galaxy-app


Namegalaxy-app JSON
Version 24.0.0 PyPI version JSON
download
home_pagehttps://github.com/galaxyproject/galaxy
SummaryGalaxy application (backend)
upload_time2024-04-03 02:48:19
maintainerNone
docs_urlNone
authorGalaxy Project and Community
requires_python>=3.8
licenseAFL
keywords galaxy
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage 
            
.. image:: https://badge.fury.io/py/galaxy-app.svg
   :target: https://pypi.org/project/galaxy-app/


Overview
--------

The Galaxy_ application logic (backend).

* Code: https://github.com/galaxyproject/galaxy

.. _Galaxy: http://galaxyproject.org/

History
-------

.. to_doc

-------------------
24.0.0 (2024-04-02)
-------------------


=========
Bug fixes
=========

* Reload built-in converters on toolbox reload by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17209 <https://github.com/galaxyproject/galaxy/pull/17209>`_
* Optional Reply-to SMTP header in tool error reports by `@neoformit <https://github.com/neoformit>`_ in `#17243 <https://github.com/galaxyproject/galaxy/pull/17243>`_
* Package tests fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17301 <https://github.com/galaxyproject/galaxy/pull/17301>`_
* Follow-up on #17274 and #17262 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17302 <https://github.com/galaxyproject/galaxy/pull/17302>`_
* Rollback invalidated transaction: catch them earlier by `@jdavcs <https://github.com/jdavcs>`_ in `#17312 <https://github.com/galaxyproject/galaxy/pull/17312>`_
* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17340 <https://github.com/galaxyproject/galaxy/pull/17340>`_
* Fix data_source and data_source_async bugs by `@wm75 <https://github.com/wm75>`_ in `#17422 <https://github.com/galaxyproject/galaxy/pull/17422>`_
* More efficient change_state queries, maybe fix deadlock by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17632 <https://github.com/galaxyproject/galaxy/pull/17632>`_
* Don't index tasks without task_uuid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17646 <https://github.com/galaxyproject/galaxy/pull/17646>`_
* Separate `ConnectedValue` from `RuntimeValue` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17678 <https://github.com/galaxyproject/galaxy/pull/17678>`_
* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17716 <https://github.com/galaxyproject/galaxy/pull/17716>`_
* Fix usage of DISTINCT by `@jdavcs <https://github.com/jdavcs>`_ in `#17759 <https://github.com/galaxyproject/galaxy/pull/17759>`_
* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17777 <https://github.com/galaxyproject/galaxy/pull/17777>`_
* Use ``hg clone --stream`` to clone repos by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17786 <https://github.com/galaxyproject/galaxy/pull/17786>`_
* Defer job attributes that are usually not needed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17795 <https://github.com/galaxyproject/galaxy/pull/17795>`_
* Fix change_datatype PJA for dynamic collections  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17803 <https://github.com/galaxyproject/galaxy/pull/17803>`_
* Fix archived histories mixing with active in histories list by `@davelopez <https://github.com/davelopez>`_ in `#17856 <https://github.com/galaxyproject/galaxy/pull/17856>`_
* Normalize extensions when loading tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17868 <https://github.com/galaxyproject/galaxy/pull/17868>`_
* Ignore user data table errors for now by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17880 <https://github.com/galaxyproject/galaxy/pull/17880>`_

============
Enhancements
============

* Add harmonize collections tool (or whatever other name) by `@lldelisle <https://github.com/lldelisle>`_ in `#16662 <https://github.com/galaxyproject/galaxy/pull/16662>`_
* Add support for Python 3.12 by `@tuncK <https://github.com/tuncK>`_ in `#16796 <https://github.com/galaxyproject/galaxy/pull/16796>`_
* SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs <https://github.com/jdavcs>`_ in `#16932 <https://github.com/galaxyproject/galaxy/pull/16932>`_
* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
* Support for OIDC API Auth and OIDC integration tests by `@nuwang <https://github.com/nuwang>`_ in `#16977 <https://github.com/galaxyproject/galaxy/pull/16977>`_
* Toward declarative help for Galaxy markdown directives. by `@jmchilton <https://github.com/jmchilton>`_ in `#16979 <https://github.com/galaxyproject/galaxy/pull/16979>`_
* Extend regex groups in stdio regex matches by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17016 <https://github.com/galaxyproject/galaxy/pull/17016>`_
* Vueify Admin User Grid by `@guerler <https://github.com/guerler>`_ in `#17030 <https://github.com/galaxyproject/galaxy/pull/17030>`_
* Remove web framework dependency from tools by `@davelopez <https://github.com/davelopez>`_ in `#17058 <https://github.com/galaxyproject/galaxy/pull/17058>`_
* Add select parameter with options from remote resources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17087 <https://github.com/galaxyproject/galaxy/pull/17087>`_
*  Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
* Vueify Admin Roles Grid by `@guerler <https://github.com/guerler>`_ in `#17118 <https://github.com/galaxyproject/galaxy/pull/17118>`_
* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17123 <https://github.com/galaxyproject/galaxy/pull/17123>`_
* Vueify Admin Groups Grid by `@guerler <https://github.com/guerler>`_ in `#17126 <https://github.com/galaxyproject/galaxy/pull/17126>`_
* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs <https://github.com/jdavcs>`_ in `#17132 <https://github.com/galaxyproject/galaxy/pull/17132>`_
* Vueify Admin Forms and Quota grids by `@guerler <https://github.com/guerler>`_ in `#17141 <https://github.com/galaxyproject/galaxy/pull/17141>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17157 <https://github.com/galaxyproject/galaxy/pull/17157>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17201 <https://github.com/galaxyproject/galaxy/pull/17201>`_
* Vendorize fastapi-utls.cbv by `@jdavcs <https://github.com/jdavcs>`_ in `#17205 <https://github.com/galaxyproject/galaxy/pull/17205>`_
* Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by `@jdavcs <https://github.com/jdavcs>`_ in `#17216 <https://github.com/galaxyproject/galaxy/pull/17216>`_
* Vueifiy History Grids by `@guerler <https://github.com/guerler>`_ in `#17219 <https://github.com/galaxyproject/galaxy/pull/17219>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17230 <https://github.com/galaxyproject/galaxy/pull/17230>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17235 <https://github.com/galaxyproject/galaxy/pull/17235>`_
* Allow job files to consume TUS uploads by `@jmchilton <https://github.com/jmchilton>`_ in `#17242 <https://github.com/galaxyproject/galaxy/pull/17242>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17247 <https://github.com/galaxyproject/galaxy/pull/17247>`_
* Migrate models to pydantic 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17262 <https://github.com/galaxyproject/galaxy/pull/17262>`_
* Consider Null inputs by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17271 <https://github.com/galaxyproject/galaxy/pull/17271>`_
* Add OIDC backend configuration schema and validation by `@uwwint <https://github.com/uwwint>`_ in `#17274 <https://github.com/galaxyproject/galaxy/pull/17274>`_
* Adds delete, purge and undelete batch operations to History Grid by `@guerler <https://github.com/guerler>`_ in `#17282 <https://github.com/galaxyproject/galaxy/pull/17282>`_
* Add ``__KEEP_SUCCESS_DATASETS__`` by `@lldelisle <https://github.com/lldelisle>`_ in `#17294 <https://github.com/galaxyproject/galaxy/pull/17294>`_
* Improve ModelManager type hints by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17299 <https://github.com/galaxyproject/galaxy/pull/17299>`_
* API endpoint that allows "changing" the objectstore for "safe" scenarios.  by `@jmchilton <https://github.com/jmchilton>`_ in `#17329 <https://github.com/galaxyproject/galaxy/pull/17329>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17333 <https://github.com/galaxyproject/galaxy/pull/17333>`_
* Add element_identifier and ext to inputs config file export by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17357 <https://github.com/galaxyproject/galaxy/pull/17357>`_
* Remove unused statements in job search function by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17361 <https://github.com/galaxyproject/galaxy/pull/17361>`_
* Enable ``warn_unreachable`` mypy option by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17365 <https://github.com/galaxyproject/galaxy/pull/17365>`_
* Fix type annotation of code using XML etree by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17367 <https://github.com/galaxyproject/galaxy/pull/17367>`_
* More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17381 <https://github.com/galaxyproject/galaxy/pull/17381>`_
* Cancel all active jobs when the user is deleted by `@davelopez <https://github.com/davelopez>`_ in `#17390 <https://github.com/galaxyproject/galaxy/pull/17390>`_
* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_
* Purge `groups` and `roles` from DB (for real) by `@davelopez <https://github.com/davelopez>`_ in `#17411 <https://github.com/galaxyproject/galaxy/pull/17411>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17420 <https://github.com/galaxyproject/galaxy/pull/17420>`_
* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17435 <https://github.com/galaxyproject/galaxy/pull/17435>`_
* Adds published histories to grid list by `@guerler <https://github.com/guerler>`_ in `#17449 <https://github.com/galaxyproject/galaxy/pull/17449>`_
* Allow filtering history datasets by object store ID and quota source. by `@jmchilton <https://github.com/jmchilton>`_ in `#17460 <https://github.com/galaxyproject/galaxy/pull/17460>`_
* `data_column` parameter: use `column_names` metadata if present by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17478 <https://github.com/galaxyproject/galaxy/pull/17478>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17486 <https://github.com/galaxyproject/galaxy/pull/17486>`_
* Consolidate resource grids into tab views by `@guerler <https://github.com/guerler>`_ in `#17487 <https://github.com/galaxyproject/galaxy/pull/17487>`_
* Update k8s docker python to 3.12 by `@nuwang <https://github.com/nuwang>`_ in `#17494 <https://github.com/galaxyproject/galaxy/pull/17494>`_
* add encode ID API endpoint by `@mira-miracoli <https://github.com/mira-miracoli>`_ in `#17510 <https://github.com/galaxyproject/galaxy/pull/17510>`_
* Fixing data_source tools and incrementing tool profile by `@wm75 <https://github.com/wm75>`_ in `#17515 <https://github.com/galaxyproject/galaxy/pull/17515>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17541 <https://github.com/galaxyproject/galaxy/pull/17541>`_
* Add `image_diff` comparison method for test output verification using images by `@kostrykin <https://github.com/kostrykin>`_ in `#17556 <https://github.com/galaxyproject/galaxy/pull/17556>`_
* Filter out subworkflow invocations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17558 <https://github.com/galaxyproject/galaxy/pull/17558>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17580 <https://github.com/galaxyproject/galaxy/pull/17580>`_
* Restore histories API behavior for `keys` query parameter by `@davelopez <https://github.com/davelopez>`_ in `#17779 <https://github.com/galaxyproject/galaxy/pull/17779>`_
* Fix datasets API custom keys encoding by `@davelopez <https://github.com/davelopez>`_ in `#17793 <https://github.com/galaxyproject/galaxy/pull/17793>`_
* Improved error messages for runtime sharing problems. by `@jmchilton <https://github.com/jmchilton>`_ in `#17794 <https://github.com/galaxyproject/galaxy/pull/17794>`_
* Allow admin to sharpen language about selected object stores. by `@jmchilton <https://github.com/jmchilton>`_ in `#17806 <https://github.com/galaxyproject/galaxy/pull/17806>`_

=============
Other changes
=============

* consistently compare profile versions by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16492 <https://github.com/galaxyproject/galaxy/pull/16492>`_

