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Changelog

What changed in each Paperclip release.

0.7.52

Latest
  • Staging preview: Data Curation turns line-backed repository claims into a live, reviewable extraction table
  • `paperclip extraction` creates schemas, ingests complete per-paper rows, synchronizes repository verification, finalizes datasets, and exports CSV
  • Large extractions use the existing batched, resumable repository commit verifier instead of one long verification request
  • Different papers can be ingested concurrently, while each paper's rows and claims remain atomic

0.7.49

  • Search retrieves a candidate pool several times deeper than the requested limit and reranks the whole pool, so the reranker orders results without dropping papers
  • `paperclip search --also PHRASING` (repeatable) fuses several phrasings server-side and reranks once; `--rerank-query` sets the question to rerank against
  • The same paper no longer takes two result slots under different identifiers (PMID, DOI, and title dedup)
  • JSON API: `queries` fan out inside the engine, `expand: true` adds LLM-generated phrasings, `num_results` up to 200

0.7.48

  • Boolean corpus grep can run as a durable background job
  • Paper Scorecards link every citation occurrence in a citing paper
  • Scorecards show citing papers that were found but not included in the score

0.7.44

  • Meta-analysis routines validate protocol requirements before Evidence work begins
  • Question and Evidence revisions now provide complete recovery steps without weakening approved-artifact hashes
  • Representative pilots, harmonization decisions, data QA, and report rendering use aligned executable contracts

0.7.42

  • `paperclip skill` now shows separate tables for available routines and loadable domain references
  • Domain guidance such as patents, proteins, and SEC is discoverable and loads with `paperclip skill <name>`

0.7.41

  • Paper Scoreboard verifies citation evidence with a one-pass full-text workflow
  • Scoreboards use a reproducible random sample when more than 100 readable citing papers are available
  • The public scorecard app is available at /scorecard with social share previews
  • Citation classifications show exact source passages and clearer sample-size caveats

0.7.37

  • Playground Search adds a source filter for corpus grep, treats trials as one source with a country filter, and shows a copyable CLI command
  • `grep --from` now saves hits as a result set so you can chain map
  • Grep reports approximate document counts
  • Citation document requests authenticate correctly
  • Default map no longer crashes before reduce, and CLI analysis workflows complete correctly
  • Docs show corpus freshness dates and clearer Clipboard help

0.7.36

  • Admin page with role-based access control for internal users
  • Invite code management UI — create codes, view redemptions, copy redeem URLs
  • User roles column (_text) for RBAC — assign admin role via SQL

0.7.35

  • Billing feature with Stripe Pro plan checkout and subscription management
  • Invite codes for promo access — redeem via /redeem?code=XXXX to grant free unlimited plan
  • PlanCard on settings page gated behind billing feature flag
  • Guided analysis workflows are now managed as Paperclip routines, distinct from the local core agent skill
  • Only standard and scaled meta-analysis routines appear in routine discovery

0.7.34

  • Paperclip starts correctly on supported Python 3.8 and 3.9 installations

0.7.33

  • Guided workflows now load current orchestrators and phases remotely without writing workflow packages into each project
  • Trusted meta-analysis helpers run from checksum-verified temporary bundles that are deleted after use

0.7.32

  • Paper Repo verification now retries malformed and failed responses without treating infrastructure errors as rejected claims
  • Meta-analysis skills keep errored or pending evidence separate from conclusive source-verification failures

0.7.31

  • Meta-analysis skill Phase 7 now requires explicit managed analysis execution with anti-fabrication gates

0.7.30

  • YAML search workflows now stream step names, operations, paper counts, result IDs, and elapsed time while they run

0.7.29

  • YAML search workflows now receive coordinated long-running timeout budgets across the CLI, proxy, backend, and Papers MCP

0.7.28

  • Large YAML search workflows now receive a dedicated backend timeout budget
  • The full PKDB candidate workflow now uses a 5,000-paper discovery limit

0.7.27

  • YAML search workflows now preserve and return their declared final result across backend and direct MCP connections
  • Workflow failures retain their error details when run through direct MCP connections

0.7.26

  • Structured map results can no longer silently lose fields — incomplete or schema-mismatched artifacts now fail closed with the full data preserved
  • Console output, results export, and later `/.gxl` reads retain complete per-paper answers from the durable map manifest

