.. to_doc

23.2
===============================

.. announce_start

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

.. major_feature


.. feature

* Initial release notes  for 23.2
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17259`_
* Make form repeat blocks reorderable
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 14892`_
* Tool Shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 15639`_
* Limit number of celery task executions per second per user
  (thanks to `@claudiofr <https://github.com/claudiofr>`__).
  `Pull Request 16232`_
* Notifications admin panel
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 16278`_
* Add Invenio RDM repository integration
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16381`_
* Add new cns, cnr and cnn datatypes (cnvkit tools)
  (thanks to `@khaled196 <https://github.com/khaled196>`__).
  `Pull Request 16503`_
* Create reusable `FilterMenu` with advanced options
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16522`_
* Support new genome browser chain file format
  (thanks to `@claudiofr <https://github.com/claudiofr>`__).
  `Pull Request 16576`_
* Workflow Comments 💬
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16612`_
* Create `GDateTime` component
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 16622`_
* History MultiView drag-drop on history picker creates new history
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16644`_
* Workflow Embed
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16657`_
* Add EGI Check-in as OIDC authentication option
  (thanks to `@enolfc <https://github.com/enolfc>`__).
  `Pull Request 16782`_
* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including
  Podman job_conf
  (thanks to `@sveinugu <https://github.com/sveinugu>`__).
  `Pull Request 16795`_
* Galaxy help forum integration
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16798`_
* Allow to permanently delete non-deleted items in Storage Dashboard Visualizations
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16944`_
* Allow switching histories from Storage Dashboard Visualizations
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16945`_
* Add support for larch datatypes
  (thanks to `@patrick-austin <https://github.com/patrick-austin>`__).
  `Pull Request 17080`_
.. enhancement_tag_viz

.. enhancement_tag_datatypes

* Implement display function for all datatypes
  (thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
  `Pull Request 15447`_
* Add stl datatype
  (thanks to `@TanguyGen <https://github.com/TanguyGen>`__).
  `Pull Request 16478`_
* Bump samtools converters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 16668`_
* Add docx datatype
  (thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
  `Pull Request 16713`_
* Optimize object store cache operations
  (thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
  `Pull Request 17025`_
.. enhancement_tag_tools

* Update cellxgene interactive tool to 1.1.1
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 15313`_
* Update interactivetool_mgnify_notebook to v1.2.2
  (thanks to `@SandyRogers <https://github.com/SandyRogers>`__).
  `Pull Request 16517`_
* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16739`_
.. enhancement_tag_workflows

* Implement default locations for data and collection parameters
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 14955`_
* Delete non-terminal jobs and subworkflow invocations when canceling invocation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16252`_
* Make it obvious that `WorkflowInvocationStep` is clickable/expandable
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16507`_
* Galaxy Markdown - add workflow image and license to Galaxy markdown
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16672`_
* Implement instance URLs in Galaxy markdown
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16675`_
* Improve invocation error reporting
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16917`_
* Remove "Create Workflow" form and allow workflow creation in editor
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16938`_
* Fix invocation report to target correct workflow version
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17008`_
* Require name for workflows on save, set default to Unnamed Workflow
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17038`_
.. enhancement_tag_ui

* Client import sorting
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16345`_
.. enhancement_tag_jobs

* Enable job resubmissions in k8s runner
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 15238`_
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy Core usage)
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16264`_
* Add HEAD route to job_files endpoint
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17072`_
.. enhancement_tag_admin

* Add carbon emissions admin configuration options
  (thanks to `@Renni771 <https://github.com/Renni771>`__).
  `Pull Request 16307`_
* Augment pgcleanup to allow periodically deleting old datasets
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16340`_
* Support configuring job metrics inline, update documentation
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 17178`_
.. enhancement