-------------------
23.2.1 (2024-02-21)
-------------------


=========
Bug fixes
=========

* pin fs.dropboxfs to >=1 by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16451 <https://github.com/galaxyproject/galaxy/pull/16451>`_
* Remove unnecessary check: item cannot be None by `@jdavcs <https://github.com/jdavcs>`_ in `#16550 <https://github.com/galaxyproject/galaxy/pull/16550>`_
* Fix: serialize `tool_shed_urls` directly from the API by `@davelopez <https://github.com/davelopez>`_ in `#16561 <https://github.com/galaxyproject/galaxy/pull/16561>`_
* Fix dependency update GitHub workflow by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16639 <https://github.com/galaxyproject/galaxy/pull/16639>`_
* Ensure Job belongs to current SA session by `@jdavcs <https://github.com/jdavcs>`_ in `#16647 <https://github.com/galaxyproject/galaxy/pull/16647>`_
* Account for shared usage between TS and galaxy apps by `@jdavcs <https://github.com/jdavcs>`_ in `#16746 <https://github.com/galaxyproject/galaxy/pull/16746>`_
* move the email and username redacting from the role loop by `@martenson <https://github.com/martenson>`_ in `#16805 <https://github.com/galaxyproject/galaxy/pull/16805>`_
* Fix shed unit test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16811 <https://github.com/galaxyproject/galaxy/pull/16811>`_
* chore: fix typos by `@afuetterer <https://github.com/afuetterer>`_ in `#16851 <https://github.com/galaxyproject/galaxy/pull/16851>`_
* Fix bug in SQLAlchemy statement by `@jdavcs <https://github.com/jdavcs>`_ in `#16881 <https://github.com/galaxyproject/galaxy/pull/16881>`_
* Ruff and flake8 fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16884 <https://github.com/galaxyproject/galaxy/pull/16884>`_
* Update help in relabel_from_file.xml by `@lldelisle <https://github.com/lldelisle>`_ in `#16891 <https://github.com/galaxyproject/galaxy/pull/16891>`_
* Fix subtle bug in listify function + simplify list munging by `@jdavcs <https://github.com/jdavcs>`_ in `#16904 <https://github.com/galaxyproject/galaxy/pull/16904>`_
* prep for updated h5py and typos by `@mr-c <https://github.com/mr-c>`_ in `#16963 <https://github.com/galaxyproject/galaxy/pull/16963>`_
* Enhancement to Tool Form page, Repeating form fields implement parameter instructions by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#17018 <https://github.com/galaxyproject/galaxy/pull/17018>`_
* Expose file_name property in DatasetFilenameWrapper by `@jdavcs <https://github.com/jdavcs>`_ in `#17107 <https://github.com/galaxyproject/galaxy/pull/17107>`_
* Fix ``to_cwl`` for nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17276 <https://github.com/galaxyproject/galaxy/pull/17276>`_
* Rollback invalidated transaction by `@jdavcs <https://github.com/jdavcs>`_ in `#17280 <https://github.com/galaxyproject/galaxy/pull/17280>`_
* Install newer celery on python 3.8+ by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17309 <https://github.com/galaxyproject/galaxy/pull/17309>`_
* Backport Rollback invalidated transaction: catch them earlier by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17315 <https://github.com/galaxyproject/galaxy/pull/17315>`_
* Discard sqlalchemy session after task completion by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17317 <https://github.com/galaxyproject/galaxy/pull/17317>`_
* Scope session for job  runner monitor loop by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17319 <https://github.com/galaxyproject/galaxy/pull/17319>`_
* Fix History contents `genome_build` filter postgresql bug by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#17384 <https://github.com/galaxyproject/galaxy/pull/17384>`_
* Update python-multipart to 0.0.7 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17429 <https://github.com/galaxyproject/galaxy/pull/17429>`_
* Build param dict before creating entrypoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17440 <https://github.com/galaxyproject/galaxy/pull/17440>`_
* Fix bug: true >> True by `@jdavcs <https://github.com/jdavcs>`_ in `#17446 <https://github.com/galaxyproject/galaxy/pull/17446>`_
* Set metadata states on dataset association, not dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17474 <https://github.com/galaxyproject/galaxy/pull/17474>`_
* Remove two print statements by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17480 <https://github.com/galaxyproject/galaxy/pull/17480>`_
* Provide working routes.url_for every ASGI request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17497 <https://github.com/galaxyproject/galaxy/pull/17497>`_

============
Enhancements
============

* Implement default locations for data and collection parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#14955 <https://github.com/galaxyproject/galaxy/pull/14955>`_
* Enable job resubmissions in k8s runner by `@pcm32 <https://github.com/pcm32>`_ in `#15238 <https://github.com/galaxyproject/galaxy/pull/15238>`_
* Add parameter name to validation errors by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15440 <https://github.com/galaxyproject/galaxy/pull/15440>`_
* Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#15639 <https://github.com/galaxyproject/galaxy/pull/15639>`_
* Add ability to assert metadata properties on input dataset parameters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15825 <https://github.com/galaxyproject/galaxy/pull/15825>`_
* Limit number of celery task executions per second per user by `@claudiofr <https://github.com/claudiofr>`_ in `#16232 <https://github.com/galaxyproject/galaxy/pull/16232>`_
* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16252 <https://github.com/galaxyproject/galaxy/pull/16252>`_
* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs <https://github.com/jdavcs>`_ in `#16264 <https://github.com/galaxyproject/galaxy/pull/16264>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16305 <https://github.com/galaxyproject/galaxy/pull/16305>`_
* Add carbon emissions admin configuration options by `@Renni771 <https://github.com/Renni771>`_ in `#16307 <https://github.com/galaxyproject/galaxy/pull/16307>`_
* Migrate a part of the users API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16341 <https://github.com/galaxyproject/galaxy/pull/16341>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16360 <https://github.com/galaxyproject/galaxy/pull/16360>`_
* Add Invenio RDM repository integration by `@davelopez <https://github.com/davelopez>`_ in `#16381 <https://github.com/galaxyproject/galaxy/pull/16381>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16389 <https://github.com/galaxyproject/galaxy/pull/16389>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16409 <https://github.com/galaxyproject/galaxy/pull/16409>`_
* Refactor FilesDialog + Remote Files API schema improvements by `@davelopez <https://github.com/davelopez>`_ in `#16420 <https://github.com/galaxyproject/galaxy/pull/16420>`_
* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs <https://github.com/jdavcs>`_ in `#16431 <https://github.com/galaxyproject/galaxy/pull/16431>`_
* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs <https://github.com/jdavcs>`_ in `#16434 <https://github.com/galaxyproject/galaxy/pull/16434>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16436 <https://github.com/galaxyproject/galaxy/pull/16436>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16485 <https://github.com/galaxyproject/galaxy/pull/16485>`_
* Rename MetadataEqualsValidator by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16489 <https://github.com/galaxyproject/galaxy/pull/16489>`_
* Add support for CILogon deployments in different regions than the US by `@uwwint <https://github.com/uwwint>`_ in `#16490 <https://github.com/galaxyproject/galaxy/pull/16490>`_
* Refactor/OIDC custos by `@uwwint <https://github.com/uwwint>`_ in `#16497 <https://github.com/galaxyproject/galaxy/pull/16497>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16521 <https://github.com/galaxyproject/galaxy/pull/16521>`_
* Move database access code out of ``galaxy.util`` by `@jdavcs <https://github.com/jdavcs>`_ in `#16526 <https://github.com/galaxyproject/galaxy/pull/16526>`_
* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16536 <https://github.com/galaxyproject/galaxy/pull/16536>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16577 <https://github.com/galaxyproject/galaxy/pull/16577>`_
* Vueify Tool Form Data Selector by `@guerler <https://github.com/guerler>`_ in `#16578 <https://github.com/galaxyproject/galaxy/pull/16578>`_
* Workflow Comments 💬 by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16612 <https://github.com/galaxyproject/galaxy/pull/16612>`_
* Switch out conditional requirement parser by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16636 <https://github.com/galaxyproject/galaxy/pull/16636>`_
* Add scroll pagination and username filter to `HistoryPublishedList` by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16642 <https://github.com/galaxyproject/galaxy/pull/16642>`_
* Bump samtools converters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16668 <https://github.com/galaxyproject/galaxy/pull/16668>`_
* Galaxy Markdown - add workflow image and license to Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16672 <https://github.com/galaxyproject/galaxy/pull/16672>`_
* Implement instance URLs in Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16675 <https://github.com/galaxyproject/galaxy/pull/16675>`_
* Change Sentry error reporting plug-in by `@kysrpex <https://github.com/kysrpex>`_ in `#16686 <https://github.com/galaxyproject/galaxy/pull/16686>`_
* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola <https://github.com/lopiola>`_ in `#16690 <https://github.com/galaxyproject/galaxy/pull/16690>`_
* Enhance task monitor composable by `@davelopez <https://github.com/davelopez>`_ in `#16695 <https://github.com/galaxyproject/galaxy/pull/16695>`_
* Misc. edits/refactorings to session handling  by `@jdavcs <https://github.com/jdavcs>`_ in `#16712 <https://github.com/galaxyproject/galaxy/pull/16712>`_
* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs <https://github.com/jdavcs>`_ in `#16724 <https://github.com/galaxyproject/galaxy/pull/16724>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16735 <https://github.com/galaxyproject/galaxy/pull/16735>`_
* Convert ISO to UTC for Date/Time in workflow reports by `@assuntad23 <https://github.com/assuntad23>`_ in `#16758 <https://github.com/galaxyproject/galaxy/pull/16758>`_
* Replace ELIXIR AAI button with Life Science login by `@sebastian-schaaf <https://github.com/sebastian-schaaf>`_ in `#16762 <https://github.com/galaxyproject/galaxy/pull/16762>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16770 <https://github.com/galaxyproject/galaxy/pull/16770>`_
* Migrate a part of the jobs API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16778 <https://github.com/galaxyproject/galaxy/pull/16778>`_
* Add EGI Check-in as OIDC authentication option by `@enolfc <https://github.com/enolfc>`_ in `#16782 <https://github.com/galaxyproject/galaxy/pull/16782>`_
* Replace file_name property with get_file_name function by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#16783 <https://github.com/galaxyproject/galaxy/pull/16783>`_
* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu <https://github.com/sveinugu>`_ in `#16795 <https://github.com/galaxyproject/galaxy/pull/16795>`_
* Galaxy help forum integration by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16798 <https://github.com/galaxyproject/galaxy/pull/16798>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16807 <https://github.com/galaxyproject/galaxy/pull/16807>`_
* Another batch of SA2.0 edits in TS2.0 (part 3) by `@jdavcs <https://github.com/jdavcs>`_ in `#16833 <https://github.com/galaxyproject/galaxy/pull/16833>`_
* Remove remaining legacy backbone form input elements by `@guerler <https://github.com/guerler>`_ in `#16834 <https://github.com/galaxyproject/galaxy/pull/16834>`_
* SQLAlchemy 2.0 upgrades (part 4) by `@jdavcs <https://github.com/jdavcs>`_ in `#16852 <https://github.com/galaxyproject/galaxy/pull/16852>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16853 <https://github.com/galaxyproject/galaxy/pull/16853>`_
* Drop unused HistoryContentManager code and related tests by `@jdavcs <https://github.com/jdavcs>`_ in `#16882 <https://github.com/galaxyproject/galaxy/pull/16882>`_
* Vueify Visualizations Grid by `@guerler <https://github.com/guerler>`_ in `#16892 <https://github.com/galaxyproject/galaxy/pull/16892>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16896 <https://github.com/galaxyproject/galaxy/pull/16896>`_
* Enable some flake8-logging-format rules in ruff by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16915 <https://github.com/galaxyproject/galaxy/pull/16915>`_
* Remove "Create Workflow" form and allow workflow creation in editor by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16938 <https://github.com/galaxyproject/galaxy/pull/16938>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16939 <https://github.com/galaxyproject/galaxy/pull/16939>`_
* Add helper to get dataset or collection via ``src`` and ``id`` by `@mr-c <https://github.com/mr-c>`_ in `#16953 <https://github.com/galaxyproject/galaxy/pull/16953>`_
* Allow non-optional integer/float params without value attribute by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16966 <https://github.com/galaxyproject/galaxy/pull/16966>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16978 <https://github.com/galaxyproject/galaxy/pull/16978>`_
* Fix invocation report to target correct workflow version. by `@jmchilton <https://github.com/jmchilton>`_ in `#17008 <https://github.com/galaxyproject/galaxy/pull/17008>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17011 <https://github.com/galaxyproject/galaxy/pull/17011>`_
* Upgrade job manager's index_query method to SA2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17020 <https://github.com/galaxyproject/galaxy/pull/17020>`_
* optimize object store cache operations by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17025 <https://github.com/galaxyproject/galaxy/pull/17025>`_
* Require name for workflows on save, set default to Unnamed Workflow by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#17038 <https://github.com/galaxyproject/galaxy/pull/17038>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17050 <https://github.com/galaxyproject/galaxy/pull/17050>`_
* Migrate groups API to fastAPI by `@arash77 <https://github.com/arash77>`_ in `#17051 <https://github.com/galaxyproject/galaxy/pull/17051>`_
* Migrate ItemTags API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#17064 <https://github.com/galaxyproject/galaxy/pull/17064>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17084 <https://github.com/galaxyproject/galaxy/pull/17084>`_
* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17342 <https://github.com/galaxyproject/galaxy/pull/17342>`_

=============
Other changes
=============

* Merge 23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16534 <https://github.com/galaxyproject/galaxy/pull/16534>`_
* Revert "[23.1] Enable job resubmissions in k8s runner" by `@nuwang <https://github.com/nuwang>`_ in `#17323 <https://github.com/galaxyproject/galaxy/pull/17323>`_
* Fix succces typo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17481 <https://github.com/galaxyproject/galaxy/pull/17481>`_

-------------------
23.1.4 (2024-01-04)
-------------------


=========
Bug fixes
=========

* Fix workflow index total matches counting by `@davelopez <https://github.com/davelopez>`_ in `#17176 <https://github.com/galaxyproject/galaxy/pull/17176>`_
* Fix `url_for` in tool error reports by `@davelopez <https://github.com/davelopez>`_ in `#17210 <https://github.com/galaxyproject/galaxy/pull/17210>`_

