* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
* Dynamics options add library dataset by `@gagayuan <https://github.com/gagayuan>`_ in `#18198 <https://github.com/galaxyproject/galaxy/pull/18198>`_
* Fix some deprecations by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18433 <https://github.com/galaxyproject/galaxy/pull/18433>`_
* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
* Update mercurial by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18686 <https://github.com/galaxyproject/galaxy/pull/18686>`_
* Replace types-pkg-resources with types-setuptools by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18708 <https://github.com/galaxyproject/galaxy/pull/18708>`_
* Fix tag processing in library upload by `@davelopez <https://github.com/davelopez>`_ in `#18714 <https://github.com/galaxyproject/galaxy/pull/18714>`_
* Update ruff to 0.6.1 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18716 <https://github.com/galaxyproject/galaxy/pull/18716>`_
* Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18755 <https://github.com/galaxyproject/galaxy/pull/18755>`_
* Fixes and tests for data fetch models. by `@jmchilton <https://github.com/jmchilton>`_ in `#18834 <https://github.com/galaxyproject/galaxy/pull/18834>`_
* data_column params: offer same columns with and without use_header_names by `@wm75 <https://github.com/wm75>`_ in `#18879 <https://github.com/galaxyproject/galaxy/pull/18879>`_
* Fix issue with generating slug for sharing by `@arash77 <https://github.com/arash77>`_ in `#18986 <https://github.com/galaxyproject/galaxy/pull/18986>`_
* Fix the bioblend test failures by `@arash77 <https://github.com/arash77>`_ in `#18991 <https://github.com/galaxyproject/galaxy/pull/18991>`_
* Fix job directory not being cleaned up by `@davelopez <https://github.com/davelopez>`_ in `#18997 <https://github.com/galaxyproject/galaxy/pull/18997>`_
* Fixes random job failures in kubernetes by `@mapk-amazon <https://github.com/mapk-amazon>`_ in `#19001 <https://github.com/galaxyproject/galaxy/pull/19001>`_
* Fix numerous issues with tool input format "21.01" by `@jmchilton <https://github.com/jmchilton>`_ in `#19030 <https://github.com/galaxyproject/galaxy/pull/19030>`_
* Fix test_stock.py unit test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19037 <https://github.com/galaxyproject/galaxy/pull/19037>`_
* quota: do not complain on no-change of default by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19045 <https://github.com/galaxyproject/galaxy/pull/19045>`_
* Normalize usernames to lowercase in OIDC authentication by `@arash77 <https://github.com/arash77>`_ in `#19131 <https://github.com/galaxyproject/galaxy/pull/19131>`_
* 2 small uv config fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19146 <https://github.com/galaxyproject/galaxy/pull/19146>`_
* Fix invocation metrics usability by providing job context. by `@jmchilton <https://github.com/jmchilton>`_ in `#19279 <https://github.com/galaxyproject/galaxy/pull/19279>`_
* Fix import of previously-deleted TRS workflow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19311 <https://github.com/galaxyproject/galaxy/pull/19311>`_
* Fix quota usage with user object stores by `@davelopez <https://github.com/davelopez>`_ in `#19323 <https://github.com/galaxyproject/galaxy/pull/19323>`_
* Fix workflows with optional non-default parameter input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19332 <https://github.com/galaxyproject/galaxy/pull/19332>`_
* Backport #19001 kubernetes api client fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19338 <https://github.com/galaxyproject/galaxy/pull/19338>`_
* Partial backport of #19331 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19342 <https://github.com/galaxyproject/galaxy/pull/19342>`_
* Use select_from_url test data from github, not usegalaxy.org by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19352 <https://github.com/galaxyproject/galaxy/pull/19352>`_
* Fix to only show ChatGXY when available. by `@dannon <https://github.com/dannon>`_ in `#19389 <https://github.com/galaxyproject/galaxy/pull/19389>`_
* Fix job parameter summary for inputs without label by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19427 <https://github.com/galaxyproject/galaxy/pull/19427>`_
* Show Keycloak provider label in UI by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19447 <https://github.com/galaxyproject/galaxy/pull/19447>`_
* Expression tool format source backport by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19466 <https://github.com/galaxyproject/galaxy/pull/19466>`_
* backport of defensive refresh tokens by `@martenson <https://github.com/martenson>`_ in `#19471 <https://github.com/galaxyproject/galaxy/pull/19471>`_
* Improve relabel from file error if file doesn't contain enough lines by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19480 <https://github.com/galaxyproject/galaxy/pull/19480>`_
* Serialize message exceptions on execution error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19483 <https://github.com/galaxyproject/galaxy/pull/19483>`_
* Fail with error message when submitting invalid request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19489 <https://github.com/galaxyproject/galaxy/pull/19489>`_
* Fix deleting lddas in batch by `@davelopez <https://github.com/davelopez>`_ in `#19506 <https://github.com/galaxyproject/galaxy/pull/19506>`_
* Skip token refresh without refresh token in psa by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19514 <https://github.com/galaxyproject/galaxy/pull/19514>`_