* Make release titles consistent
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17341`_
* Use python-isal for fast zip deflate compression in rocrate export
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17342`_
* Improve embed performance
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17326`_
* Add parameter name to validation errors
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 15440`_
* Add framework test for profile behavior of `format="input"`
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 15482`_
* Add ability to assert metadata properties on input dataset parameters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 15825`_
* Vueify _fieldDialog
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 16236`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16305`_
* Add Python string formatting best practices
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16312`_
* Migrate a part of the users API to FastAPI
  (thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
  `Pull Request 16341`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16360`_
* Exclude auto-generated schema file from labeler
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16378`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16389`_
* Update carbon emissions methodology page to match current feature specifications
  (thanks to `@Renni771 <https://github.com/Renni771>`__).
  `Pull Request 16392`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16409`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16436`_
* Vueify Data Uploader
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 16472`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16485`_
* Add support for CILogon deployments in different regions than the US
  (thanks to `@uwwint <https://github.com/uwwint>`__).
  `Pull Request 16490`_
* Published Workflow Sharing page overhaul
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16510`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16521`_
* Tweak tool memory use and optimize shared memory when using preload
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16536`_
* Document that required text parameters need a validator
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 16538`_
* Make tool id searchable in side panel search
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16543`_
* Add uploader test cases, consolidate payload processing
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 16554`_
* Implement datatype upload warnings
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16564`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16577`_
* Vueify Tool Form Data Selector
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 16578`_
* Run eslint autofix as a part of client format when using Makefile
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16586`_
* Add scroll pagination and username filter to `HistoryPublishedList`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16642`_
* Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16649`_
* cwl testing: use the proposed 1.2.1 CWL conformance tests
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 16658`_
* Clarify documentation on how to build a job runner
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16665`_
* Enhance disk quota usage summary
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16670`_
* Include `regex` when linting validators
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16684`_
* Change Sentry error reporting plug-in
  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
  `Pull Request 16686`_
* Use fs.onedatarestfs for Onedata files source plugin implementation
  (thanks to `@lopiola <https://github.com/lopiola>`__).
  `Pull Request 16690`_
* Skip node installation for ``check_indexes`` tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16694`_
* Migrate `collection elements` store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16725`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16735`_
* Improve collection items scrolling
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16738`_
* Don't copy collection elements in ``test_dataset_collection_hide_originals``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16747`_
* Selective bold text
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 16748`_
* Workflow report enhancement: add time format to generated text
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 16757`_
* Workflow report enhancement: convert ISO to UTC for invocation date/time
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 16758`_
* Workflow report enhancement: expose workflow version as workflow checkpoint
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 16760`_
* Replace ELIXIR AAI button with Life Science login
  (thanks to `@sebastian-schaaf <https://github.com/sebastian-schaaf>`__).
  `Pull Request 16762`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16770`_
* Add ClientSearchMiss Sentry capture
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16789`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16807`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16853`_
* Visually indicate currently viewed/edited dataset
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16859`_
* Allow partial matches in workflow name tag search and search all tags for unquoted query
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16860`_
* Vueify visualizations grid
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 16892`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16896`_
* Remove record access handling for Invenio RDM plugin
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16900`_
* Test link data with extended metadata
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16921`_
* Publish Tool Shed frontend to npm
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16924`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16939`_
* Adds `biii` as supported xref reference type
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 16952`_
* Remove sentry.py from mypy exclusions
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16959`_
* Enhance Invenio RDM integration
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16964`_
* Allow non-optional integer/float params without value attribute
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16966`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 16978`_
* Update API tool_panels route conditions
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16991`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17011`_
* Restyle Vue multiselect and adapt option order
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17015`_
* Show current tool panel view name on top of tool panel
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17021`_
* Change broadcast notifications style
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17032`_
* Open `HistoryStorageOverview` in center panel from `HistoryPanel`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17043`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17050`_
* Enhance xsd schema and allow simpler assertion lists
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17134`_
* Disable workflow report and generate PDF buttons unless workflow is successful
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 17149`_
* Add rerun and show details buttons in expanded collection
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17182`_
.. small_enhancement

