.. to_doc

24.2
===============================

.. announce_start

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

.. major_feature

.. feature

Features
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Backport of Workflow Editor Activity Bar
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19212`_
* Add onedata templates
  (thanks to `@bwalkowi <https://github.com/bwalkowi>`__).
  `Pull Request 18457`_
* Add linter to check validity of output filters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19114`_
* FITS file table graph visualization plugin
  (thanks to `@francoismg <https://github.com/francoismg>`__).
  `Pull Request 19003`_
* Experimental galactic wizard
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 15860`_
* Allow OAuth 2.0 user defined file sources (w/Dropbox integration)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18272`_
* Add job metrics per invocation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19048`_
* Feature - stdout live reporting
  (thanks to `@gecage952 <https://github.com/gecage952>`__).
  `Pull Request 16975`_

.. enhancement_tag_viz

Vizualization enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Fix MSA viz, new dependency specification options
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18760`_
* Parse stored config details to script-based visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18651`_
* Migrate NGL viewer to npm package
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18946`_
* Support deferred datasets in visualizations
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19097`_
* Openlayer update to npm package
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 19134`_
* Replace static Cytoscape plugin with npm package
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 19127`_
* Update tiff viewer to use script entry_point
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19151`_
* Migrate Venn Diagram to Script-Tag
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19153`_
* Remove OpenLayers legacy files and add SVG logo
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19135`_

.. enhancement_tag_datatypes

Datatype enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Add pod5 datatype
  (thanks to `@TomHarrop <https://github.com/TomHarrop>`__).
  `Pull Request 18419`_
* Handle compressed content in dataset preview for all sequence classes
  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
  `Pull Request 18776`_
* Improve usability of Directory datatype
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 17614`_
* Add some Zarr-based datatypes
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19040`_
* Add XML based `vtk` datatype
  (thanks to `@tStehling <https://github.com/tStehling>`__).
  `Pull Request 19104`_

.. enhancement_tag_tools

Tool enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Update GPU JupyterLab tool
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 18220`_
* Add Tool-Centric APIs to the Tool Shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18524`_
* Add BlobToolkit to the list of interactive tools
  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
  `Pull Request 18630`_
* Remove some unused dynamic drill down options
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18892`_
* Add filter null collection operation tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18928`_
* Jupyter Interactive Tool 1.0.1/24.07
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 18861`_
* Add Interactive Tool Ilastik
  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
  `Pull Request 16837`_

.. enhancement_tag_workflows

* Fix problem with multiple layers in workflow metrics
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19283`_
* Fix workflow metrics chart style
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19291`_
Workflow enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Fix usability of workflow best practice attribute checking.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19230`_
* Workflow Inputs Activity
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19252`_
* Fix default value handling for parameters connected to required parameters
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19219`_
* Allow connecting text param into data column parameter
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18674`_
* Allow specifying multi-select workflow parameters
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18715`_
* Allow access to invocation via shared or published history
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18707`_
* Modelling for Test Assertions
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18787`_
* Implement Pydantic model for workflow test format.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18884`_
* Improvements to Planemo test format based on feedback/discussions
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18889`_
* Allow CORS requests to /api/workflow_landings
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18963`_
* Workflow landing improvements
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18979`_
* Always validate hashes when provided
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19110`_
* Workflow Landing Requests
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18807`_
* Implement Declarative Testing for Workflow Behaviors
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18542`_
* Allow recovering a normalized version of workflow request state from API
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18985`_

.. enhancement_tag_ui

UI enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Enable verbatimModuleSyntax, fix jest usage
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18595`_
* Make vite tool shed client proxy configurable
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18988`_
* Upgrade `openapi-typescript` to 7.0.2 + swap to `openapi-fetch`
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18532`_

.. enhancement_tag_jobs

Job enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Record container id and type in core job metrics
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18579`_
* Add type annotations to ``JobRunnerMapper`` and related code
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19115`_
* Allow to overwrite `real_system_username` per destination
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18945`_

