.. to_doc

24.1
===============================

.. announce_start

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

.. major_feature


.. feature

* Release notes
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18218`_
* Implement a page object accessibility dialog
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17225`_
* Enable all-vs-all collection analysis patterns
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17366`_
* Visualizing workflow runs with an invocation graph view
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17413`_
* Enables activity bar by default
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17531`_
* Add onedata objectstore
  (thanks to `@bwalkowi <https://github.com/bwalkowi>`__).
  `Pull Request 17540`_
* Add content assertion XML tags for test output verification using images
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17581`_
* Workflow editor item selection
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17615`_
* Workflow editor undo/redo
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17774`_
* Enable managing object store usage within a history.
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17853`_
* Add `email` notifications channel
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17914`_
* Script for deleting userless histories from database + testing + drop unused model testing code
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18079`_
* Add Net datatype
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 18080`_
* Overhaul Azure storage infrastructure
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18087`_
* Empower users to bring their own storage and file sources
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18127`_
* More unit testing for object store stuff
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18136`_
* Add an Invocations Panel for the Invocations activity
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18137`_
.. enhancement_tag_viz

* Update parcel-built visualizations to use parcel v2
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18311`_
.. enhancement_tag_datatypes

* Tighten axt sniffer
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 18204`_
* 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`_
* Add colabfold tar file datatype
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 17567`_
* Set minimal metadata also for empty bed datasets
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 17586`_
* Add support for additional media types
  (thanks to `@arash77 <https://github.com/arash77>`__).
  `Pull Request 18054`_
.. enhancement_tag_tools

* Backport Qiskit Jupyter Notebook update to 24.1
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 18310`_
* Rename JupyTool to something more searchable (i.e. JupyterLab which includes the substring Jupyter)
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 17849`_
.. enhancement_tag_workflows

* Allow running and editing workflows for specific versions
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18378`_
* Update labels in Markdown editor when workflow labels change
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17863`_
* Add galaxy to user agent
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18003`_
.. enhancement_tag_ui

* Add vue sentry integration
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18120`_
.. enhancement_tag_jobs

* Only include tool stdout/stderr in HDA info
  (thanks to `@natefoo <https://github.com/natefoo>`__).
  `Pull Request 16730`_
* Fix boto3-stubs typecheck dependency
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18173`_
.. enhancement_tag_admin

* Add some admin facing docs on data tables
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17585`_
* Make urgent notifications mandatory
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17975`_
* Add middleware for logging start and end of request
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18046`_
.. enhancement