0.7.24

  • Guided meta-analysis projects now pause for review at Question, Evidence, and Results checkpoints
  • Large-paper extraction is resumable, automatically split when needed, and records verification and model provenance

0.7.23

  • New Citation Explorer finds papers cited by a reference paper and ranks them with configurable filters and scorecards
  • Run Citation Explorer from the Paperclip CLI or use the dedicated web app for an interactive workflow

0.7.22

  • Paper fetch is more reliable and can use browser HTML capture when a publisher blocks direct downloads
  • Moving Clipboard files now routes through the server correctly
  • Uploads that reach the added state now complete successfully

0.7.18

  • Clipboard replaces Workspace across the CLI and web app, with uploads, folders, search, previews, exports, sharing, and Google Drive import
  • Analogical and threshold-based search make it easier to find related work and control result quality
  • Map jobs are more durable: interrupted streams recover, long output is preserved, and exhaustive workers can resume safely
  • Paper Repos validate structured claims earlier and provide more reliable collection and verification workflows
  • Meta-analysis reports use a deterministic pipeline and can repair incomplete agent-authored reports

0.6.0

  • New: browse 575K+ UniProt proteins, 256K+ PDB structures, and 2.9M+ ChEMBL compounds in Paperclip
  • Query proteins, structures, and bioactivities together with SQL — joins across UniProt, PDB, and ChEMBL are built in
  • Access everything under `/proteins/` with the same filesystem commands you already use (`cat`, `grep`, `ls`, `sql`)
  • Ask your agent to use UniProt, PDB, or ChEMBL directly with Paperclip

0.5.13

  • Verification no longer confuses timeouts with real failures — infra errors now show as [!] instead of [X]
  • Re-committing a repo skips claims that already passed or failed — no more re-verifying everything from scratch
  • Transient network hiccups won't silently flip your previously-verified [OK] claims to [X]

0.5.7

  • Fixed annotations not saving on bioRxiv, medRxiv, arXiv, FDA, and clinical trial papers
  • Better status indicators and clearer error messages when things go wrong

0.5.6

  • Upload Word docs, PowerPoint slides, HTML files, and EPUBs — not just PDFs
  • See real-time progress when uploading multiple files (e.g. "3 of 19 complete")
  • Check processing status of uploaded documents with `paperclip sync status`
  • Clearer error messages when uploads fail (file too large, network issues, etc.)

0.5.5

  • Upload files to your clipboard with `paperclip cp` (originals stay on your computer)
  • No more getting logged out unexpectedly — sessions refresh automatically
  • See exactly which files failed and why when uploading a batch
  • Paperclip now auto-updates when your version is out of sync

0.5.3

  • Running `paperclip update` now refreshes all skill files across your projects
  • Improved AI tool integration for more reliable responses

0.5.2

  • Type `repos` as a shortcut for the repo command
  • More accurate citation counts powered by OpenAlex (covers 250M+ works)

0.5.1

  • Faster, simpler login — fewer steps and no more copy-pasting codes
  • If you're already signed in on the web, login completes automatically

0.5.0

  • Paper Repos: organize papers into collections you can branch, merge, and synthesize
  • Use `reduce` to generate AI summaries across an entire repo of papers

0.4.3

  • Choose which source to search with the `-s` flag (e.g. `-s pmc`, `-s fda`, `-s trials`)
  • Cleaned up command list — removed retired commands for a simpler experience

0.4.2

  • Search now covers all sources by default — papers, FDA docs, clinical trials, and more
  • No configuration needed; use `-s` to narrow to a specific source when you want

0.4.0

  • New: search 217K+ FDA regulatory documents directly from the CLI
  • New: search 110K+ clinical trials (ClinicalTrials.gov + WHO ICTRP)
  • Access structured trial data and regulatory metadata in search results

0.3.0

  • Interactive shell mode — stay in Paperclip and run commands without re-typing `paperclip`
  • Read complete papers with `cat --full`
  • New: search arXiv preprints and conference abstracts
  • Better error messages when authentication expires

0.2.0

  • Initial release of Paperclip
  • Search 3.4M+ biomedical papers from PubMed Central, bioRxiv, and medRxiv
  • AI-powered semantic search — find papers by meaning, not just keywords
  • Full-text search within papers using grep
  • Cite specific passages with block-level references
  • Secure login with your browser (no API keys needed)
  • Ask questions about individual papers and get AI-powered answers
  • Analyze many papers at once with parallel map/reduce