-------------------
23.1.3 (2023-12-01)
-------------------

No recorded changes since last release

-------------------
23.1.2 (2023-11-29)
-------------------


=========
Bug fixes
=========

* Fix unbound ``runner`` variable when there is an error in the job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16906 <https://github.com/galaxyproject/galaxy/pull/16906>`_
* Fix discarded dataset ordering in Storage Dashboard by `@davelopez <https://github.com/davelopez>`_ in `#16929 <https://github.com/galaxyproject/galaxy/pull/16929>`_
* Include owner's annotation when exporting workflow by `@dannon <https://github.com/dannon>`_ in `#16930 <https://github.com/galaxyproject/galaxy/pull/16930>`_
* Skip state filtering in ``__MERGE_COLLECTION__`` tool  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16937 <https://github.com/galaxyproject/galaxy/pull/16937>`_
* Prevent Singular external auth users from disconnecting identity by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16961 <https://github.com/galaxyproject/galaxy/pull/16961>`_
* Prevent workflow submission with missing input values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17048 <https://github.com/galaxyproject/galaxy/pull/17048>`_
* Fix extra files collection if using ``store_by="id"`` and `outputs_to_working_directory` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17067 <https://github.com/galaxyproject/galaxy/pull/17067>`_
* Remove rollback from ``__check_jobs_at_startup`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17085 <https://github.com/galaxyproject/galaxy/pull/17085>`_

============
Enhancements
============

* Improve invocation error reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16917 <https://github.com/galaxyproject/galaxy/pull/16917>`_

-------------------
23.1.1 (2023-10-23)
-------------------


=========
Bug fixes
=========

* read job_conf directly from `config_dir` instead of computing it again from `config_file` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15596 <https://github.com/galaxyproject/galaxy/pull/15596>`_
* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_
* Fix filesource file url support by `@nuwang <https://github.com/nuwang>`_ in `#15794 <https://github.com/galaxyproject/galaxy/pull/15794>`_
* Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by `@jdavcs <https://github.com/jdavcs>`_ in `#15811 <https://github.com/galaxyproject/galaxy/pull/15811>`_
* Change confusing pulsar logs message by `@kysrpex <https://github.com/kysrpex>`_ in `#16038 <https://github.com/galaxyproject/galaxy/pull/16038>`_
* Fix and test startup with Python 3.11 on macOS by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16082 <https://github.com/galaxyproject/galaxy/pull/16082>`_
* Fix : Ignore error messages for admin created accounts by `@jvanbraekel <https://github.com/jvanbraekel>`_ in `#16132 <https://github.com/galaxyproject/galaxy/pull/16132>`_
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
* Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by `@jdavcs <https://github.com/jdavcs>`_ in `#16208 <https://github.com/galaxyproject/galaxy/pull/16208>`_
* Fix ordering of data libraries from API by `@martenson <https://github.com/martenson>`_ in `#16300 <https://github.com/galaxyproject/galaxy/pull/16300>`_
* qualify querying for an api-key by `@martenson <https://github.com/martenson>`_ in `#16320 <https://github.com/galaxyproject/galaxy/pull/16320>`_
* Fix tags ownership by `@davelopez <https://github.com/davelopez>`_ in `#16339 <https://github.com/galaxyproject/galaxy/pull/16339>`_
* Job cache fixes for DCEs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16384 <https://github.com/galaxyproject/galaxy/pull/16384>`_
* Fix histories count by `@davelopez <https://github.com/davelopez>`_ in `#16400 <https://github.com/galaxyproject/galaxy/pull/16400>`_
* Fix select statement syntax for SQLAlchemy 2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#16421 <https://github.com/galaxyproject/galaxy/pull/16421>`_
* Fix up unit tests for local use by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16483 <https://github.com/galaxyproject/galaxy/pull/16483>`_
* Run through tmp_dir_creation_statement only once by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16529 <https://github.com/galaxyproject/galaxy/pull/16529>`_
* Fix double-encoding notification content by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16530 <https://github.com/galaxyproject/galaxy/pull/16530>`_
* Limit tool document cache to tool configs with explicit cache path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16537 <https://github.com/galaxyproject/galaxy/pull/16537>`_
* Fix `multiple` remote test data by `@davelopez <https://github.com/davelopez>`_ in `#16542 <https://github.com/galaxyproject/galaxy/pull/16542>`_
* Ignore errors with user-set job resources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16579 <https://github.com/galaxyproject/galaxy/pull/16579>`_
* Fix replacement parameters for subworkflows. by `@jmchilton <https://github.com/jmchilton>`_ in `#16592 <https://github.com/galaxyproject/galaxy/pull/16592>`_
* make sure that TMP, TEMP, and TMPDIR are set by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16594 <https://github.com/galaxyproject/galaxy/pull/16594>`_
* Bump minimum tpv version to 2.3.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16597 <https://github.com/galaxyproject/galaxy/pull/16597>`_
* Backport tool mem fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16601 <https://github.com/galaxyproject/galaxy/pull/16601>`_
* Reload toolbox after forking when using `--preload` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16620 <https://github.com/galaxyproject/galaxy/pull/16620>`_
* Account for expires/expires_in when refreshing token by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16621 <https://github.com/galaxyproject/galaxy/pull/16621>`_
* Fixes for conditional subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16632 <https://github.com/galaxyproject/galaxy/pull/16632>`_
* Fix nested conditional workflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16641 <https://github.com/galaxyproject/galaxy/pull/16641>`_
* Ensure Job belongs to current SA session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16655 <https://github.com/galaxyproject/galaxy/pull/16655>`_
* Fix expression evaluation for nested state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16656 <https://github.com/galaxyproject/galaxy/pull/16656>`_
* Make sort_collection tool require terminal datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16661 <https://github.com/galaxyproject/galaxy/pull/16661>`_
* Push to object store even if ``set_meta`` fails by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16667 <https://github.com/galaxyproject/galaxy/pull/16667>`_
* Fix metadata setting in extended metadata + outputs_to_working_directory mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16678 <https://github.com/galaxyproject/galaxy/pull/16678>`_
* Fix regex validation for global inline flags by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16683 <https://github.com/galaxyproject/galaxy/pull/16683>`_
* Fix closed transaction error on galaxy startup/check jobs by `@jdavcs <https://github.com/jdavcs>`_ in `#16687 <https://github.com/galaxyproject/galaxy/pull/16687>`_
* Add missing join condition in job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16710 <https://github.com/galaxyproject/galaxy/pull/16710>`_
* Fix job search query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16714 <https://github.com/galaxyproject/galaxy/pull/16714>`_
* Copy the collection contents by default when copying a collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16717 <https://github.com/galaxyproject/galaxy/pull/16717>`_
* Fix collection id encoding by `@davelopez <https://github.com/davelopez>`_ in `#16718 <https://github.com/galaxyproject/galaxy/pull/16718>`_
* Workaround for XML nodes of job resource parameters losing their children by `@kysrpex <https://github.com/kysrpex>`_ in `#16728 <https://github.com/galaxyproject/galaxy/pull/16728>`_
* move the email and username redacting from the role loop by `@martenson <https://github.com/martenson>`_ in `#16820 <https://github.com/galaxyproject/galaxy/pull/16820>`_
* Fix parameter display in job info page for tools with sections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16821 <https://github.com/galaxyproject/galaxy/pull/16821>`_
* Fix workflow preview display if tool state does not contain all parameter values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16829 <https://github.com/galaxyproject/galaxy/pull/16829>`_
* Fix up local tool version handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16836 <https://github.com/galaxyproject/galaxy/pull/16836>`_
* Fix and prevent persisting null file_size by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16855 <https://github.com/galaxyproject/galaxy/pull/16855>`_
* Allow referring to steps by label only in markdown editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16861 <https://github.com/galaxyproject/galaxy/pull/16861>`_
* Fix safe update version handling in run form by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16865 <https://github.com/galaxyproject/galaxy/pull/16865>`_
* Remove more flushes in database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16875 <https://github.com/galaxyproject/galaxy/pull/16875>`_
* Fix tag ownership check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16877 <https://github.com/galaxyproject/galaxy/pull/16877>`_

============
Enhancements
============

* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15019 <https://github.com/galaxyproject/galaxy/pull/15019>`_
* Add slack error reporting plugin by `@hexylena <https://github.com/hexylena>`_ in `#15025 <https://github.com/galaxyproject/galaxy/pull/15025>`_
* Various Tool Shed Cleanup by `@jmchilton <https://github.com/jmchilton>`_ in `#15247 <https://github.com/galaxyproject/galaxy/pull/15247>`_
* Add Storage Management API by `@davelopez <https://github.com/davelopez>`_ in `#15295 <https://github.com/galaxyproject/galaxy/pull/15295>`_
* OIDC tokens by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#15300 <https://github.com/galaxyproject/galaxy/pull/15300>`_
* Expose additional beaker caching backends  by `@claudiofr <https://github.com/claudiofr>`_ in `#15349 <https://github.com/galaxyproject/galaxy/pull/15349>`_
* Add support for visualizing HDF5 datasets. by `@jarrah42 <https://github.com/jarrah42>`_ in `#15394 <https://github.com/galaxyproject/galaxy/pull/15394>`_
* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs <https://github.com/jdavcs>`_ in `#15421 <https://github.com/galaxyproject/galaxy/pull/15421>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15435 <https://github.com/galaxyproject/galaxy/pull/15435>`_
* Fix for new style conda packages by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15446 <https://github.com/galaxyproject/galaxy/pull/15446>`_
* Move database access code out of tool_util by `@jdavcs <https://github.com/jdavcs>`_ in `#15467 <https://github.com/galaxyproject/galaxy/pull/15467>`_
* Protection against problematic boolean parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#15493 <https://github.com/galaxyproject/galaxy/pull/15493>`_
* Use connection instead of session for ItemGrabber by `@jdavcs <https://github.com/jdavcs>`_ in `#15496 <https://github.com/galaxyproject/galaxy/pull/15496>`_
* Unify url handling with filesources by `@nuwang <https://github.com/nuwang>`_ in `#15497 <https://github.com/galaxyproject/galaxy/pull/15497>`_
* Move TS to Alembic by `@jdavcs <https://github.com/jdavcs>`_ in `#15509 <https://github.com/galaxyproject/galaxy/pull/15509>`_
* Explore tool remote test data by `@davelopez <https://github.com/davelopez>`_ in `#15510 <https://github.com/galaxyproject/galaxy/pull/15510>`_
* Handle "email_from" config option consistently, as per schema description by `@jdavcs <https://github.com/jdavcs>`_ in `#15557 <https://github.com/galaxyproject/galaxy/pull/15557>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15564 <https://github.com/galaxyproject/galaxy/pull/15564>`_
* Drop workflow exports to myexperiment.org by `@dannon <https://github.com/dannon>`_ in `#15576 <https://github.com/galaxyproject/galaxy/pull/15576>`_
* Update database_heartbeat for SA 2.0 compatibility by `@jdavcs <https://github.com/jdavcs>`_ in `#15611 <https://github.com/galaxyproject/galaxy/pull/15611>`_
* Add suggested Training material to Tool Form by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#15628 <https://github.com/galaxyproject/galaxy/pull/15628>`_
* Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by `@jdavcs <https://github.com/jdavcs>`_ in `#15643 <https://github.com/galaxyproject/galaxy/pull/15643>`_
* Add Galaxy Notification System by `@davelopez <https://github.com/davelopez>`_ in `#15663 <https://github.com/galaxyproject/galaxy/pull/15663>`_
* Unpin Beaker requirement by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15665 <https://github.com/galaxyproject/galaxy/pull/15665>`_
* Add transactional state to JobHandlerStopQueue by `@jdavcs <https://github.com/jdavcs>`_ in `#15671 <https://github.com/galaxyproject/galaxy/pull/15671>`_
* Verify that activation and reset emails are properly generated by `@guerler <https://github.com/guerler>`_ in `#15681 <https://github.com/galaxyproject/galaxy/pull/15681>`_
* Add transactional state to workflow scheduling manager by `@jdavcs <https://github.com/jdavcs>`_ in `#15683 <https://github.com/galaxyproject/galaxy/pull/15683>`_
* Remove DELETED_NEW job state from code base by `@jdavcs <https://github.com/jdavcs>`_ in `#15690 <https://github.com/galaxyproject/galaxy/pull/15690>`_
* Fix/Enhance recalculate disk usage API endpoint by `@davelopez <https://github.com/davelopez>`_ in `#15739 <https://github.com/galaxyproject/galaxy/pull/15739>`_
* Add API test and refactor code for related:hid history filter by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15786 <https://github.com/galaxyproject/galaxy/pull/15786>`_
* Migrate to MyST-Parser for Markdown docs by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15844 <https://github.com/galaxyproject/galaxy/pull/15844>`_
* Drop use_legacy_history from config  by `@dannon <https://github.com/dannon>`_ in `#15861 <https://github.com/galaxyproject/galaxy/pull/15861>`_
* Drop database views by `@jdavcs <https://github.com/jdavcs>`_ in `#15876 <https://github.com/galaxyproject/galaxy/pull/15876>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15890 <https://github.com/galaxyproject/galaxy/pull/15890>`_
* Allow pending inputs in some collection operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15892 <https://github.com/galaxyproject/galaxy/pull/15892>`_
* Updated doc and tests for attribute value filter by `@tuncK <https://github.com/tuncK>`_ in `#15929 <https://github.com/galaxyproject/galaxy/pull/15929>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15942 <https://github.com/galaxyproject/galaxy/pull/15942>`_
* Record input datasets and collections at full parameter path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15978 <https://github.com/galaxyproject/galaxy/pull/15978>`_
* Export tool citations configurable message by `@minh-biocommons <https://github.com/minh-biocommons>`_ in `#15998 <https://github.com/galaxyproject/galaxy/pull/15998>`_
* Add History Archival feature by `@davelopez <https://github.com/davelopez>`_ in `#16003 <https://github.com/galaxyproject/galaxy/pull/16003>`_
* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16035 <https://github.com/galaxyproject/galaxy/pull/16035>`_
* Add missing fields to HistorySummary schema model by `@davelopez <https://github.com/davelopez>`_ in `#16041 <https://github.com/galaxyproject/galaxy/pull/16041>`_
* Vendorise ``packaging.versions.LegacyVersion`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16058 <https://github.com/galaxyproject/galaxy/pull/16058>`_
* Add Repository owner field to ToolSearch by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16061 <https://github.com/galaxyproject/galaxy/pull/16061>`_
* Add count support for listing filters by `@davelopez <https://github.com/davelopez>`_ in `#16075 <https://github.com/galaxyproject/galaxy/pull/16075>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16086 <https://github.com/galaxyproject/galaxy/pull/16086>`_
* Improved Cache Monitoring for Object Stores by `@jmchilton <https://github.com/jmchilton>`_ in `#16110 <https://github.com/galaxyproject/galaxy/pull/16110>`_
* Integrate accessibility testing into Selenium testing by `@jmchilton <https://github.com/jmchilton>`_ in `#16122 <https://github.com/galaxyproject/galaxy/pull/16122>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16123 <https://github.com/galaxyproject/galaxy/pull/16123>`_
* Improve histories and datasets immutability checks by `@davelopez <https://github.com/davelopez>`_ in `#16143 <https://github.com/galaxyproject/galaxy/pull/16143>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16153 <https://github.com/galaxyproject/galaxy/pull/16153>`_
* Migrate display applications API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16156 <https://github.com/galaxyproject/galaxy/pull/16156>`_
* adjust grid sharing indicators by `@martenson <https://github.com/martenson>`_ in `#16163 <https://github.com/galaxyproject/galaxy/pull/16163>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16182 <https://github.com/galaxyproject/galaxy/pull/16182>`_
* Drop workarounds for old ro-crate-py and docutils versions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16198 <https://github.com/galaxyproject/galaxy/pull/16198>`_
* Remove various fallback behaviors by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16199 <https://github.com/galaxyproject/galaxy/pull/16199>`_
* bring grids for (published) pages on par with workflows by `@martenson <https://github.com/martenson>`_ in `#16209 <https://github.com/galaxyproject/galaxy/pull/16209>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16227 <https://github.com/galaxyproject/galaxy/pull/16227>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16267 <https://github.com/galaxyproject/galaxy/pull/16267>`_
* Fix tool remote test data by `@davelopez <https://github.com/davelopez>`_ in `#16311 <https://github.com/galaxyproject/galaxy/pull/16311>`_
* Hide conditionally skipped output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16356 <https://github.com/galaxyproject/galaxy/pull/16356>`_
* Fix Storage Dashboard missing archived histories by `@davelopez <https://github.com/davelopez>`_ in `#16473 <https://github.com/galaxyproject/galaxy/pull/16473>`_
* Bump bx-python to 0.10.0 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16484 <https://github.com/galaxyproject/galaxy/pull/16484>`_
* Drop expunge_all() call in WebTransactionRequest by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16606 <https://github.com/galaxyproject/galaxy/pull/16606>`_