* Backport `#18197 <https://github.com/galaxyproject/galaxy/issues/18197>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18212`_
* Drop restriction to switch to immutable histories
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18234`_
* Allow bookmarking public workflows
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18247`_
* More structured indexing for user data objects
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18291`_
* Display error message if not an image in reports
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18309`_
* Add copy link to published workflow in `WorkflowCard`
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18370`_
* Onedada object store and files source stability fixes
  (thanks to `@bwalkowi <https://github.com/bwalkowi>`__).
  `Pull Request 18372`_
* Persistent toggle sections of job info
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 16983`_
* Enable storage management by object store
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17500`_
* Automatically bind `galaxy_data_manager_data_path` in containers
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17596`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17653`_
* Tool linter: check for valid bio.tools entries
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17655`_
* Tool linter: check for leaf nodes with unstripped text content
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17656`_
* Addition of release process doc
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17680`_
* Issue `#17631 <https://github.com/galaxyproject/galaxy/issues/17631>`__: Make it possible to use custom invfile.lua if needed
  (thanks to `@martin-g <https://github.com/martin-g>`__).
  `Pull Request 17693`_
* Add browser and operating system info to issue template
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17696`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17764`_
* SQLAlchemy 2.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17778`_
* Add support for floating point TIFF files in verification of image-based tool outputs
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17797`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17819`_
* Add tool linting for valid EDAM terms
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17839`_
* Add `pin_labels` attribute for `image_diff` comparison method
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17866`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17870`_
* Add admin activity to activity bar
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17877`_
* Disable published item copy button when editing slug
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17888`_
* Outline use of type_annotation_map to fix mypy issues
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17902`_
* Do not save workflow on Run without user confirmation
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17907`_
* Update config docs about Celery
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17918`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17923`_
* Adds pages to the activity bar
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17925`_
* Revises visualizations activity
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17931`_
* Error reporting unit tests
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17968`_
* Update _thanks.rst in the User Release Notes to include new socials and remove inactive ones
  (thanks to `@natwhitaker <https://github.com/natwhitaker>`__).
  `Pull Request 17971`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 17982`_
* Add tags to data dialog display, restores update_time and extension columns
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17992`_
* Reduce notifications polling frequency
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18010`_
* Consolidate Visualization container, avoid using default iframe
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18016`_
* Document syntax for accessing nested parameters in `change_format` - `when` tags
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18018`_
* Add Zenodo integration
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18022`_
* Add a button that filters out a tool section in the tool panel
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18034`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18035`_
* Add datasets/collections filter to history panel filters
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18039`_
* Add pagination support to Files Source plugins
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18059`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18063`_
* Add Attributes section to Edit Collection view as well
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18071`_
* Enhance form drilldown
  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
  `Pull Request 18074`_
* Change `InvocationsList` into a grid using `GridList`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18088`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18095`_
* Workflow preview improvements
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18108`_
* Drop "?" (Help) from DatasetActions list
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18124`_
* Update Python dependencies
  (thanks to `@galaxybot <https://github.com/galaxybot>`__).
  `Pull Request 18125`_
* Revises handling of warnings in the workflow run form
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18126`_
* Display DOIs in Archived Histories
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18134`_
* Update s3fs dependency
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18135`_
* Harden User Object Store and File Source Creation
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18172`_
* Move activity panel go to button to top
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18182`_
* Update db revision 24.1 release tags
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18183`_
* Play nice with password managers
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 18206`_
.. small_enhancement

* Remove deprecated BCO export endpoint
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 16645`_
* Login components refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17564`_
* Collections common refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17571`_
* Modernization and cleanup of job state related client code
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17593`_
* Type annotation improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17601`_
* Type annotation and CWL-related improvements
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17630`_
* Collection components refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17647`_
* Code cleanups from ruff and pyupgrade
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17654`_
* Activity bar preference handling fixes
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17701`_
* Datasets refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17799`_
* Consolidates data dialog components
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17802`_
* Dataset information refactors
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 17804`_
* Mailing list wording tweaks
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17867`_
* Model edits and bug fixes
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17922`_
* Fix client types around history items
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17924`_
* Model typing and SA2.0 follow-up
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17958`_
* Use typed API client for reporting job errors
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17969`_
* Drop unused workflow controller methods
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17974`_
* Enable ``warn_unused_ignores`` mypy option
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17991`_
* Refactor convert HistoryExport component to Typescript
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18028`_
* More typing in galaxy.files
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18037`_
* Refactor galaxy.files plugin loading + config handling
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18049`_
* Add stronger type annotations in file sources + refactoring
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18050`_
* Enable flake8-implicit-str-concat ruff rules
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18067`_
* Ensure history `update_time` is set when exporting
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18086`_
* De-duplication of onedata objectstore code
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18174`_


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

.. major_bug


.. bug_tag_viz

* Check various preconditions in FeatureLocationIndexDataProvider
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18283`_
* Adds pinia to manually mounted vue components
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18299`_
* Fix visualizations compatible dataset filtering
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18343`_
* Fix pca 3d rendering of tabular files and visualization error handling in general
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18211`_
.. bug_tag_datatypes

* Don't set dataset peek for errored jobs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18231`_
* Npz sniffing: do not read the whole file
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17672`_
* Never fail dataset serialization if display_peek fails
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17937`_
.. bug_tag_tools

