
.. to_doc

21.05
===============================

.. announce_start

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

.. major_feature

* Beta History scrolling behavior and polling efficiency tuning
  `Pull Request 11693`_
* Add FastAPI routes for tours
  `Pull Request 11089`_
* Add FastAPI routes for datatypes
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11098`_
* Add cache_dir to schema
  `Pull Request 11202`_
* Allow requesting extra scopes
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 11561`_
* Github workflow for updating dependencies
  `Pull Request 11570`_
* Allow line break html tag in markdown pages
  `Pull Request 11592`_
* Allow workflow imports in pages
  `Pull Request 11607`_
* Add option to download collections in markdown pages
  `Pull Request 11676`_
* Add the SimText shiny app as Interactive Tool
  (thanks to `@dlal-group <https://github.com/dlal-group>`__).
  `Pull Request 11680`_
* Replace sqlalchemy-utilities with local implementation
  `Pull Request 11696`_
* Circus + Celery - MVP
  `Pull Request 11720`_
* Support role and group permissions in file sources plugins
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11769`_
* Add circus + gunicorn option when using run.sh
  `Pull Request 11772`_
* Run history export setup via celery, if configured
  `Pull Request 11789`_
* Allow importing histories through pages / reports
  `Pull Request 11863`_
* Migrate api/genomes to fastapi
  `Pull Request 11241`_
* Add FlowCytometry and MetaCyto datatypes
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 9807`_
* Add mrc datatype (and Python dependency)
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 11220`_
* Add HHR datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 11661`_
* add meryldb datatype
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 11694`_
* Add datatype for PretextMap output
  `Pull Request 11747`_
* add new datatype class for meryldb
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 11758`_
* Add Avivator GEDA and sniffer for ome.tiff datatype
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 11801`_
* jellyfish db datatype
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 11802`_
* Add new datatype JPEG 2000 in Galaxy
  (thanks to `@annefou <https://github.com/annefou>`__).
  `Pull Request 11812`_
* Adding h5_model datatype for machine leaning models
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 11825`_
* Add support for the Relion STAR data format
  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
  `Pull Request 11831`_
* Add minerva display app for covid
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 11880`_
* Add toml datatype
  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
  `Pull Request 11909`_
* grep, tail, head: add option to keep header
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11859`_
* add a bit of docs to the add tags tool
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11874`_
* Add failed-to-submit error handling for simplified workflow run form
  `Pull Request 12124`_
* Selenium test case for invocation grid + display.
  `Pull Request 11160`_
* be more verbose on output filter errors
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11197`_
* Add UpgradeAllSteps workflow refactor action
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 11429`_
* Guess tool name when extracting workflows with imported datasets
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11483`_
* Avoid appending imported source on workflow name multiple times.
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11671`_
* Switch default handler assignment to skip locked or transaction isolation if possible
  `Pull Request 11792`_
* Client testing/linting updates and followup
  `Pull Request 11121`_
* replaced global vue with test vue in unit tests
  `Pull Request 11138`_
* Manage folder rewrite in Vue & VueRouter
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11259`_
* Copy to Clipboard button next to the tool id in job information
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11478`_
* Better webpack-dev-server handling.
  `Pull Request 11566`_
* Speed up get history list
  `Pull Request 11883`_
* Implement switch to history modal for beta history panel
  `Pull Request 11895`_
* Store job_id on Dataset table.
  `Pull Request 10222`_
* Handle unschedulable jobs in k8s runner
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 10496`_
* Establish a best practice for trans dependency management.
  `Pull Request 11113`_
* Adding GALAXY_MEMORY_MB_PER_SLOT to k8s runner
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 11227`_
* add reworked chronos job runner
  (thanks to `@mtangaro <https://github.com/mtangaro>`__).
