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Merge branch 'release_26.0' into dev

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mvdbeek
2026-03-09 17:33:09 +01:00
parent 9b03fe65f0 3124ebcec6
commit 8de15ef52c
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packages/app/HISTORY.rst
+21
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@@ -9,6 +9,27 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Add selenium test and fix inline images in workflow report tables by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21698 <https://github.com/galaxyproject/galaxy/pull/21698>`_
* Allow workflow download with missing file source references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21814 <https://github.com/galaxyproject/galaxy/pull/21814>`_
* Fix AWS Batch monitor crash, delete copied monitor method by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21818 <https://github.com/galaxyproject/galaxy/pull/21818>`_
* Fix tool credentials on containerized (Singularity/Docker) destinations by `@arash77 <https://github.com/arash77>`_ in `#21821 <https://github.com/galaxyproject/galaxy/pull/21821>`_
* Add `builtin_converters` section to integrated tool panel by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21838 <https://github.com/galaxyproject/galaxy/pull/21838>`_
* Fix output dataset permission guessing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21862 <https://github.com/galaxyproject/galaxy/pull/21862>`_
* Enforce storage quota for Celery-based data fetch jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21941 <https://github.com/galaxyproject/galaxy/pull/21941>`_
* Fix optional parameter persisting ``NO_REPLACEMENT`` sentinel when not provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21964 <https://github.com/galaxyproject/galaxy/pull/21964>`_
* Fix recording duplicate workflow_request_input_step_parameter rows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21980 <https://github.com/galaxyproject/galaxy/pull/21980>`_
* Fix NoReplacement handling in workflow callback_helper by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21994 <https://github.com/galaxyproject/galaxy/pull/21994>`_
* Fix pick_value output inheriting hidden state from input datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21995 <https://github.com/galaxyproject/galaxy/pull/21995>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/auth/HISTORY.rst
+6
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/config/HISTORY.rst
+18
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@@ -9,6 +9,24 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Add missing enable_beta_tool_formats config option by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21190 <https://github.com/galaxyproject/galaxy/pull/21190>`_
============
Enhancements
============
* Add Deacon idx format by `@SantaMcCloud <https://github.com/SantaMcCloud>`_ in `#21632 <https://github.com/galaxyproject/galaxy/pull/21632>`_
* Add amnis cif flow cytometry data type by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21829 <https://github.com/galaxyproject/galaxy/pull/21829>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/data/HISTORY.rst
+20
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@@ -9,6 +9,26 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Fix private dataset sharing error handling by `@davelopez <https://github.com/davelopez>`_ in `#21689 <https://github.com/galaxyproject/galaxy/pull/21689>`_
* Fix database migration error from 25.0 > 25.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#21737 <https://github.com/galaxyproject/galaxy/pull/21737>`_
* Make database heartbeat more robust (backport) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21812 <https://github.com/galaxyproject/galaxy/pull/21812>`_
* Fix recording duplicate workflow_request_input_step_parameter rows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21980 <https://github.com/galaxyproject/galaxy/pull/21980>`_
=============
Other changes
=============
* Fix worker segfault in gunicorn preload mode on OSX by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21837 <https://github.com/galaxyproject/galaxy/pull/21837>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/files/HISTORY.rst
+6
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/job_execution/HISTORY.rst
+6
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/job_metrics/HISTORY.rst
+6
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/meta/HISTORY.rst
+54
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@@ -9,6 +9,60 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Add missing enable_beta_tool_formats config option by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21190 <https://github.com/galaxyproject/galaxy/pull/21190>`_
* Properly parse build info from requirement info by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21481 <https://github.com/galaxyproject/galaxy/pull/21481>`_
* Fix private dataset sharing error handling by `@davelopez <https://github.com/davelopez>`_ in `#21689 <https://github.com/galaxyproject/galaxy/pull/21689>`_
* Add selenium test and fix inline images in workflow report tables by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21698 <https://github.com/galaxyproject/galaxy/pull/21698>`_
* Fix route to workflow editor with version does not load expected version by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21711 <https://github.com/galaxyproject/galaxy/pull/21711>`_
* Fix database migration error from 25.0 > 25.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#21737 <https://github.com/galaxyproject/galaxy/pull/21737>`_
* Fix npm trusted publishing in 25.1 release workflow by `@dannon <https://github.com/dannon>`_ in `#21747 <https://github.com/galaxyproject/galaxy/pull/21747>`_
* Make galaxy-web-apps package compatible with latest FastAPI by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21753 <https://github.com/galaxyproject/galaxy/pull/21753>`_
* Fix disable_local_accounts displays register link by `@davelopez <https://github.com/davelopez>`_ in `#21764 <https://github.com/galaxyproject/galaxy/pull/21764>`_
* Fix help forum integration by `@davelopez <https://github.com/davelopez>`_ in `#21773 <https://github.com/galaxyproject/galaxy/pull/21773>`_
* Fix workflow rename modal is not reactive to prop changes by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21785 <https://github.com/galaxyproject/galaxy/pull/21785>`_
* Fix tag dropdown not closing on outside click, and not selecting in Safari by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21797 <https://github.com/galaxyproject/galaxy/pull/21797>`_
* Make database heartbeat more robust (backport) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21812 <https://github.com/galaxyproject/galaxy/pull/21812>`_
* Allow workflow download with missing file source references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21814 <https://github.com/galaxyproject/galaxy/pull/21814>`_
* Fix AWS Batch monitor crash, delete copied monitor method by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21818 <https://github.com/galaxyproject/galaxy/pull/21818>`_
* Fix form number negative handling by `@davelopez <https://github.com/davelopez>`_ in `#21819 <https://github.com/galaxyproject/galaxy/pull/21819>`_