* Raise exception when extracting dataset from collection without datasets
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18249`_
* Fix null inputs in database operation tools
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18385`_
.. bug_tag_workflows

* Drop unnecessary escaping for workflow name and annotation
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18376`_
* Fix invocation step_job_summary for new collections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18402`_
* Fix `input_step_parameters` missing values that don't have a label
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18405`_
* Fixes for mapping workflow labels to markdown dialogs
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17424`_
* Fix workflow run form failing on certain histories
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17869`_
* Make sure step removal also resets mapOver state
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17915`_
* Fix workflow run form for workflows with null rename PJA
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17929`_
* Fix missing implicit conversion for mapped over jobs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17952`_
* Fix `LengthValidator` if no value passed
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17983`_
* Use or copy StoredWorkflow when copying step
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17988`_
* Don't commit in ``DeleteIntermediatesAction``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18131`_
* Fix submitted value in workflow run form if data is constrained by tag filter
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18193`_
.. bug_tag_ui

* Bump es5-ext from 0.10.62 to 0.10.63 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17555`_
* Bump webpack-dev-middleware from 5.3.3 to 5.3.4 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17820`_
* Bump express from 4.18.1 to 4.19.2 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17840`_
* Bump undici from 5.28.3 to 5.28.4 in /client
  (thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
  `Pull Request 17905`_
* Update prebuilt client
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18000`_
* Fix tag regex pattern
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18025`_
.. bug_tag_jobs

* Restrict job_files access to jobs that are not terminal
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18217`_
* Raise appropriate exception if accessing deleted input file
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18223`_
* Fix seek in slurm memory check
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18338`_
* Do not copy purged outputs to object store
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18342`_
* Kill pulsar job if job stopped on galaxy side
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18348`_
* Always discard session after __handle_waiting_jobs is done
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17913`_
* Fix tool form building if select filters from unavailable dataset metadata
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17930`_
* Fix ``InvalidRequestError: Can't operate on closed transaction inside context manager.  Please complete the context manager before emitting further
  commands.``
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17932`_
* Downgrade missing output file in working directory to warning for failed jobs
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18123`_
* Drop redundant error message
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18156`_
* Don't fail metadata if we only have an extra output files dir
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18179`_
* Avoid object store path lookup when constructing JobState object
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18190`_
.. bug_tag_admin

* Only log error if deleting directory really failed
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18236`_
* Rebuild Galaxy config
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 18325`_
* Downgrade doi fetch error to debug
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18330`_
* Include exception info when something goes wrong while refreshing tokens
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18008`_
* Don't log exception if cancelled slurm job doesn't have stderr file
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18121`_
* Downgrade count lines error to warning
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18175`_
* Emit warning when user-cancelled job already complete
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18178`_
* Include stack when reporting delete error
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18208`_
.. bug

