.. to_doc

24.0
===============================

.. announce_start

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

.. major_feature


.. feature

* 24.0 release notes
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17610`_
* New Workflow List and Card View
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 16607`_
* Add harmonize collections tool (or whatever other name)
  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
  `Pull Request 16662`_
* Add support for Python 3.12
  (thanks to `@tuncK <https://github.com/tuncK>`__).
  `Pull Request 16796`_
* Support for OIDC API Auth and OIDC integration tests
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 16977`_
* New select component for selecting a large amount of options
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17059`_
* Qiskit in galaxy
  (thanks to `@thepineapplepirate <https://github.com/thepineapplepirate>`__).
  `Pull Request 17170`_
* Add accepted extensions to form data input
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17238`_
* Allow job files to consume TUS uploads
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17242`_
* API endpoint that allows "changing" the objectstore for "safe" scenarios.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17329`_
* Allow using tool data bundles as inputs to reference data select parameters
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17435`_
* Tag Autocomplete Rework
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17469`_
* Add magres datatype
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17499`_
* Add encode ID API endpoint
  (thanks to `@mira-miracoli <https://github.com/mira-miracoli>`__).
  `Pull Request 17510`_
* Fixing data_source tools and incrementing tool profile
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 17515`_
* Add npy datatype
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 17517`_
* Add basic TIFF Image visualization
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17553`_
.. enhancement_tag_viz

* Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17415`_
* Enhance Avivator display app to support regular Tiffs
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17554`_
.. enhancement_tag_datatypes

* Make columns types an empty list for empty tabular data
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 13918`_
* Add support for (fast5.tar).xz binary compressed files
  (thanks to `@tuncK <https://github.com/tuncK>`__).
  `Pull Request 17106`_
* Add a3m datatype
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 17217`_
* Add binary datatypes for intermediate output of fastk tools
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 17265`_
* Faster FASTA and FASTQ metadata setting
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17462`_
* Feature SBOL datatypes
  (thanks to `@guillaume-gricourt <https://github.com/guillaume-gricourt>`__).
  `Pull Request 17482`_
* Better display of estimated line numbers and add number of columns for tabular
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17492`_
.. enhancement_tag_tools

* Hide wig_to_bigWig tool
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17328`_
* Update RStudio GxIT to use the reworked 23.1 image
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 17533`_
.. enhancement_tag_workflows

* Toward declarative help for Galaxy markdown directives
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16979`_
* Add select parameter with options from remote resources
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17087`_
*  Expose more tool information / navigability in UI
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17105`_
* Overhaul Galaxy Markdown Help
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17228`_
* Consider Null inputs
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17271`_
* Display workflow invocation counts
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17488`_
* Filter out subworkflow invocations
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17558`_
* Links to individual invocations
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17566`_
* Add help text to workflow invocation states
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17569`_
.. enhancement_tag_ui

.. enhancement_tag_jobs

* Enable job resubmissions in k8s runner
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17324`_
.. enhancement_tag_admin

* Proxy Access-Control-* headers when using x-accel-redirect
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17842`_
* Add docs for tool panel and panel view administration
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17078`_
* Convert sample object store configuration to YAML and support configuring inline
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 17222`_
* Add documentation on how to use vault keys in file sources
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17498`_
.. enhancement