  `Pull Request 11228`_
* Generalise rule helper to detect whether tools can use any container
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 11274`_
* Only return a subset of jobs ready to run per user when querying for jobs ready to run
  `Pull Request 11358`_
* ITs on Kubernetes
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 11383`_
* Read cgroups from cgroup filesystem mount rather than cgget, which is not always installed
  `Pull Request 11393`_
* SLURM: stop editing job stderr file
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11575`_
* Fixes for extended metadata working with Pulsar.
  `Pull Request 11788`_
* Fix collection state updates by setting collection update time
  `Pull Request 11849`_
* Test a better Pulsar configuration for extended metadata.
  `Pull Request 11852`_
* Add handler column in admin jobs, remove webcontroller
  `Pull Request 11868`_
* improve three debug messages
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11908`_
* Add documentation on how to setup Pulsar's two-container job runner
  `Pull Request 11557`_
* sortable columns in Admin->Users
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11665`_
* Create install database with create_db.sh
  `Pull Request 11753`_
* Include more info on test input staging exception
  `Pull Request 11953`_
* Add indexes on update_time columns used in ORDER BY clauses
  `Pull Request 11988`_
* Don't assert output_metadata state
  `Pull Request 12100`_
* Fix and enhance subworkflow step upgrade messages
  `Pull Request 12120`_
* Performance testing infrastructure.
  `Pull Request 10117`_
* Stub MQ docs
  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
  `Pull Request 10347`_
* Implement read-only conda resolver.
  `Pull Request 10810`_
* really test variables in conditionals
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11111`_
* Updated API Design Guidelines
  `Pull Request 11115`_
* uvicorn-compatible factory function for fastapi.
  `Pull Request 11116`_
* Dynamic discovery of FastAPI routers.
  `Pull Request 11124`_
* FastAPI routes for configuration
  `Pull Request 11126`_
* Start type signature for UniverseApplication.
  `Pull Request 11142`_
* Various testing framework cleanups.
  `Pull Request 11156`_
* FastAPI routes for tool data tables
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11167`_
* Recommend 2FA and commit signing
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11173`_
* Warns that build_mulled_singularity requires docker
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 11176`_
* Documentation and helpers for using galaxy-selenium package within Jupyter
  `Pull Request 11177`_
* History beta poll decay time reset
  `Pull Request 11178`_
* Holistic approach to dependency injection.
  `Pull Request 11180`_
* Selenium test for ``library_import_dir``
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11188`_
* Replace pipenv with poetry. Update all dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11192`_
* Add missing xml:lang attribute to documentation annotations
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11198`_
* Selenium tests for user library import dir
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11203`_
* FastAPI route for remote files
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11211`_
* More debug info for failed integration selenium tests during CI.
  `Pull Request 11217`_
* Implement abstraction around InferringApiRouter tailored to typical Galaxy usage.
  `Pull Request 11219`_
* FastAPI route for tags (Disabled)
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11224`_
* Remove `folder_up` button from data folder
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11230`_
* add ActionChains example in documentation of galaxy-selenium package within Jupyter
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11232`_
* Sync x-frame-options handling across frameworks and test.
  `Pull Request 11235`_
* FastAPI/ASGI CORS handling.
  `Pull Request 11240`_
* FastAPI routes for Pages (Disabled)
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11262`_
* Don't fail silently in `User.system_user_pwent()`
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11272`_
* Move docstring linting to GitHub workflows
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11300`_
* Add Nuwan Goonasekera to the committers group
  `Pull Request 11304`_
* ignore subdirectories if recurse is false
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11307`_
* Fix transiently failing roles API test.
  `Pull Request 11319`_
* Allow `GET /api/dataset_collections/{hdca_id}` without specifying `instance_type`
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11346`_
* Add support for Plausible analytics and Matomo analytics
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 11351`_
* Lint for optional or multiple selects with radio display
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11385`_
* Test library dataset permissions
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11402`_
* Use request id middleware to scope session
  `Pull Request 11411`_
* Move unit tests to GitHub workflows, test also under Python 3.9
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11452`_
* Allow anonymous access to S3 buckets via file sources plugins.