* Pin pydantic to >=2.7.4
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18423`_
* do not expand datasets that are known to be inaccessible
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17818`_
* Prevent anonymous and inactive users from running workflows
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18192`_
* Revert some requests import changes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18199`_
* Check dataset state when attempting to acces dataset contents
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18214`_
* Raise ``RequestParameterInvalidException`` if url can't be verified
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18230`_
* Reset content-length for unhandled exceptions
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18233`_
* Fix element serialization for collections that aren't populated yet
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18235`_
* Fix userOwnsHistory conditions
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18243`_
* Small bug fixes for user data plugins
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18246`_
* Transparently open compressed files in DatasetDataProvider
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18248`_
* Skip tests if toolshed, dx.doi not responding
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18250`_
* Fix history export error handling
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18251`_
* Remove linter for unstripped text content for tool xml leaves
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18252`_
* Fix Invenio credentials handling
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18255`_
* Set page importable to false when serializing
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18263`_
* Add missing TS migration
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18267`_
* Format with black
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18273`_
* Fix handler: access to result row items changed in SA2.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18274`_
* Don't attempt to download purged datasets
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18278`_
* Fix first_dataset_element type hint
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18284`_
* Redirect anonymous users to home when importing public histories
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18286`_
* Use correct link for log in or register in Copy Modal
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18289`_
* Add TS db revision tags for 24.0
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18294`_
* Move tool shed specific driver function to tool_shed.test
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18296`_
* Fix various packages' issues
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18301`_
* Fix "label updated" popup triggers too often
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 18303`_
* Adapt Tool prediction API to Transformer-based deep learning architecture
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 18305`_
* Fix word bleeding in modals, sharing page and history rename
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18306`_
* Don't serialize display application links for deleted datasets
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18307`_
* Fix non-history items drag&drop into histories
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18308`_
* Filter data dialog entries by dataset state, only display `ok` state
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18313`_
* Fix pinia in manually mounted components
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18315`_
* Disable state filter for collections in `HistoryFilters`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18324`_
* Fix users API serialization when listing users
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18329`_
* Fix authentication error for anonymous users querying jobs
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18333`_
* Make sure that all Linter subclasses are imported for listing them
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18339`_
* Fix anonymous user job retrieval logic
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18358`_
* Fix check for anonymous
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18364`_
* Fix update group API payload model
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18374`_
* Sanitize FormElement error messages
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18377`_
* Fix empty usernames in database + bug in username generation
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18379`_
* Fix user's private role can be missing
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18381`_
* Fix duplicated requests when browsing files sources with pagination
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18387`_
* Fix dataset details polling re-render
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18388`_
* Assign default ``data`` extension on discovered collection output
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18389`_
* Fix workflow editor tool form scroll memory
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 18390`_
* Reset current page when browsing sub-folders in FilesSources
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18395`_
* Fix workflow tags initialisation in workflow editor
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18396`_
* Fix ``get_accessible_job`` if called without session
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18400`_
* Allow in_range validator for selects
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18403`_
* Ensure datatypes match on dragging elements into FormData
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18410`_
* Really allow in-range validator for txt
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 18411`_
* Fix collection map over status for dragged collections
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18416`_
* Add TypedDict for JobsSummary
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18418`_
* Serialize purged flag for datasets in collections
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18420`_
* Unpin social-auth-core dependency
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17607`_
* remove reference to a non-existent component
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 17686`_
* Add carbon_intensity.csv to package
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 17748`_
* Fix bug in image_util.py
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17749`_
* Fix bug in galaxy.xsd
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17752`_
* Fix bug in `assert_has_image_n_labels`
  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
  `Pull Request 17754`_
* Fix odd object store exception
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 17810`_
* Fix permissions for temporary upload file for API uploads
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 17850`_
* Fix tool version switch in editor
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17858`_
* Remove duplicate tool panel insertion, rely on activity bar
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17872`_
* Fix hasOwner function for histories in client
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 17886`_
* Always serialize element_count and populated when listing contents
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17890`_
* Make `wait_for_history_jobs` look at jobs, not datasets
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17892`_
* Fix release notes
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17894`_
* Fix deadlock that can occur when changing job state
