opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'release_25.1' into dev

Browse Source
This commit is contained in:
mvdbeek
2025-11-18 16:02:31 +01:00
parent 8b52821f51 231ea7db6e
commit bef42b43ca
25 changed files with 339 additions and 25 deletions
Download Patch File Download Diff File Expand all files Collapse all files
packages/app/HISTORY.rst
+27 -1
View File
@@ -4,11 +4,37 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Check for expiration in refresh token dictionary by `@jdavcs <https://github.com/jdavcs>`_ in `#20954 <https://github.com/galaxyproject/galaxy/pull/20954>`_
* Deactivate user file source on unknown error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20962 <https://github.com/galaxyproject/galaxy/pull/20962>`_
* 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>`_
* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
* Store pulsar job prep error messages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21013 <https://github.com/galaxyproject/galaxy/pull/21013>`_
* Require OK datasets for filtering empty datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21023 <https://github.com/galaxyproject/galaxy/pull/21023>`_
* Fix `InvalidRequestError` when saving workflow step with dynamic tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21056 <https://github.com/galaxyproject/galaxy/pull/21056>`_
* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
* 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>`_
* Fix refresh token expiration retrieval logic by `@nuwang <https://github.com/nuwang>`_ in `#21213 <https://github.com/galaxyproject/galaxy/pull/21213>`_
============
Enhancements
============
* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/auth/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/config/HISTORY.rst
+30 -1
View File
@@ -4,11 +4,40 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
* Fix MIME type for LAZ datatype by `@kysrpex <https://github.com/kysrpex>`_ in `#21202 <https://github.com/galaxyproject/galaxy/pull/21202>`_
============
Enhancements
============
* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
* Add LAS and LAZ file format by `@bgruening <https://github.com/bgruening>`_ in `#21049 <https://github.com/galaxyproject/galaxy/pull/21049>`_
* New datatype addition: gam for vg toolkit by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21096 <https://github.com/galaxyproject/galaxy/pull/21096>`_
* support ZARR v3 for Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
=============
Other changes
=============
* New datatype addition: beast.trees datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21055 <https://github.com/galaxyproject/galaxy/pull/21055>`_
* Add display_in_upload to LAZ and LAS by `@bgruening <https://github.com/bgruening>`_ in `#21060 <https://github.com/galaxyproject/galaxy/pull/21060>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/data/HISTORY.rst
+26 -1
View File
@@ -4,11 +4,36 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
* Skip sam metadata if we have too many references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20820 <https://github.com/galaxyproject/galaxy/pull/20820>`_
* Backport of #20984 by `@davelopez <https://github.com/davelopez>`_ in `#20994 <https://github.com/galaxyproject/galaxy/pull/20994>`_
* Backport fix anndata datatype update by `@nilchia <https://github.com/nilchia>`_ in `#21111 <https://github.com/galaxyproject/galaxy/pull/21111>`_
* 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>`_
* Fix optional param unset in RO-Crate export by `@davelopez <https://github.com/davelopez>`_ in `#21192 <https://github.com/galaxyproject/galaxy/pull/21192>`_
============
Enhancements
============
* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
* support ZARR v3 for Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/files/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/job_execution/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/job_metrics/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/meta/HISTORY.rst
+57 -1
View File
@@ -4,11 +4,67 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
* Skip sam metadata if we have too many references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20820 <https://github.com/galaxyproject/galaxy/pull/20820>`_
* Fix select field cut off in dataset view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20947 <https://github.com/galaxyproject/galaxy/pull/20947>`_
* Check for expiration in refresh token dictionary by `@jdavcs <https://github.com/jdavcs>`_ in `#20954 <https://github.com/galaxyproject/galaxy/pull/20954>`_
* Deactivate user file source on unknown error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20962 <https://github.com/galaxyproject/galaxy/pull/20962>`_
* 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>`_
* 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>`_
* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
* Backport of #20984 by `@davelopez <https://github.com/davelopez>`_ in `#20994 <https://github.com/galaxyproject/galaxy/pull/20994>`_
* Improves zip file type detection for uploads under windows by `@caroott <https://github.com/caroott>`_ in `#20999 <https://github.com/galaxyproject/galaxy/pull/20999>`_
* Store pulsar job prep error messages by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21013 <https://github.com/galaxyproject/galaxy/pull/21013>`_
* Require OK datasets for filtering empty datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21023 <https://github.com/galaxyproject/galaxy/pull/21023>`_
* Fix `InvalidRequestError` when saving workflow step with dynamic tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21056 <https://github.com/galaxyproject/galaxy/pull/21056>`_
* Fix has_size assertion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21081 <https://github.com/galaxyproject/galaxy/pull/21081>`_
* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
* Fix workflow run form input restrictions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21095 <https://github.com/galaxyproject/galaxy/pull/21095>`_
* Backport fix anndata datatype update by `@nilchia <https://github.com/nilchia>`_ in `#21111 <https://github.com/galaxyproject/galaxy/pull/21111>`_
* Prefix download link by `@martenson <https://github.com/martenson>`_ in `#21112 <https://github.com/galaxyproject/galaxy/pull/21112>`_