  `Pull Request 11458`_
* add copy tooldID btn
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11477`_
* Libraries rewrite
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11485`_
* adding nameSuggestion to PairCollectionCreator
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11489`_
* xsd: use validator as child of param
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11497`_
* add sshfs plugin to the new file infrastructure
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 11507`_
* add ftp files.plugin
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 11508`_
* Add ready-to-go gitpod config
  `Pull Request 11509`_
* Create pull_request_template.md
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11530`_
* Add more filtering options to api/jobs endpoint
  (thanks to `@rikeshi <https://github.com/rikeshi>`__).
  `Pull Request 11560`_
* Migrate metrics API to FastAPI
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11568`_
* Sample conf for dropbox and owncloud file sources
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 11580`_
* An attempt to improve dependency management
  `Pull Request 11619`_
* Overhaul make-based release process
  `Pull Request 11641`_
* Pin fs.webdavfs requirement to latest version
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 11648`_
* Update all Python dependencies
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11649`_
* update to cope with impending changes to cwltool internals
  (thanks to `@rupertnash <https://github.com/rupertnash>`__).
  `Pull Request 11655`_
* Lint for duplicated options
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11662`_
* Single User Mode - Disable irrelevant and broken options
  `Pull Request 11669`_
* Swap 'Analyze Data' to home icon
  `Pull Request 11674`_
* Bugfix/11476/disabled upload button explanation
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11682`_
* Break up dynamic dataset collection into chunks
  `Pull Request 11697`_
* enable the S3 plugin to use non-AWS resrouces
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 11703`_
* Implement selenium tests for exporting library datasets to history collections.
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11716`_
* lint for checkboxes select
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11727`_
* Refactor stdout/stderr in Job Information
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11731`_
* Copy collections dbkey
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11732`_
* Fix CI docs build for feature branches
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11740`_
* Updated Code of Conduct to point to the exact copy of this CoC on the hub.
  `Pull Request 11750`_
* Allow AWS s3 access for ec2 instances without hardcoding credentials
  (thanks to `@crashGoBoom <https://github.com/crashGoBoom>`__).
  `Pull Request 11757`_
* Add an explicit statement of assent to licensing to the pull request template
  `Pull Request 11777`_
* Fixes for installed Galaxy
  `Pull Request 11779`_
* Update Python dependencies
  `Pull Request 11782`_
* Handle deprecated postgresql db urls; update postgres version in ci
  `Pull Request 11790`_
* Update localisation options to include Español
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 11791`_
* Open update deps PRs from galaxybot's fork
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11795`_
* Make k8s container 39 MB smaller by using vim-tiny
  (thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
  `Pull Request 11826`_
* Make tool parameter options capable of referring to metadata file
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 11832`_
* Restore triggers dropped in `#10821 <https://github.com/galaxyproject/galaxy/issues/10821>`__
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11843`_
* Do not invoke workflow if not all tools are available
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 11844`_
* Improve error handling when creating a new History with the master API key
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11846`_
* Expose StoredWorkflowId in invocation API
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 11871`_
* Create FastAPI entry points for Tool Shed and Reports
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11872`_
* Rev mypy.
  `Pull Request 11877`_
* Backport `#11871 <https://github.com/galaxyproject/galaxy/issues/11871>`__
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 11881`_
* Allow to filter /api/invocations by job_id
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 11882`_
* Complete Spanish language version
  (thanks to `@nomadscientist <https://github.com/nomadscientist>`__).
  `Pull Request 11891`_
* Add subpathing to k8s_persistent_volume_claims
  (thanks to `@anvilproject <https://github.com/anvilproject>`__).
  `Pull Request 11899`_
* Make _metadata regular JSONType field
  `Pull Request 11902`_
* Abstraction for fetching qualified app URL across webapp types
  `Pull Request 11904`_
* Add ``delete account`` selenium test
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11905`_
* Update framework dependencies
  `Pull Request 11907`_
* expose copied_from_ldda_id on dataset api endpoint
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 11922`_
* Fix remaining issues reported by bugbear; add it to flake8 reqs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11153`_
* Fix all E203, E741 and W504 flake8 errors
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11155`_
* Remove unused TS methods.
