Create version 25.1.1

Author: mvdbeek

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxyproject/galaxy-client",
-  "version": "25.1.1.dev0",
+  "version": "25.1.1",
   "description": "Galaxy client application build system",
   "keywords": [
     "galaxy"

lib/galaxy/version.py

@@ -1,3 +1,3 @@
 VERSION_MAJOR = "25.1"
-VERSION_MINOR = "1.dev0"
+VERSION_MINOR = "1"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxyproject/galaxy",
-  "version": "25.1.0",
+  "version": "25.1.1",
   "description": ".. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg    :alt: Galaxy Logo",
   "main": "index.js",
   "scripts": {
@@ -17,7 +17,7 @@
   },
   "homepage": "https://github.com/galaxyproject/galaxy#readme",
   "dependencies": {
-    "@galaxyproject/galaxy-client": "25.1.0",
+    "@galaxyproject/galaxy-client": "25.1.1",
     "cpy-cli": "^5.0.0"
   },
   "packageManager": "[email protected]+sha512.a6b2f7906b721bba3d67d4aff083df04dad64c399707841b7acf00f6b133b7ac24255f2652fa22ae3534329dc6180534e98d17432037ff6fd140556e2bb3137e"

packages/app/HISTORY.rst

@@ -3,11 +3,36 @@ History
 
 .. to_doc
 
------------
-25.1.1.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/app/setup.cfg

@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-app
 url = https://github.com/galaxyproject/galaxy
-version = 25.1.1.dev0
+version = 25.1.1
 
 [options]
 include_package_data = True

packages/auth/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-25.1.1.dev0
------------
-
+-------------------
+25.1.1 (2026-02-03)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 25.1.0 (2025-12-12)

packages/auth/setup.cfg

@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-auth
 url = https://github.com/galaxyproject/galaxy
-version = 25.1.1.dev0
+version = 25.1.1
 
 [options]
 include_package_data = True

packages/config/HISTORY.rst

@@ -3,11 +3,30 @@ History
 
 .. to_doc
 
------------
-25.1.1.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/config/setup.cfg

@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-config
 url = https://github.com/galaxyproject/galaxy
-version = 25.1.1.dev0
+version = 25.1.1
 
 [options]
 include_package_data = True

packages/data/HISTORY.rst

@@ -3,11 +3,34 @@ History
 
 .. to_doc
 
------------
-25.1.1.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)