* Fix tool credentials on containerized (Singularity/Docker) destinations by `@arash77 <https://github.com/arash77>`_ in `#21821 <https://github.com/galaxyproject/galaxy/pull/21821>`_
* Pin setuptools<82 for galaxy-files package - Backport #21824 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21826 <https://github.com/galaxyproject/galaxy/pull/21826>`_
* Add `builtin_converters` section to integrated tool panel by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21838 <https://github.com/galaxyproject/galaxy/pull/21838>`_
* Fix Galaxy UI nesting in data manager job info view by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21840 <https://github.com/galaxyproject/galaxy/pull/21840>`_
* Fix output dataset permission guessing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21862 <https://github.com/galaxyproject/galaxy/pull/21862>`_
* Fix loading non-tool files from watched tool directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21880 <https://github.com/galaxyproject/galaxy/pull/21880>`_
* Fix credential validation logic in tool form component by `@itisAliRH <https://github.com/itisAliRH>`_ in `#21889 <https://github.com/galaxyproject/galaxy/pull/21889>`_
* Ensure markdown elements do not render if argument is undefined by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21908 <https://github.com/galaxyproject/galaxy/pull/21908>`_
* Fix "Create New" in workflow editor not resetting editor state by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21918 <https://github.com/galaxyproject/galaxy/pull/21918>`_
* Enforce storage quota for Celery-based data fetch jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21941 <https://github.com/galaxyproject/galaxy/pull/21941>`_
* Fix optional parameter persisting ``NO_REPLACEMENT`` sentinel when not provided by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21964 <https://github.com/galaxyproject/galaxy/pull/21964>`_
* Fix recording duplicate workflow_request_input_step_parameter rows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21980 <https://github.com/galaxyproject/galaxy/pull/21980>`_
* Fix AttributeError when requesting invalid metadata file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21985 <https://github.com/galaxyproject/galaxy/pull/21985>`_
* Fix NoReplacement handling in workflow callback_helper by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21994 <https://github.com/galaxyproject/galaxy/pull/21994>`_
* Fix pick_value output inheriting hidden state from input datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21995 <https://github.com/galaxyproject/galaxy/pull/21995>`_
============
Enhancements
============
* Add Deacon idx format by `@SantaMcCloud <https://github.com/SantaMcCloud>`_ in `#21632 <https://github.com/galaxyproject/galaxy/pull/21632>`_
* Add amnis cif flow cytometry data type by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21829 <https://github.com/galaxyproject/galaxy/pull/21829>`_
=============
Other changes
=============
* Fix worker segfault in gunicorn preload mode on OSX by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21837 <https://github.com/galaxyproject/galaxy/pull/21837>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/navigation/HISTORY.rst
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/objectstore/HISTORY.rst
+6
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/schema/HISTORY.rst
+11
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@@ -9,6 +9,17 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Fix help forum integration by `@davelopez <https://github.com/davelopez>`_ in `#21773 <https://github.com/galaxyproject/galaxy/pull/21773>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/selenium/HISTORY.rst
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/test_api/HISTORY.rst
+12
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@@ -9,6 +9,18 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Allow workflow download with missing file source references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21814 <https://github.com/galaxyproject/galaxy/pull/21814>`_
* Fix pick_value output inheriting hidden state from input datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21995 <https://github.com/galaxyproject/galaxy/pull/21995>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/test_base/HISTORY.rst
+12
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@@ -9,6 +9,18 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Add selenium test and fix inline images in workflow report tables by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21698 <https://github.com/galaxyproject/galaxy/pull/21698>`_
* Fix tool credentials on containerized (Singularity/Docker) destinations by `@arash77 <https://github.com/arash77>`_ in `#21821 <https://github.com/galaxyproject/galaxy/pull/21821>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/test_driver/HISTORY.rst
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-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/tool_shed/HISTORY.rst
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-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/tool_shed_schema/HISTORY.rst
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/tool_util/HISTORY.rst
+12
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@@ -9,6 +9,18 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Properly parse build info from requirement info by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21481 <https://github.com/galaxyproject/galaxy/pull/21481>`_
* Fix loading non-tool files from watched tool directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21880 <https://github.com/galaxyproject/galaxy/pull/21880>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/tool_util_models/HISTORY.rst
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-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/tours/HISTORY.rst
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-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/util/HISTORY.rst
+6
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/web_apps/HISTORY.rst
+12
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@@ -9,6 +9,18 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
=========
Bug fixes
=========
* Make galaxy-web-apps package compatible with latest FastAPI by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21753 <https://github.com/galaxyproject/galaxy/pull/21753>`_
* Fix AttributeError when requesting invalid metadata file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21985 <https://github.com/galaxyproject/galaxy/pull/21985>`_
-------------------
25.1.1 (2026-02-03)
-------------------
packages/web_client/HISTORY.rst
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/web_framework/HISTORY.rst
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-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------
packages/web_stack/HISTORY.rst
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@@ -9,6 +9,12 @@ History
-------------------
25.1.2 (2026-03-09)
-------------------
No recorded changes since last release
-------------------
25.1.1 (2026-02-03)
-------------------