
.. to_doc

25.0
===============================

.. announce_start

Enhancements
-------------------------------

.. major_feature


.. feature

* Add Vizarr visualization
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19061`_
* Workflow Editor Activity Bar
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 18729`_
* Workflow Editor Auto Zoom
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19451`_
* Prevent users from reusing a banned email after account is purged
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19413`_
* Add Breadcrumb Heading Component
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19656`_
* Allow to send notifications when Admins cancel jobs
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19547`_
* Add basic support for icons in tools
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19850`_
* Data-source tool for DICED database (https://diced.lerner.ccf.org/) added
  (thanks to `@jaidevjoshi83 <https://github.com/jaidevjoshi83>`__).
  `Pull Request 19689`_
* Add cell-based markdown editor for pages
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19769`_
* Add share button for invocations
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19959`_
* Allow different AI providers (as long as they are openai compatible)
  (thanks to `@uwwint <https://github.com/uwwint>`__).
  `Pull Request 19989`_
* Add kepler.gl visualization
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20005`_
* Add Niivue viewer
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19995`_
* Add VTK Visualization Toolkit Plugin
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20028`_
* Add sample datasets for visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20046`_
* Add flac audio format
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20057`_
* Drop old galaxy_session records
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19872`_
* Add Molstar
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20101`_
* Add alignment.js for multiple sequence alignment rendering
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20110`_
* Add client package
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20171`_
* Add rerun option for workflows
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20032`_
* Add ZIP explorer to import individual files from local or remote ZIP archives
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20054`_
* Standalone Galaxy API Client Package
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20181`_
* Empower Users to Build More Kinds of Collections, More Intelligently
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19377`_
* Add User-Defined Tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19434`_
* Add Katex Equation rendering plugin to Markdown Editor
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19988`_
* IT Activity Panel
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19996`_
* Add markdown datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20056`_
* Workflow Run Form Enhancements
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19294`_
* Add eLabFTW file source from file source templates
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19493`_
* Add workflow selection and bulk actions
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19336`_
* eLabFTW integration via Galaxy file source
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19319`_
* Add Vitessce Viewer
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19227`_
* Add JupyterLite
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20174`_
* Add history sharing and accessibility management view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19786`_
* Dataset View Component
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20154`_
* Visualization-First Display functionality
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20190`_
* Add Dataverse RDM repository integration
  (thanks to `@KaiOnGitHub <https://github.com/KaiOnGitHub>`__).
  `Pull Request 19367`_
* Implement file source to integrate Galaxy with RSpace
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 20167`_
.. enhancement_tag_viz

* Update tiffviewer to latest version supporting more formats
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20457`_
* Add ``/api/datasets/{dataset_id}/extra_files/raw/{filename:path}``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20468`_
* Move phylocanvas to script entry point
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19193`_
* Move heatmap visualization to new script endpoint
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19176`_
* Add plotly.js
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19206`_
* Update visualizations to latest charts package
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19213`_
* Allow embedding vitessce visualizations
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19909`_
* Add support for Markdown help text in visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20043`_
* Adds Example Datasets and Help Text for Visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20097`_
* Add updated PCA plot
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20140`_
* Add visualization test data
  (thanks to `@nilchia <https://github.com/nilchia>`__).
  `Pull Request 20183`_
* Add plotly 6.0.1 to JupyterLite
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20201`_
* Browse multiple trees in phylocanvas
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20141`_
* Migrate ChiraViz
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20214`_
* Enable visualizations for anonymous user
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20210`_
* Improve handling of very large files in Tabulator
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20271`_
.. enhancement_tag_datatypes

* Add Aladin as standard FITS viewer
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20465`_
* Add molstar as default viewer for some molecule formats
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20467`_
* Enhance UTF-8 support for filename handling in downloads
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 19161`_
* Calculate hash for new non-deferred datasets when finishing a job
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19181`_
* Add IGB display support for CRAM files
  (thanks to `@paige-kulzer <https://github.com/paige-kulzer>`__).
  `Pull Request 19428`_
* Add fastk_ktab_tar datatype required for fastk tool
  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
  `Pull Request 19615`_
* Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 2
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19726`_
* Add bwa_mem2_index directory datatype, framework enhancements for testing directories
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19694`_
* Add rDock prm datatype
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19783`_
* Bump up max_peek_size to 50MB
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19823`_
* Populate image metadata without allocating memory for the entire image content
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 19830`_
* Extend image metadata
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 18951`_
* Add vitesscejson datatype
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20027`_
* Add specific datatypes for Cytoscape and Kepler.gl
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20117`_
* Add rd datatype
  (thanks to `@richard-burhans <https://github.com/richard-burhans>`__).
  `Pull Request 20060`_
* Add more metadata, esp `infer_from` to datatypes configuration
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20142`_
* Add docx datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20055`_
* Add bigbed to bed converter and tests
  (thanks to `@d-callan <https://github.com/d-callan>`__).
  `Pull Request 19787`_
.. enhancement_tag_tools