.. enhancement_tag_admin

Admin enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Remove `defaults` channel for conda usage
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18757`_
* Allow setting a few global defaults for file source plugin types
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18909`_
* Bring your own file sources: Add the WebDAV template and configuration
  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
  `Pull Request 18598`_
* Decouple user email from role name
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18966`_
* Support high-availability setups for the interactive tools proxy
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 18481`_
* Minor config documentation enhancements
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 18499`_
* Better cleanup of sharing roles on user purge
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19096`_

.. enhancement

* List private file sources first in Remote Files Dialog
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19455`_
* Various list of pairs builder usability fixes
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19248`_
* Fix to not display upload when creating collections from existing datasets
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19373`_
Misc. enhancements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Activity bar add new workflow button
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19281`_
* Guide users to collection builders
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18857`_
* Updates the About Page
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18461`_
* Moves Libraries from Masthead to Activity Bar
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18468`_
* Adds an option to restore activity bar defaults
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18469`_
* Add errors fast api
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18093`_
* Add task expiration to persistent task monitor
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18551`_
* Improve datasets permissions API schema typing
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18563`_
* Group tool templating exceptions in sentry
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18570`_
* Add a new version of the production s3fs file source template with the writable configuration variable added
  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
  `Pull Request 18575`_
* Move history multiview item actions to top
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18265`_
* Improve update user API payload schema
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18602`_
* Improve update history payload schema
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18618`_
* Rev pinned gxformat2
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18624`_
* Improve typing for archived histories API schema
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18586`_
* Reduce unnecessary requests when browsing tool repositories in Admin Panel
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18632`_
* Improve types around User in schema and client
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18645`_
* Rip repository_registry out of tool shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18647`_
* Improve accept header API schema
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18668`_
* Another round of parameter model improvements
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18673`_
* Another round of parameter model enhancements and tool tests
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18678`_
* Dynamic Models for Tool Test Validation
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18679`_
* Implement tool upgrade assistant
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18728`_
* Cache pip directory as part of `setup-python` action
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18789`_
* Refactor FolderTopBar to TypeScript
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18488`_
* Update Visualization FastAPI
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18792`_
* Add Alireza to committers group
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18613`_
* Improvements to help terms & tool help
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18722`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18578`_
* Add wizard-like export view for workflow invocations
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18796`_
* Improvements to parameter models for test case inputs
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18743`_
* Add docs on indexing for filter column
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18844`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18864`_
* Add unique constraints to the email and username fields in the galaxy_user table
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18493`_
* Replace History Dataset Picker in Library Folder
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18518`_
* Allow using tracks and groups in visualization xml
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18779`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18904`_
* Add support for arbitrarily ordered image axes in image content assertions
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 18891`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18943`_
* Add BioBlend tests
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18975`_
* Optimize to_history_dataset_association in create_datasets_from_library_folder
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18970`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18982`_
* Add workflow to update PR title based on target branch version
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18835`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19031`_
* Enable extra user preferences for remotely authorized users
  (thanks to `@maartenschermer <https://github.com/maartenschermer>`__).
  `Pull Request 18887`_
* UI Improvements for Tool Shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19041`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19062`_
* Annotate ``DatasetAssociationManager`` as generic type
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19063`_
* Better logging around tool loading
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19029`_
* Add `galaxy-upload` link to `UploadModal`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19055`_
* Do not skip CI tests on missing tools
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19002`_
* Add a filter for `labels` (tags) in Tool Search
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19076`_
* Replace poetry with uv
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19075`_
* Add Python 3.13 support
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18449`_
* Allow deferred datasets to behave as URIs
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19077`_
* uv: Do not recalculate dependencies when exporting
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19099`_
* Test hash validation also for upload by path
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19109`_
* Integrate Tool Parameter Modeling into Linting (for Planemo)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19073`_
* Better search stuff in Tool Shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19047`_
* Enable specifying dataset hash in test jobs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19113`_
* Access public history in job cache / job search
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19108`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 19123`_
* Also use miniforge docker for container building
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19128`_
* Silence the quota manager for updates
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19046`_
* Enhance relabel_from_file to work with any column pair in mapping file
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 19022`_
* Irods ssl connection
  (thanks to `@pauldg <https://github.com/pauldg>`__).
  `Pull Request 19014`_
* Update Japanese locale.js
  (thanks to `@manabuishii <https://github.com/manabuishii>`__).
  `Pull Request 19101`_
* Update vizarr version to 0.1.5
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19142`_
* Fix word wrapping in invocation panel list items
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19141`_
* Add Workflow Title and Annotation sections
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 18762`_
* Assert that `data_column` parameters have a valid `data_ref`
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18949`_
* Switch update annotate image to new script entry_point
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19150`_
* Workflow license and creator edit keyboard access
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18936`_
* More data access tests, some refactoring and cleanup
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18312`_
* Add hint to the tool schema about runtime conditional changes
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 18996`_
* Undo stack UI
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 18548`_
* Run installed Galaxy with no config and a simplified entry point
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 19050`_
* A variety of improvements around tool parameter modeling (second try)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19027`_
* Parameter Model Improvements
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18641`_
* Masthead Revision
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17927`_
* Workflow Invocation view improvements
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18615`_
* Add linters for datatypes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17600`_