* Downgrade 'InteractiveTools are not enabled' to warning by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19518 <https://github.com/galaxyproject/galaxy/pull/19518>`_
* Fix extracting workflows from purged and deleted histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19525 <https://github.com/galaxyproject/galaxy/pull/19525>`_
* Fix error message when subworkflow input connection missing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19526 <https://github.com/galaxyproject/galaxy/pull/19526>`_
* Fix remap for parameter called id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19532 <https://github.com/galaxyproject/galaxy/pull/19532>`_
* Fix admin cancel job message not being displayed to the user by `@davelopez <https://github.com/davelopez>`_ in `#19537 <https://github.com/galaxyproject/galaxy/pull/19537>`_
* Use instance wide default ``real_system_username`` if not defined on destination by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19544 <https://github.com/galaxyproject/galaxy/pull/19544>`_
============
Enhancements
============
* Add clean up job working directory as celery task by `@sanjaysrikakulam <https://github.com/sanjaysrikakulam>`_ in `#15816 <https://github.com/galaxyproject/galaxy/pull/15816>`_
* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
* Feature - stdout live reporting by `@gecage952 <https://github.com/gecage952>`_ in `#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18226 <https://github.com/galaxyproject/galaxy/pull/18226>`_
* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
* More data access tests, some refactoring and cleanup by `@jdavcs <https://github.com/jdavcs>`_ in `#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18406 <https://github.com/galaxyproject/galaxy/pull/18406>`_
* Add Python 3.13 support by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18449 <https://github.com/galaxyproject/galaxy/pull/18449>`_
* Add onedata templates by `@bwalkowi <https://github.com/bwalkowi>`_ in `#18457 <https://github.com/galaxyproject/galaxy/pull/18457>`_
* Support high-availability setups for the interactive tools proxy by `@kysrpex <https://github.com/kysrpex>`_ in `#18481 <https://github.com/galaxyproject/galaxy/pull/18481>`_
* Add unique constraints to the email and username fields in the galaxy_user table by `@jdavcs <https://github.com/jdavcs>`_ in `#18493 <https://github.com/galaxyproject/galaxy/pull/18493>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18505 <https://github.com/galaxyproject/galaxy/pull/18505>`_
* Improvements for K8S deployment (especially ITs) by `@almahmoud <https://github.com/almahmoud>`_ in `#18514 <https://github.com/galaxyproject/galaxy/pull/18514>`_
* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
* Improvements to Tool Test Parsing by `@jmchilton <https://github.com/jmchilton>`_ in `#18560 <https://github.com/galaxyproject/galaxy/pull/18560>`_
* Group tool templating exceptions in sentry by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18570 <https://github.com/galaxyproject/galaxy/pull/18570>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18578 <https://github.com/galaxyproject/galaxy/pull/18578>`_
* Record container id and type in core job metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18579 <https://github.com/galaxyproject/galaxy/pull/18579>`_
* Rev pinned gxformat2. by `@jmchilton <https://github.com/jmchilton>`_ in `#18624 <https://github.com/galaxyproject/galaxy/pull/18624>`_
* Better Typing for Tool Execution Plumbing by `@jmchilton <https://github.com/jmchilton>`_ in `#18626 <https://github.com/galaxyproject/galaxy/pull/18626>`_
* Remove unused functions in dataset managers by `@jmchilton <https://github.com/jmchilton>`_ in `#18631 <https://github.com/galaxyproject/galaxy/pull/18631>`_
* Parameter Model Improvements by `@jmchilton <https://github.com/jmchilton>`_ in `#18641 <https://github.com/galaxyproject/galaxy/pull/18641>`_
* Parse stored config details to script-based visualizations by `@guerler <https://github.com/guerler>`_ in `#18651 <https://github.com/galaxyproject/galaxy/pull/18651>`_
* Another round of parameter model improvements. by `@jmchilton <https://github.com/jmchilton>`_ in `#18673 <https://github.com/galaxyproject/galaxy/pull/18673>`_
* Allow access to invocation via shared or published history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18707 <https://github.com/galaxyproject/galaxy/pull/18707>`_
* Allow specifying multi-select workflow parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18715 <https://github.com/galaxyproject/galaxy/pull/18715>`_
* Improvements to help terms & tool help. by `@jmchilton <https://github.com/jmchilton>`_ in `#18722 <https://github.com/galaxyproject/galaxy/pull/18722>`_
* Add a retry when deleting a k8s job by `@afgane <https://github.com/afgane>`_ in `#18744 <https://github.com/galaxyproject/galaxy/pull/18744>`_
* More typing, docs, and decomposition around tool execution by `@jmchilton <https://github.com/jmchilton>`_ in `#18758 <https://github.com/galaxyproject/galaxy/pull/18758>`_
* Add Workflow Title and Annotation sections by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18762 <https://github.com/galaxyproject/galaxy/pull/18762>`_
* Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18773 <https://github.com/galaxyproject/galaxy/pull/18773>`_
* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
* Allow using tracks and groups in visualization xml by `@guerler <https://github.com/guerler>`_ in `#18779 <https://github.com/galaxyproject/galaxy/pull/18779>`_
* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
* Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18811 <https://github.com/galaxyproject/galaxy/pull/18811>`_
* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18864 <https://github.com/galaxyproject/galaxy/pull/18864>`_
* Implement Pydantic model for workflow test format. by `@jmchilton <https://github.com/jmchilton>`_ in `#18884 <https://github.com/galaxyproject/galaxy/pull/18884>`_
* Remove some unused dynamic drill down options. by `@jmchilton <https://github.com/jmchilton>`_ in `#18892 <https://github.com/galaxyproject/galaxy/pull/18892>`_
* Enable ``ignore-without-code`` mypy error code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18898 <https://github.com/galaxyproject/galaxy/pull/18898>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18904 <https://github.com/galaxyproject/galaxy/pull/18904>`_
* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
* Add filter null collection operation tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18928 <https://github.com/galaxyproject/galaxy/pull/18928>`_
* Remove outdated fimo wrapper and galaxy-sequence-utils dependency by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18937 <https://github.com/galaxyproject/galaxy/pull/18937>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18943 <https://github.com/galaxyproject/galaxy/pull/18943>`_
* Allow to overwrite `real_system_username` per destination by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18945 <https://github.com/galaxyproject/galaxy/pull/18945>`_
* Assert that `data_column` parameters have a valid `data_ref` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18949 <https://github.com/galaxyproject/galaxy/pull/18949>`_
* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18982 <https://github.com/galaxyproject/galaxy/pull/18982>`_
* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
* Enhance relabel_from_file to work with any column pair in mapping file by `@wm75 <https://github.com/wm75>`_ in `#19022 <https://github.com/galaxyproject/galaxy/pull/19022>`_
* A variety of improvements around tool parameter modeling (second try) by `@jmchilton <https://github.com/jmchilton>`_ in `#19027 <https://github.com/galaxyproject/galaxy/pull/19027>`_
* Better logging around tool loading by `@jmchilton <https://github.com/jmchilton>`_ in `#19029 <https://github.com/galaxyproject/galaxy/pull/19029>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19031 <https://github.com/galaxyproject/galaxy/pull/19031>`_
* Silence the quota manager for updates by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19046 <https://github.com/galaxyproject/galaxy/pull/19046>`_
* Add job metrics per invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19062 <https://github.com/galaxyproject/galaxy/pull/19062>`_
* Annotate ``DatasetAssociationManager`` as generic type by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19063 <https://github.com/galaxyproject/galaxy/pull/19063>`_
* Move TRS import into WorkflowContentManager by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19070 <https://github.com/galaxyproject/galaxy/pull/19070>`_
* Replace poetry with uv by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19075 <https://github.com/galaxyproject/galaxy/pull/19075>`_
* Allow deferred datasets to behave as URIs by `@davelopez <https://github.com/davelopez>`_ in `#19077 <https://github.com/galaxyproject/galaxy/pull/19077>`_
* Implement workflow parameter validators. by `@jmchilton <https://github.com/jmchilton>`_ in `#19092 <https://github.com/galaxyproject/galaxy/pull/19092>`_
* Allow directory_uri workflow parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#19093 <https://github.com/galaxyproject/galaxy/pull/19093>`_
* Better cleanup of sharing roles on user purge by `@jdavcs <https://github.com/jdavcs>`_ in `#19096 <https://github.com/galaxyproject/galaxy/pull/19096>`_
* Support deferred datasets in visualizations by `@davelopez <https://github.com/davelopez>`_ in `#19097 <https://github.com/galaxyproject/galaxy/pull/19097>`_
* uv: Do not recalculate dependencies when exporting by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19099 <https://github.com/galaxyproject/galaxy/pull/19099>`_
* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
* Test hash validation also for upload by path by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19109 <https://github.com/galaxyproject/galaxy/pull/19109>`_
* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
* Add type annotations to ``JobRunnerMapper`` and related code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19115 <https://github.com/galaxyproject/galaxy/pull/19115>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19123 <https://github.com/galaxyproject/galaxy/pull/19123>`_
* Allow a posix file source to prefer linking. by `@jmchilton <https://github.com/jmchilton>`_ in `#19132 <https://github.com/galaxyproject/galaxy/pull/19132>`_
* Remove OpenLayers legacy files and add SVG logo by `@guerler <https://github.com/guerler>`_ in `#19135 <https://github.com/galaxyproject/galaxy/pull/19135>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19149 <https://github.com/galaxyproject/galaxy/pull/19149>`_
* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
* Workflow Inputs Activity by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#19252 <https://github.com/galaxyproject/galaxy/pull/19252>`_
=============
Other changes
=============
* Fix workflow invocation accessibility check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18746 <https://github.com/galaxyproject/galaxy/pull/18746>`_
* Fix destentation typo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19140 <https://github.com/galaxyproject/galaxy/pull/19140>`_