* Fix Multi-History status bar reactivity
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17812`_
* Allow admin to sharpen language about selected object stores
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17806`_
* Fix activity bar unreachable in some pages
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17860`_
* Record missing outputs as test errors
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17874`_
* Moves archived histories from Masthead to Histories Grid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17649`_
* Change user-facing language from "object store" to "storage location"
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17763`_
* Restore histories API behavior for `keys` query parameter
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17779`_
* Prompt user to change default history permissions
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17782`_
* Fix datasets API custom keys encoding
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17793`_
* Improved error messages for runtime sharing problems
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17794`_
* build_mulled: also use namespace for building singularity images
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 15657`_
* Implement Galaxy Markdown directive history_dataset_as_table
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16681`_
* Add test and doc showing how dynamic selects are used
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 16885`_
* Dataset Display : force reload on subsequent clicks
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16982`_
* Extend regex groups in stdio regex matches
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17016`_
* Add Ahmed as a committer
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17017`_
* Vueify Admin User Grid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17030`_
* Migrate ItemTags API to FastAPI
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 17064`_
* Use eventbus to emit route request in grid list
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17070`_
* Split linters in separate classes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17081`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17084`_
* Enhance Notification Broadcasts Admin Panel
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17090`_
* Make notification message input multi-line
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17091`_
* Make flex panel drag handle more obvious
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17113`_
* Vueify Admin Roles Grid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17118`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17123`_
* Vueify Admin Groups Grid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17126`_
* Vueify Admin Forms and Quota grids
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17141`_
* Create pydantic model for the return of show operation -  get: `/api/jobs/{job_id}`
  (thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
  `Pull Request 17153`_
* Adding object store plugin for Rucio
  (thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
  `Pull Request 17156`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17157`_
* Don't require admin user to list ``/api/tool_data``
  (thanks to `@jozh2008 <https://github.com/jozh2008>`__).
  `Pull Request 17161`_
* Much simpler default dataset permissions for typical users
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17166`_
* Add future=True flag to SA engine
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17174`_
* Add future=True flag to SA session
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17179`_
* Clarify the meaning of lexical sorting of discovered datasets
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17190`_
* Accept any number of arguments to the secret decoder ring
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 17191`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17201`_
* Vueifiy History Grids
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17219`_
* Improve links to Hub, Matrix and WGs in ``CONTRIBUTING.md``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17221`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17230`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17235`_
* Workflow node connector improvements
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17240`_
* Workflow node connector improvements followup
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17244`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17247`_
* Add History Multiview activity+panel, add "Show Recent" mode to multiview
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17251`_
* Add OIDC backend configuration schema and validation
  (thanks to `@uwwint <https://github.com/uwwint>`__).
  `Pull Request 17274`_
* Adds delete, purge and undelete batch operations to History Grid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17282`_
* Fix any type for tool_data_file_path
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17293`_
* Add ``__KEEP_SUCCESS_DATASETS__``
  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
  `Pull Request 17294`_
* Make Workflow Editor Toolbar Toggleable
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17297`_
* Adjust  Flex Panel Drag Handle and Collapse Button
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17298`_
* New Activity bar - Notifications
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17300`_
* Fix s3fs templating
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 17311`_
* Document SQLAlchemy session lifespan
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17322`_
* Add documentation for data source tool
  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
  `Pull Request 17327`_
* Custom Multiselect
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17331`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17333`_
* Unify continuous polling with composable
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17355`_
* Add element_identifier and ext to inputs config file export
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17357`_
* Add name_eq and genome_build_eq filters to HistoryFilters
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17389`_
* Cancel all active jobs when the user is deleted
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17390`_
* Some additional typing for test interactor stuff
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17398`_
* Allow removing last value from multi select field
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17403`_
* Enable comments in package dag file
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17408`_
* Purge `groups` and `roles` from DB (for real)
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17411`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17420`_
* Add signpost to training material
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17421`_
* UI for "relocating" a dataset to a new object store (when safe)
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17437`_
* Freeze (make sticky) header row in tabular files
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 17455`_
* Move Activity Bar Settings to Activity
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17457`_
* Move Visualizations Activity to Side Panel
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17458`_
* Allow filtering history datasets by object store ID and quota source
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17460`_
* Update release process documentation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17461`_
* Use short link for TPV shared database
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17467`_
* `data_column` parameter: use `column_names` metadata if present
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17478`_
* Type annotation and refactoring of tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17484`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17486`_
* Consolidate resource grids into tab views
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17487`_
* Update k8s docker python to 3.12
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17494`_
* Add multiple drag/drop and keyboard accessible selection to `HistoryPanel` items
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17502`_
* Add gxadmin to docker and update branch
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17521`_
* Enable workflow buttons right click
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17529`_
* Workflow list small tweaks
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17538`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17541`_
* Remove virtual scroller from History
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17546`_
* Add `image_diff` comparison method for test output verification using images
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17556`_
* Add shm_size based on ShmSize
  (thanks to `@richard-burhans <https://github.com/richard-burhans>`__).
  `Pull Request 17565`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17580`_
* Add migrations revision identifier for 24.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17589`_
.. small_enhancement

