Create version 24.0.1

galaxyproject · May 2, 2024 · 592cf1e · 592cf1e
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commit 592cf1e
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diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
 VERSION_MAJOR = "24.0"
-VERSION_MINOR = "1.dev0"
+VERSION_MINOR = "1"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
@@ -3,11 +3,49 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix tool version switch in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17858 <https://github.com/galaxyproject/galaxy/pull/17858>`_
+* Fix workflow run form failing on certain histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17869 <https://github.com/galaxyproject/galaxy/pull/17869>`_
+* Always serialize element_count and populated when listing contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17890 <https://github.com/galaxyproject/galaxy/pull/17890>`_
+* Fix saving workflows with freehand_comments only by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17901 <https://github.com/galaxyproject/galaxy/pull/17901>`_
+* Always discard session after __handle_waiting_jobs is done by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17913 <https://github.com/galaxyproject/galaxy/pull/17913>`_
+* Fix workflow run form for workflows with null rename PJA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17929 <https://github.com/galaxyproject/galaxy/pull/17929>`_
+* Revert unnecessary error change by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17948 <https://github.com/galaxyproject/galaxy/pull/17948>`_
+* Fix missing implicit conversion for mapped over jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17952 <https://github.com/galaxyproject/galaxy/pull/17952>`_
+* Fix get_content_as_text for compressed text datatypes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17976 <https://github.com/galaxyproject/galaxy/pull/17976>`_
+* Backport: Fix bug: call unique() on result, not select stmt by `@jdavcs <https://github.com/jdavcs>`_ in `#17981 <https://github.com/galaxyproject/galaxy/pull/17981>`_
+* Fix `LengthValidator` if no value passed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17983 <https://github.com/galaxyproject/galaxy/pull/17983>`_
+* Raise ``RequestParameterInvalidException`` if collection element has unknown extension by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17985 <https://github.com/galaxyproject/galaxy/pull/17985>`_
+* Don't attempt to commit in dry_run mode by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17987 <https://github.com/galaxyproject/galaxy/pull/17987>`_
+* Don't fail if reporting invalid parameter values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18002 <https://github.com/galaxyproject/galaxy/pull/18002>`_
+* Include exception info when something goes wrong while refreshing tokens by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18008 <https://github.com/galaxyproject/galaxy/pull/18008>`_
+* Avoid exception when opening apply rules tool and no collection in history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18011 <https://github.com/galaxyproject/galaxy/pull/18011>`_
+* Don't commit without having set a hid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18014 <https://github.com/galaxyproject/galaxy/pull/18014>`_
+* Raise appropriate exception if user forces a collection that is not populated with elements as input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18023 <https://github.com/galaxyproject/galaxy/pull/18023>`_
+* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
+* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
+* Change wrong quota_source value from KeyError to ValueError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18040 <https://github.com/galaxyproject/galaxy/pull/18040>`_
+* Check database connection to issue a rollback if no connection by `@jdavcs <https://github.com/jdavcs>`_ in `#18070 <https://github.com/galaxyproject/galaxy/pull/18070>`_
 
+============
+Enhancements
+============
+
+* Fix remote files sources error handling by `@davelopez <https://github.com/davelopez>`_ in `#18027 <https://github.com/galaxyproject/galaxy/pull/18027>`_
+
+=============
+Other changes
+=============
 
+* Drop left-over debug statement by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17939 <https://github.com/galaxyproject/galaxy/pull/17939>`_
 
 -------------------
 24.0.0 (2024-04-02)
@@ -52,7 +90,7 @@ Enhancements
 * Vueify Admin User Grid by `@guerler <https://github.com/guerler>`_ in `#17030 <https://github.com/galaxyproject/galaxy/pull/17030>`_
 * Remove web framework dependency from tools by `@davelopez <https://github.com/davelopez>`_ in `#17058 <https://github.com/galaxyproject/galaxy/pull/17058>`_
 * Add select parameter with options from remote resources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17087 <https://github.com/galaxyproject/galaxy/pull/17087>`_
-*  Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
+* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
 * Vueify Admin Roles Grid by `@guerler <https://github.com/guerler>`_ in `#17118 <https://github.com/galaxyproject/galaxy/pull/17118>`_
 * SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_
 * Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17123 <https://github.com/galaxyproject/galaxy/pull/17123>`_

diff --git a/packages/app/setup.cfg b/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 = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
-
+-------------------
+24.0.1 (2024-05-02)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/auth/setup.cfg b/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 = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
@@ -3,11 +3,32 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Invenio plugin fixes by `@davelopez <https://github.com/davelopez>`_ in `#17997 <https://github.com/galaxyproject/galaxy/pull/17997>`_
+* clarify the object store relocate functionality by `@martenson <https://github.com/martenson>`_ in `#18033 <https://github.com/galaxyproject/galaxy/pull/18033>`_
+* Updated the datatypes name for FASTK tool by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#18053 <https://github.com/galaxyproject/galaxy/pull/18053>`_
 