.. small_enhancement

* Release testing - selenium tests for workflow invocation export
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19262`_
* Update versions of GitHub actions
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18197`_
* Update openapi-typescript dependency to version 6.7.6
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18519`_
* Mixed enhancements from CWL branch
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18539`_
* Fix some Toolshed 2.0 development paper-cuts
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18538`_
* Improvements to Tool Test Parsing
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18560`_
* Drop unused datasets controller methods
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18568`_
* Consistent type imports, fixes and linting
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18589`_
* Tighten user notification API response types
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18599`_
* More tool test typing
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18590`_
* Remove unused functions in dataset managers
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18631`_
* Better Typing for Tool Execution Plumbing
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18626`_
* De-couple XML from tool interface for test collections
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18676`_
* Update ExportToRemoteModal.vue to use TypeScript
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18706`_
* More typing, docs, and decomposition around tool execution
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18758`_
* Migrate Visualizations API to FastAPI
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18721`_
* Refactor ``LibraryDatasetsManager`` and fix type annotation issue
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18773`_
* Update Mypy to 1.11.2 and fix new signature override errors
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18811`_
* Remove Build Dataset Pair option from history actions
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18740`_
* Backend handling of setting user-role, user-group, and group-role associations
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18777`_
* Refactor migration testing setup code
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18886`_
* Enable ``ignore-without-code`` mypy error code
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18898`_
* Raise exception if CompressedFile used on incompatible file
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18888`_
* Type annotations and fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18911`_
* Remove outdated fimo wrapper and galaxy-sequence-utils dependency
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18937`_
* Migrate Library Contents API to FastAPI
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18838`_
* Fix extra files path type hint
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18958`_
* Move TRS import into WorkflowContentManager
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19070`_
* More concise, readable tool execution testing
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18977`_
* Libraries Modernisation: Directory Dataset Picker
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18638`_


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

.. major_bug


.. bug_tag_viz

* Prevent cycling through failing conversion jobs in trackster
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19494`_
Vizualization fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Update visualizations package versions
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19232`_
* Install npm-package viz to the package prefix explicitly
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18950`_
* Restore access to saved visualizations
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19136`_

.. bug_tag_datatypes

Datatype fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Add gtf to auto_compressed_types
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19175`_

.. bug_tag_tools

Tool fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Drop "Send to cloud" tool and associated cloudauthz code
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18196`_
* Fix commas that shouldn't be in biotools_mappings.tsv
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18919`_

.. bug_tag_workflows

* Fix error message when subworkflow input connection missing
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19526`_
* Also check `trs_tool_id` for imported workflow indicator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19460`_
* Set a hard limit of 100 invocations per request in api/invocations
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19497`_
* Fix import of previously-deleted TRS workflow
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19311`_
Workflow fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Fix workflows with optional non-default parameter input
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19332`_
* Fix cancellation of workflow scheduling
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19238`_
* Fix collection type drag and drop validation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18623`_