  `Pull Request 11179`_
* Remove some seemingly unused cruft in GalaxyWebTransaction
  `Pull Request 11234`_
* Drop unused transfer_manager.py
  `Pull Request 11238`_
* Get rid of legacy decorator in api/tours
  `Pull Request 11253`_
* Update vscode dev instructions, drop helper script
  `Pull Request 11258`_
* Replace $.isArray with Array prototype check
  `Pull Request 11264`_
* Drop docker testing image
  `Pull Request 11329`_
* Renamed virtualscroller since it is no longer virtual
  `Pull Request 11331`_
* Dataset lib permissions Vue rewrite
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11347`_
* Refactor libraries API logic into LibrariesManager
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11359`_
* Refactor display_applications API logic into DisplayApplicationsManager
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11386`_
* Repair styleguide
  `Pull Request 11404`_
* Refactor groups API logic into GroupsManager
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11412`_
* Refactor group_roles API logic into GroupRolesManager
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11417`_
* Refactor group_users API logic into GroupUsersManager
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11418`_
* Pin mypy to 0.790 to prevent linting errors when running v 0.8
  `Pull Request 11422`_
* Use galaxy Router instead of InferringRouter
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11591`_
* Front-end Library Routing refactor
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11614`_
* Remove unused `TraceLogger` class
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11616`_
* Refactor library folder API logic into FoldersService
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11631`_
* Rewrite Library Permissions
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11637`_
* Fix prop mutation in FolderTopBar
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11638`_
* Refactor library folder contents api
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11686`_
* Update Python dependencies
  `Pull Request 11702`_
* Partial refactor ShareableMixin into ShareableService
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11712`_
* Incorporate changes from Pulsar's copy of galaxy.jobs.runners.util
  `Pull Request 11810`_
* Separate tests for "remote" and "remote + extended" metadata.
  `Pull Request 11840`_
* Unify security decode id exceptions
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11856`_
* Optimized beta history polling by leveraging history.update_time + loading behavior bug fixes
  `Pull Request 11884`_
* Eslint tweaks
  `Pull Request 11925`_


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

* Shared visualization display fix
  `Pull Request 11906`_
* remove duplicated qcml from datatypes_conf sample
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11378`_
* Limit max column in tabular dataset preview
  `Pull Request 11901`_
* Use keep_original in pysam.tabix_index to not remove original data
  `Pull Request 11913`_
* Open input file in read mode in liftover wrapper
  `Pull Request 12001`_
* Resolve session problems, enabled pages and tags fastAPI routes
  `Pull Request 11342`_
* Make filter work with file containing header
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11365`_
* Fix copying text in workflow editor
  `Pull Request 12118`_
* Make failure to save workflow dismissible
  `Pull Request 12122`_
* Allow trs_version to refer to name or id field
  `Pull Request 12021`_
* Workflow editor null/zero fixes
  `Pull Request 11265`_
* Fix reconnecting terminals
  `Pull Request 11660`_
* Fix tags not included when importing shared workflow
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11663`_
* Fix workflow rename dropping metadata.
  `Pull Request 11670`_
* Use Modal to show wrong RuntimeValue
  `Pull Request 11678`_
* Ensure new outputs have correct mapOver state
  `Pull Request 11683`_
* Redraw connections when adding or removing inputs
  `Pull Request 11684`_
* Fix displaying data column parameters in workflow editor
  `Pull Request 11692`_
* Fix workflow refactor schema parsing for pydantic 1.8.
  `Pull Request 11778`_
* fix undefined error in ui-file-source
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11586`_
* Remove filter from list:paired element names when filter is not _1
  `Pull Request 11486`_
* Beta history current history mismatch with legacy code.