* Drop release notes webhook
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17675`_
* Port invocation API to fastapi
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 16707`_
* SQLAlchemy 2.0 upgrades (part 5)
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16932`_
* Python 3.8 as minimum
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 16954`_
* Migrate groups API to fastAPI
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 17051`_
* Remove web framework dependency from tools
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17058`_
* Migrate job destination parameters store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17119`_
* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path"
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17122`_
* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17132`_
* Migrate dataset extra files store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17145`_
* Add simpleKeyStore composable
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17148`_
* Remove legacy tool versions list from admin panel
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17155`_
* Convert dataset path destination store to composable
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17175`_
* Replace discouraged Mambaforge with Miniforge3
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17177`_
* Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17184`_
* Migrate workflow invocation store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17203`_
* Vendorize fastapi-utls.cbv
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17205`_
* Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17216`_
* Reuse test instance during non-integration tests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17234`_
* Refactor two of the missing invocation routes to FastAPI
  (thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
  `Pull Request 17237`_
* Build and cache galaxy client for selenium and startup tests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17239`_
* Migrate models to pydantic 2
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17262`_
* Improve ModelManager type hints
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17299`_
* Scoped Store Refactor and Store Composition Refactor
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17304`_
* Port HistoryPanel component to composition API and typescript
  (thanks to `@Renni771 <https://github.com/Renni771>`__).
  `Pull Request 17318`_
* Remove remaining Vuex stores and dependencies
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17348`_
* History refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17353`_
* Convert entryPointStore to composition API + TS
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17356`_
* Remove unused statements in job search function
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17361`_
* Enable ``warn_unreachable`` mypy option
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17365`_
* Fix type annotation of code using XML etree
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17367`_
* Combines legacy qv-pattern and advanced filter pattern in history index endpoint
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17368`_
* Add explicit cache_ok attribute to JSONType subclass
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17376`_
* More specific type annotation for ``BaseJobExec.parse_status()``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17381`_
* Update to black 2024 stable style
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17391`_
* Refactor MarkdownDialog.vue to ts+composition
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17399`_
* Update current version to 24.0.dev0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17402`_
* Removes outdated Grid controller and backbone modules
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17434`_
* Modernize bits and pieces of storage display
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17436`_
* Refactor Common components
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17441`_
* Adds published histories to grid list
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17449`_
* Refactor Workflow API routes - Part 1
  (thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
  `Pull Request 17463`_
* Citation refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17483`_
* Refactor Workflow Import components
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17495`_
* Removes legacy history xml makos
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17505`_
* Remove legacy phyloviz, circster and sweepster artifacts
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17573`_


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

.. major_bug


.. bug_tag_viz

* Fix for fits_image_viewer visualization plugin
  (thanks to `@francoismg <https://github.com/francoismg>`__).
  `Pull Request 17002`_
.. bug_tag_datatypes

* Fix for converter tests
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17188`_
* Correct dbkey for minerva display app
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 17196`_
.. bug_tag_tools

.. bug_tag_workflows

* Make WorkflowInput label, value and uuid optional
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17638`_
* Prevent 500 for anon /api/invocations
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17640`_
* Fix step type serialization for StoredWorkflowDetailed models
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17716`_
* Fix input parameter step type
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17767`_
* Fix ``include_nested_invocations`` parameter use
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17768`_
* Fix change_datatype PJA for dynamic collections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17803`_
* Render Useful Markdown Components for Mapped Over Steps
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17198`_
* Fix invocation serialization if no state was set
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17278`_
* Fix workflow report markdown editor toolbox becoming non-responsive
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17427`_
* Workflow anonymous user buttons
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17537`_
.. bug_tag_ui

* Fix typescript warning for grid list operation
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17065`_
* Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17115`_
* Bump yaml from 2.1.1 to 2.3.4 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17125`_
* Bump follow-redirects from 1.15.1 to 1.15.4 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17260`_
* Bump undici from 5.26.5 to 5.28.3 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17485`_
.. bug_tag_jobs

* Ignore user data table errors for now
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17880`_
* Also set extension and metadata on copies of job outputs when finishing job
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17777`_
.. bug_tag_admin

* Optional Reply-to SMTP header in tool error reports
  (thanks to `@neoformit <https://github.com/neoformit>`__).
  `Pull Request 17243`_
.. bug