* 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>`_
* 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>`_
* Fix optional param unset in RO-Crate export by `@davelopez <https://github.com/davelopez>`_ in `#21192 <https://github.com/galaxyproject/galaxy/pull/21192>`_
* Fix MIME type for LAZ datatype by `@kysrpex <https://github.com/kysrpex>`_ in `#21202 <https://github.com/galaxyproject/galaxy/pull/21202>`_
* Fix refresh token expiration retrieval logic by `@nuwang <https://github.com/nuwang>`_ in `#21213 <https://github.com/galaxyproject/galaxy/pull/21213>`_
* Fix direct tool execution not using the latest version by `@jmchilton <https://github.com/jmchilton>`_ in `#21240 <https://github.com/galaxyproject/galaxy/pull/21240>`_
* Fix proxy url validation for non-printable characters by `@davelopez <https://github.com/davelopez>`_ in `#21280 <https://github.com/galaxyproject/galaxy/pull/21280>`_
* Swap to NPM trusted publishing for prebuilt client by `@dannon <https://github.com/dannon>`_ in `#21290 <https://github.com/galaxyproject/galaxy/pull/21290>`_
============
Enhancements
============
* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
* Add LAS and LAZ file format by `@bgruening <https://github.com/bgruening>`_ in `#21049 <https://github.com/galaxyproject/galaxy/pull/21049>`_
* New datatype addition: gam for vg toolkit by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21096 <https://github.com/galaxyproject/galaxy/pull/21096>`_
* Harden proxy redirect validation by `@davelopez <https://github.com/davelopez>`_ in `#21185 <https://github.com/galaxyproject/galaxy/pull/21185>`_
* support ZARR v3 for Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
=============
Other changes
=============
* New datatype addition: beast.trees datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21055 <https://github.com/galaxyproject/galaxy/pull/21055>`_
* Add display_in_upload to LAZ and LAS by `@bgruening <https://github.com/bgruening>`_ in `#21060 <https://github.com/galaxyproject/galaxy/pull/21060>`_
* Backport `Fix proxy endpoint encoding` by `@davelopez <https://github.com/davelopez>`_ in `#21184 <https://github.com/galaxyproject/galaxy/pull/21184>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/navigation/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/objectstore/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/schema/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/selenium/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/test_api/HISTORY.rst
+29 -1
View File
@@ -4,11 +4,39 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Fix PUT /api/workflows for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20987 <https://github.com/galaxyproject/galaxy/pull/20987>`_
* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
* Fix workflow run form input restrictions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21095 <https://github.com/galaxyproject/galaxy/pull/21095>`_
* 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>`_
* Fix proxy url validation for non-printable characters by `@davelopez <https://github.com/davelopez>`_ in `#21280 <https://github.com/galaxyproject/galaxy/pull/21280>`_
============
Enhancements
============
* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
* Harden proxy redirect validation by `@davelopez <https://github.com/davelopez>`_ in `#21185 <https://github.com/galaxyproject/galaxy/pull/21185>`_
=============
Other changes
=============
* Backport `Fix proxy endpoint encoding` by `@davelopez <https://github.com/davelopez>`_ in `#21184 <https://github.com/galaxyproject/galaxy/pull/21184>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/test_base/HISTORY.rst
+12 -1
View File
@@ -4,11 +4,22 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Run landing request state through validator by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21087 <https://github.com/galaxyproject/galaxy/pull/21087>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/test_driver/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/tool_shed/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/tool_shed_schema/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/tool_util/HISTORY.rst
+14 -1
View File
@@ -4,11 +4,24 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* Fix has_size assertion by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21081 <https://github.com/galaxyproject/galaxy/pull/21081>`_
* Fix workflow run form input restrictions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21095 <https://github.com/galaxyproject/galaxy/pull/21095>`_
* Fix direct tool execution not using the latest version by `@jmchilton <https://github.com/jmchilton>`_ in `#21240 <https://github.com/galaxyproject/galaxy/pull/21240>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/tool_util_models/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/tours/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/util/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/web_apps/HISTORY.rst
+25 -1
View File
@@ -4,11 +4,35 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
=========
Bug fixes
=========
* 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>`_
* Fix proxy url validation for non-printable characters by `@davelopez <https://github.com/davelopez>`_ in `#21280 <https://github.com/galaxyproject/galaxy/pull/21280>`_
============
Enhancements
============
* Harden proxy redirect validation by `@davelopez <https://github.com/davelopez>`_ in `#21185 <https://github.com/galaxyproject/galaxy/pull/21185>`_
=============
Other changes
=============
* Backport `Fix proxy endpoint encoding` by `@davelopez <https://github.com/davelopez>`_ in `#21184 <https://github.com/galaxyproject/galaxy/pull/21184>`_
-------------------
25.0.3 (2025-09-23)
-------------------
packages/web_client/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/web_framework/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------
packages/web_stack/HISTORY.rst
+7 -1
View File
@@ -4,11 +4,17 @@ History
.. to_doc
---------
25.1.dev0
26.0.dev0
---------
-------------------
25.0.4 (2025-11-18)
-------------------
No recorded changes since last release
-------------------
25.0.3 (2025-09-23)
-------------------