* Update RStudio IT
  (thanks to `@afgane <https://github.com/afgane>`__).
  `Pull Request 19711`_
* More user feedback in FormRulesEdit (for Apply Rules tool)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19827`_
* RStudio IT updates to work on .org
  (thanks to `@afgane <https://github.com/afgane>`__).
  `Pull Request 19924`_
.. enhancement_tag_workflows

* Selenium tests for various 24.2 features
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20215`_
* Implement workflow parameter validators
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19092`_
* Allow directory_uri workflow parameters.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19093`_
* Fix UP031 errors - Part 3
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19218`_
* Type annotation improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19485`_
* Move Workflow Editor save button
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19761`_
* Workflow Run Form Enhancements follow up
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19825`_
* Job cache allow different names when possible
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19962`_
* Add help text popovers for workflow runtime settings
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20031`_
* Migrate WF Collection Input Form Definition to Client Side
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19313`_
* Move README to center panel in workflow editor
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20029`_
* Implement dataset collection support in workflow landing requests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20004`_
* Client refactorings ahead of `#19377 <https://github.com/galaxyproject/galaxy/issues/19377>`__.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20059`_
* Expand workflow metadata for readme.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19591`_
.. enhancement_tag_ui

* Generate correct types for Dataset source transformations on backend
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19666`_
* Enable lazy loading for ace-builds
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19847`_
* Webpack build performance improvements
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19851`_
* Migrate from Prism to Monaco for ToolSource display
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19861`_
* Upgrade bundled/requested node version to 22.15.0
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18710`_
* Gulp build improvements, update
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19405`_
* G modal implementation
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 20168`_
* Add more descriptions to custom tool source schema
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20266`_
.. enhancement_tag_jobs

* Syntactic sugar to ease TPV configuration
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19834`_
* Define simple models for job messages
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19688`_
* Run the tool working dir backup/restore on Pulsar
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 16696`_
.. enhancement_tag_admin

* Add failed jobs working directory cleanup as a celery periodic task
  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
  `Pull Request 19594`_
* Button replacement batch 1
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19963`_
* Support setting and displaying timezone with the core metrics plugin
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 19527`_
* Add config options for tool dependency installs
  (thanks to `@afgane <https://github.com/afgane>`__).
  `Pull Request 19565`_
* Button replacement batch 2
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19990`_
.. enhancement