  `Pull Request 11850`_
* Reposition history scroller during new updates
  `Pull Request 11879`_
* ITs on K8S tweaks and SSL
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 11947`_
* Fix anonymous user job walltime query
  `Pull Request 11951`_
* Fix container port parsing if IPv6 hostname is ``::``
  `Pull Request 11955`_
* Fix isolated job home dir on pulsar
  `Pull Request 12037`_
* Don't start workflow scheduler for handler in job pool
  `Pull Request 12075`_
* Fix set metadata for primary discovered outputs
  `Pull Request 12088`_
* Fix mule job messaging
  `Pull Request 11148`_
* Deal with empty claim names in k8s runner
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 11223`_
* Fix SLURM runner for real user setups and avoid uneccesary chowns
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11403`_
* Prevent endless fail_job cycles
  `Pull Request 11673`_
* Fix value of 'unknown_error' resubmit condition variable
  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
  `Pull Request 11749`_
* Pulsar: mark cancelled jobs as finished
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 11763`_
* Lower tool id case while populating resource params
  (thanks to `@eancelet <https://github.com/eancelet>`__).
  `Pull Request 11793`_
* Don't overwrite $GALAXY_MEMORY_MB if it's already set
  `Pull Request 11808`_
* Transfer fewer unneeded files back to Galaxy when using remote extended metadata with Pulsar.
  `Pull Request 11814`_
* Don't write job and job-related attributes when creating export model
  `Pull Request 11815`_
* Handle resubmission before changing job state in CLI runner
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 11886`_
* fix broken docs links
  `Pull Request 11384`_
* Add missing ssl keyword in nginx example [docs]
  (thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
  `Pull Request 11633`_
* Create history_audit table to avoid write deadlocks during history.update_time updates
  `Pull Request 11914`_
* Fix `GET /api/datasets/` docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11933`_
* Don't move the `update_time` goalpost
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11934`_
* Force galaxy_id to string in galactic_job_json
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 11965`_
* Update default base images, make DEFAULT_CHANNELS configurable via env var
  `Pull Request 11966`_
* Fix mulled singularity building
  `Pull Request 11979`_
* restrict invalid input in library pagination
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11996`_
* Fix breadcrumb in dataset details in libraries
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11998`_
* Fix deleted libs for user
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12011`_
* fix library dataset permissions
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12015`_
* Disable import button during "Import to History"
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12016`_
* Hide edit libraries for users
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12023`_
* Fix downloading (sub)folders from data-libraries
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12028`_
* Fix subworkflow / update all steps upgrade action
  `Pull Request 12029`_
* Fix uploading multiple files in ftp upload / choose remote files
  `Pull Request 12030`_
* add GALAXY_MEMORY_MB* to passt hrough
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 12039`_
* invocation_time report fix
  `Pull Request 12070`_
* Fix edit field reactivity in libraries
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12080`_
* Fix select all in import from history backbone modal
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12082`_
* Fix export select_all in collections
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12086`_
* fix library search filter
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 12087`_
* Fix name of datasets with invalid contents
  `Pull Request 12107`_
* Beta History: implement missing advanced search filters
  `Pull Request 10972`_
* Fix mypy error with Union in response_model
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11132`_
* Minor spelling error fix
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 11135`_
* Fix permission in user dir library import
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11137`_
* fix error message
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11157`_
* changing tooltip to match functionality
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11204`_
* Copy only dataset tags in Extract Dataset tool
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 11206`_
* Fix regression of 'disabled' masthead items.
  `Pull Request 11215`_
* fix `test_user_library_import_dir_warning`
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11226`_
* Make OIDC email matching case-insensitive
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 11251`_
* Tool XML container requirements: fix example
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 11271`_
* Bugfix/8488/rule builder fails for one bad url
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11276`_
* Fix printing non-dict output in api/display script
  `Pull Request 11278`_
* Fix images in workflow PDF report
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11296`_
* consider collections in all tests
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11313`_
* Replace Query with Path
  `Pull Request 11320`_
* Custos `aud` handling fix
  `Pull Request 11322`_
* Get latest pull request labels in maintenance bot
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11326`_
* Update OIDC links
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 11362`_
* fix profile logic for configfile generation
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11380`_
* Standardise tool param attribute docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11390`_
* Run maintainance bot on ready_for_review and edit
  `Pull Request 11400`_
* Decrease verbosity of messages in poetry
  `Pull Request 11405`_
* Rename fixtures to fix test database object name conflict
  `Pull Request 11424`_
* Check for binary files at the middle of the file instead of at the beginning
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 11425`_
* Set default USE_UVICORN to true only on python >= 3.7
  `Pull Request 11454`_
* Fix galaxy.files.sources plugin unit tests being missed by CI.