=============
Other changes
=============

* Follow up on object store selection PR. by `@jmchilton <https://github.com/jmchilton>`_ in `#15654 <https://github.com/galaxyproject/galaxy/pull/15654>`_
* merge release_23.0 into dev by `@martenson <https://github.com/martenson>`_ in `#15830 <https://github.com/galaxyproject/galaxy/pull/15830>`_
* Move axe-selenium-python to dev dependencies by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16162 <https://github.com/galaxyproject/galaxy/pull/16162>`_
* Bump msal version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16285 <https://github.com/galaxyproject/galaxy/pull/16285>`_
* Fix error_reports linting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16465 <https://github.com/galaxyproject/galaxy/pull/16465>`_

-------------------
23.0.6 (2023-10-23)
-------------------


=========
Bug fixes
=========

* Fix upload paramfile handling (for real user setups) by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16504 <https://github.com/galaxyproject/galaxy/pull/16504>`_
* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
* Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16569 <https://github.com/galaxyproject/galaxy/pull/16569>`_
* Fix conditional step evaluation with datasets in repeats by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16584 <https://github.com/galaxyproject/galaxy/pull/16584>`_
* Don't read request body into memory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16585 <https://github.com/galaxyproject/galaxy/pull/16585>`_
* Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_
* Lazy load tool data tables in celery worker by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16640 <https://github.com/galaxyproject/galaxy/pull/16640>`_
* Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer by `@simonbray <https://github.com/simonbray>`_ in `#16659 <https://github.com/galaxyproject/galaxy/pull/16659>`_

============
Enhancements
============

* Update pulsar client library to 0.15.5 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16701 <https://github.com/galaxyproject/galaxy/pull/16701>`_

-------------------
23.0.5 (2023-07-29)
-------------------


=========
Bug fixes
=========

* Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16403 <https://github.com/galaxyproject/galaxy/pull/16403>`_
* Fix test discovery in vscode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16413 <https://github.com/galaxyproject/galaxy/pull/16413>`_
* Fixes for (gitlab) error reporting by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16424 <https://github.com/galaxyproject/galaxy/pull/16424>`_

-------------------
23.0.4 (2023-06-30)
-------------------


=========
Bug fixes
=========

* Fix default when statement evaluation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16332 <https://github.com/galaxyproject/galaxy/pull/16332>`_
* Redact private role name and description when purging user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16349 <https://github.com/galaxyproject/galaxy/pull/16349>`_

-------------------
23.0.3 (2023-06-26)
-------------------


=========
Bug fixes
=========

* Bump galaxy-release-util version to 0.1.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16241 <https://github.com/galaxyproject/galaxy/pull/16241>`_

============
Enhancements
============

* When importing tool data bundles, use the first loc file for the matching table by `@natefoo <https://github.com/natefoo>`_ in `#16247 <https://github.com/galaxyproject/galaxy/pull/16247>`_

=============
Other changes
=============

* Forward port of slugify username received from oidc by `@nuwang <https://github.com/nuwang>`_ in `#16271 <https://github.com/galaxyproject/galaxy/pull/16271>`_

-------------------
23.0.2 (2023-06-13)
-------------------


=========
Bug fixes
=========

* Fix ``Text File Busy`` errors at the source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16212 <https://github.com/galaxyproject/galaxy/pull/16212>`_

============
Enhancements
============

* Point release deps fixes and docs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16214 <https://github.com/galaxyproject/galaxy/pull/16214>`_
* Use galaxy-release-util to upload python packages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16240 <https://github.com/galaxyproject/galaxy/pull/16240>`_

-------------------
23.0.1 (2023-06-08)
-------------------


=========
Bug fixes
=========

* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_
* Fix mixed outputs_to_working_directory pulsar destinations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15927 <https://github.com/galaxyproject/galaxy/pull/15927>`_
* Update Gravity to 1.0.3 by `@natefoo <https://github.com/natefoo>`_ in `#15939 <https://github.com/galaxyproject/galaxy/pull/15939>`_
* Various fixes to path prefix handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16033 <https://github.com/galaxyproject/galaxy/pull/16033>`_
* Fix case sensitive filtering by name in histories by `@davelopez <https://github.com/davelopez>`_ in `#16036 <https://github.com/galaxyproject/galaxy/pull/16036>`_
* Fix gcsfs test discovery by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16039 <https://github.com/galaxyproject/galaxy/pull/16039>`_
* Replace httpbin service with pytest-httpserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16042 <https://github.com/galaxyproject/galaxy/pull/16042>`_
* Update pulsar to 0.15.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16050 <https://github.com/galaxyproject/galaxy/pull/16050>`_
* Anonymous User tool link bug fix by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16065 <https://github.com/galaxyproject/galaxy/pull/16065>`_
* Fix BCO export by updating gxformat2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16081 <https://github.com/galaxyproject/galaxy/pull/16081>`_
* Fix job failure handling when condor indicates job failure by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16096 <https://github.com/galaxyproject/galaxy/pull/16096>`_
* Fix dataype_change not updating HDCA update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16099 <https://github.com/galaxyproject/galaxy/pull/16099>`_
* Extract HDA for code_file validate_input hook by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16120 <https://github.com/galaxyproject/galaxy/pull/16120>`_
* Fix sort error when re-running job with DCE collection input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16126 <https://github.com/galaxyproject/galaxy/pull/16126>`_
* Fix related-hid in bulk contents API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16128 <https://github.com/galaxyproject/galaxy/pull/16128>`_
* Fix rank calculation for jobs waiting to be run by anonymous users by `@jdavcs <https://github.com/jdavcs>`_ in `#16137 <https://github.com/galaxyproject/galaxy/pull/16137>`_
* Tool warnings can either be None or a Dictionary but not a String by `@guerler <https://github.com/guerler>`_ in `#16183 <https://github.com/galaxyproject/galaxy/pull/16183>`_
* Pin minimum tpv version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16201 <https://github.com/galaxyproject/galaxy/pull/16201>`_

=============
Other changes
=============

* Startup fix when tool removed between reboot by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16175 <https://github.com/galaxyproject/galaxy/pull/16175>`_

-------------------
20.9.0 (2020-10-15)
-------------------

* First release from the 20.09 branch of Galaxy.

-------------------
20.5.0 (2020-07-04)
-------------------

* First release from the 20.05 branch of Galaxy.