* Fix Invenio file source downloads not working with some Invenio instances
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19930`_
* Improve performance of job cache query
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20319`_
* DatasetView and Card Polish
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20342`_
* Deprecate ``enable_tool_document_cache``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20433`_
* Allow a posix file source to prefer linking
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19132`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19149`_
* Dynamic options: add data table filter
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 12941`_
* Fix UP031 errors - Part 1
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19194`_
* Fix UP031 errors - Part 2
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19204`_
* Explicitly add cwl-utils to dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19257`_
* Drop thumbs up reaction as pull request approval method
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19202`_
* Minor drag style adjustment for activities
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19299`_
* Update pydantic to 2.10.3
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19326`_
* Refactor and add tests for Popovers
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19337`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19190`_
* Use popper wrapper for help text popover
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19340`_
* Make conditional discriminators literals instead of generic string/bool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19374`_
* Remove apptainer-version pin
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19380`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19366`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19418`_
* Set safe default extraction filter for tar archives
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19406`_
* Let file sources choose a path for uploaded files
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19154`_
* Type annotations improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19442`_
* Update main citation to 2024 community paper
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19453`_
* Reset invocation export wizard after completion
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19449`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19464`_
* Document `$__user_name__`
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19433`_
* Improve asynchronous tasks error handling and reporting
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19448`_
* Handles S3 listing errors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19446`_
* Add author and tools details in RO-Crate
  (thanks to `@Marie59 <https://github.com/Marie59>`__).
  `Pull Request 18820`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19510`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19567`_
* Change galaxy system user uid for K8s image
  (thanks to `@afgane <https://github.com/afgane>`__).
  `Pull Request 19403`_
* Add vue-tsc baseline comparison to client-lint workflow
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19593`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19623`_
* Use correct `plugin_kind` in user file sources
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19622`_
* Add InvenioRDM file source template
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19619`_
* Make tool ids readable in invocation metrics
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19634`_
* Mention default values for truevalue and falsevalue
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 19657`_
* Enhance ListHeader Component for Reusability
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19655`_
* More Vue Typescript Fixes
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19663`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19682`_
* Workflow landing request - collapse activity bar by default
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19652`_
* Add webdavclient3 to conditional-requirements.txt
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 19671`_
* Add forgotten linter test
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19690`_
* Add Zenodo file source template
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19638`_
* Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 1
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19706`_
* Improved simplicity and isolation in transiently failing test
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19709`_
* Type annotation improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19642`_
* Move Markdown components to subdirectory for modularity
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19719`_
* Move vega wrapper to shared common directory and add error handler
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19718`_
* Augments popper wrapper, add click and escape handler
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19717`_
* ToolShed2 - Add more context when navigating between tools an repositories
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19738`_
* Enhance breadcrumb navigation UX in small screen sizes
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19737`_
* Refactor dependencies for tool output actions
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19662`_
* Skip slow tests for manage_db, db_dev scripts
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19744`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19727`_
* Fix Tours and add tooltips to history items
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19734`_
* Hide outdated visualizations from visualizations activity panel
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19353`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19772`_
* ToolShed 2.1 - Various bugfixes and enhancements.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19722`_
* Preserve workflow labels in final invocation reports
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19721`_
* Click to edit history name in `HistoryPanel`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19665`_
* Rework some form components for reuse
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19347`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19816`_
* Improve markdown editor modularity and structure
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19835`_
* Point install_requires at requirements.txt file
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19864`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19874`_
* Add visualization framework interface to cell-based markdown editor
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19775`_
* Use direct icon references in FormSelectMany.vue
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19829`_
* Improve type annotations of ``ModelPersistenceContext`` and derived classes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19852`_
* Various styling improvements to Workflow Run and Invocation views
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19905`_
* Show workflow help (and readme?) in run form
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19736`_
* Replace backend-based page creation controller endpoint
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19914`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19929`_
* Decrease sentry_sdk.errors log level to INFO
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 19951`_
* Allow PathLike parameters in ``make_fast_zipfile()``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19955`_
* Add link to view history on dataset info page
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 19956`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19964`_
* First steps of bootstrap replacement
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19946`_
* Adds a trimInputs prop to FormGeneric to trim string values on submit
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19971`_
* Overhaul workflow runtime settings display
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19906`_
* Improve type annotation of tool parameter wrapping
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19991`_
* Update selectable object stores after adding or editing them
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19992`_
* Allow resizing Visualizations in Markdown editor
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19958`_
* Adds validation and alerts for Markdown elements
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19952`_
* Enable ``warn_redundant_casts`` mypy option and drop redundant casts
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20008`_
* Merge Inputs/Parameters and Outputs/Collections Tabs
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20019`_
* Remove tags used
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19576`_
* Improvements to package decomposition.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19759`_
* Selenium test cases for running workflow from form upload
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19997`_
* GCard Full Description
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 20064`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19998`_
* Enhance Storage Dashboard Selected Item UI
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 20070`_
* Use visualization dropdown solely for examples
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20094`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 20096`_
* Flexible mapping from collection parameter types to collection builder components
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20082`_
* Add activity panel width to local storage
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20072`_
* Improve type annotation of `galaxy.util` submodules
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20104`_
* Route to creating a new file source in remote file browser modal
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20084`_
* Speedup mulled build test
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19712`_
* Show workflow README in split view next to the form inputs
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20026`_
* Run integration tests on latest Ubuntu
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20118`_
* Create working dir output outside of tool evaluator
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20153`_
* Show job ids on job success
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20145`_
* Revise transiently failing data source test
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20157`_
* Add Tapis auth support
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19887`_
* Improve docs for output filters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19904`_
* Implement tool markdown reports
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19054`_
* Rename tool "Citations" to "References"
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19770`_
* Improved rule builder display for non-nested lists (most of them)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20156`_
* GLink implementation
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 20063`_
* Add mandatory RO-Crate metadata when exporting
  (thanks to `@elichad <https://github.com/elichad>`__).
  `Pull Request 19846`_
* Rucio templates
  (thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
  `Pull Request 19720`_
* Allow overriding datatypes for planemo lint
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 19780`_
* Documentation around highlighting PRs for release notes
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19390`_
* Show pre-populated landing data values in workflow run form
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19935`_
* Irods objectstore templates
  (thanks to `@pauldg <https://github.com/pauldg>`__).
  `Pull Request 19415`_
* xsd: use CollectionType for collections in tests
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19802`_
* Allow controlling strict channel priority in mulled-build
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19425`_
* Isolate singularity containers more thoroughly for better reproducibility
  (thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
  `Pull Request 18628`_
* Add a script to reorganize tool data based on the new layout for genomic Data Managers
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 19728`_
* Avoid persisting credentials on checkout step of the Github actions
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 19089`_
* Improve type annotation of ``galaxy.model.dataset_collections``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20194`_
* Make preferences drop down available in single user deployments
  (thanks to `@ksuderman <https://github.com/ksuderman>`__).
  `Pull Request 19888`_
* Add replacement_dataset option to collection filter tools
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 20166`_
* Clarify that extra_scopes is sometimes non-optional
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 19385`_
* Introduce reusable GCard component for unified card layout
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19785`_
* Strip galaxy filename annotation on upload
  (thanks to `@GomeChas <https://github.com/GomeChas>`__).
  `Pull Request 18561`_
* Remote File Sources and Storage Locations redesign
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19521`_
* Enable cloning subworkflows
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19420`_
* Clarify that higher python versions are also supported
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 19156`_
* Have `make dist` in the web_client package build the client
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20195`_
* Enhance external login interface styling
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20100`_
* Display invocation inputs and outputs in workflow report
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20222`_
* Support setting masthead height in a theme
  (thanks to `@ksuderman <https://github.com/ksuderman>`__).
  `Pull Request 19581`_
* Add three AAI providers
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 20165`_
* Drop old job metrics
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19936`_
* Enable retrieving contents from extra file paths when request contains leading `/`
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20336`_
* Add DOI to workflow metadata
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 20033`_
* Enhance OpenAI Chat Integration
  (thanks to `@uwwint <https://github.com/uwwint>`__).
  `Pull Request 19612`_
.. small_enhancement