* Fix tool panel loading delay
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17847`_
* Fix archived histories mixing with active in histories list
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17856`_
* Minor refactor of query building logic for readability
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17835`_
* Fix help forum integration uses long ID
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17844`_
* Embed fix
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17852`_
* Embed download fix
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17861`_
* Wait for config to load with user prefs options
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17865`_
* Fix bugs relating to history keyboard navigation
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17587`_
* Fix ``test_oidc_login_existing_user`` test
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17612`_
* Increase ContentItem clickable area
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17621`_
* Do not link to invocations for workflow that has never run
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17626`_
* Add basic model import attribute validation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17628`_
* Make latest_workflow_uuid optional
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17629`_
* More efficient change_state queries, maybe fix deadlock
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17632`_
* Fix tool panel workflow and favorites button bugs
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17634`_
* Default sort all grid histories the same
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17635`_
* Fix workflow person validation
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17636`_
* Fix DataResult type
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17639`_
* Don't fail for anon /api/users request
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17645`_
* Don't index tasks without task_uuid
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17646`_
* Fix history panel arrow navigate by id bug, add `HistoryOperations` to `HistoryView` and prevent item selection in unowned histories
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17648`_
* Fix shared item details and initial filters
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17651`_
* Fix history filters taking up space in `GridList`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17652`_
* Fix syntax for SA2.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17663`_
* Grid filtering bug fixes
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17684`_
* Purge history from history panel
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17685`_
* Fix contentitem display routing.
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17687`_
* Workflow Comment Indexing
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17700`_
* Fix incorrect history item count in histories lists
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17714`_
* Improve published histories listing performance in UI
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17717`_
* Fix archived histories tab anonymous access
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17719`_
* Fix Collection Scrolling not showing all items
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17720`_
* Fix Workflow Name Display in `WorkflowCard` to Prevent Bleeding Over Borders
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17721`_
* Always display grid pagination on the right
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17722`_
* Fix histories API index_query serialization
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17726`_
* Fix source history update_time being updated when importing a public history
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17728`_
* Handle missing indexer for a dataset
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17736`_
* Fix overflowing and hiding of storage popovers
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17742`_
* Revise language around non-private object stores
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17744`_
* Fix tag sorting
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17753`_
* Datasets list anonymous access and history link fixes
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17756`_
* Fix usage of DISTINCT
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17759`_
* Prevent dragover for item from same history in history panel
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17761`_
* Improve Shift+Click select in history panel and add it for `ContentItem` selector checkboxes as well
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17762`_
* Don't require history to calculate anon disk usage
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17765`_
* Fix anon user values again
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17772`_
* Add missing fields in histories listings
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17775`_
* Fix anonymous user create, run and import workflows
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17776`_
* Use ``hg clone --stream`` to clone repos
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17786`_
* Avoid showing a shareable URL with the default slug/username
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17788`_
* Swap history dropdown from using the tiny caret to faBars.
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17791`_
* Fix visualization activity plugin list images
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17792`_
* Defer job attributes that are usually not needed
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17795`_
* Fix new default history creation when in remote or single user mode
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17796`_
* Return published histories first in display_by_username_and_slug
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17808`_
* Show full Data menu when in single user mode
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17815`_
* Remove link to non existent page from Data menu
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17816`_
* Simplify nested collection joins
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17817`_
* Fix very slow user data table query
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17830`_
* Fix optional types in Help Forum API
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17832`_
* Update db revision 24.0 release tags
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17834`_
* Update tour testing selector usage
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 14005`_
* Enhance Global Drag-and-Drop feature for Upload component
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 16995`_
* Add history items display state for collections/lists with failed or new populated_state
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16996`_
* Enhancement to Tool Form page, Repeating form fields implement parameter instructions
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 17018`_
* Prevent excessive `api/tool_panels` calls by keeping views in store
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17039`_
* Allow relative URLs in broadcasts action links
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17042`_
* xsd: reorder choices for permissive boolean
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17187`_
* Update DatasetError.vue to fix broken link
  (thanks to `@jennaj <https://github.com/jennaj>`__).
  `Pull Request 17193`_
* Reload built-in converters on toolbox reload
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17209`_
* tus wants a json response from v2.0.0
  (thanks to `@mira-miracoli <https://github.com/mira-miracoli>`__).
  `Pull Request 17246`_
* Add missing re-usable commit-id output
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17248`_
* Allow for upper case container tags
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17254`_
* Fixes for output discovery
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17266`_
* Fix Workflow Comment Model for Pydantic 2
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17296`_
* Package tests fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17301`_
* Follow-up on `#17274 <https://github.com/galaxyproject/galaxy/issues/17274>`__ and `#17262 <https://github.com/galaxyproject/galaxy/issues/17262>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17302`_
* LDAP3 fix for attributes returned as strings
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17305`_
* Fix quotas ID encoding
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17335`_
* Fixes for flake8-bugbear 24.1.17
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17340`_
* Fix model store exports that include implicit conversions.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17346`_
* Escape pipe character in tool XSD docs
  (thanks to `@neoformit <https://github.com/neoformit>`__).
  `Pull Request 17359`_
* XSD schema doc building: quote pipe characters in attribute tables
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17364`_
* Fix minor oidc_backends_config comment bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17385`_
* Fix activity-settings hidden behind left side panel bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17392`_
* Fix z-index in BroadcastContainer.vue
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17401`_
* Fix IUC best practices links, mention data_source_async in XSD
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 17409`_
* Fix data_source and data_source_async bugs
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 17422`_
* Only check access permissions in ``/api/{history_dataset_collection_id}/contents/{dataset_collection_id}``
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17444`_
* More defensive access of extra props in filesources
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17445`_
* Fix `datasetStore.saveDatasets` bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17448`_
* Fix text to match options in HistoryStorageOverview
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17450`_
* Add tool XML schema documention for outputs - collection - data
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17465`_
* Fix for a regression change - auto-select/highlight file name text
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 17466`_
* Exclude password reset link from login form where users don't have the ability to manage accounts
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17473`_
* has_size assertion: implement size (as synonym for value)
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17490`_
* Stringify cgroups metrics formatted value return
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17520`_
* Fix ``test_index_advanced_filter`` API test re-running
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17547`_
* Change default milestone to target 24.1
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17549`_
* Drop plugin-based new user welcome
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17568`_
* Apply default theme to theme selector
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17583`_

.. include:: 24.0_prs.rst