Raw data

            {
    "_id": null,
    "home_page": "https://github.com/galaxyproject/galaxy",
    "name": "galaxy-app",
    "maintainer": null,
    "docs_url": null,
    "requires_python": ">=3.8",
    "maintainer_email": null,
    "keywords": "Galaxy",
    "author": "Galaxy Project and Community",
    "author_email": "galaxy-committers@lists.galaxyproject.org",
    "download_url": "https://files.pythonhosted.org/packages/10/8a/8722621711150c5522028ae4f5ecd1a7e12cd7e430a6b9cf2f8f4d1ff409/galaxy-app-24.0.0.tar.gz",
    "platform": null,
    "description": "\n.. image:: https://badge.fury.io/py/galaxy-app.svg\n   :target: https://pypi.org/project/galaxy-app/\n\n\nOverview\n--------\n\nThe Galaxy_ application logic (backend).\n\n* Code: https://github.com/galaxyproject/galaxy\n\n.. _Galaxy: http://galaxyproject.org/\n\nHistory\n-------\n\n.. to_doc\n\n-------------------\n24.0.0 (2024-04-02)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Reload built-in converters on toolbox reload by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17209 <https://github.com/galaxyproject/galaxy/pull/17209>`_\n* Optional Reply-to SMTP header in tool error reports by `@neoformit <https://github.com/neoformit>`_ in `#17243 <https://github.com/galaxyproject/galaxy/pull/17243>`_\n* Package tests fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17301 <https://github.com/galaxyproject/galaxy/pull/17301>`_\n* Follow-up on #17274 and #17262 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17302 <https://github.com/galaxyproject/galaxy/pull/17302>`_\n* Rollback invalidated transaction: catch them earlier by `@jdavcs <https://github.com/jdavcs>`_ in `#17312 <https://github.com/galaxyproject/galaxy/pull/17312>`_\n* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17340 <https://github.com/galaxyproject/galaxy/pull/17340>`_\n* Fix data_source and data_source_async bugs by `@wm75 <https://github.com/wm75>`_ in `#17422 <https://github.com/galaxyproject/galaxy/pull/17422>`_\n* More efficient change_state queries, maybe fix deadlock by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17632 <https://github.com/galaxyproject/galaxy/pull/17632>`_\n* Don't index tasks without task_uuid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17646 <https://github.com/galaxyproject/galaxy/pull/17646>`_\n* Separate `ConnectedValue` from `RuntimeValue` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17678 <https://github.com/galaxyproject/galaxy/pull/17678>`_\n* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17716 <https://github.com/galaxyproject/galaxy/pull/17716>`_\n* Fix usage of DISTINCT by `@jdavcs <https://github.com/jdavcs>`_ in `#17759 <https://github.com/galaxyproject/galaxy/pull/17759>`_\n* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17777 <https://github.com/galaxyproject/galaxy/pull/17777>`_\n* Use ``hg clone --stream`` to clone repos by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17786 <https://github.com/galaxyproject/galaxy/pull/17786>`_\n* Defer job attributes that are usually not needed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17795 <https://github.com/galaxyproject/galaxy/pull/17795>`_\n* Fix change_datatype PJA for dynamic collections  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17803 <https://github.com/galaxyproject/galaxy/pull/17803>`_\n* Fix archived histories mixing with active in histories list by `@davelopez <https://github.com/davelopez>`_ in `#17856 <https://github.com/galaxyproject/galaxy/pull/17856>`_\n* Normalize extensions when loading tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17868 <https://github.com/galaxyproject/galaxy/pull/17868>`_\n* Ignore user data table errors for now by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17880 <https://github.com/galaxyproject/galaxy/pull/17880>`_\n\n============\nEnhancements\n============\n\n* Add harmonize collections tool (or whatever other name) by `@lldelisle <https://github.com/lldelisle>`_ in `#16662 <https://github.com/galaxyproject/galaxy/pull/16662>`_\n* Add support for Python 3.12 by `@tuncK <https://github.com/tuncK>`_ in `#16796 <https://github.com/galaxyproject/galaxy/pull/16796>`_\n* SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs <https://github.com/jdavcs>`_ in `#16932 <https://github.com/galaxyproject/galaxy/pull/16932>`_\n* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_\n* Support for OIDC API Auth and OIDC integration tests by `@nuwang <https://github.com/nuwang>`_ in `#16977 <https://github.com/galaxyproject/galaxy/pull/16977>`_\n* Toward declarative help for Galaxy markdown directives. by `@jmchilton <https://github.com/jmchilton>`_ in `#16979 <https://github.com/galaxyproject/galaxy/pull/16979>`_\n* Extend regex groups in stdio regex matches by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17016 <https://github.com/galaxyproject/galaxy/pull/17016>`_\n* Vueify Admin User Grid by `@guerler <https://github.com/guerler>`_ in `#17030 <https://github.com/galaxyproject/galaxy/pull/17030>`_\n* Remove web framework dependency from tools by `@davelopez <https://github.com/davelopez>`_ in `#17058 <https://github.com/galaxyproject/galaxy/pull/17058>`_\n* Add select parameter with options from remote resources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17087 <https://github.com/galaxyproject/galaxy/pull/17087>`_\n*  Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_\n* Vueify Admin Roles Grid by `@guerler <https://github.com/guerler>`_ in `#17118 <https://github.com/galaxyproject/galaxy/pull/17118>`_\n* SA2.0 updates: handling \"object is being merged into a Session along the backref cascade path\" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17123 <https://github.com/galaxyproject/galaxy/pull/17123>`_\n* Vueify Admin Groups Grid by `@guerler <https://github.com/guerler>`_ in `#17126 <https://github.com/galaxyproject/galaxy/pull/17126>`_\n* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs <https://github.com/jdavcs>`_ in `#17132 <https://github.com/galaxyproject/galaxy/pull/17132>`_\n* Vueify Admin Forms and Quota grids by `@guerler <https://github.com/guerler>`_ in `#17141 <https://github.com/galaxyproject/galaxy/pull/17141>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17157 <https://github.com/galaxyproject/galaxy/pull/17157>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17201 <https://github.com/galaxyproject/galaxy/pull/17201>`_\n* Vendorize fastapi-utls.cbv by `@jdavcs <https://github.com/jdavcs>`_ in `#17205 <https://github.com/galaxyproject/galaxy/pull/17205>`_\n* Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by `@jdavcs <https://github.com/jdavcs>`_ in `#17216 <https://github.com/galaxyproject/galaxy/pull/17216>`_\n* Vueifiy History Grids by `@guerler <https://github.com/guerler>`_ in `#17219 <https://github.com/galaxyproject/galaxy/pull/17219>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17230 <https://github.com/galaxyproject/galaxy/pull/17230>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17235 <https://github.com/galaxyproject/galaxy/pull/17235>`_\n* Allow job files to consume TUS uploads by `@jmchilton <https://github.com/jmchilton>`_ in `#17242 <https://github.com/galaxyproject/galaxy/pull/17242>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17247 <https://github.com/galaxyproject/galaxy/pull/17247>`_\n* Migrate models to pydantic 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17262 <https://github.com/galaxyproject/galaxy/pull/17262>`_\n* Consider Null inputs by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17271 <https://github.com/galaxyproject/galaxy/pull/17271>`_\n* Add OIDC backend configuration schema and validation by `@uwwint <https://github.com/uwwint>`_ in `#17274 <https://github.com/galaxyproject/galaxy/pull/17274>`_\n* Adds delete, purge and undelete batch operations to History Grid by `@guerler <https://github.com/guerler>`_ in `#17282 <https://github.com/galaxyproject/galaxy/pull/17282>`_\n* Add ``__KEEP_SUCCESS_DATASETS__`` by `@lldelisle <https://github.com/lldelisle>`_ in `#17294 <https://github.com/galaxyproject/galaxy/pull/17294>`_\n* Improve ModelManager type hints by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17299 <https://github.com/galaxyproject/galaxy/pull/17299>`_\n* API endpoint that allows \"changing\" the objectstore for \"safe\" scenarios.  by `@jmchilton <https://github.com/jmchilton>`_ in `#17329 <https://github.com/galaxyproject/galaxy/pull/17329>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17333 <https://github.com/galaxyproject/galaxy/pull/17333>`_\n* Add element_identifier and ext to inputs config file export by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17357 <https://github.com/galaxyproject/galaxy/pull/17357>`_\n* Remove unused statements in job search function by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17361 <https://github.com/galaxyproject/galaxy/pull/17361>`_\n* Enable ``warn_unreachable`` mypy option by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17365 <https://github.com/galaxyproject/galaxy/pull/17365>`_\n* Fix type annotation of code using XML etree by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17367 <https://github.com/galaxyproject/galaxy/pull/17367>`_\n* More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17381 <https://github.com/galaxyproject/galaxy/pull/17381>`_\n* Cancel all active jobs when the user is deleted by `@davelopez <https://github.com/davelopez>`_ in `#17390 <https://github.com/galaxyproject/galaxy/pull/17390>`_\n* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_\n* Purge `groups` and `roles` from DB (for real) by `@davelopez <https://github.com/davelopez>`_ in `#17411 <https://github.com/galaxyproject/galaxy/pull/17411>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17420 <https://github.com/galaxyproject/galaxy/pull/17420>`_\n* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17435 <https://github.com/galaxyproject/galaxy/pull/17435>`_\n* Adds published histories to grid list by `@guerler <https://github.com/guerler>`_ in `#17449 <https://github.com/galaxyproject/galaxy/pull/17449>`_\n* Allow filtering history datasets by object store ID and quota source. by `@jmchilton <https://github.com/jmchilton>`_ in `#17460 <https://github.com/galaxyproject/galaxy/pull/17460>`_\n* `data_column` parameter: use `column_names` metadata if present by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17478 <https://github.com/galaxyproject/galaxy/pull/17478>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17486 <https://github.com/galaxyproject/galaxy/pull/17486>`_\n* Consolidate resource grids into tab views by `@guerler <https://github.com/guerler>`_ in `#17487 <https://github.com/galaxyproject/galaxy/pull/17487>`_\n* Update k8s docker python to 3.12 by `@nuwang <https://github.com/nuwang>`_ in `#17494 <https://github.com/galaxyproject/galaxy/pull/17494>`_\n* add encode ID API endpoint by `@mira-miracoli <https://github.com/mira-miracoli>`_ in `#17510 <https://github.com/galaxyproject/galaxy/pull/17510>`_\n* Fixing data_source tools and incrementing tool profile by `@wm75 <https://github.com/wm75>`_ in `#17515 <https://github.com/galaxyproject/galaxy/pull/17515>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17541 <https://github.com/galaxyproject/galaxy/pull/17541>`_\n* Add `image_diff` comparison method for test output verification using images by `@kostrykin <https://github.com/kostrykin>`_ in `#17556 <https://github.com/galaxyproject/galaxy/pull/17556>`_\n* Filter out subworkflow invocations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17558 <https://github.com/galaxyproject/galaxy/pull/17558>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17580 <https://github.com/galaxyproject/galaxy/pull/17580>`_\n* Restore histories API behavior for `keys` query parameter by `@davelopez <https://github.com/davelopez>`_ in `#17779 <https://github.com/galaxyproject/galaxy/pull/17779>`_\n* Fix datasets API custom keys encoding by `@davelopez <https://github.com/davelopez>`_ in `#17793 <https://github.com/galaxyproject/galaxy/pull/17793>`_\n* Improved error messages for runtime sharing problems. by `@jmchilton <https://github.com/jmchilton>`_ in `#17794 <https://github.com/galaxyproject/galaxy/pull/17794>`_\n* Allow admin to sharpen language about selected object stores. by `@jmchilton <https://github.com/jmchilton>`_ in `#17806 <https://github.com/galaxyproject/galaxy/pull/17806>`_\n\n=============\nOther changes\n=============\n\n* consistently compare profile versions by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16492 <https://github.com/galaxyproject/galaxy/pull/16492>`_\n\n-------------------\n23.2.1 (2024-02-21)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* pin fs.dropboxfs to >=1 by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16451 <https://github.com/galaxyproject/galaxy/pull/16451>`_\n* Remove unnecessary check: item cannot be None by `@jdavcs <https://github.com/jdavcs>`_ in `#16550 <https://github.com/galaxyproject/galaxy/pull/16550>`_\n* Fix: serialize `tool_shed_urls` directly from the API by `@davelopez <https://github.com/davelopez>`_ in `#16561 <https://github.com/galaxyproject/galaxy/pull/16561>`_\n* Fix dependency update GitHub workflow by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16639 <https://github.com/galaxyproject/galaxy/pull/16639>`_\n* Ensure Job belongs to current SA session by `@jdavcs <https://github.com/jdavcs>`_ in `#16647 <https://github.com/galaxyproject/galaxy/pull/16647>`_\n* Account for shared usage between TS and galaxy apps by `@jdavcs <https://github.com/jdavcs>`_ in `#16746 <https://github.com/galaxyproject/galaxy/pull/16746>`_\n* move the email and username redacting from the role loop by `@martenson <https://github.com/martenson>`_ in `#16805 <https://github.com/galaxyproject/galaxy/pull/16805>`_\n* Fix shed unit test by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16811 <https://github.com/galaxyproject/galaxy/pull/16811>`_\n* chore: fix typos by `@afuetterer <https://github.com/afuetterer>`_ in `#16851 <https://github.com/galaxyproject/galaxy/pull/16851>`_\n* Fix bug in SQLAlchemy statement by `@jdavcs <https://github.com/jdavcs>`_ in `#16881 <https://github.com/galaxyproject/galaxy/pull/16881>`_\n* Ruff and flake8 fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16884 <https://github.com/galaxyproject/galaxy/pull/16884>`_\n* Update help in relabel_from_file.xml by `@lldelisle <https://github.com/lldelisle>`_ in `#16891 <https://github.com/galaxyproject/galaxy/pull/16891>`_\n* Fix subtle bug in listify function + simplify list munging by `@jdavcs <https://github.com/jdavcs>`_ in `#16904 <https://github.com/galaxyproject/galaxy/pull/16904>`_\n* prep for updated h5py and typos by `@mr-c <https://github.com/mr-c>`_ in `#16963 <https://github.com/galaxyproject/galaxy/pull/16963>`_\n* Enhancement to Tool Form page, Repeating form fields implement parameter instructions by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#17018 <https://github.com/galaxyproject/galaxy/pull/17018>`_\n* Expose file_name property in DatasetFilenameWrapper by `@jdavcs <https://github.com/jdavcs>`_ in `#17107 <https://github.com/galaxyproject/galaxy/pull/17107>`_\n* Fix ``to_cwl`` for nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17276 <https://github.com/galaxyproject/galaxy/pull/17276>`_\n* Rollback invalidated transaction by `@jdavcs <https://github.com/jdavcs>`_ in `#17280 <https://github.com/galaxyproject/galaxy/pull/17280>`_\n* Install newer celery on python 3.8+ by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17309 <https://github.com/galaxyproject/galaxy/pull/17309>`_\n* Backport Rollback invalidated transaction: catch them earlier by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17315 <https://github.com/galaxyproject/galaxy/pull/17315>`_\n* Discard sqlalchemy session after task completion by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17317 <https://github.com/galaxyproject/galaxy/pull/17317>`_\n* Scope session for job  runner monitor loop by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17319 <https://github.com/galaxyproject/galaxy/pull/17319>`_\n* Fix History contents `genome_build` filter postgresql bug by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#17384 <https://github.com/galaxyproject/galaxy/pull/17384>`_\n* Update python-multipart to 0.0.7 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17429 <https://github.com/galaxyproject/galaxy/pull/17429>`_\n* Build param dict before creating entrypoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17440 <https://github.com/galaxyproject/galaxy/pull/17440>`_\n* Fix bug: true >> True by `@jdavcs <https://github.com/jdavcs>`_ in `#17446 <https://github.com/galaxyproject/galaxy/pull/17446>`_\n* Set metadata states on dataset association, not dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17474 <https://github.com/galaxyproject/galaxy/pull/17474>`_\n* Remove two print statements by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17480 <https://github.com/galaxyproject/galaxy/pull/17480>`_\n* Provide working routes.url_for every ASGI request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17497 <https://github.com/galaxyproject/galaxy/pull/17497>`_\n\n============\nEnhancements\n============\n\n* Implement default locations for data and collection parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#14955 <https://github.com/galaxyproject/galaxy/pull/14955>`_\n* Enable job resubmissions in k8s runner by `@pcm32 <https://github.com/pcm32>`_ in `#15238 <https://github.com/galaxyproject/galaxy/pull/15238>`_\n* Add parameter name to validation errors by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15440 <https://github.com/galaxyproject/galaxy/pull/15440>`_\n* Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#15639 <https://github.com/galaxyproject/galaxy/pull/15639>`_\n* Add ability to assert metadata properties on input dataset parameters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15825 <https://github.com/galaxyproject/galaxy/pull/15825>`_\n* Limit number of celery task executions per second per user by `@claudiofr <https://github.com/claudiofr>`_ in `#16232 <https://github.com/galaxyproject/galaxy/pull/16232>`_\n* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16252 <https://github.com/galaxyproject/galaxy/pull/16252>`_\n* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs <https://github.com/jdavcs>`_ in `#16264 <https://github.com/galaxyproject/galaxy/pull/16264>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16305 <https://github.com/galaxyproject/galaxy/pull/16305>`_\n* Add carbon emissions admin configuration options by `@Renni771 <https://github.com/Renni771>`_ in `#16307 <https://github.com/galaxyproject/galaxy/pull/16307>`_\n* Migrate a part of the users API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16341 <https://github.com/galaxyproject/galaxy/pull/16341>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16360 <https://github.com/galaxyproject/galaxy/pull/16360>`_\n* Add Invenio RDM repository integration by `@davelopez <https://github.com/davelopez>`_ in `#16381 <https://github.com/galaxyproject/galaxy/pull/16381>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16389 <https://github.com/galaxyproject/galaxy/pull/16389>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16409 <https://github.com/galaxyproject/galaxy/pull/16409>`_\n* Refactor FilesDialog + Remote Files API schema improvements by `@davelopez <https://github.com/davelopez>`_ in `#16420 <https://github.com/galaxyproject/galaxy/pull/16420>`_\n* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs <https://github.com/jdavcs>`_ in `#16431 <https://github.com/galaxyproject/galaxy/pull/16431>`_\n* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs <https://github.com/jdavcs>`_ in `#16434 <https://github.com/galaxyproject/galaxy/pull/16434>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16436 <https://github.com/galaxyproject/galaxy/pull/16436>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16485 <https://github.com/galaxyproject/galaxy/pull/16485>`_\n* Rename MetadataEqualsValidator by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16489 <https://github.com/galaxyproject/galaxy/pull/16489>`_\n* Add support for CILogon deployments in different regions than the US by `@uwwint <https://github.com/uwwint>`_ in `#16490 <https://github.com/galaxyproject/galaxy/pull/16490>`_\n* Refactor/OIDC custos by `@uwwint <https://github.com/uwwint>`_ in `#16497 <https://github.com/galaxyproject/galaxy/pull/16497>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16521 <https://github.com/galaxyproject/galaxy/pull/16521>`_\n* Move database access code out of ``galaxy.util`` by `@jdavcs <https://github.com/jdavcs>`_ in `#16526 <https://github.com/galaxyproject/galaxy/pull/16526>`_\n* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16536 <https://github.com/galaxyproject/galaxy/pull/16536>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16577 <https://github.com/galaxyproject/galaxy/pull/16577>`_\n* Vueify Tool Form Data Selector by `@guerler <https://github.com/guerler>`_ in `#16578 <https://github.com/galaxyproject/galaxy/pull/16578>`_\n* Workflow Comments \ud83d\udcac by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16612 <https://github.com/galaxyproject/galaxy/pull/16612>`_\n* Switch out conditional requirement parser by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16636 <https://github.com/galaxyproject/galaxy/pull/16636>`_\n* Add scroll pagination and username filter to `HistoryPublishedList` by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16642 <https://github.com/galaxyproject/galaxy/pull/16642>`_\n* Bump samtools converters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16668 <https://github.com/galaxyproject/galaxy/pull/16668>`_\n* Galaxy Markdown - add workflow image and license to Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16672 <https://github.com/galaxyproject/galaxy/pull/16672>`_\n* Implement instance URLs in Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16675 <https://github.com/galaxyproject/galaxy/pull/16675>`_\n* Change Sentry error reporting plug-in by `@kysrpex <https://github.com/kysrpex>`_ in `#16686 <https://github.com/galaxyproject/galaxy/pull/16686>`_\n* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola <https://github.com/lopiola>`_ in `#16690 <https://github.com/galaxyproject/galaxy/pull/16690>`_\n* Enhance task monitor composable by `@davelopez <https://github.com/davelopez>`_ in `#16695 <https://github.com/galaxyproject/galaxy/pull/16695>`_\n* Misc. edits/refactorings to session handling  by `@jdavcs <https://github.com/jdavcs>`_ in `#16712 <https://github.com/galaxyproject/galaxy/pull/16712>`_\n* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs <https://github.com/jdavcs>`_ in `#16724 <https://github.com/galaxyproject/galaxy/pull/16724>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16735 <https://github.com/galaxyproject/galaxy/pull/16735>`_\n* Convert ISO to UTC for Date/Time in workflow reports by `@assuntad23 <https://github.com/assuntad23>`_ in `#16758 <https://github.com/galaxyproject/galaxy/pull/16758>`_\n* Replace ELIXIR AAI button with Life Science login by `@sebastian-schaaf <https://github.com/sebastian-schaaf>`_ in `#16762 <https://github.com/galaxyproject/galaxy/pull/16762>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16770 <https://github.com/galaxyproject/galaxy/pull/16770>`_\n* Migrate a part of the jobs API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16778 <https://github.com/galaxyproject/galaxy/pull/16778>`_\n* Add EGI Check-in as OIDC authentication option by `@enolfc <https://github.com/enolfc>`_ in `#16782 <https://github.com/galaxyproject/galaxy/pull/16782>`_\n* Replace file_name property with get_file_name function by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#16783 <https://github.com/galaxyproject/galaxy/pull/16783>`_\n* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu <https://github.com/sveinugu>`_ in `#16795 <https://github.com/galaxyproject/galaxy/pull/16795>`_\n* Galaxy help forum integration by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16798 <https://github.com/galaxyproject/galaxy/pull/16798>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16807 <https://github.com/galaxyproject/galaxy/pull/16807>`_\n* Another batch of SA2.0 edits in TS2.0 (part 3) by `@jdavcs <https://github.com/jdavcs>`_ in `#16833 <https://github.com/galaxyproject/galaxy/pull/16833>`_\n* Remove remaining legacy backbone form input elements by `@guerler <https://github.com/guerler>`_ in `#16834 <https://github.com/galaxyproject/galaxy/pull/16834>`_\n* SQLAlchemy 2.0 upgrades (part 4) by `@jdavcs <https://github.com/jdavcs>`_ in `#16852 <https://github.com/galaxyproject/galaxy/pull/16852>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16853 <https://github.com/galaxyproject/galaxy/pull/16853>`_\n* Drop unused HistoryContentManager code and related tests by `@jdavcs <https://github.com/jdavcs>`_ in `#16882 <https://github.com/galaxyproject/galaxy/pull/16882>`_\n* Vueify Visualizations Grid by `@guerler <https://github.com/guerler>`_ in `#16892 <https://github.com/galaxyproject/galaxy/pull/16892>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16896 <https://github.com/galaxyproject/galaxy/pull/16896>`_\n* Enable some flake8-logging-format rules in ruff by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16915 <https://github.com/galaxyproject/galaxy/pull/16915>`_\n* Remove \"Create Workflow\" form and allow workflow creation in editor by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16938 <https://github.com/galaxyproject/galaxy/pull/16938>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16939 <https://github.com/galaxyproject/galaxy/pull/16939>`_\n* Add helper to get dataset or collection via ``src`` and ``id`` by `@mr-c <https://github.com/mr-c>`_ in `#16953 <https://github.com/galaxyproject/galaxy/pull/16953>`_\n* Allow non-optional integer/float params without value attribute by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16966 <https://github.com/galaxyproject/galaxy/pull/16966>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16978 <https://github.com/galaxyproject/galaxy/pull/16978>`_\n* Fix invocation report to target correct workflow version. by `@jmchilton <https://github.com/jmchilton>`_ in `#17008 <https://github.com/galaxyproject/galaxy/pull/17008>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17011 <https://github.com/galaxyproject/galaxy/pull/17011>`_\n* Upgrade job manager's index_query method to SA2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17020 <https://github.com/galaxyproject/galaxy/pull/17020>`_\n* optimize object store cache operations by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17025 <https://github.com/galaxyproject/galaxy/pull/17025>`_\n* Require name for workflows on save, set default to Unnamed Workflow by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#17038 <https://github.com/galaxyproject/galaxy/pull/17038>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17050 <https://github.com/galaxyproject/galaxy/pull/17050>`_\n* Migrate groups API to fastAPI by `@arash77 <https://github.com/arash77>`_ in `#17051 <https://github.com/galaxyproject/galaxy/pull/17051>`_\n* Migrate ItemTags API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#17064 <https://github.com/galaxyproject/galaxy/pull/17064>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17084 <https://github.com/galaxyproject/galaxy/pull/17084>`_\n* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17342 <https://github.com/galaxyproject/galaxy/pull/17342>`_\n\n=============\nOther changes\n=============\n\n* Merge 23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16534 <https://github.com/galaxyproject/galaxy/pull/16534>`_\n* Revert \"[23.1] Enable job resubmissions in k8s runner\" by `@nuwang <https://github.com/nuwang>`_ in `#17323 <https://github.com/galaxyproject/galaxy/pull/17323>`_\n* Fix succces typo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17481 <https://github.com/galaxyproject/galaxy/pull/17481>`_\n\n-------------------\n23.1.4 (2024-01-04)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Fix workflow index total matches counting by `@davelopez <https://github.com/davelopez>`_ in `#17176 <https://github.com/galaxyproject/galaxy/pull/17176>`_\n* Fix `url_for` in tool error reports by `@davelopez <https://github.com/davelopez>`_ in `#17210 <https://github.com/galaxyproject/galaxy/pull/17210>`_\n\n-------------------\n23.1.3 (2023-12-01)\n-------------------\n\nNo recorded changes since last release\n\n-------------------\n23.1.2 (2023-11-29)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Fix unbound ``runner`` variable when there is an error in the job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16906 <https://github.com/galaxyproject/galaxy/pull/16906>`_\n* Fix discarded dataset ordering in Storage Dashboard by `@davelopez <https://github.com/davelopez>`_ in `#16929 <https://github.com/galaxyproject/galaxy/pull/16929>`_\n* Include owner's