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17896`_
* Fix search and version menu in docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 17898`_
* Fix conditional Image imports
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17899`_
* Fix lost reports when switching workflow versions
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17904`_
* Fix saving user preferences crashes tab
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 17917`_
* Ensures that the activity bar is not shown when use_panels is set to false
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 17926`_
* Replace sample Celery result_backend in config
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 17949`_
* Show dataset image in workflow_outputs display listing
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17964`_
* Fix get_content_as_text for compressed text datatypes
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17976`_
* History import - show user feedback on completion
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 17980`_
* Backport: Fix bug: call unique() on result, not select stmt
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 17981`_
* Raise ``RequestParameterInvalidException`` if collection element has unknown extension
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17985`_
* Don't attempt to commit in dry_run mode
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 17987`_
* Don't fail if reporting invalid parameter values
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18002`_
* Preserve surrounding whitespace when localizing complex nodes
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18005`_
* Add section divider to activity bar, fix click handler
  (thanks to `@guerler <https://github.com/guerler>`__).
  `Pull Request 18007`_
* Raise ``MessageException`` when report references invalid workflow output
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18009`_
* Avoid exception when opening apply rules tool and no collection in history
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18011`_
* Don't commit without having set a hid
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18014`_
* Make celery fixture available in framework tests
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18020`_
* Add a link to histories list in history import message for situations…
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18021`_
* Raise appropriate exception if user forces a collection that is not populated with elements as input
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18023`_
* Fix ``test_get_tags_histories_content`` test
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18026`_
* Clarify the object store relocate functionality
  (thanks to `@martenson <https://github.com/martenson>`__).
  `Pull Request 18033`_
* Fix History Dataset Association creation so that hid is always set
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18036`_
* Change wrong quota_source value from KeyError to ValueError
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18040`_
* Ensure that offset and limit are never negative
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18044`_
* Fix comments lost on import
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 18060`_
* Fix (I think) a transiently failing selenium error
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18065`_
* Check database connection to issue a rollback if no connection
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18070`_
* Fix toolbar header z-index
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18084`_
* Dynamic tool fixes
  (thanks to `@dcore94 <https://github.com/dcore94>`__).
  `Pull Request 18085`_
* Raise exception if collection elements missing during download
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18094`_
* Tests and bugfixes for cloudbridge object store
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18099`_
* Fix AWS object store for us-east-2
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18100`_
* Hide bookmark toggle on deleted workflows
  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
  `Pull Request 18103`_
* Fix for unexpected OIDC XML validation error
  (thanks to `@Edmontosaurus <https://github.com/Edmontosaurus>`__).
  `Pull Request 18106`_
* Fix vanishing connections on workflow upgrade
  (thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
  `Pull Request 18107`_
* Fix activity bar touch events on iOS devices
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18109`_
* Fairly critical fix for `#18087 <https://github.com/galaxyproject/galaxy/issues/18087>`__
  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
  `Pull Request 18110`_
* Fix and unify axios error handling
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18112`_
* Fix switching between nested collection elements
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18115`_
* Ignore AdminRequired and RegisteredUserRequired Sentry events
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18118`_
* Fix deprecated `deprecated` argument
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18119`_
* Include traceback when logging email PJA exception
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18122`_
* Fix listing possibly untitled records in Invenio Plugin
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18130`_
* Fix data default values not getting added to history
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18132`_
* Fix undefined `reading 'produces_entry_points'` TypeError
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18141`_
* Fix config access in StorageManager
  (thanks to `@dannon <https://github.com/dannon>`__).
  `Pull Request 18143`_
* Fix Legacy HTML page view
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18145`_
* Delay tool form rendering until config is loaded
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18151`_
* Raise ``RequestParameterInvalidException`` when url is invalid
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18155`_
* Fix error message when accessing restricted Zenodo records
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18169`_
* Small refinements and fixes to new release process doc
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 18170`_
* Add message to Invocations panel for no invocations
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18180`_
* Fix typos in create release documentation page
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18181`_
* Change default milestone to target 24.2
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18186`_
* Fix Edit Dataset UI when there is an error retrieving the dataset
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18188`_
* Fix file source search query with empty string value
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18191`_
* Replace `Multiselect` `selectLabel` with icons in `FormSelect`
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18194`_
* Fix `make all histories private` with immutable histories
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18200`_
* Fix selection highlight in Files Dialog when using items provider
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 18201`_
* Remove legacy code, reference to sqlalchemy migrate
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18202`_
* Add `GenericItem` error handling
  (thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
  `Pull Request 18203`_
* Add string cast for dbkey / genome_build
  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
  `Pull Request 18207`_
* Use config_section to distinguish between galaxy and ts or other apps
  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
  `Pull Request 18215`_

.. include:: 24.1_prs.rst