.. bug_tag_ui

UI fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Bump requirejs from 2.3.6 to 2.3.7 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 18610`_
* Bump axios from 1.6.2 to 1.7.4 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 18717`_
* Bump webpack from 5.89.0 to 5.94.0 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 18768`_
* Bump express from 4.19.2 to 4.21.0 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 18808`_
* Bump dompurify from 3.0.6 to 3.1.3 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 18821`_
* Bump http-proxy-middleware from 2.0.6 to 2.0.7 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 19060`_
* Bump dompurify from 2.3.10 to 3.1.6 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 18880`_

.. bug_tag_jobs

* Use instance wide default ``real_system_username`` if not defined on destination
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19544`_
* Fix job parameter summary for inputs without label
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19427`_
* Serialize message exceptions on execution error
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19483`_
* Partial backport of `#19331 <https://github.com/galaxyproject/galaxy/issues/19331>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19342`_
* Fixes for console logging
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19381`_
Job fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Fixes random job failures in kubernetes
  (thanks to `@mapk-amazon <https://github.com/mapk-amazon>`__).
  `Pull Request 19001`_

.. bug_tag_admin

* Downgrade 'InteractiveTools are not enabled' to warning
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19518`_
.. bug

* Use visualizations api in trackster
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19495`_
* Fix extracting workflows from purged and deleted histories
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19525`_
* Fix WSGI response status handling in controller methods
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19520`_
* Fix remap for parameter called id
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19532`_
* Fix admin cancel job message not being displayed to the user
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19537`_
* Provide guidance in case of deadlock during db migration
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19551`_
* Update 24.2 db revision tags
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19550`_
* Fix to only show ChatGXY when available
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19389`_
* Display upload help highlight only once and include Rule-based upload info
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19393`_
* Show message for mixed extensions in collection creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19404`_
* Fix Activity Bar state lost on page reload
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19426`_
* Show Keycloak provider label in UI
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19447`_
* `mulled-build-tool` fix for packages wo version
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19450`_
* Fix parsing of validators with inf limits
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19459`_
* Fix help text overflow breaking tool inspector
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19465`_
* Fix object not found handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19468`_
* Remove print statement
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19469`_
* Bump typescript target to es2020
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19473`_
* Fail with error message when submitting invalid request
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19489`_
* Fix invocation query in JobInformation.vue component
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19496`_
* Fix minor typo in event name in collection creator
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19499`_
* Fix library dataset current user potentially null
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19505`_
* Fix workflowID assignment in Markdown.vue
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19507`_
* Skip token refresh without refresh token in psa
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19514`_
* Fix tool search constantly loading bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19528`_
* Add tool_id index on job table
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19543`_
* Outputs filter linter fixes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19208`_
* Fix some collection builder help and language choices
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19244`_
* Only allow moving activity bar icons when editing the bar
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19258`_
* Fix CollectionCreatorModal being reopened on history
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19276`_
* Fix invocation metrics usability by providing job context
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19279`_
* Fix inconsistent tab handling in invocation view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19298`_
* Don't show published workflows in workflow activity of workflow editor
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19312`_
* Fix timeout handling for planemo / galaxy-tool-util
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19384`_
* Fix for empty string in regex validator message
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19387`_
Misc. fixes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