* Remove legacy visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20173`_
* Use TUS streaming and remove redundant IndexDB temp store in Zip Explorer
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20226`_
* Switch h5web to script endpoint
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19211`_
* Fix UP031 errors - Part 4
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19235`_
* Refactor for better reuse of workflow parameter type constants
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19260`_
* Fix UP031 errors - Part 5
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19282`_
* Fix UP031 errors - Part 6
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19314`_
* Extract and typescript-ify datatype selection in wfeditor
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19304`_
* Misc fixes 202412
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19341`_
* Type annotation fixes for mypy 1.14.0
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19372`_
* SQLAlchemy 2.0 follow-up
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19388`_
* Remove transaction helper
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19407`_
* Add test that verifies workflow source_metadata is preserved on landing claim
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19454`_
* Use discriminated unions in object stores and file source template configs
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19621`_
* Format code with black 25.1.0
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19625`_
* Remove unused/deprecated Cloud Authorization preference
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19643`_
* Relax job status check in test_delete_user_cancel_all_jobs
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19661`_
* Update test_create_dataset_in_subfolder to check for the dataset presence
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19660`_
* Remove unused(?) data_dialog form element type
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19669`_
* Drop support for Python 3.8
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19685`_
* Move RequiredAppT back into galaxy packages
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19704`_
* Update TypeScript version to 5.7.3
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19713`_
* Move history watcher and minor fixes
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19732`_
* Fix MarkdownDialog types
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19703`_
* Client circular dependency check
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19858`_
* Remove unnecessary code duplications
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19921`_
* FITS Graph Viewer - script name tweak
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19902`_
* Migrate Page editing controller endpoint to API
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19923`_
* Fix local import in ``__resolvers_dict``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19944`_
* Add type hints around collection copying and job things
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19961`_
* Removes outdated Markdown visualization insertion wizard
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19898`_
* Update vitessce version
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20016`_
* Set node version to 22.13.0
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20095`_
* Add role creation form
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20119`_
* Add logo, description and help for aequatus
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20128`_
* Drop now unused controller method
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20129`_
* Migrate Transition Systems Visualization
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20125`_
* Additional type hints for ``toolbox.get_tool`` / ``toolbox.has_tool``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20150`_
* Yaml parser fixes and improvements (part 1)
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20158`_
* Hide non-functional and replaced visualizations (e.g. Nora, MSA)
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20077`_
* Clarify is_active method usage for Python Social Auth in Galaxy
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19899`_
* Fix remaining vue-tsc errors
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20163`_
* Bump vega from 5.30.0 to 5.32.0 in /client
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20188`_
* Restore Visualization insertion options in Reports Editor
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20000`_
* Touch up Dataset View
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20290`_
* Remove backbone-based charts modules
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19892`_
* Remove type import side-effects
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 20321`_


