What's Changed
- Fix: an interrupted self-update broke the Desktop bundle's launch by @gasvn in #759
- Add bounded PDB inventory and coincident-coordinate diagnostics by @gasvn in #757
- Fix: the tool index lost its final newline on every build by @gasvn in #760
- Close skill/tool gaps vs. the life-sciences tool marketplace and beyond, plus a new protocols.io tool by @gasvn in #606
- Feature: reproduction code for the published benchmark results by @gasvn in #538
- Add a BixBench reproduction package under benchmarks/ by @gasvn in #510
- Add protein input diagnostics for MSA, SEQRES and PDB LINK records by @gasvn in #761
- Report SEQRES declarations and coordinate-only PDB inputs by @gasvn in #762
- Add local distance audit for explicit PDB LINK connections by @gasvn in #763
- Complete PROPKA partner comparisons with retained components and carboxylates by @gasvn in #765
- Retain explicitly selected components in free-partner PROPKA comparisons by @gasvn in #764
- Add protein design campaign skill and correct pH validation guidance by @gasvn in #766
- FDA_get_drug_label: find labels openFDA never linked (osimertinib/Tagrisso) by @gasvn in #767
- Fix: re-pin Genomic Intelligence predict_expression after upstream description change by @gasvn in #770
- Harden administrator-only Docker LLM provisioning by @gasvn in #422
- Add safe explicit Verified Source Directory core by @gasvn in #413
- Expose AgenticTool prompts and add scientific peer-review skill by @gasvn in #435
- Fix: say the iPTMnet API is down and name working PTM alternatives by @gasvn in #771
- Skills that let the assistant share, publish and set up logins for the user by @gasvn in #772
- Fix: PubMed_convert_article_ids failed on current Python builds (PMC 403) by @gasvn in #773
- Monarch searches keep items: [] when nothing matches by @gasvn in #774
- DDBJ reads the organism of BioProject records by @gasvn in #775
- GWAS: move SNP-by-gene and trait-name lookup off the retired v1 API by @gasvn in #776
- MediaDive_get_ingredient describes its usage counts correctly by @gasvn in #777
- SABIO-RK and BRENDA kinetics return the measured Km/kcat/Ki values by @gasvn in #778
- load_tools(categories=...) no longer returns tools from other categories by @gasvn in #779
- Bring the opt-in live test tier up to date with current tool contracts by @gasvn in #780
- Live-tier tests follow the GWAS v2 and SABIO-RK Json changes by @gasvn in #782
- Make sharing work when an assistant runs it: --detach, and skills from a real run by @gasvn in #781
- Add EWAS Atlas tools as the EWAS fallback while the EWAS Catalog is down by @gasvn in #783
- HTTP errors quote the service's reason, not its HTML error page by @gasvn in #784
- Fix #787: move USGS water tools to the Water Data OGC API by @gasvn in #790
- Add RFdiffusion2 as a validated remote tool by @krudo-taco in #768
- Link CCB workshop under Workshops and Education by @gasvn in #793
- OpenFDA_search_drug_labels: guide retries when a label has no openFDA fields by @gasvn in #792
- Add a GEANT4 depth-dose simulation tool (closes #252) by @gasvn in #796
- Fix: a tool needing any one API key gave network advice, and hid one of the keys by @gasvn in #795
- Refresh the tool hash #792 left stale by @gasvn in #797
- fix: keep DESeq2 and enrichGO result CSVs after R exits by @starvingarc in #791
- Reject gross protein backbone defects before PROPKA prediction by @gasvn in #785
- Add local protein sequence and structure similarity tools by @gasvn in #786
- Fix: clinical guideline searches that failed, timed out or never searched by @gasvn in #788
- Feature: StatPearls, LactMed and LiverTox from a local NCBI Bookshelf index, and case report search by @gasvn in #789
- Treat the R tools' arguments as data, not as R code by @gasvn in #798
- Let a gated tool be unlocked by the keys its error names by @gasvn in #799
- Ship every data file in the wheel, not just the directories named one by one by @gasvn in #801
- Release tooluniverse 1.5.7 by @gasvn in #803
Full Changelog: v1.5.6...v1.5.7