* Ensure release notes include all PRs added during the freeze by re-running the release note bootstrapping
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17344`_
* Tool Shed client build separation
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 15000`_
* Migrate cloud API to FastAPI
  (thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
  `Pull Request 16296`_
* Drop (admin only) userskeys controller
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16318`_
* Migrate some Remote Files Export components to composition API + TS
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16391`_
* Standardize, lint vue component name casing
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16398`_
* Refactor FilesDialog services to use Fetcher
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16414`_
* Refactor FilesDialog + Remote Files API schema improvements
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16420`_
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy ORM usage in /test)
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16431`_
* SQLAlchemy 2.0 upgrades to ORM usage in /lib
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16434`_
* Force makefile client targets to use .venv-shipped node if it exists
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16462`_
* Rename MetadataEqualsValidator
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 16489`_
* Refactor/OIDC custos
  (thanks to `@uwwint <https://github.com/uwwint>`__).
  `Pull Request 16497`_
* Migrate configuration store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16514`_
* Scope Workflow Stores to Workflow ID
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16523`_
* Move database access code out of ``galaxy.util``
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16526`_
* Drop syncConfigToGalaxy
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16562`_
* Switch out conditional requirement parser
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16636`_
* Fix flaky test timing issue in DiskUsageSummary component
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16685`_
* Enhance task monitor composable
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16695`_
* Migrate `dataset` store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16709`_
* Enhance Short Term Storage Composable
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16711`_
* Misc. edits/refactorings to session handling
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16712`_
* SQLAlchemy 2.0 upgrades (part 2)
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16724`_
* Reset autocommit to False
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16745`_
* Migrate `collection attributes` store to Pinia
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16752`_
* Drop legacy server-side search
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16755`_
* Optimize iteration in DatasetInstance model + SA2.0 fix
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16776`_
* Migrate a part of the jobs API to FastAPI
  (thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
  `Pull Request 16778`_
* Replace file_name property with get_file_name function
  (thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
  `Pull Request 16783`_
* SQLAlchemy 2.0 fixes for TS2.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16791`_
* Another batch of SQLAlchemy 2.0 edits in TS 2.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16799`_
* Use vue modal instead of global backbone modal in user preferences
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 16830`_
* Another batch of SQLAlchemy 2.0 edits in TS 2.0 (part 3)
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16833`_
* Remove remaining legacy backbone form input elements
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 16834`_
* Adjust tz inclusion in workflow reports
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16835`_
* Refactor dataset services
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16839`_
* Refactor client API packages
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16847`_
* SQLAlchemy 2.0 upgrades (part 4)
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16852`_
* Update client dependencies
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16867`_
* Convert `historyItemsStore` to ts+composition
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16873`_
* Drop unused HistoryContentManager code and related tests
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16882`_
* Bump undici from 5.19.1 to 5.26.5 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 16897`_
* Enable some flake8-logging-format rules in ruff
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16915`_
* Fix import in historyItemsStore.ts
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16916`_
* Change `api/tool_panel` to `api/tool_panels/...`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16928`_
* Standardize to W3C naming for color
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16949`_
* Add helper to get dataset or collection via ``src`` and ``id``
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 16953`_
* Move and re-use persist_extra_files
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16955`_
* Upgrade job manager's index_query method to SA2.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17020`_
* Remove eventHub custom module, swap to appropriate alternatives
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17037`_


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

.. major_bug


.. bug_tag_viz

* Fix and update visualization plugins
  (thanks to `@mahendrapaipuri <https://github.com/mahendrapaipuri>`__).
  `Pull Request 16119`_
* Allow the legacy DELETE dataset endpoint to accept any string for the history_id
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 16593`_
.. bug_tag_datatypes

* MINERVA display application: enable cors, add for tabular datasets
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 16737`_
* Prep for updated h5py
  (thanks to `@mr-c <https://github.com/mr-c>`__).
  `Pull Request 16963`_
* Update tar_to_directory dependency
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17009`_
* Fix display application link generation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17227`_
* Display application fixes and tests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17233`_
.. bug_tag_tools

* Add back 1.1.0 version of Filtering1 tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16883`_
* Add missing requirements to perl tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16763`_
* Fix typos across code base
  (thanks to `@afuetterer <https://github.com/afuetterer>`__).
  `Pull Request 16851`_
* Fix missing grep input in sort1 tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16910`_
* Fix maf_thread_for_species.py
  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
  `Pull Request 16971`_
* Fix duplicated tools in tool panel view section copying
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17036`_
.. bug_tag_workflows