Fixes
-------------------------------

.. major_bug


.. bug_tag_viz

* Fix phylocanvas visualization build
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19138`_
* Update Vizarr package version to 0.1.6
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19228`_
* Fix and migrate Drawrna
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20102`_
.. bug_tag_datatypes

* Dataset Display and Preferred Viz fixes
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20439`_
* Make optional edam-ontology in datatypes registry optional
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20492`_
* Handle isatools dependency
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19582`_
* Fail request explicitly when sqlite provider used on non-sqlite file
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19630`_
* Raise ``MessageException`` when using data provider on incompatible data
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19639`_
* Fix anndata metadata setting for data with integer indexes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19774`_
* Fix parameter model constructions with leading underscores, fixes converter linting
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19790`_
* Fix tabular metadata setting on pulsar with remote metadata
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19891`_
* Let pysam use extra threads available in job
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19917`_
* Add new line to vtpascii test file
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20051`_
* Update tabular_csv.py to use less memory in tsv->csv conversion
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 20187`_
* Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20239`_
.. bug_tag_tools

* Handle directories with percents directories with export_remote.xml
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19865`_
* Also chown R lib in RStudio BioC tool
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20025`_
* Add missing tool test file
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19763`_
.. bug_tag_workflows

* Link workflow invocation outputs upon importing invocation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20485`_
* Allow unused query params in ``workflows/export_to_file``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19574`_
* Fix invocation failure dataset reference
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20200`_
* Bug fix: allow any collection type in FormCollectionType
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20403`_
* Better handling of public pages and workflows authored by deleted users
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19394`_
* Fix dangling workflow store references
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19618`_
* Raise serializable exception on invalid workflow connection
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19636`_
* Fix Selenium workflow tests not updating param type properly.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19810`_
* Fix broken optimisation introduced in `#19852 <https://github.com/galaxyproject/galaxy/issues/19852>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19871`_
* Skip ``data_meta`` filter in run form
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19895`_
* Fix attempt restriction on multiple connections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19948`_
* Sort intersected options
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19953`_
* Move `FormBoolean` back to `FormElement` field in workflow run form
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19938`_
* Restrict job cache to terminal jobs (and other fixes)
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19978`_
* Ensure job states are fetched in invocation view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20010`_
* Allow tool state changes in refactor actions
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19730`_
* Skip ``param_value`` filter if ref value is runtime value
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20144`_
* Fix certain cases of collection parameter handling during workflow execution
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20152`_
* Rerun workflows for the correct version/instance
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20313`_
* Fix workflow bookmark filtering
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20325`_
.. bug_tag_ui

* Force Monaco into a separate bundle
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20396`_
* Bump cross-spawn from 7.0.3 to 7.0.5 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 19152`_
* Stabilize HistoryView.test.js
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19165`_
* Cleanup Jest Test Output (part 2)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19178`_
* Cleanup Jest Test Output (part 3)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19185`_
* Cleanup Jest Test Output (part 4)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19186`_
* Cleanup test output console for tool panel tests
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19210`_
* Fix more vue tsc indicated type issues
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19650`_
* Fix a vue-tsc issue - Login.vue
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19647`_
* Yet More Vue Typing Error Fixes
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19680`_
* Bump axios from 1.7.4 to 1.8.2 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 19773`_
* Fix most new vue typescript errors discovered in `#19851 <https://github.com/galaxyproject/galaxy/issues/19851>`__
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19862`_
* Unwind more client dependencies at top of stack.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19983`_
* Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 20086`_
.. bug_tag_jobs

