Create version 23.2.1

lib/galaxy/version.py

@@ -1,3 +1,3 @@
 VERSION_MAJOR = "23.2"
-VERSION_MINOR = "1.dev0"
+VERSION_MINOR = "1"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True
@@ -86,4 +86,4 @@ console_scripts =
 [options.packages.find]
 exclude =
     galaxy.tools.bundled*
-    tests*
+    tests*

packages/auth/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
-
+-------------------
+23.2.1 (2024-02-21)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 23.1.4 (2024-01-04)

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True

packages/config/HISTORY.rst

@@ -3,11 +3,55 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* pin fs.dropboxfs to >=1 by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16451 <https://github.com/galaxyproject/galaxy/pull/16451>`_
+* MINERVA display application: enable cors, add for tabular by `@hexylena <https://github.com/hexylena>`_ in `#16737 <https://github.com/galaxyproject/galaxy/pull/16737>`_
+* chore: fix typos by `@afuetterer <https://github.com/afuetterer>`_ in `#16851 <https://github.com/galaxyproject/galaxy/pull/16851>`_
+* Add back 1.1.0 version of Filtering1 tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16883 <https://github.com/galaxyproject/galaxy/pull/16883>`_
+* Set webdav file source to use temp files by default by `@davelopez <https://github.com/davelopez>`_ in `#17388 <https://github.com/galaxyproject/galaxy/pull/17388>`_
 
+============
+Enhancements
+============
+
+* Update cellxgene interactive tool to 1.1.1 by `@pcm32 <https://github.com/pcm32>`_ in `#15313 <https://github.com/galaxyproject/galaxy/pull/15313>`_
+* Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#15639 <https://github.com/galaxyproject/galaxy/pull/15639>`_
+* Limit number of celery task executions per second per user by `@claudiofr <https://github.com/claudiofr>`_ in `#16232 <https://github.com/galaxyproject/galaxy/pull/16232>`_
+* Add carbon emissions admin configuration options by `@Renni771 <https://github.com/Renni771>`_ in `#16307 <https://github.com/galaxyproject/galaxy/pull/16307>`_
+* Add Invenio RDM repository integration by `@davelopez <https://github.com/davelopez>`_ in `#16381 <https://github.com/galaxyproject/galaxy/pull/16381>`_
+* Add new datatype: STL by `@TanguyGen <https://github.com/TanguyGen>`_ in `#16478 <https://github.com/galaxyproject/galaxy/pull/16478>`_
+* add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools by `@khaled196 <https://github.com/khaled196>`_ in `#16503 <https://github.com/galaxyproject/galaxy/pull/16503>`_
+* Tweak tool memory use and optimize shared memory when using preload by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16536 <https://github.com/galaxyproject/galaxy/pull/16536>`_
+* Implement datatype upload warnings by `@jmchilton <https://github.com/jmchilton>`_ in `#16564 <https://github.com/galaxyproject/galaxy/pull/16564>`_
+* Support new genome browser chain file format by `@claudiofr <https://github.com/claudiofr>`_ in `#16576 <https://github.com/galaxyproject/galaxy/pull/16576>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16577 <https://github.com/galaxyproject/galaxy/pull/16577>`_
+* Implement instance URLs in Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16675 <https://github.com/galaxyproject/galaxy/pull/16675>`_
+*  Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola <https://github.com/lopiola>`_ in `#16690 <https://github.com/galaxyproject/galaxy/pull/16690>`_
+* Update datatypes_conf.xml.sample with docx type by `@yvanlebras <https://github.com/yvanlebras>`_ in `#16713 <https://github.com/galaxyproject/galaxy/pull/16713>`_
+* Replace ELIXIR AAI button with Life Science login by `@sebastian-schaaf <https://github.com/sebastian-schaaf>`_ in `#16762 <https://github.com/galaxyproject/galaxy/pull/16762>`_
+* Add EGI Check-in as OIDC authentication option by `@enolfc <https://github.com/enolfc>`_ in `#16782 <https://github.com/galaxyproject/galaxy/pull/16782>`_
+* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu <https://github.com/sveinugu>`_ in `#16795 <https://github.com/galaxyproject/galaxy/pull/16795>`_
+* Galaxy help forum integration by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16798 <https://github.com/galaxyproject/galaxy/pull/16798>`_
+* Remove record access handling for Invenio RDM plugin by `@davelopez <https://github.com/davelopez>`_ in `#16900 <https://github.com/galaxyproject/galaxy/pull/16900>`_
+* optimize object store cache operations by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17025 <https://github.com/galaxyproject/galaxy/pull/17025>`_
+* Support configuring job metrics inline, update documentation by `@natefoo <https://github.com/natefoo>`_ in `#17178 <https://github.com/galaxyproject/galaxy/pull/17178>`_
+* Add binary datatypes for intermediate output of fastk tools by `@astrovsky01 <https://github.com/astrovsky01>`_ in `#17265 <https://github.com/galaxyproject/galaxy/pull/17265>`_
+* Add magres datatype by `@martenson <https://github.com/martenson>`_ in `#17499 <https://github.com/galaxyproject/galaxy/pull/17499>`_
+
+=============
+Other changes
+=============
 
