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Merge branch 'release_25.0' into release_25.1
# 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
2 parents bf9aef3 + f764acd commit 231ea7d

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‎packages/app/HISTORY.rst‎

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=========
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Bug fixes
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=========
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* Check for expiration in refresh token dictionary by `@jdavcs <https://github.com/jdavcs>`_ in `#20954 <https://github.com/galaxyproject/galaxy/pull/20954>`_
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* Deactivate user file source on unknown error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20962 <https://github.com/galaxyproject/galaxy/pull/20962>`_
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* Don't create workflow outputs to recover input parameter outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20980 <https://github.com/galaxyproject/galaxy/pull/20980>`_
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* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
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* Store pulsar job prep error messages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21013 <https://github.com/galaxyproject/galaxy/pull/21013>`_
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* Require OK datasets for filtering empty datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21023 <https://github.com/galaxyproject/galaxy/pull/21023>`_
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* Fix `InvalidRequestError` when saving workflow step with dynamic tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21056 <https://github.com/galaxyproject/galaxy/pull/21056>`_
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* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
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* Create new datasets when creating skipped database operation tool outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21142 <https://github.com/galaxyproject/galaxy/pull/21142>`_
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* Fix refresh token expiration retrieval logic by `@nuwang <https://github.com/nuwang>`_ in `#21213 <https://github.com/galaxyproject/galaxy/pull/21213>`_
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============
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Enhancements
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============
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* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
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‎packages/auth/HISTORY.rst‎

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‎packages/config/HISTORY.rst‎

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-------------------
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25.0.4 (2025-11-18)
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-------------------
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=========
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Bug fixes
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=========
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* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
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* Fix MIME type for LAZ datatype by `@kysrpex <https://github.com/kysrpex>`_ in `#21202 <https://github.com/galaxyproject/galaxy/pull/21202>`_
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============
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Enhancements
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============
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* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
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* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
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* Add LAS and LAZ file format by `@bgruening <https://github.com/bgruening>`_ in `#21049 <https://github.com/galaxyproject/galaxy/pull/21049>`_
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* New datatype addition: gam for vg toolkit by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21096 <https://github.com/galaxyproject/galaxy/pull/21096>`_
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* support ZARR v3 for Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
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=============
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Other changes
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=============
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* New datatype addition: beast.trees datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21055 <https://github.com/galaxyproject/galaxy/pull/21055>`_
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* Add display_in_upload to LAZ and LAS by `@bgruening <https://github.com/bgruening>`_ in `#21060 <https://github.com/galaxyproject/galaxy/pull/21060>`_
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‎packages/data/HISTORY.rst‎

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-------------------
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25.0.4 (2025-11-18)
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-------------------
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=========
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Bug fixes
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=========
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* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
22+
* Skip sam metadata if we have too many references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20820 <https://github.com/galaxyproject/galaxy/pull/20820>`_
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* Backport of #20984 by `@davelopez <https://github.com/davelopez>`_ in `#20994 <https://github.com/galaxyproject/galaxy/pull/20994>`_
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* Backport fix anndata datatype update by `@nilchia <https://github.com/nilchia>`_ in `#21111 <https://github.com/galaxyproject/galaxy/pull/21111>`_
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* Create new datasets when creating skipped database operation tool outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21142 <https://github.com/galaxyproject/galaxy/pull/21142>`_
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* Fix optional param unset in RO-Crate export by `@davelopez <https://github.com/davelopez>`_ in `#21192 <https://github.com/galaxyproject/galaxy/pull/21192>`_
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============
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Enhancements
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============
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* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
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* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
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* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
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* support ZARR v3 for Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
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‎packages/files/HISTORY.rst‎

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-------------------
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25.0.4 (2025-11-18)
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-------------------
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No recorded changes since last release
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‎packages/job_execution/HISTORY.rst‎

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25.1rc1
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-------
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-------------------
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25.0.4 (2025-11-18)
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-------------------
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No recorded changes since last release
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‎packages/job_metrics/HISTORY.rst‎

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25.1rc1
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-------
99

1010

1111

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-------------------
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25.0.4 (2025-11-18)
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-------------------
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No recorded changes since last release
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‎packages/meta/HISTORY.rst‎

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25.1rc1
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-------
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910