* Set ``GALAXY_CONFIG_FILE`` env var if starting handler with `-c`
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20449`_
* Fix job rerun with tool version change
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20417`_
* Don't calculate dataset hash for datasets in non-OK state
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19191`_
* Use ``resource_path()`` to access datatypes_conf.xml.sample as a package resource
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19331`_
* Alternative `format_source` fix
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19395`_
* Make k8s user and group ids overriddable per job
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 19568`_
* Use materialized datasets in pulsar job runner
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19807`_
* Fix various job concurrency limit issues
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19824`_
* Fix Galaxy ignoring job object_store_id for quota check
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19854`_
* Use ``make_fast_zipfile`` directly
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19947`_
* Add missing job state history entry for queued state
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19977`_
* Fix dynamic filter option access when building command line
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19982`_
* Fix setting env and tags on resubmission
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19753`_
.. bug_tag_admin

* Fix searching roles in admin UI
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 20394`_
* Fixes for the admin jobs interface
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 20405`_
* Update eLabFTW file source template docs
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19632`_
* Updated registration warning message
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19598`_
* Fix default ordering of items sorted by name
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19853`_
* Fix broken admin navigation option and add missing menu items
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20333`_
.. bug

* Change wording of the client side storage handling
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 19815`_
* Fix `mulled-search --destination quay`, add index reuse
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20107`_
* Data Libraries - persist number of entries displayed in folders
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20455`_
* Fix copying of job metrics for cached jobs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20436`_
* Fix multiple remote file upload to collection creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20456`_
* Fix pagination state in FilesDialog
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20452`_
* Fix inconsistent styling in List Collection Builder selector
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20442`_
* Fix bug with handling compressed file names while auto-pairing.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20459`_
* Fix dataset error button not using router
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20472`_
* Prevent running datatype autodetect on purged datasets
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20479`_
* Fix legacy get_metadata_file controller route
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20477`_
* Make response header values strings
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20475`_
* More fixes to `FormData` drag and drop and typing
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19900`_
* Replace Bootstrap Popover with Popper wrapper
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20246`_
* Recreate triggers
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 20491`_
* Use DatasetAsImage component for DatasetView image display
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20488`_
* Bug fix: paired_or_unpaired also endswith paired
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20458`_
* Don't fit workflow if it doesn't have steps
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20480`_
* Fix libraries folder include deleted
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19553`_
* Fix "export datasets" tool displaying dialog right away
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19555`_
* Fix saved visualization (non-trackster ones) not displaying
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19561`_
* Add Python 3.13 classifier to packages
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19569`_
* Fix job paused on user defined object store
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19578`_
* Fix collection load error handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19585`_
* Fix mulled tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19626`_
* Apply exec options to connection
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19651`_
* Initialize dictionary used to set connection execution options
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19653`_
* Pin mercurial to >=6.8.1 for Python 3.12 support
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19693`_
* Fix container building
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19714`_
* Check if index exists before creating
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19873`_
* Fall back to name in job summary if no input label given
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20258`_
* Group Tool Versions in IT Panel
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20244`_
* Fix vue-tsc issue in ParameterStep
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20245`_
* Remove rename modal from List Collection Creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20487`_
* Add user-facing explanation for legacy workflow run form usage
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20431`_
* Wrap Tool and Workflow run headers properly
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20440`_
* Fix add button is enabled when empty tag list
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20443`_
* Fix unit tests returning values
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20413`_
* Update pulsar-galaxy-lib to 0.15.8
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20419`_
* Fix css alignment styling of login page
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20429`_
* Update triggers
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 20425`_
* Fix toolshed-installed tool icons
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20399`_
* Fix $app attribute access in cheetah templates
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20414`_
* Fix workflow logo URL not being persisted
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20428`_
* Upgrade tensorflow conditional dependency version to 2.15.1
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 20434`_
* Make invocation errors more compact
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20369`_
* Fix create file source button, show only at root
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20385`_
* Fix interactive activity highlighting
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20276`_
* Avoid displaying dataset tab view in window manager
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20317`_
* Fix form select input sorting
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20401`_
* Add job config variable for singularity `--contain`
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 20400`_
* Prevent waiting for history item state to be ok in uploader
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20397`_