  `Pull Request 11469`_
* Fix exception handling in datasets display API.
  `Pull Request 11482`_
* Mark some tool reload tests as expected to fail
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11496`_
* Fix clearing of search inputs
  `Pull Request 11526`_
* Fix bug with Pulsar and $__tool_directory__
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 11599`_
* Allow any extra field in Pages API
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11600`_
* Fix workflow labelling
  `Pull Request 11604`_
* Pin refgenconf to <0.10.0
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11627`_
* Pin SQAlchemy to <1.4.0
  `Pull Request 11629`_
* Change Upload button tooltip position
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11634`_
* Set minimum requirements for starlette-context and fastapi
  `Pull Request 11643`_
* Match environment variable set up by doc building workflow
  `Pull Request 11646`_
* Don't check for missing `kind/` label for `minor` merged PRs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11647`_
* Library folder_contents API tests + small fixes
  (thanks to `@davelopez <https://github.com/davelopez>`__).
  `Pull Request 11650`_
* Refactor default mounting of $tmp_directory in containers
  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
  `Pull Request 11654`_
* Fix datatype defined column name display
  `Pull Request 11664`_
* Expose command line if expose_dataset_path is set
  `Pull Request 11687`_
* Hotfix/paired list builder from data library
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11700`_
* Make extra user preferences behave like defaultdict
  `Pull Request 11708`_
* Fix importing collections to new history and import correct elements
  `Pull Request 11718`_
* Removedreference to remove-extensions
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 11724`_
* Refgenie table del
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 11728`_
* Fix job filtering by `date_range_max` / `date_range_mix`
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11736`_
* Fix a bug when unzipping collections with nametags.
  `Pull Request 11741`_
* Fix API job filtering by workflow or invocation
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11751`_
* Assorted tool shed fixes
  `Pull Request 11762`_
* Fix format="input" with implicit conversions
  `Pull Request 11764`_
* galaxy.webapps.tool_shed to webapp.tool_shed
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 11765`_
* Fix auto-pair naming in list paired creator.
  `Pull Request 11773`_
* Fix library scrolling
  `Pull Request 11776`_
* Use `assertRaisesRegex()` to fix new B017 linting errors
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11783`_
* Fix typo in `upstream_mod_zip` admin docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11794`_
* Fix tool profile details in schema docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11798`_
* Activate virtualenv in `updateucsc.sh.sample`
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 11800`_
* Backport `#11815 <https://github.com/galaxyproject/galaxy/issues/11815>`__: Don't write job and job-related attributes when creating export model
  `Pull Request 11816`_
* do not chown pasted urls
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 11818`_
* Fixed uploader link on tool list and legacy empty history message
  `Pull Request 11830`_
* Join QueueWorker thread
  `Pull Request 11835`_
* Patch to click the button which should be more stable
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 11838`_
* fix data stickiness on folder change
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 11845`_
* BUGFIX: Also check for boolean True, not just string 'True' when evaluating conditional dependencies.
  (thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
  `Pull Request 11861`_
* Fix ``Delete account`` visibility
  `Pull Request 11897`_
* Fix S3 backend support in iRODS object store
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 11910`_
* fix GalaxyInteractorApi get_tool_tests
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 11911`_
* Stabilize test_history_options selenium test
  `Pull Request 11918`_
* update legacy_framework.grids.StateColumn (bug fix)
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 11923`_

.. include:: 21.05_prs.rst