annotation when exporting workflow by `@dannon <https://github.com/dannon>`_ in `#16930 <https://github.com/galaxyproject/galaxy/pull/16930>`_\n* Skip state filtering in ``__MERGE_COLLECTION__`` tool  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16937 <https://github.com/galaxyproject/galaxy/pull/16937>`_\n* Prevent Singular external auth users from disconnecting identity by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16961 <https://github.com/galaxyproject/galaxy/pull/16961>`_\n* Prevent workflow submission with missing input values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17048 <https://github.com/galaxyproject/galaxy/pull/17048>`_\n* Fix extra files collection if using ``store_by=\"id\"`` and `outputs_to_working_directory` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17067 <https://github.com/galaxyproject/galaxy/pull/17067>`_\n* Remove rollback from ``__check_jobs_at_startup`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17085 <https://github.com/galaxyproject/galaxy/pull/17085>`_\n\n============\nEnhancements\n============\n\n* Improve invocation error reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16917 <https://github.com/galaxyproject/galaxy/pull/16917>`_\n\n-------------------\n23.1.1 (2023-10-23)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* read job_conf directly from `config_dir` instead of computing it again from `config_file` by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15596 <https://github.com/galaxyproject/galaxy/pull/15596>`_\n* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_\n* Fix filesource file url support by `@nuwang <https://github.com/nuwang>`_ in `#15794 <https://github.com/galaxyproject/galaxy/pull/15794>`_\n* Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by `@jdavcs <https://github.com/jdavcs>`_ in `#15811 <https://github.com/galaxyproject/galaxy/pull/15811>`_\n* Change confusing pulsar logs message by `@kysrpex <https://github.com/kysrpex>`_ in `#16038 <https://github.com/galaxyproject/galaxy/pull/16038>`_\n* Fix and test startup with Python 3.11 on macOS by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16082 <https://github.com/galaxyproject/galaxy/pull/16082>`_\n* Fix : Ignore error messages for admin created accounts by `@jvanbraekel <https://github.com/jvanbraekel>`_ in `#16132 <https://github.com/galaxyproject/galaxy/pull/16132>`_\n* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_\n* Fix \"database is locked\" error (occurring in the context of workflow testing under SQLite) by `@jdavcs <https://github.com/jdavcs>`_ in `#16208 <https://github.com/galaxyproject/galaxy/pull/16208>`_\n* Fix ordering of data libraries from API by `@martenson <https://github.com/martenson>`_ in `#16300 <https://github.com/galaxyproject/galaxy/pull/16300>`_\n* qualify querying for an api-key by `@martenson <https://github.com/martenson>`_ in `#16320 <https://github.com/galaxyproject/galaxy/pull/16320>`_\n* Fix tags ownership by `@davelopez <https://github.com/davelopez>`_ in `#16339 <https://github.com/galaxyproject/galaxy/pull/16339>`_\n* Job cache fixes for DCEs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16384 <https://github.com/galaxyproject/galaxy/pull/16384>`_\n* Fix histories count by `@davelopez <https://github.com/davelopez>`_ in `#16400 <https://github.com/galaxyproject/galaxy/pull/16400>`_\n* Fix select statement syntax for SQLAlchemy 2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#16421 <https://github.com/galaxyproject/galaxy/pull/16421>`_\n* Fix up unit tests for local use by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16483 <https://github.com/galaxyproject/galaxy/pull/16483>`_\n* Run through tmp_dir_creation_statement only once by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16529 <https://github.com/galaxyproject/galaxy/pull/16529>`_\n* Fix double-encoding notification content by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16530 <https://github.com/galaxyproject/galaxy/pull/16530>`_\n* Limit tool document cache to tool configs with explicit cache path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16537 <https://github.com/galaxyproject/galaxy/pull/16537>`_\n* Fix `multiple` remote test data by `@davelopez <https://github.com/davelopez>`_ in `#16542 <https://github.com/galaxyproject/galaxy/pull/16542>`_\n* Ignore errors with user-set job resources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16579 <https://github.com/galaxyproject/galaxy/pull/16579>`_\n* Fix replacement parameters for subworkflows. by `@jmchilton <https://github.com/jmchilton>`_ in `#16592 <https://github.com/galaxyproject/galaxy/pull/16592>`_\n* make sure that TMP, TEMP, and TMPDIR are set by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16594 <https://github.com/galaxyproject/galaxy/pull/16594>`_\n* Bump minimum tpv version to 2.3.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16597 <https://github.com/galaxyproject/galaxy/pull/16597>`_\n* Backport tool mem fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16601 <https://github.com/galaxyproject/galaxy/pull/16601>`_\n* Reload toolbox after forking when using `--preload` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16620 <https://github.com/galaxyproject/galaxy/pull/16620>`_\n* Account for expires/expires_in when refreshing token by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16621 <https://github.com/galaxyproject/galaxy/pull/16621>`_\n* Fixes for conditional subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16632 <https://github.com/galaxyproject/galaxy/pull/16632>`_\n* Fix nested conditional workflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16641 <https://github.com/galaxyproject/galaxy/pull/16641>`_\n* Ensure Job belongs to current SA session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16655 <https://github.com/galaxyproject/galaxy/pull/16655>`_\n* Fix expression evaluation for nested state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16656 <https://github.com/galaxyproject/galaxy/pull/16656>`_\n* Make sort_collection tool require terminal datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16661 <https://github.com/galaxyproject/galaxy/pull/16661>`_\n* Push to object store even if ``set_meta`` fails by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16667 <https://github.com/galaxyproject/galaxy/pull/16667>`_\n* Fix metadata setting in extended metadata + outputs_to_working_directory mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16678 <https://github.com/galaxyproject/galaxy/pull/16678>`_\n* Fix regex validation for global inline flags by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16683 <https://github.com/galaxyproject/galaxy/pull/16683>`_\n* Fix closed transaction error on galaxy startup/check jobs by `@jdavcs <https://github.com/jdavcs>`_ in `#16687 <https://github.com/galaxyproject/galaxy/pull/16687>`_\n* Add missing join condition in job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16710 <https://github.com/galaxyproject/galaxy/pull/16710>`_\n* Fix job search query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16714 <https://github.com/galaxyproject/galaxy/pull/16714>`_\n* Copy the collection contents by default when copying a collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16717 <https://github.com/galaxyproject/galaxy/pull/16717>`_\n* Fix collection id encoding by `@davelopez <https://github.com/davelopez>`_ in `#16718 <https://github.com/galaxyproject/galaxy/pull/16718>`_\n* Workaround for XML nodes of job resource parameters losing their children by `@kysrpex <https://github.com/kysrpex>`_ in `#16728 <https://github.com/galaxyproject/galaxy/pull/16728>`_\n* move the email and username redacting from the role loop by `@martenson <https://github.com/martenson>`_ in `#16820 <https://github.com/galaxyproject/galaxy/pull/16820>`_\n* Fix parameter display in job info page for tools with sections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16821 <https://github.com/galaxyproject/galaxy/pull/16821>`_\n* Fix workflow preview display if tool state does not contain all parameter values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16829 <https://github.com/galaxyproject/galaxy/pull/16829>`_\n* Fix up local tool version handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16836 <https://github.com/galaxyproject/galaxy/pull/16836>`_\n* Fix and prevent persisting null file_size by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16855 <https://github.com/galaxyproject/galaxy/pull/16855>`_\n* Allow referring to steps by label only in markdown editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16861 <https://github.com/galaxyproject/galaxy/pull/16861>`_\n* Fix safe update version handling in run form by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16865 <https://github.com/galaxyproject/galaxy/pull/16865>`_\n* Remove more flushes in database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16875 <https://github.com/galaxyproject/galaxy/pull/16875>`_\n* Fix tag ownership check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16877 <https://github.com/galaxyproject/galaxy/pull/16877>`_\n\n============\nEnhancements\n============\n\n* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_\n* External Login Flow: Redirect users if account already exists by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15019 <https://github.com/galaxyproject/galaxy/pull/15019>`_\n* Add slack error reporting plugin by `@hexylena <https://github.com/hexylena>`_ in `#15025 <https://github.com/galaxyproject/galaxy/pull/15025>`_\n* Various Tool Shed Cleanup by `@jmchilton <https://github.com/jmchilton>`_ in `#15247 <https://github.com/galaxyproject/galaxy/pull/15247>`_\n* Add Storage Management API by `@davelopez <https://github.com/davelopez>`_ in `#15295 <https://github.com/galaxyproject/galaxy/pull/15295>`_\n* OIDC tokens by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#15300 <https://github.com/galaxyproject/galaxy/pull/15300>`_\n* Expose additional beaker caching backends  by `@claudiofr <https://github.com/claudiofr>`_ in `#15349 <https://github.com/galaxyproject/galaxy/pull/15349>`_\n* Add support for visualizing HDF5 datasets. by `@jarrah42 <https://github.com/jarrah42>`_ in `#15394 <https://github.com/galaxyproject/galaxy/pull/15394>`_\n* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs <https://github.com/jdavcs>`_ in `#15421 <https://github.com/galaxyproject/galaxy/pull/15421>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15435 <https://github.com/galaxyproject/galaxy/pull/15435>`_\n* Fix for new style conda packages by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#15446 <https://github.com/galaxyproject/galaxy/pull/15446>`_\n* Move database access code out of tool_util by `@jdavcs <https://github.com/jdavcs>`_ in `#15467 <https://github.com/galaxyproject/galaxy/pull/15467>`_\n* Protection against problematic boolean parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#15493 <https://github.com/galaxyproject/galaxy/pull/15493>`_\n* Use connection instead of session for ItemGrabber by `@jdavcs <https://github.com/jdavcs>`_ in `#15496 <https://github.com/galaxyproject/galaxy/pull/15496>`_\n* Unify url handling with filesources by `@nuwang <https://github.com/nuwang>`_ in `#15497 <https://github.com/galaxyproject/galaxy/pull/15497>`_\n* Move TS to Alembic by `@jdavcs <https://github.com/jdavcs>`_ in `#15509 <https://github.com/galaxyproject/galaxy/pull/15509>`_\n* Explore tool remote test data by `@davelopez <https://github.com/davelopez>`_ in `#15510 <https://github.com/galaxyproject/galaxy/pull/15510>`_\n* Handle \"email_from\" config option consistently, as per schema description by `@jdavcs <https://github.com/jdavcs>`_ in `#15557 <https://github.com/galaxyproject/galaxy/pull/15557>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15564 <https://github.com/galaxyproject/galaxy/pull/15564>`_\n* Drop workflow exports to myexperiment.org by `@dannon <https://github.com/dannon>`_ in `#15576 <https://github.com/galaxyproject/galaxy/pull/15576>`_\n* Update database_heartbeat for SA 2.0 compatibility by `@jdavcs <https://github.com/jdavcs>`_ in `#15611 <https://github.com/galaxyproject/galaxy/pull/15611>`_\n* Add suggested Training material to Tool Form by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#15628 <https://github.com/galaxyproject/galaxy/pull/15628>`_\n* Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by `@jdavcs <https://github.com/jdavcs>`_ in `#15643 <https://github.com/galaxyproject/galaxy/pull/15643>`_\n* Add Galaxy Notification System by `@davelopez <https://github.com/davelopez>`_ in `#15663 <https://github.com/galaxyproject/galaxy/pull/15663>`_\n* Unpin Beaker requirement by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15665 <https://github.com/galaxyproject/galaxy/pull/15665>`_\n* Add transactional state to JobHandlerStopQueue by `@jdavcs <https://github.com/jdavcs>`_ in `#15671 <https://github.com/galaxyproject/galaxy/pull/15671>`_\n* Verify that activation and reset emails are properly generated by `@guerler <https://github.com/guerler>`_ in `#15681 <https://github.com/galaxyproject/galaxy/pull/15681>`_\n* Add transactional state to workflow scheduling manager by `@jdavcs <https://github.com/jdavcs>`_ in `#15683 <https://github.com/galaxyproject/galaxy/pull/15683>`_\n* Remove DELETED_NEW job state from code base by `@jdavcs <https://github.com/jdavcs>`_ in `#15690 <https://github.com/galaxyproject/galaxy/pull/15690>`_\n* Fix/Enhance recalculate disk usage API endpoint by `@davelopez <https://github.com/davelopez>`_ in `#15739 <https://github.com/galaxyproject/galaxy/pull/15739>`_\n* Add API test and refactor code for related:hid history filter by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#15786 <https://github.com/galaxyproject/galaxy/pull/15786>`_\n* Migrate to MyST-Parser for Markdown docs by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15844 <https://github.com/galaxyproject/galaxy/pull/15844>`_\n* Drop use_legacy_history from config  by `@dannon <https://github.com/dannon>`_ in `#15861 <https://github.com/galaxyproject/galaxy/pull/15861>`_\n* Drop database views by `@jdavcs <https://github.com/jdavcs>`_ in `#15876 <https://github.com/galaxyproject/galaxy/pull/15876>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15890 <https://github.com/galaxyproject/galaxy/pull/15890>`_\n* Allow pending inputs in some collection operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15892 <https://github.com/galaxyproject/galaxy/pull/15892>`_\n* Updated doc and tests for attribute