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Changelog

New features, improvements, and fixes in each Paperclip release.

0.6.0

Latest
  • •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