* Fix handling of step id offsets when duplicating selections
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 19351`_
* Fix simple activity panel item style
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19350`_
* Fixes window manager scrolling and resizing
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 19308`_
* Fix activity-bar-id handling wrt activityStore
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19316`_
* Login redirect followup
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19251`_
* Build collection only if populated in collection builder
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19250`_
* Avoid a class of unhelpful accepted format drop downs
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19241`_
* Improve the empty history message for guiding users to collections.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19242`_
* Fix PSA Redirect
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19247`_
* release testing - UI tests for new workflow parameters
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19182`_
* Return generic message for password reset email
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18479`_
* Raise Message Exception when displaying binary data
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18503`_
* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18510`_
* Follow-up on `#18212 <https://github.com/galaxyproject/galaxy/issues/18212>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18516`_
* Fix "worklfow" typo here and there
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 18523`_
* Fix MessageException handling in get_edit
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18529`_
* Fix bugs in tool shed tool API
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18558`_
* Fix Archive header encoding
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18583`_
* Fix for not-null in 'column_list' object
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 18553`_
* Fix API key reveals on mouse hover
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18593`_
* Fix for Numeric form field to allow Null min/max values in validation methods
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 18585`_
* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18605`_
* Fixes for errors reported by mypy 1.11.0
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18608`_
* Bug fix for invalid duplicate id in function test tools
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18644`_
* Handle output parsing when tool is not available for tool-centric API
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18643`_
* Restore interactive tools watcher
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18581`_
* Strip whitespace when listifying admin users
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18656`_
* Update mercurial
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18686`_
* Restore repository update in the tool shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18655`_
* Fix "Latest Updates" order in tool shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16894`_
* Replace types-pkg-resources with types-setuptools
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18708`_
* Update ruff to 0.6.1
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18716`_
* Fix new flake8-bugbear B039 and mypy type-var errors
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18755`_
* Fixing RegisterForm.vue not appending prefix when set
  (thanks to `@mcuaya1 <https://github.com/mcuaya1>`__).
  `Pull Request 18786`_
* Fix response if dataset requested by display application is deleted
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18803`_
* Fix alert handling in workflow label handler
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18836`_
* Fix transiently failing selenium tooltip issues
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18847`_
* Fix flaky `test/integration_selenium/test_toolbox_filters.py::TestToolboxFiltersSeleniumIntegration::test_toolbox_filters`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18854`_
* Fix migration data fixes tests
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18885`_
* data_column params: offer same columns with and without use_header_names
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 18879`_
* Allow users with 'can_modify_folder' permission to delete items in libraries
  (thanks to `@npinter <https://github.com/npinter>`__).
  `Pull Request 18924`_
* Fix `WorkflowInvocationHeader` import type and current user errors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18956`_
* Explicitly display dataset preview in pages and workflow reports
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18968`_
* Ignore preflight options in API schema
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18983`_
* Define environment variables in ``env:`` section
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18987`_
* Fix the bioblend test failures
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18991`_
* Fix job directory not being cleaned up
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18997`_
* Fix job search statement building
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19010`_
* Fix test_stock.py unit test
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 19037`_
* add data source doc to the list in index
  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
  `Pull Request 18742`_
* Fix auto-detect metadata from Edit Dataset Attributes panel
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 19025`_
* Fix numerous issues with tool input format "21.01"
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 19030`_
* Prevent purged users from logging in
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19094`_
* Fixes and tests for data fetch models
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18834`_
* Run ``uv lock`` under Python 3.9
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 19111`_
* Allow modes `z` and `Z` for docker volumes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18998`_
* Fix handling of v2 hashes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18522`_
* Dynamics options add library dataset
  (thanks to `@gagayuan <https://github.com/gagayuan>`__).
  `Pull Request 18198`_
* Add merge migration to merge 2 heads
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 19163`_
* Disallow /tool_runner? in robots.txt
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19020`_
* Avoid possible negative offset in LibraryFolder
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 19090`_
* Fix backend role sharing bug
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18942`_
* Update a localized word with a more appropriate one
  (thanks to `@mpalmada <https://github.com/mpalmada>`__).
  `Pull Request 18910`_
* Fix tag processing in library upload
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18714`_
* Update plausible script name in mako templates
  (thanks to `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`__).
  `Pull Request 18458`_
* Fix issue with generating slug for sharing
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18986`_
* Consolidate tag validation
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 19166`_
* Move invocation view running actions and improve styling of annotation section
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 19168`_
* Fix mulled_hash
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19199`_
* Add requirement/resource to schema docs
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 19172`_
* Normalize usernames to lowercase in OIDC authentication
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 19131`_

.. include:: 24.2_prs.rst