* Fix ``to_cwl`` for nested collections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17276`_
* Fix workflow output display without label
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16749`_
* Fix up local tool version handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16836`_
* Fix safe update version handling in run form
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16865`_
* Fix workflow import losing tool_version
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16869`_
* Remove more flushes in database operation tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16875`_
* Include owner's annotation when exporting workflow
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16930`_
* Skip change_datatype things if we're not actually changing the extension
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16931`_
* Add execute back to published workflows list
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16934`_
* Skip state filtering in ``__MERGE_COLLECTION__`` tool
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16937`_
* Prevent workflow submission with missing input values
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17048`_
.. bug_tag_ui

* Replace Persistedstate Pinia Plugin with User-Scoped Composable
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16371`_
* Bump tough-cookie from 4.1.2 to 4.1.3 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 16385`_
* Bump semver from 5.7.1 to 5.7.2 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 16388`_
* Bump word-wrap from 1.2.3 to 1.2.4 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 16417`_
* Bump @babel/traverse from 7.18.11 to 7.23.2 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 16874`_
* Client publication
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16999`_
* Upgrade axios to 1.6.2
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17053`_
* Ensure that plugin build hash actually has a git hash to compare with otherwise force rebuild
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17104`_
.. bug_tag_jobs

* Rollback invalidated transaction
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17280`_
* Rollback invalidated transaction: catch them earlier
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17312`_
* Ensure Job belongs to current SQLAlchemy session
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16647`_
* Fix and prevent persisting null file_size
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16855`_
* Fix tag ownership check
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16877`_
* Ruff and flake8 fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16884`_
* Fix unbound ``runner`` variable when there is an error in the job config
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16906`_
* Assert that ``DatasetCollectioElement`` has an associated object
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17071`_
* Remove rollback from ``__check_jobs_at_startup``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17085`_
* Fix cardinality violation error: subquery returns multiple results
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17224`_
.. bug_tag_admin

* Fix: serialize `tool_shed_urls` directly from the API
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16561`_
* Change log level for duplicate data table entries to warning
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16988`_
* Quote singularity env parameters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17055`_
.. bug

