v25.1.1

What's Changed

🔧 Enhancements

• [25.0] Add Sourmash sig new datatype by @SaimMomin12 in #21469
• [25.0] add new datatype for kmindex index data by @Smeds in #21429
• [25.1] Add sample sheet support to many database operation tools by @mvdbeek in #21465
• [25.1] Adds object_expires_after_days example usage to sample config by @davelopez in #21547
• [25.1] Add new jupyter version by @bgruening in #21531
• [25.1] Add tool credentials system documentation and schema updates by @arash77 in #21561
• [25.1] Add new datatype pg and hg for pangenomics by @SaimMomin12 in #21620
• [25.1] Add database operation tool to convert sample sheets to list collections by @mvdbeek in #21625
• [25.1] Add new datatypes required for VG tool by @SaimMomin12 in #21644
• [25.1] Add a few datatypes from the digital humanities domain by @bgruening in #21596
• [25.1] Document security considerations for using secrets by @bernt-matthias in #21654

🐛 Bug Fixes

• [25.1] Update 25.1 release notes with config changes by @ahmedhamidawan in #21444
• [25.1] Fix 25.1 release month on user facing notes by @ahmedhamidawan in #21450
• [25.1] Sample sheet column fix by @mvdbeek in #21446
• [25.1] Fix sample_sheet column display by @mvdbeek in #21457
• [25.1] Maintain column definitions on map over by @mvdbeek in #21468
• [25.1] Record input parameter invocation inputs by @mvdbeek in #21452
• [25.1] Remove ref and polish release-drafter workflow by @ahmedhamidawan in #21467
• [25.0] Add missing test file for sig datatype by @SaimMomin12 in #21473
• [25.1] Remove release-drafter workflow and add a release config file to improve generated notes by @ahmedhamidawan in #21478
• [25.0] Add missing ending newline to test.sig test data file by @nsoranzo in #21485
• [25.1] change locuszoom package version to 0.0.7 by @elmedjadjirayane in #21494
• [25.1] Fix subworkflow runs for disconnected required inputs with defaults by @mvdbeek in #21488
• [25.0] Pin release prebuilt client package exactly by @dannon in #21498
• [25.1] Fix exception message to enable debugging of missing dataset issue. by @jmchilton in #21504
• [25.1] Usability fixes for sample sheet selection. by @jmchilton in #21503
• [25.1] Do not update a user's update_time when an admin archives (and purges) a history by @natefoo in #21484
• [25.0] Fix type annotation for invocation report errors field by @mvdbeek in #21508
• [25.1] Add missing dependencies to galaxy-files package by @nsoranzo in #21518
• [25.1] Filter out failed_metadata HDAs from job cache by @mvdbeek in #21544
• [25.1] Fix job cache collection copy by @mvdbeek in #21558
• [25.1] Show "Expires today" instead of "Expires soon" in Expiration Warning by @mvdbeek in #21560
• [25.1] Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557
• [25.1] Supports Dataverse file access via both persistent and database IDs by @davelopez in #21569
• [25.1] Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by @jmchilton in #21584
• [25.1] Fix passing user id to preferences by @guerler in #21576
• [25.1] Use quotes for Galaxy citation bibtex by @bernt-matthias in #21563
• [25.1] Add belated deprecation of Python 3.9 support by @nsoranzo in #21598
• [25.0] Fix race condition in workflow collection populated state check by @mvdbeek in #21613
• [25.1] Harden Dataverse integration by @davelopez in #21624
• [25.1] Fix loading of credentials when associated tools are missing by @arash77 in #21599
• [25.1] Fix Pulsar with default_file_action: none by @mvdbeek in #21578
• [25.1] Fix condor typo by @gsaudade99 in #21651
• [25.1] Add split paired or unpaired tool to sample tool conf by @bernt-matthias in #21647
• [25.1] Fix secret credential editing and add clear button by @itisAliRH in #21650
• [25.1] Fix HTCondor runner unwatching jobs when stopping containers by @kysrpex in #21656
• [25.1] Fixes storage management check for anonymous users by @davelopez in #21680
• [25.1] Resets selection filter when loading dialog by @davelopez in #21681
• [25.1] Fixes duplicated entries in "share with individual users" component by @davelopez in #21683
• [25.0] Fix data manager .loc file selection logic by @jdavcs in #21664
• [25.1] Remove Discover Tools button in the workflow tool panel by @ahmedhamidawan in #21697
• [25.1] Simplify docker build, use node as specified in requirements by @mvdbeek in #21695
• [25.0] Fix option propagation for workflow inputs connected to multiple subworkflows by @mvdbeek in #21712
• [25.1] Fix collection job state not preserved during history export/import by @mvdbeek in #21716
• [25.1] Strip inline comments in conditional requirements by @mvdbeek in #21720
• [25.1] Exclude node_modules at all depths in Docker builds by @mvdbeek in #21721
• [25.0] Add missing filter_failed_collection_1.1.0.xml tool by @mvdbeek in #21719

🧪 Testing

• [25.1] Improve tempdir cleanup in integration tests by @mvdbeek in #21520

New Contributors

• @gsaudade99 made their first contribution in #21651

Full Changelog: v25.1.0...v25.1.1