+* Merge 23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16534 <https://github.com/galaxyproject/galaxy/pull/16534>`_
+* Remove xml remnant in sample yml job conf by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16609 <https://github.com/galaxyproject/galaxy/pull/16609>`_
 
 -------------------
 23.1.4 (2024-01-04)

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True

packages/data/HISTORY.rst

@@ -3,11 +3,75 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Rename to_dict to populate in FormDefintion to fix bug by `@jdavcs <https://github.com/jdavcs>`_ in `#16553 <https://github.com/galaxyproject/galaxy/pull/16553>`_
+* MINERVA display application: enable cors, add for tabular by `@hexylena <https://github.com/hexylena>`_ in `#16737 <https://github.com/galaxyproject/galaxy/pull/16737>`_
+* Use AlignedSegment.to_string by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16803 <https://github.com/galaxyproject/galaxy/pull/16803>`_
+* Ruff and flake8 fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16884 <https://github.com/galaxyproject/galaxy/pull/16884>`_
+* prep for updated h5py and typos by `@mr-c <https://github.com/mr-c>`_ in `#16963 <https://github.com/galaxyproject/galaxy/pull/16963>`_
+* Fix cardinality violation error: subquery returns multiple results by `@jdavcs <https://github.com/jdavcs>`_ in `#17224 <https://github.com/galaxyproject/galaxy/pull/17224>`_
+* Fix Display Application link generation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17227 <https://github.com/galaxyproject/galaxy/pull/17227>`_
+* Display application fixes and tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17233 <https://github.com/galaxyproject/galaxy/pull/17233>`_
+* Rollback invalidated transaction by `@jdavcs <https://github.com/jdavcs>`_ in `#17280 <https://github.com/galaxyproject/galaxy/pull/17280>`_
+* Set metadata states on dataset association, not dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17474 <https://github.com/galaxyproject/galaxy/pull/17474>`_
+* Provide working routes.url_for every ASGI request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17497 <https://github.com/galaxyproject/galaxy/pull/17497>`_
 
