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galaxy/packages/test_base/HISTORY.rst
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mvdbeek ac8ec8c08d Merge branch 'release_25.0' into dev 
# Conflicts:
#	client/package.json
#	lib/galaxy/version.py
#	package.json
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/meta/HISTORY.rst
#	packages/meta/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_shed_schema/HISTORY.rst
#	packages/tool_shed_schema/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tool_util_models/HISTORY.rst
#	packages/tool_util_models/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_client/HISTORY.rst
#	packages/web_client/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
2025-09-23 19:10:06 +02:00

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History
-------
.. to_doc
---------
25.1.dev0
---------
-------------------
25.0.3 (2025-09-23)
-------------------
No recorded changes since last release
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25.0.2 (2025-08-13)
-------------------
=========
Bug fixes
=========
* Fix deferred datasets in multiple dataset parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#20650 <https://github.com/galaxyproject/galaxy/pull/20650>`_
-------------------
25.0.1 (2025-06-20)
-------------------
No recorded changes since last release
-------------------
25.0.0 (2025-06-18)
-------------------
=========
Bug fixes
=========
* Use ``resource_path()`` to access datatypes_conf.xml.sample as a package resource by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19331 <https://github.com/galaxyproject/galaxy/pull/19331>`_
* Fix ownership check in history contents update route by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19969 <https://github.com/galaxyproject/galaxy/pull/19969>`_
* Add test for workflow instance download fix by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20326 <https://github.com/galaxyproject/galaxy/pull/20326>`_
============
Enhancements
============
* Calculate hash for new non-deferred datasets when finishing a job by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19181 <https://github.com/galaxyproject/galaxy/pull/19181>`_
* Empower Users to Build More Kinds of Collections, More Intelligently by `@jmchilton <https://github.com/jmchilton>`_ in `#19377 <https://github.com/galaxyproject/galaxy/pull/19377>`_
* Add User-Defined Tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19434 <https://github.com/galaxyproject/galaxy/pull/19434>`_
* Format code with black 25.1.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19625 <https://github.com/galaxyproject/galaxy/pull/19625>`_
* Improved simplicity and isolation in transiently failing test. by `@jmchilton <https://github.com/jmchilton>`_ in `#19709 <https://github.com/galaxyproject/galaxy/pull/19709>`_
* Implement dataset collection support in workflow landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20004 <https://github.com/galaxyproject/galaxy/pull/20004>`_
-------------------
24.2.4 (2025-06-17)
-------------------
=========
Bug fixes
=========
* Restrict job cache to terminal jobs (and other fixes) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19978 <https://github.com/galaxyproject/galaxy/pull/19978>`_
* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
-------------------
24.2.3 (2025-03-16)
-------------------
No recorded changes since last release
-------------------
24.2.2 (2025-03-08)
-------------------
============
Enhancements
============
* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
-------------------
24.2.1 (2025-02-28)
-------------------
No recorded changes since last release
-------------------
24.2.0 (2025-02-11)
-------------------
=========
Bug fixes
=========
* Fix some deprecations by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18433 <https://github.com/galaxyproject/galaxy/pull/18433>`_
* Fix tag processing in library upload by `@davelopez <https://github.com/davelopez>`_ in `#18714 <https://github.com/galaxyproject/galaxy/pull/18714>`_
============
Enhancements
============
* Mixed enhancements from CWL branch by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18539 <https://github.com/galaxyproject/galaxy/pull/18539>`_
* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
* Migrate Library Contents API to FastAPI by `@arash77 <https://github.com/arash77>`_ in `#18838 <https://github.com/galaxyproject/galaxy/pull/18838>`_
* Implement Pydantic model for workflow test format. by `@jmchilton <https://github.com/jmchilton>`_ in `#18884 <https://github.com/galaxyproject/galaxy/pull/18884>`_
* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
* Allow CORS requests to /api/workflow_landings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18963 <https://github.com/galaxyproject/galaxy/pull/18963>`_
* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
* More concise, readable tool execution testing. by `@jmchilton <https://github.com/jmchilton>`_ in `#18977 <https://github.com/galaxyproject/galaxy/pull/18977>`_
* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
* A variety of improvements around tool parameter modeling (second try) by `@jmchilton <https://github.com/jmchilton>`_ in `#19027 <https://github.com/galaxyproject/galaxy/pull/19027>`_
* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
* Release testing - selenium tests for workflow invocation export. by `@jmchilton <https://github.com/jmchilton>`_ in `#19262 <https://github.com/galaxyproject/galaxy/pull/19262>`_
=============
Other changes
=============
* Fix workflow invocation accessibility check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18746 <https://github.com/galaxyproject/galaxy/pull/18746>`_
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
-------------------
24.1.3 (2024-10-25)
-------------------
=========
Bug fixes
=========
* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
* Access tool data table filters in workflow building mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18900 <https://github.com/galaxyproject/galaxy/pull/18900>`_
-------------------
24.1.2 (2024-09-25)
-------------------
=========
Bug fixes
=========
* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18751 <https://github.com/galaxyproject/galaxy/pull/18751>`_
* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
* Fix data_column ref to nested collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18875 <https://github.com/galaxyproject/galaxy/pull/18875>`_
-------------------
24.1.1 (2024-07-02)
-------------------
=========
Bug fixes
=========
* Revert some requests import changes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18199 <https://github.com/galaxyproject/galaxy/pull/18199>`_
* Fix subwofklow tags serialization type by `@arash77 <https://github.com/arash77>`_ in `#18456 <https://github.com/galaxyproject/galaxy/pull/18456>`_
============
Enhancements
============
* Remove deprecated BCO export endpoint by `@martenson <https://github.com/martenson>`_ in `#16645 <https://github.com/galaxyproject/galaxy/pull/16645>`_
* Enable all-vs-all collection analysis patterns. by `@jmchilton <https://github.com/jmchilton>`_ in `#17366 <https://github.com/galaxyproject/galaxy/pull/17366>`_
* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17654 <https://github.com/galaxyproject/galaxy/pull/17654>`_
* Error reporting unit tests by `@jmchilton <https://github.com/jmchilton>`_ in `#17968 <https://github.com/galaxyproject/galaxy/pull/17968>`_
* Add galaxy to user agent by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18003 <https://github.com/galaxyproject/galaxy/pull/18003>`_
* Empower users to bring their own storage and file sources by `@jmchilton <https://github.com/jmchilton>`_ in `#18127 <https://github.com/galaxyproject/galaxy/pull/18127>`_
* More structured indexing for user data objects. by `@jmchilton <https://github.com/jmchilton>`_ in `#18291 <https://github.com/galaxyproject/galaxy/pull/18291>`_
-------------------
24.0.3 (2024-06-28)
-------------------
=========
Bug fixes
=========
* Fix submitted value in workflow run form if data is constrained by tag filter by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18193 <https://github.com/galaxyproject/galaxy/pull/18193>`_
-------------------
24.0.2 (2024-05-07)
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No recorded changes since last release
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24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Make `wait_for_history_jobs` look at jobs, not datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17892 <https://github.com/galaxyproject/galaxy/pull/17892>`_
* Fix missing implicit conversion for mapped over jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17952 <https://github.com/galaxyproject/galaxy/pull/17952>`_
-------------------
24.0.0 (2024-04-02)
-------------------
============
Enhancements
============
* port invocation API to fastapi by `@martenson <https://github.com/martenson>`_ in `#16707 <https://github.com/galaxyproject/galaxy/pull/16707>`_
* 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>`_
* Reuse test instance during non-integration tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17234 <https://github.com/galaxyproject/galaxy/pull/17234>`_