1011

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-------------------
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25.0.4 (2025-11-18)
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-------------------
15+
16+
17+
=========
18+
Bug fixes
19+
=========
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* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
22+
* Skip sam metadata if we have too many references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20820 <https://github.com/galaxyproject/galaxy/pull/20820>`_
23+
* Fix select field cut off in dataset view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20947 <https://github.com/galaxyproject/galaxy/pull/20947>`_
24+
* Check for expiration in refresh token dictionary by `@jdavcs <https://github.com/jdavcs>`_ in `#20954 <https://github.com/galaxyproject/galaxy/pull/20954>`_
25+
* Deactivate user file source on unknown error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20962 <https://github.com/galaxyproject/galaxy/pull/20962>`_
26+
* Don't create workflow outputs to recover input parameter outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20980 <https://github.com/galaxyproject/galaxy/pull/20980>`_
27+
* Fix ``test_multiple_decorators`` unit test for FastAPI 0.118.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20982 <https://github.com/galaxyproject/galaxy/pull/20982>`_
28+
* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
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* Backport of #20984 by `@davelopez <https://github.com/davelopez>`_ in `#20994 <https://github.com/galaxyproject/galaxy/pull/20994>`_
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* Improves zip file type detection for uploads under windows by `@caroott <https://github.com/caroott>`_ in `#20999 <https://github.com/galaxyproject/galaxy/pull/20999>`_
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* Store pulsar job prep error messages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21013 <https://github.com/galaxyproject/galaxy/pull/21013>`_
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* Require OK datasets for filtering empty datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21023 <https://github.com/galaxyproject/galaxy/pull/21023>`_
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* Fix `InvalidRequestError` when saving workflow step with dynamic tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21056 <https://github.com/galaxyproject/galaxy/pull/21056>`_
34+
* Fix has_size assertion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21081 <https://github.com/galaxyproject/galaxy/pull/21081>`_
35+
* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
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* Fix workflow run form input restrictions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21095 <https://github.com/galaxyproject/galaxy/pull/21095>`_
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* Backport fix anndata datatype update by `@nilchia <https://github.com/nilchia>`_ in `#21111 <https://github.com/galaxyproject/galaxy/pull/21111>`_
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* Prefix download link by `@martenson <https://github.com/martenson>`_ in `#21112 <https://github.com/galaxyproject/galaxy/pull/21112>`_
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* Create new datasets when creating skipped database operation tool outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21142 <https://github.com/galaxyproject/galaxy/pull/21142>`_
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* Fix workflow landing rendering if public query param not provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21165 <https://github.com/galaxyproject/galaxy/pull/21165>`_
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* Fix optional param unset in RO-Crate export by `@davelopez <https://github.com/davelopez>`_ in `#21192 <https://github.com/galaxyproject/galaxy/pull/21192>`_
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* Fix MIME type for LAZ datatype by `@kysrpex <https://github.com/kysrpex>`_ in `#21202 <https://github.com/galaxyproject/galaxy/pull/21202>`_
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* Fix refresh token expiration retrieval logic by `@nuwang <https://github.com/nuwang>`_ in `#21213 <https://github.com/galaxyproject/galaxy/pull/21213>`_
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* Fix direct tool execution not using the latest version by `@jmchilton <https://github.com/jmchilton>`_ in `#21240 <https://github.com/galaxyproject/galaxy/pull/21240>`_
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* Fix proxy url validation for non-printable characters by `@davelopez <https://github.com/davelopez>`_ in `#21280 <https://github.com/galaxyproject/galaxy/pull/21280>`_
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* Swap to NPM trusted publishing for prebuilt client by `@dannon <https://github.com/dannon>`_ in `#21290 <https://github.com/galaxyproject/galaxy/pull/21290>`_
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============
49+
Enhancements
50+
============
51+
52+
* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
53+
* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
54+
* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
55+
* Add LAS and LAZ file format by `@bgruening <https://github.com/bgruening>`_ in `#21049 <https://github.com/galaxyproject/galaxy/pull/21049>`_
56+
* New datatype addition: gam for vg toolkit by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21096 <https://github.com/galaxyproject/galaxy/pull/21096>`_
57+
* Harden proxy redirect validation by `@davelopez <https://github.com/davelopez>`_ in `#21185 <https://github.com/galaxyproject/galaxy/pull/21185>`_
58+
* support ZARR v3 for Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
59+
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=============
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Other changes
62+
=============
63+
64+
* New datatype addition: beast.trees datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21055 <https://github.com/galaxyproject/galaxy/pull/21055>`_
65+
* Add display_in_upload to LAZ and LAS by `@bgruening <https://github.com/bgruening>`_ in `#21060 <https://github.com/galaxyproject/galaxy/pull/21060>`_
66+
* Backport `Fix proxy endpoint encoding` by `@davelopez <https://github.com/davelopez>`_ in `#21184 <https://github.com/galaxyproject/galaxy/pull/21184>`_
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‎packages/navigation/HISTORY.rst‎

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-------
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-------------------
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25.0.4 (2025-11-18)
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-------------------
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No recorded changes since last release
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-------------------
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-------------------

‎packages/objectstore/HISTORY.rst‎

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-------
99

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-------------------
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25.0.4 (2025-11-18)
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-------------------
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No recorded changes since last release
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-------------------
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25.0.3 (2025-09-23)
1420
-------------------

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