mims-harvard/ToolUniverse v1.5.5

Release v1.5.5

on GitHub

What's Changed

• Fix: republish the bundle when it installs an older release than this one by @gasvn in #665
• Fix: let the bundle install on Python 3.14 by @gasvn in #666
• Fix: correct the MCPB manifest licence and listing metadata by @gasvn in #667
• Fix: validation errors named an array index instead of the parameter by @Om-singhaI in #669
• Fix: listing metadata that had drifted away from the catalogue by @gasvn in #670
• Feature: gather a drug-target profile from several databases in one call by @gasvn in #671
• Fix: notes that invited the wrong reading of an approved indication by @gasvn in #672
• Stop a domain noun from becoming a verb when one more tool is registered by @gasvn in #673
• Docs: state the macOS 14 requirement on Apple Silicon by @gasvn in #674
• Fix: regenerate the static lazy registry and pin it to its generator by @gasvn in #675
• Fix: stop reporting healthy tools as returning None against their schema by @gasvn in #676
• Fix: examples that the tool itself refuses to run by @gasvn in #677
• Feature: serve several remote providers from one process, starting each on demand by @gasvn in #679
• Record how a cold model is waited out, now that the platform absorbs it by @gasvn in #680
• Admit providers on measured GPU memory, not only on a count by @gasvn in #681
• Stop telling a caller about the host it is borrowing by @gasvn in #682
• Give a provider only the environment it declared, not the owner's whole shell by @gasvn in #686
• Feature: one command to share, whatever you are sharing by @gasvn in #687
• Fix: the Windows launcher could never start the bundle by @gasvn in #688
• Fix: FDA label tools that could not match, and schemas that rejected them by @gasvn in #678
• Fix ERepo CAid/ClinVar lookups returning false negatives by @milkshake0901 in #685
• Fix: the publish gate never started the bundle on Windows by @gasvn in #689
• Fix: five schema nodes that disagreed with what the API returns by @gasvn in #690
• Fix: three ways the Open Targets API moved on without us by @gasvn in #691
• Fix: validate against what the return_schema says it describes by @gasvn in #692
• Fix: DailyMed could not search, and the NCI resources API is gone by @gasvn in #693
• Fix: read RNA editing from UniProt, because EBI's dataset is empty by @gasvn in #694
• Name a shared machine after itself, so two machines are two machines by @gasvn in #695
• Say what is wrong in words someone can act on by @gasvn in #696
• Offer the command that removes the terminal from the picture by @gasvn in #697
• Fix: the weekly canary could not report, for three separate reasons by @gasvn in #698
• Fix: 24 weekly-check failures that were missing credentials, not defects by @gasvn in #699
• Fix: Rfam's /structures endpoint needs a query parameter, not a header by @gasvn in #700
• Fix: read SAbDab's API, which a trailing slash made look unreachable by @gasvn in #701
• Fix: declare the credentials four more tool families cannot work without by @gasvn in #703
• Fix: one blocked User-Agent took out every TDC dataset load by @gasvn in #706
• Fix: the 429s were our own concurrency, and the limiter already existed by @gasvn in #713
• Fix: a third of the weekly report's failures were the sweep skipping tools by @gasvn in #702
• Fix: the weekly report could not tell a broken tool from an overloaded upstream by @gasvn in #708
• Fix: a schema declaring data inside a oneOf branch was read as a payload by @gasvn in #709
• Fix: "ols" is inside "tools", so one category tested 647 config files by @gasvn in #710
• Fix: four leftovers from the sweep triage, and STITCH recorded by @gasvn in #711
• Fix: three 403s, three causes — a default User-Agent, and naming Cloudflare by @gasvn in #707
• Fix: GtoPdb reads the open bulk downloads now that its REST service is gated by @gasvn in #704
• Fix: the xml category was OOM-killed at 120 GB on every weekly sweep by @gasvn in #705
• Fix: WormBase reads the Alliance API, since its own host is unreachable by @gasvn in #712
• Fix: report an upstream that cannot be repaired as what it is by @gasvn in #714
• Say when --pass-env names a variable that is not set by @gasvn in #715
• Fix: 157 wrappers had a file and no import line, so they imported as modules by @gasvn in #716
• Fix: NASA DONKI moved host, and the old one serves a web page by @gasvn in #717
• Fix: errors that blamed the caller, and a skip reason nothing read by @gasvn in #719
• Fix: MouseMine falls back to MGI's own reports while it is down by @gasvn in #721
• Fix: tu serve with a bare Namespace, broken by #687 by @gasvn in #718
• Fix: the borrower's path through tu connect, end to end by @gasvn in #720
• Fix: the AI-assistant path to a borrowed machine, through tu serve by @gasvn in #722
• Fix: register MCPProxyTool as the class again, not describe_remote_call_failure by @gasvn in #730
• Fix: using a published tool connected from the marketplace by @gasvn in #723
• Fix: tu remote login hung over SSH on a machine with a text browser by @gasvn in #725
• Fix: when a machine's owner withdraws access, say so instead of blaming the key by @gasvn in #726
• Fix: stop calling this computer's sharing key a "private connection" by @gasvn in #727
• Fix: what a caller gets back from a scientist's own @remote_tool function by @gasvn in #732
• Fix: from tooluniverse import remote_tool could return a module instead of the decorator by @gasvn in #733
• Fix: tu serve my_tool.py --share shared another program when its port was taken by @gasvn in #734
• Fix: a tool file's own helper modules failed to import outside its folder by @gasvn in #735
• Fix: an assistant now picks up a borrowed machine that comes back online by @gasvn in #736
• Fix: after tu connect, name the tools and say what to do next by @gasvn in #729
• Fix: a borrowed model call longer than five minutes failed in the client by @gasvn in #731
• Fix: say why a shared machine refused (request limit, ended period), not that it was offline by @gasvn in #737
• Fix: the weekly summary called skipped categories unreached by @gasvn in #724
• Fix NIM prediction output formats and false successes by @gasvn in #728
• Fix: a published tool that runs longer than two minutes failed for the person calling it by @gasvn in #739
• fix: correct Census presence matrix axis description by @starvingarc in #738
• Fix: the weekly report can say why a category failed, and RDKit is declared by @gasvn in #740
• Fix: the Claude Code setup line registered ToolUniverse for one folder only by @gasvn in #742
• Fix: name the real file a key is saved in, not ~/.tooluniverse/.env by @gasvn in #743
• Fix: say that a share code can run out of uses or reach its end date by @gasvn in #744
• After tu connect, give the Codex command as well as Claude Code's by @gasvn in #745
• Fix: the weekly summary counted failures the serial re-run had cleared by @gasvn in #746
• Fix: STITCH interactions work again, sweep failures say why, baseline pruned by @gasvn in #747
• Release tooluniverse 1.5.5 by @gasvn in #748

New Contributors

• @milkshake0901 made their first contribution in #685
• @starvingarc made their first contribution in #738

Full Changelog: v1.5.4...v1.5.5