value filter by `@tuncK <https://github.com/tuncK>`_ in `#15929 <https://github.com/galaxyproject/galaxy/pull/15929>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15942 <https://github.com/galaxyproject/galaxy/pull/15942>`_\n* Record input datasets and collections at full parameter path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15978 <https://github.com/galaxyproject/galaxy/pull/15978>`_\n* Export tool citations configurable message by `@minh-biocommons <https://github.com/minh-biocommons>`_ in `#15998 <https://github.com/galaxyproject/galaxy/pull/15998>`_\n* Add History Archival feature by `@davelopez <https://github.com/davelopez>`_ in `#16003 <https://github.com/galaxyproject/galaxy/pull/16003>`_\n* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16035 <https://github.com/galaxyproject/galaxy/pull/16035>`_\n* Add missing fields to HistorySummary schema model by `@davelopez <https://github.com/davelopez>`_ in `#16041 <https://github.com/galaxyproject/galaxy/pull/16041>`_\n* Vendorise ``packaging.versions.LegacyVersion`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16058 <https://github.com/galaxyproject/galaxy/pull/16058>`_\n* Add Repository owner field to ToolSearch by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16061 <https://github.com/galaxyproject/galaxy/pull/16061>`_\n* Add count support for listing filters by `@davelopez <https://github.com/davelopez>`_ in `#16075 <https://github.com/galaxyproject/galaxy/pull/16075>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16086 <https://github.com/galaxyproject/galaxy/pull/16086>`_\n* Improved Cache Monitoring for Object Stores by `@jmchilton <https://github.com/jmchilton>`_ in `#16110 <https://github.com/galaxyproject/galaxy/pull/16110>`_\n* Integrate accessibility testing into Selenium testing by `@jmchilton <https://github.com/jmchilton>`_ in `#16122 <https://github.com/galaxyproject/galaxy/pull/16122>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16123 <https://github.com/galaxyproject/galaxy/pull/16123>`_\n* Improve histories and datasets immutability checks by `@davelopez <https://github.com/davelopez>`_ in `#16143 <https://github.com/galaxyproject/galaxy/pull/16143>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16153 <https://github.com/galaxyproject/galaxy/pull/16153>`_\n* Migrate display applications API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16156 <https://github.com/galaxyproject/galaxy/pull/16156>`_\n* adjust grid sharing indicators by `@martenson <https://github.com/martenson>`_ in `#16163 <https://github.com/galaxyproject/galaxy/pull/16163>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16182 <https://github.com/galaxyproject/galaxy/pull/16182>`_\n* Drop workarounds for old ro-crate-py and docutils versions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16198 <https://github.com/galaxyproject/galaxy/pull/16198>`_\n* Remove various fallback behaviors by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16199 <https://github.com/galaxyproject/galaxy/pull/16199>`_\n* bring grids for (published) pages on par with workflows by `@martenson <https://github.com/martenson>`_ in `#16209 <https://github.com/galaxyproject/galaxy/pull/16209>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16227 <https://github.com/galaxyproject/galaxy/pull/16227>`_\n* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16267 <https://github.com/galaxyproject/galaxy/pull/16267>`_\n* Fix tool remote test data by `@davelopez <https://github.com/davelopez>`_ in `#16311 <https://github.com/galaxyproject/galaxy/pull/16311>`_\n* Hide conditionally skipped output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16356 <https://github.com/galaxyproject/galaxy/pull/16356>`_\n* Fix Storage Dashboard missing archived histories by `@davelopez <https://github.com/davelopez>`_ in `#16473 <https://github.com/galaxyproject/galaxy/pull/16473>`_\n* Bump bx-python to 0.10.0 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16484 <https://github.com/galaxyproject/galaxy/pull/16484>`_\n* Drop expunge_all() call in WebTransactionRequest by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16606 <https://github.com/galaxyproject/galaxy/pull/16606>`_\n\n=============\nOther changes\n=============\n\n* Follow up on object store selection PR. by `@jmchilton <https://github.com/jmchilton>`_ in `#15654 <https://github.com/galaxyproject/galaxy/pull/15654>`_\n* merge release_23.0 into dev by `@martenson <https://github.com/martenson>`_ in `#15830 <https://github.com/galaxyproject/galaxy/pull/15830>`_\n* Move axe-selenium-python to dev dependencies by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16162 <https://github.com/galaxyproject/galaxy/pull/16162>`_\n* Bump msal version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16285 <https://github.com/galaxyproject/galaxy/pull/16285>`_\n* Fix error_reports linting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16465 <https://github.com/galaxyproject/galaxy/pull/16465>`_\n\n-------------------\n23.0.6 (2023-10-23)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Fix upload paramfile handling (for real user setups) by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16504 <https://github.com/galaxyproject/galaxy/pull/16504>`_\n* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_\n* Make sure job_wrapper uses a consistent metadata strategy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16569 <https://github.com/galaxyproject/galaxy/pull/16569>`_\n* Fix conditional step evaluation with datasets in repeats by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16584 <https://github.com/galaxyproject/galaxy/pull/16584>`_\n* Don't read request body into memory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16585 <https://github.com/galaxyproject/galaxy/pull/16585>`_\n* Fixes for extra files handling and cached object stores  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16595 <https://github.com/galaxyproject/galaxy/pull/16595>`_\n* Lazy load tool data tables in celery worker by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16640 <https://github.com/galaxyproject/galaxy/pull/16640>`_\n* Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer by `@simonbray <https://github.com/simonbray>`_ in `#16659 <https://github.com/galaxyproject/galaxy/pull/16659>`_\n\n============\nEnhancements\n============\n\n* Update pulsar client library to 0.15.5 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16701 <https://github.com/galaxyproject/galaxy/pull/16701>`_\n\n-------------------\n23.0.5 (2023-07-29)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16403 <https://github.com/galaxyproject/galaxy/pull/16403>`_\n* Fix test discovery in vscode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16413 <https://github.com/galaxyproject/galaxy/pull/16413>`_\n* Fixes for (gitlab) error reporting by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16424 <https://github.com/galaxyproject/galaxy/pull/16424>`_\n\n-------------------\n23.0.4 (2023-06-30)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Fix default when statement evaluation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16332 <https://github.com/galaxyproject/galaxy/pull/16332>`_\n* Redact private role name and description when purging user by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16349 <https://github.com/galaxyproject/galaxy/pull/16349>`_\n\n-------------------\n23.0.3 (2023-06-26)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Bump galaxy-release-util version to 0.1.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16241 <https://github.com/galaxyproject/galaxy/pull/16241>`_\n\n============\nEnhancements\n============\n\n* When importing tool data bundles, use the first loc file for the matching table by `@natefoo <https://github.com/natefoo>`_ in `#16247 <https://github.com/galaxyproject/galaxy/pull/16247>`_\n\n=============\nOther changes\n=============\n\n* Forward port of slugify username received from oidc by `@nuwang <https://github.com/nuwang>`_ in `#16271 <https://github.com/galaxyproject/galaxy/pull/16271>`_\n\n-------------------\n23.0.2 (2023-06-13)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Fix ``Text File Busy`` errors at the source by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16212 <https://github.com/galaxyproject/galaxy/pull/16212>`_\n\n============\nEnhancements\n============\n\n* Point release deps fixes and docs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16214 <https://github.com/galaxyproject/galaxy/pull/16214>`_\n* Use galaxy-release-util to upload python packages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16240 <https://github.com/galaxyproject/galaxy/pull/16240>`_\n\n-------------------\n23.0.1 (2023-06-08)\n-------------------\n\n\n=========\nBug fixes\n=========\n\n* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_\n* Fix mixed outputs_to_working_directory pulsar destinations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15927 <https://github.com/galaxyproject/galaxy/pull/15927>`_\n* Update Gravity to 1.0.3 by `@natefoo <https://github.com/natefoo>`_ in `#15939 <https://github.com/galaxyproject/galaxy/pull/15939>`_\n* Various fixes to path prefix handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16033 <https://github.com/galaxyproject/galaxy/pull/16033>`_\n* Fix case sensitive filtering by name in histories by `@davelopez <https://github.com/davelopez>`_ in `#16036 <https://github.com/galaxyproject/galaxy/pull/16036>`_\n* Fix gcsfs test discovery by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16039 <https://github.com/galaxyproject/galaxy/pull/16039>`_\n* Replace httpbin service with pytest-httpserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16042 <https://github.com/galaxyproject/galaxy/pull/16042>`_\n* Update pulsar to 0.15.2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16050 <https://github.com/galaxyproject/galaxy/pull/16050>`_\n* Anonymous User tool link bug fix by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16065 <https://github.com/galaxyproject/galaxy/pull/16065>`_\n* Fix BCO export by updating gxformat2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16081 <https://github.com/galaxyproject/galaxy/pull/16081>`_\n* Fix job failure handling when condor indicates job failure by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16096 <https://github.com/galaxyproject/galaxy/pull/16096>`_\n* Fix dataype_change not updating HDCA update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16099 <https://github.com/galaxyproject/galaxy/pull/16099>`_\n* Extract HDA for code_file validate_input hook by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16120 <https://github.com/galaxyproject/galaxy/pull/16120>`_\n* Fix sort error when re-running job with DCE collection input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16126 <https://github.com/galaxyproject/galaxy/pull/16126>`_\n* Fix related-hid in bulk contents API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16128 <https://github.com/galaxyproject/galaxy/pull/16128>`_\n* Fix rank calculation for jobs waiting to be run by anonymous users by `@jdavcs <https://github.com/jdavcs>`_ in `#16137 <https://github.com/galaxyproject/galaxy/pull/16137>`_\n* Tool warnings can either be None or a Dictionary but not a String by `@guerler <https://github.com/guerler>`_ in `#16183 <https://github.com/galaxyproject/galaxy/pull/16183>`_\n* Pin minimum tpv version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16201 <https://github.com/galaxyproject/galaxy/pull/16201>`_\n\n=============\nOther changes\n=============\n\n* Startup fix when tool removed between reboot by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16175 <https://github.com/galaxyproject/galaxy/pull/16175>`_\n\n-------------------\n20.9.0 (2020-10-15)\n-------------------\n\n* First release from the 20.09 branch of Galaxy.\n\n-------------------\n20.5.0 (2020-07-04)\n-------------------\n\n* First release from the 20.05 branch of Galaxy.\n",
    "bugtrack_url": null,
    "license": "AFL",
    "summary": "Galaxy application (backend)",
    "version": "24.0.0",
    "project_urls": {
        "Homepage": "https://github.com/galaxyproject/galaxy"
    },
    "split_keywords": [
        "galaxy"
    ],
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "237237370b092b6ea34491efdb854990cba6068b4a3b6eef26947c2ab1274f69",
                "md5": "a665279da4036b317ecb09734602e03f",
                "sha256": "8907d469d117c4828c1fdd19aafed8986c569b59e3fc00ee5ea75ded0f8339dc"
            },
            "downloads": -1,
            "filename": "galaxy_app-24.0.0-py3-none-any.whl",
            "has_sig": false,
            "md5_digest": "a665279da4036b317ecb09734602e03f",
            "packagetype": "bdist_wheel",
            "python_version": "py3",
            "requires_python": ">=3.8",
            "size": 1457182,
            "upload_time": "2024-04-03T02:48:17",
            "upload_time_iso_8601": "2024-04-03T02:48:17.183896Z",
            "url": "https://files.pythonhosted.org/packages/23/72/37370b092b6ea34491efdb854990cba6068b4a3b6eef26947c2ab1274f69/galaxy_app-24.0.0-py3-none-any.whl",
            "yanked": false,
            "yanked_reason": null
        },
        {
            "comment_text": "",
            "digests": {
                "blake2b_256": "108a8722621711150c5522028ae4f5ecd1a7e12cd7e430a6b9cf2f8f4d1ff409",
                "md5": "c7d0b182a738cfff967dd5bb1bf93895",
                "sha256": "2e0e85d2abc067044a9dcbde5f7605e1111db026ebac2bdf8fc950204a04e4d6"
            },
            "downloads": -1,
            "filename": "galaxy-app-24.0.0.tar.gz",
            "has_sig": false,
            "md5_digest": "c7d0b182a738cfff967dd5bb1bf93895",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.8",
            "size": 1187202,
            "upload_time": "2024-04-03T02:48:19",
            "upload_time_iso_8601": "2024-04-03T02:48:19.889570Z",
            "url": "https://files.pythonhosted.org/packages/10/8a/8722621711150c5522028ae4f5ecd1a7e12cd7e430a6b9cf2f8f4d1ff409/galaxy-app-24.0.0.tar.gz",
            "yanked": false,
            "yanked_reason": null
        }
    ],
    "upload_time": "2024-04-03 02:48:19",
    "github": true,
    "gitlab": false,
    "bitbucket": false,
    "codeberg": false,
    "github_user": "galaxyproject",
    "github_project": "galaxy",
    "travis_ci": false,
    "coveralls": true,
    "github_actions": true,
    "circle": true,
    "requirements": [],
    "tox": true,
    "lcname": "galaxy-app"
}
Galaxy Project and Community
Elapsed time: 0.55852s