+============
+Enhancements
+============
+
+* Added 4dn_pairs and 4dn_pairsam datatypes by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#17875 <https://github.com/galaxyproject/galaxy/pull/17875>`_
+* Add middleware for logging start and end of request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18046 <https://github.com/galaxyproject/galaxy/pull/18046>`_
+
+=============
+Other changes
+=============
 
+* Rebuild config samples by `@davelopez <https://github.com/davelopez>`_ in `#17911 <https://github.com/galaxyproject/galaxy/pull/17911>`_
+* Backport colabfold tar file datatype by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18029 <https://github.com/galaxyproject/galaxy/pull/18029>`_
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/config/setup.cfg b/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 = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
@@ -3,11 +3,28 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* Always serialize element_count and populated when listing contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17890 <https://github.com/galaxyproject/galaxy/pull/17890>`_
+* Fix deadlock that can occur when changing job state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17896 <https://github.com/galaxyproject/galaxy/pull/17896>`_
+* Fix tool form building if select filters from unavailable dataset metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17930 <https://github.com/galaxyproject/galaxy/pull/17930>`_
+* Fix ``InvalidRequestError: Can't operate on closed transaction inside context manager.  Please complete the context manager before emitting further commands.`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17932 <https://github.com/galaxyproject/galaxy/pull/17932>`_
+* Never fail dataset serialization if display_peek fails by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17937 <https://github.com/galaxyproject/galaxy/pull/17937>`_
+* Fix output datatype when uncompressing a dataset with incorrect datatype by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17944 <https://github.com/galaxyproject/galaxy/pull/17944>`_
+* Use or copy StoredWorkflow when copying step by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17988 <https://github.com/galaxyproject/galaxy/pull/17988>`_
+* Raise ``MessageException`` when report references invalid workflow output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18009 <https://github.com/galaxyproject/galaxy/pull/18009>`_
+* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
+* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
+* Fix history export with missing dataset hids by `@davelopez <https://github.com/davelopez>`_ in `#18052 <https://github.com/galaxyproject/galaxy/pull/18052>`_
+* Fix comments lost on import by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#18060 <https://github.com/galaxyproject/galaxy/pull/18060>`_
+* Fix history update time after bulk operation by `@davelopez <https://github.com/davelopez>`_ in `#18068 <https://github.com/galaxyproject/galaxy/pull/18068>`_
 
 -------------------
 24.0.0 (2024-04-02)
@@ -51,7 +68,7 @@ Enhancements
 * port invocation API to fastapi by `@martenson <https://github.com/martenson>`_ in `#16707 <https://github.com/galaxyproject/galaxy/pull/16707>`_
 * SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs <https://github.com/jdavcs>`_ in `#16932 <https://github.com/galaxyproject/galaxy/pull/16932>`_
 * Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
-*  Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
+* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
 * Add support for (fast5.tar).xz binary compressed files by `@tuncK <https://github.com/tuncK>`_ in `#17106 <https://github.com/galaxyproject/galaxy/pull/17106>`_
 * SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_
 * Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs <https://github.com/jdavcs>`_ in `#17132 <https://github.com/galaxyproject/galaxy/pull/17132>`_

diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-data
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst
@@ -3,11 +3,22 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
 
+=========
+Bug fixes
+=========
+
+* Invenio plugin fixes by `@davelopez <https://github.com/davelopez>`_ in `#17997 <https://github.com/galaxyproject/galaxy/pull/17997>`_
+
+============
+Enhancements
+============
 
+* Fix remote files sources error handling by `@davelopez <https://github.com/davelopez>`_ in `#18027 <https://github.com/galaxyproject/galaxy/pull/18027>`_
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-files
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
-
+-------------------
+24.0.1 (2024-05-02)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-job-execution
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
-
+-------------------
+24.0.1 (2024-05-02)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-job-metrics
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
-
+-------------------
+24.0.1 (2024-05-02)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-navigation
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
-
+-------------------
+24.0.1 (2024-05-02)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg
@@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-objectstore
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst
@@ -3,11 +3,17 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
+* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-schema
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
@@ -3,11 +3,16 @@ History
 
 .. to_doc
 
------------
-24.0.1.dev0
------------
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
 
+=========
+Bug fixes
+=========
 
+* Set from_tool_form: true when saving new workflow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17972 <https://github.com/galaxyproject/galaxy/pull/17972>`_
 
 -------------------
 24.0.0 (2024-04-02)

diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg
@@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst
 long_description_content_type = text/x-rst
 name = galaxy-selenium
 url = https://github.com/galaxyproject/galaxy
-version = 24.0.1.dev0
+version = 24.0.1
 
 [options]
 include_package_data = True