Merge branch 'release_26.0' into dev

Author: mvdbeek

packages/app/HISTORY.rst

@@ -4,11 +4,42 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Record input parameter invocation inputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21452 <https://github.com/galaxyproject/galaxy/pull/21452>`_
+* Maintain column definitions on map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21468 <https://github.com/galaxyproject/galaxy/pull/21468>`_
+* Do not update a user's update_time when an admin archives (and purges) a history by `@natefoo <https://github.com/natefoo>`_ in `#21484 <https://github.com/galaxyproject/galaxy/pull/21484>`_
+* Fix subworkflow runs for disconnected required inputs with defaults by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21488 <https://github.com/galaxyproject/galaxy/pull/21488>`_
+* Usability fixes for sample sheet selection.  by `@jmchilton <https://github.com/jmchilton>`_ in `#21503 <https://github.com/galaxyproject/galaxy/pull/21503>`_
+* Fix type annotation for invocation report ``errors`` field by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21508 <https://github.com/galaxyproject/galaxy/pull/21508>`_
+* Filter out failed_metadata HDAs from job cache by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21544 <https://github.com/galaxyproject/galaxy/pull/21544>`_
+* Fix pulsar with ``rewrite_parameters: false`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21557 <https://github.com/galaxyproject/galaxy/pull/21557>`_
+* Fix Pulsar with ``default_file_action: none`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21578 <https://github.com/galaxyproject/galaxy/pull/21578>`_
+* Fix condor typo by `@gsaudade99 <https://github.com/gsaudade99>`_ in `#21651 <https://github.com/galaxyproject/galaxy/pull/21651>`_
+* Fix HTCondor runner unwatching jobs when stopping containers by `@kysrpex <https://github.com/kysrpex>`_ in `#21656 <https://github.com/galaxyproject/galaxy/pull/21656>`_
+* Fix option propagation for workflow inputs connected to multiple subworkflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21712 <https://github.com/galaxyproject/galaxy/pull/21712>`_
+* Add missing filter_failed_collection_1.1.0.xml tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21719 <https://github.com/galaxyproject/galaxy/pull/21719>`_
+* Strip inline comments in conditional requirements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21720 <https://github.com/galaxyproject/galaxy/pull/21720>`_
+
+============
+Enhancements
+============
+
+* Add sample sheet support to many database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21465 <https://github.com/galaxyproject/galaxy/pull/21465>`_
+* Add database operation tool to convert sample sheets to list collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21625 <https://github.com/galaxyproject/galaxy/pull/21625>`_
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------

packages/auth/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------

packages/config/HISTORY.rst

@@ -4,11 +4,36 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Use quotes for Galaxy citation bibtex by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21563 <https://github.com/galaxyproject/galaxy/pull/21563>`_
+* Add split paired or unpaired tool to sample tool conf by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#21647 <https://github.com/galaxyproject/galaxy/pull/21647>`_
+* Add missing filter_failed_collection_1.1.0.xml tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21719 <https://github.com/galaxyproject/galaxy/pull/21719>`_
+
+============
+Enhancements
+============
+
+* add new datatype for kmindex index data by `@Smeds <https://github.com/Smeds>`_ in `#21429 <https://github.com/galaxyproject/galaxy/pull/21429>`_
+* Add Sourmash sig new datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21469 <https://github.com/galaxyproject/galaxy/pull/21469>`_
+* Adds object_expires_after_days example usage to sample config by `@davelopez <https://github.com/davelopez>`_ in `#21547 <https://github.com/galaxyproject/galaxy/pull/21547>`_
+* Add a few datatypes from the digital humanities domain by `@bgruening <https://github.com/bgruening>`_ in `#21596 <https://github.com/galaxyproject/galaxy/pull/21596>`_
+* Add new datatype pg and hg for pangenomics by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21620 <https://github.com/galaxyproject/galaxy/pull/21620>`_
+* Add database operation tool to convert sample sheets to list collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21625 <https://github.com/galaxyproject/galaxy/pull/21625>`_
+* Add new datatypes required for VG tool by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21644 <https://github.com/galaxyproject/galaxy/pull/21644>`_
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------

packages/data/HISTORY.rst

@@ -4,11 +4,40 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Sample sheet column fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21446 <https://github.com/galaxyproject/galaxy/pull/21446>`_
+* Maintain column definitions on map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21468 <https://github.com/galaxyproject/galaxy/pull/21468>`_
+* Add missing test file for sig datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21473 <https://github.com/galaxyproject/galaxy/pull/21473>`_
+* Do not update a user's update_time when an admin archives (and purges) a history by `@natefoo <https://github.com/natefoo>`_ in `#21484 <https://github.com/galaxyproject/galaxy/pull/21484>`_
+* Add missing ending newline to test.sig test data file by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21485 <https://github.com/galaxyproject/galaxy/pull/21485>`_
+* Usability fixes for sample sheet selection.  by `@jmchilton <https://github.com/jmchilton>`_ in `#21503 <https://github.com/galaxyproject/galaxy/pull/21503>`_
+* Fix exception message to enable debugging of missing dataset issue. by `@jmchilton <https://github.com/jmchilton>`_ in `#21504 <https://github.com/galaxyproject/galaxy/pull/21504>`_
+* Add missing dependencies to ``galaxy-files`` package by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21518 <https://github.com/galaxyproject/galaxy/pull/21518>`_
+* Fix job cache collection copy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21558 <https://github.com/galaxyproject/galaxy/pull/21558>`_
+* Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by `@jmchilton <https://github.com/jmchilton>`_ in `#21584 <https://github.com/galaxyproject/galaxy/pull/21584>`_
+* Fix race condition in workflow collection populated state check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21613 <https://github.com/galaxyproject/galaxy/pull/21613>`_
+* Fix collection job state not preserved during history export/import by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21716 <https://github.com/galaxyproject/galaxy/pull/21716>`_
+
+============
+Enhancements
+============
+
+* Add Sourmash sig new datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21469 <https://github.com/galaxyproject/galaxy/pull/21469>`_
+* Add database operation tool to convert sample sheets to list collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21625 <https://github.com/galaxyproject/galaxy/pull/21625>`_
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------

packages/files/HISTORY.rst

@@ -4,11 +4,24 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Add missing dependencies to ``galaxy-files`` package by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21518 <https://github.com/galaxyproject/galaxy/pull/21518>`_
+* Supports Dataverse file access via both persistent and database IDs by `@davelopez <https://github.com/davelopez>`_ in `#21569 <https://github.com/galaxyproject/galaxy/pull/21569>`_
+* Harden Dataverse integration by `@davelopez <https://github.com/davelopez>`_ in `#21624 <https://github.com/galaxyproject/galaxy/pull/21624>`_
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------

packages/job_execution/HISTORY.rst

@@ -4,11 +4,22 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix pulsar with ``rewrite_parameters: false`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21557 <https://github.com/galaxyproject/galaxy/pull/21557>`_
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------

packages/job_metrics/HISTORY.rst

@@ -4,11 +4,17 @@ History
 .. to_doc
 
 ---------
-26.0.dev0
+26.1.dev0
 ---------
 
 
 
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+No recorded changes since last release
+
 -------------------
 25.1.0 (2025-12-12)
 -------------------