserved in the repository at the archive/pre-deslop-0.3.49 git tag. To recover a piece, check it out from that tag, for example git checkout archive/pre-deslop-0.3.49 -- src/workbench workbench-web, or install @companion-ai/feynman@0.3.49 to keep using the workbench.

Paper search

• Semantic Scholar source: feynman_science_database_search gains source: "semanticscholar". By default it runs a bulk search sorted by citation count and keeps the top results (up to 20), which found 7 of 9 seminal papers in the search benchmark versus 2 for OpenAlex keyword search. sort: "relevance" uses relevance search and sort: "pub_date" returns newest first. Set SEMANTIC_SCHOLAR_API_KEY (free on request) to use your own rate limit; without it, a 429 from the shared anonymous pool is retried once and then reported with instructions.
• OpenAlex semantic search and key guidance: prefix an openalex query with semantic: to use OpenAlex's embedding search (search.semantic), which found the test-time-compute paper at rank 1 where keyword search missed it. OPENALEX_API_KEY is still sent as the api_key parameter when set; when it is missing, results and 401/403/429 errors now say how to get a free key.
• Researcher and verifier guidance: the researcher now routes by need (Semantic Scholar for general ML/CS papers, PubMed and Europe PMC for biomedicine, OpenAlex for citation graphs and semantic search, web_search for web sources with keyless Parallel MCP as a fallback, direct ID lookup for known papers) and runs 2–4 reworded queries per question instead of trusting one. The verifier cross-checks each cited paper's DOI or arXiv ID against two indexes and flags title/ID mismatches. Both agents can now call feynman_science_database_search. If you customized ~/.feynman/agent/agents/researcher.md or verifier.md, Feynman keeps your copy, so merge these changes by hand.

alphaXiv

• Updated the bundled alphaXiv client to @companion-ai/alpha-hub@0.1.5, which now ships the fixes Feynman used to patch in at install time: opening the login browser from WSL, printing the login URL when no browser opens, and falling back to REST search when discover_papers is unavailable. It also adds a paste-the-URL login for headless sessions, fixes a hang in parallel searches, and writes the token file with 0600 permissions. Feynman no longer patches alpha-hub.
• Updated @companion-ai/alpha-hub to 0.1.6. Expired alphaXiv tokens are now refreshed before paper tool calls instead of failing with "Invalid Authorization", concurrent calls share one refresh, logging out can no longer be undone by an in-flight refresh, the auth file is written atomically with 0600 permissions, and feynman alpha status checks the login with the alphaXiv server.