* Fix ``mull_targets()`` with mamba 2.x
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20416`_
* 2 small uv config fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19146`_
* Fix Pesky warning with PersistentTaskProgressMonitorAlert.test.ts
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19180`_
* Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 19189`_
* Update PR title handling for changing base ref
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 19195`_
* Create harmonized collections from correct tool outputs
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 19222`_
* Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 19233`_
* Require importlib-resources also for Python 3.9-3.11
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19358`_
* Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 19369`_
* Node 22 unreachable fixes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19378`_
* Use ``id`` entity attribute when setting ``exampleOfWork`` property
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19396`_
* Display email activation help only if user activation is enabled
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19402`_
* Prevent negative offset
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19409`_
* Fix wrong id in test_combined_mapping_and_subcollection_mapping
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19481`_
* Fix preferred object store id reactivity
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19491`_
* Fix wrong URI written to `ExportObjectResultMetadata` when exporting histories to eLabFTW
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19541`_
* Fix missing name in user-defined object store list
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19599`_
* Add ``upgrade_codes.json`` to tool-util package
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19605`_
* Fix user preferences secret (without vault) lost on save
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19610`_
* Set content-type to text/plain if dataset not safe
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19563`_
* Remove redundant `Create Collection` ok button from collection creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19613`_
* Remove unused and broken methods
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19614`_
* Fix `test_mulled_build.py::test_mulled_build_files_cli` with `use_mamba=True`
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19545`_
* Raise ``RequestParameterInvalidException`` on invalid ``input_format`` parameter
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19631`_
* Disable chatgxy wizard for anon users
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19628`_
* Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19620`_
* xsd: fix format
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19683`_
* Fix validation of required floats specified as empty strings in tool XML
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19701`_
* Update fs.dropboxfs conditional dependency version to 1.0.3
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19741`_
* Fix conditional dependency path resolution
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19723`_
* Fix incorrect type in tool_util.deps and fix package structure
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19702`_
* Add linter argument to linter report function calls
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19708`_
* Refactor tool panel handling, resolve transiently failing jest test
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19733`_
* Fix various bugs around tool data table bundles
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19659`_
* Use fissix also when python3-lib2to3 is not installed
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19749`_
* Fix dataypes linter: allow auto for output tags
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19757`_
* Fix RDM token access for user-defined file sources
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19768`_
* Follow-up to `#19651 <https://github.com/galaxyproject/galaxy/issues/19651>`__: Do not reassign: method modifies object in-place
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19746`_
* Assertion linter fixes
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19715`_
* Fix recording transform action name
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19672`_
* Jest Cleanup (Part 5)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19743`_
* Fix masthead webhook click/nav
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19764`_
* Update webdav user file source template help text
  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
  `Pull Request 19784`_
* Revise consistently failing edam tool panel view test
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19762`_
* Fix private role name performance issue
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19679`_
* Fix wording of API doc string
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19776`_
* Add better `WorkflowSummary` type
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19779`_
* Fix workflow run graph non input steps not appearing bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19781`_
* Fix tool directory pulsar transfer
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19799`_
* Reduce default framework tool test timeout to 60 seconds
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19819`_
* Backport `#19810 <https://github.com/galaxyproject/galaxy/issues/19810>`__: Fix workflow param tests not updating param type
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19820`_
* Try to recover from recurring activation link error
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19844`_
* Create rucio.cfg from inside Rucio objectstore
  (thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
  `Pull Request 19863`_
* Don't collect unnamed outputs twice in extended metadata mode
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19868`_
* Move some store types out into own file to reduce circular dependencies
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19860`_
* Cleanup circular dependencies around utils.ts
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19857`_
* Lazy-load invocation step jobs as needed
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19877`_
* Fix drag and drop for dataset collection elements
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19866`_
* Fix various mypy issues around mapped attributes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19883`_
* Decode/encode FormDirectory paths to allow spaces (and other characters)
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19841`_
* Fix collection builder input states
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19797`_
* Drop unused alembic-utils from galaxy-data package requirements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19896`_
* Fix duplicate extensions for data inputs
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19903`_
* Add spacing between workflow author and invocation count
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19849`_
* Skip implicit HDA conversions in DataToolParameter options
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19911`_
* Fix duplicate entries when using drag and drop in multiple mode
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19913`_
* Handle special charater in raw SQL
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19925`_
* Report TestCaseValidation as linter error for 24.2 and above
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19928`_