* 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 to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_
* 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>`_
* Refactor Workflow API routes - Part 1 by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#17463 <https://github.com/galaxyproject/galaxy/pull/17463>`_
* Filter out subworkflow invocations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17558 <https://github.com/galaxyproject/galaxy/pull/17558>`_
-------------------
23.2.1 (2024-02-21)
-------------------
=========
Bug fixes
=========
* Restore ToolsApi and create new api route for new panel structure by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16872 <https://github.com/galaxyproject/galaxy/pull/16872>`_
============
Enhancements
============
* Implement default locations for data and collection parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#14955 <https://github.com/galaxyproject/galaxy/pull/14955>`_
* 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>`_
* Augment pgcleanup to allow periodically deleting old datasets. by `@jmchilton <https://github.com/jmchilton>`_ in `#16340 <https://github.com/galaxyproject/galaxy/pull/16340>`_
* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16739 <https://github.com/galaxyproject/galaxy/pull/16739>`_
* Change `api/tool_panel` to `api/tool_panels/...` by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16928 <https://github.com/galaxyproject/galaxy/pull/16928>`_
-------------------
23.1.4 (2024-01-04)
-------------------
No recorded changes since last release
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
-------------------
=========
Bug fixes
=========
* Fix duplicated tools in tool panel view section copying by `@jmchilton <https://github.com/jmchilton>`_ in `#17036 <https://github.com/galaxyproject/galaxy/pull/17036>`_
-------------------
23.1.1 (2023-10-23)
-------------------
=========
Bug fixes
=========
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
============
Enhancements
============
* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
* Outline Deployment Tests by `@jmchilton <https://github.com/jmchilton>`_ in `#15420 <https://github.com/galaxyproject/galaxy/pull/15420>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15890 <https://github.com/galaxyproject/galaxy/pull/15890>`_
* Add History Archival feature by `@davelopez <https://github.com/davelopez>`_ in `#16003 <https://github.com/galaxyproject/galaxy/pull/16003>`_
* Dataset chunking tests (and small fixes) by `@jmchilton <https://github.com/jmchilton>`_ in `#16069 <https://github.com/galaxyproject/galaxy/pull/16069>`_
* Improve histories and datasets immutability checks by `@davelopez <https://github.com/davelopez>`_ in `#16143 <https://github.com/galaxyproject/galaxy/pull/16143>`_
* bring grids for (published) pages on par with workflows by `@martenson <https://github.com/martenson>`_ in `#16209 <https://github.com/galaxyproject/galaxy/pull/16209>`_
* Small test decorator improvements. by `@jmchilton <https://github.com/jmchilton>`_ in `#16220 <https://github.com/galaxyproject/galaxy/pull/16220>`_
=============
Other changes
=============
* Tweaks to new object store and quota APIs by `@jmchilton <https://github.com/jmchilton>`_ in `#15709 <https://github.com/galaxyproject/galaxy/pull/15709>`_
-------------------
23.0.6 (2023-10-23)
-------------------
No recorded changes since last release
-------------------
23.0.5 (2023-07-29)
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No recorded changes since last release
-------------------
23.0.4 (2023-06-30)
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No recorded changes since last release
-------------------
23.0.3 (2023-06-26)
-------------------
No recorded changes since last release
-------------------
23.0.2 (2023-06-13)
-------------------
No recorded changes since last release
-------------------
23.0.1 (2023-06-08)
-------------------
=========
Bug fixes
=========
* Ensure history export contains all expected datasets by `@davelopez <https://github.com/davelopez>`_ in `#16013 <https://github.com/galaxyproject/galaxy/pull/16013>`_
* Fix extended metadata file size handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16109 <https://github.com/galaxyproject/galaxy/pull/16109>`_
-------------------
20.9.0 (2020-10-15)
-------------------
* Initial release from the 20.09 branch of Galaxy.
-------------------
20.5.0 (2020-07-04)
-------------------
* Initial import from the 20.05 branch of Galaxy.
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