* Write to a temp filename in posix file source plugin
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 17350`_
* Always store multi select data input values in fixed order
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17352`_
* Remove duplicates when copying sections for tool panel view
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17117`_
* Tagging component performance improvements
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17253`_
* Always copy datasets in collection builder modals
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17268`_
* Install newer celery on python 3.8+
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17309`_
* Backport Rollback invalidated transaction: catch them earlier
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17315`_
* Discard SQLAlchemy session after task completion
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17317`_
* Scope session for job  runner monitor loop
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17319`_
* Fix subworkflow edit button
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17330`_
* Disable verbose parso logging in db_shell.py
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16410`_
* Fix SQLAlchemy 2.0 syntax in scripts/helper.py, fix ancient bug
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16425`_
* Pin fs.dropboxfs to >=1
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 16451`_
* Fix labeler for UI UX labels
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16456`_
* Never consider `_galaxy_` conda env as unused
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 16460`_
* Adjust test_data_download method in GalaxyInteractorApi so an admin user is not required
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 16482`_
* Test that object store cache file gets updated
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16493`_
* Remove unnecessary check: item cannot be None
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16550`_
* Rename to_dict to populate in FormDefintion to fix bug
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16553`_
* Run poetry under Python 3.8
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16638`_
* Fix dependency update GitHub workflow
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16639`_
* Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 16659`_
* Update build_a_job_runner.rst
  (thanks to `@maikenp <https://github.com/maikenp>`__).
  `Pull Request 16673`_
* Fix notifications icon not showing in Masthead
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16679`_
* Fix package version handling for initial minor releases
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16743`_
* Account for shared usage between TS and galaxy apps
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16746`_
* Fix large gap between labels and form elements
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16753`_
* Add deprecation notice for api/search
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16756`_
* Don't allow empty selection on required select field
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16759`_
* Fix public archived histories not importable
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16766`_
* Provide specific example for API docs - tags
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 16769`_
* Fix ItemOwnerShipException in tag removal
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16773`_
* Initial bug fixes for Tool Shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16787`_
* Fix short ids in tool panel views.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16800`_
* Use AlignedSegment.to_string
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16803`_
* Move the email and username redacting from the role loop
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 16805`_
* Move history and tool panel tooltips out of the way
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 16808`_
* Fix tool panel views for versionless tool ids
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16809`_
* Fix duplicate key eslint error
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16810`_
* Fix shed unit test
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16811`_
* Fix collection drilling
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16819`_
* Fix parameter display in job info page for tools with sections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16821`_
* Tool Shed 2.0 fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16825`_
* Fix workflow preview display if tool state does not contain all parameter values
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16829`_
* Specify uid for the k8s image
  (thanks to `@afgane <https://github.com/afgane>`__).
  `Pull Request 16844`_
* Exclude on_opened and on_closed from watcher events
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16850`_
* Allow referring to steps by label only in markdown editor
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16861`_
* Restore ToolsApi and create new api route for new panel structure
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 16872`_
* Fix delete collection + elements
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16879`_
* Fix join condition for nested collection query
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16880`_
* Fix bug in SQLAlchemy statement
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16881`_
* Fix bug in SQLAlchemy statement: desc() applied to column, not statement
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16887`_
* Update help in relabel_from_file.xml
  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
  `Pull Request 16891`_
* Fix link to mercurial tip in Tool Shed 2.0
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16895`_
* Fix type annotation of ``lib/tool_shed/test/functional/``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16901`_
* Fix navigation error in Tool Shed tests
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16902`_
* Fix subtle bug in listify function + simplify list munging
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 16904`_
* Provide error message instead of internal server error
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16905`_
* Fix selenium selector for Workflow Run warnings
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16908`_
* Fix GQL infinite scrolling in Tool Shed
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16914`_
* Fix library import from path linking files
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16919`_
* Fix discarded dataset ordering in Storage Dashboard
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 16929`_
* Fix select parameter doesn't show parameter name in UI
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 16942`_
* Backport Fix select parameter doesn't show parameter name in UI
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16943`_
* Don't store job in JobIO instance attributes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 16965`_
* Workaround issue in Routes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 16981`_
* Fix rendering of an empty page
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16985`_
* Empty page render fix - backport
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16992`_
* Fixes for job metrics Galaxy markdown component
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 16994`_
* Fix copying metadata to copied job outputs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17007`_
* Upgrade minimum conda to be compatible with latest conda-build
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17013`_
* Fix filtering of active broadcasts for admins
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17049`_
* Use debounce instead of timeout utility
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17057`_
* Disable conda_auto_init in embedded pulsar test cases
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17061`_
* Fix testing of the galaxy-tool-shed package
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17062`_
* Make job state param optional again
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17077`_
* Fix input dates in notifications: consider timezone offset
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17088`_
* Allow relative URLs in broadcasts action links
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17093`_
* Fix web_apps dependencies
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17099`_
* Implement missing upload for S3 file sources
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17100`_
* Set correct tool_path for packaged galaxy
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17102`_
* Expose file_name property in DatasetFilenameWrapper
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17107`_
* Fix hid/elementindex for collection displays
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17110`_
* Tool panel views overflow bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17112`_
* Disable admin notifications management if notifications are disabled in config
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17114`_
* Add missing optional description field, fixes ephemeris data library example
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17116`_
* Fix CSS issue affecting all dropdown menus
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17124`_
* Fix job search when ``command_version`` is None
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17129`_
* Assert that tus uploader instance has URL
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17133`_
* Make payload optional again for create tag API
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17144`_
* Fix select option appears for single select
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17146`_
* Add support for Cgroupsv2
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 17169`_
* Fix workflow index total matches counting
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17176`_
* Fix job destination extra params
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17186`_
* Fix tools missing in panel bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17192`_
* Fix Multiselect in BModal overflows out of view bug
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17197`_
* Remove `SingleItemSelector` deselect label, fix history filters hidden on smaller screen
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17199`_
* Fix `url_for` in tool error reports
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17210`_
* Fix `ToolSearch` bug for `StaticToolPanelView`s
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17213`_
* Fix categories in ToolShed repo create API
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17218`_
* Fix job parameter display
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17226`_
* Fix User.current_galaxy_session
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17232`_
* Separate collection and non-collection data element
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17236`_

.. include:: 23.2_prs.rst