* Use FA Component (w/svg) instead of span+font in RunWorkflow header
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19901`_
* Change wording in the google drive user file source template
  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
  `Pull Request 19927`_
* Better interactive tool entry point query
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19942`_
* Drop unnecessary job cache job subquery
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19945`_
* Fix ``test_in_directory`` on osx
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19943`_
* Fix adding tags popup closing logic on focus out
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19950`_
* Remove circular dependency around user store
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19859`_
* Remove hgv_sift from tool_conf.xml.sample
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 19972`_
* HelpText improvements (content, sizing) and WorkflowInvocationHeader tweaks
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19792`_
* Remove unused (define* - compiler macro) imports from TextEditor.vue
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19793`_
* Fix ownership check in history contents update route
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19969`_
* Do not display default labels obscuring selectable options in a vue-multiselect component
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19981`_
* Always set copy_elements to true
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19985`_
* ChatGXY Error Handling
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19987`_
* Fix various parameter validation issues
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19949`_
* Fix `keyedCache` never allowing multiple fetches
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20020`_
* Use lower case extension for setting datatype in data discovery
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19954`_
* Pass host url to visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20022`_
* Update breadcrumb item 'to' type for better routing support
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 20065`_
* Fix edit permission for datasets delete button in storage dashboard overview by location
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 20066`_
* Fix `test_workflow_run` export selenium
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20089`_
* Remove collapse invocations panel on mouseleave feature
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20074`_
* Always render Outputs tab in invocation view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20073`_
* Add hid to selection field in visualization creation form
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20108`_
* Wait for Gbutton to become enabled
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20131`_
* Sort visualization datasets by hid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20123`_
* Allow deferred and ok state datasets for vis
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20143`_
* Fix edam selenium test
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20134`_
* Yaml parser fixes part2
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20162`_
* Remove only the Docker images specific for the test
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20109`_
* Fixes for GButtons with disabled state
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20121`_
* Fix ``DataCollectionParameterModel`` factory
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20164`_
* Job cache backports
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20078`_
* Use ``backports.zoneinfo`` in ``job_metrics`` package under Python <3.9
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20178`_
* Renew access tokens from PSA using valid refresh tokens
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 20040`_
* Fix tapis module typing errors
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 20175`_
* Corrects header levels in Visualization Help Markdown
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20199`_
* Fix `#19515 <https://github.com/galaxyproject/galaxy/issues/19515>`__ - invalid citation handling changed with 24.2
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19716`_
* Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING`
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 20209`_
* Fix linting with markdown in tool help
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20058`_
* Avoid using custos refresh tokens which are expired
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 19411`_
* Add missing linter name argument to linter report function calls
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19707`_
* Fix next milestone
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 20219`_
* Package fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 20208`_
* Move UnprivilegedToolResponse into api
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20207`_
* Fix theme selector
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20275`_
* Add non-dev httpx dependency
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20281`_
* Fix WF Run RO-Crate logo width in Firefox
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20305`_
* Add test for workflow instance download fix
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20326`_
* Do not reorder options in FormSelect component when multiselect disabled
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19837`_
* Add basic validation to workflow creator attribute
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 20328`_
* Remove redundant badge when creating collection from upload
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20367`_
* Fix inconsistent header sizes
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20277`_
* Remove duplicated job id in job success view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20289`_
* Skip multiple pasted URLs when checking for remote Zip
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20300`_
* Increase proxy API robustness by validating URL before use
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20311`_
* Fix display urls
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20318`_
* Error on duplicate labels
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 20335`_
* Small UI fixes for ag-grid based rule grid
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 20358`_
* Fix selection issue when adding tags to workflows in bulk
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20362`_
* Log invalid vault paths
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 20363`_
* Generate a tenant-unique UID for tapis
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 20370`_
* Use router to route to creating a new file source
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 20374`_
* Fix radio button options in CopyModal
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 20378`_
* Fix conda_link to use platform.machine() for architecture detection
  (thanks to `@chrisagrams <https://github.com/chrisagrams>`__).
  `Pull Request 20381`_
* Fix masthead logo height
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 20302`_
* Do not print OIDC access tokens to the logs
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19966`_
* Renew OIDC access tokens using valid refresh tokens
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 19967`_
* Fix bug in psa-authnz redirect handling
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19968`_
* Fix NFDI auth
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 20217`_

.. include:: 25.0_prs.rst