+============
+Enhancements
+============
+
+* Implement default locations for data and collection parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#14955 <https://github.com/galaxyproject/galaxy/pull/14955>`_
+* Display beginning of non-text files as text instead of triggering a download by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#15447 <https://github.com/galaxyproject/galaxy/pull/15447>`_
+* Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#15639 <https://github.com/galaxyproject/galaxy/pull/15639>`_
+* Limit number of celery task executions per second per user by `@claudiofr <https://github.com/claudiofr>`_ in `#16232 <https://github.com/galaxyproject/galaxy/pull/16232>`_
+* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16252 <https://github.com/galaxyproject/galaxy/pull/16252>`_
+* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs <https://github.com/jdavcs>`_ in `#16264 <https://github.com/galaxyproject/galaxy/pull/16264>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16409 <https://github.com/galaxyproject/galaxy/pull/16409>`_
+* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs <https://github.com/jdavcs>`_ in `#16431 <https://github.com/galaxyproject/galaxy/pull/16431>`_
+* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs <https://github.com/jdavcs>`_ in `#16434 <https://github.com/galaxyproject/galaxy/pull/16434>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16436 <https://github.com/galaxyproject/galaxy/pull/16436>`_
+* Implement datatype upload warnings by `@jmchilton <https://github.com/jmchilton>`_ in `#16564 <https://github.com/galaxyproject/galaxy/pull/16564>`_
+* Support new genome browser chain file format by `@claudiofr <https://github.com/claudiofr>`_ in `#16576 <https://github.com/galaxyproject/galaxy/pull/16576>`_
+* Workflow Comments 💬 by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16612 <https://github.com/galaxyproject/galaxy/pull/16612>`_
+* Bump samtools converters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16668 <https://github.com/galaxyproject/galaxy/pull/16668>`_
+* Misc. edits/refactorings to session handling  by `@jdavcs <https://github.com/jdavcs>`_ in `#16712 <https://github.com/galaxyproject/galaxy/pull/16712>`_
+* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs <https://github.com/jdavcs>`_ in `#16724 <https://github.com/galaxyproject/galaxy/pull/16724>`_
+* Migrate `collection elements` store to Pinia by `@davelopez <https://github.com/davelopez>`_ in `#16725 <https://github.com/galaxyproject/galaxy/pull/16725>`_
+* Reset autocommit to False by `@jdavcs <https://github.com/jdavcs>`_ in `#16745 <https://github.com/galaxyproject/galaxy/pull/16745>`_
+* Drop legacy server-side search by `@jdavcs <https://github.com/jdavcs>`_ in `#16755 <https://github.com/galaxyproject/galaxy/pull/16755>`_
+* Optimize iteration in DatasetInstance model + SA2.0 fix by `@jdavcs <https://github.com/jdavcs>`_ in `#16776 <https://github.com/galaxyproject/galaxy/pull/16776>`_
+* Migrate a part of the jobs API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16778 <https://github.com/galaxyproject/galaxy/pull/16778>`_
+* Replace file_name property with get_file_name function by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#16783 <https://github.com/galaxyproject/galaxy/pull/16783>`_
+* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu <https://github.com/sveinugu>`_ in `#16795 <https://github.com/galaxyproject/galaxy/pull/16795>`_
+* Allow partial matches in workflow name tag search and search all tags for unquoted query by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16860 <https://github.com/galaxyproject/galaxy/pull/16860>`_
+* Vueify Visualizations Grid by `@guerler <https://github.com/guerler>`_ in `#16892 <https://github.com/galaxyproject/galaxy/pull/16892>`_
+* Standardize to W3C naming for color. by `@dannon <https://github.com/dannon>`_ in `#16949 <https://github.com/galaxyproject/galaxy/pull/16949>`_
+* Move and re-use persist_extra_files by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16955 <https://github.com/galaxyproject/galaxy/pull/16955>`_
+* Fix invocation report to target correct workflow version. by `@jmchilton <https://github.com/jmchilton>`_ in `#17008 <https://github.com/galaxyproject/galaxy/pull/17008>`_
+* optimize object store cache operations by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17025 <https://github.com/galaxyproject/galaxy/pull/17025>`_
+* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17342 <https://github.com/galaxyproject/galaxy/pull/17342>`_
+* Add magres datatype by `@martenson <https://github.com/martenson>`_ in `#17499 <https://github.com/galaxyproject/galaxy/pull/17499>`_
+
+=============
+Other changes
+=============
 
+* Merge 23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16534 <https://github.com/galaxyproject/galaxy/pull/16534>`_
+* Merge release_23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16768 <https://github.com/galaxyproject/galaxy/pull/16768>`_
+* Create db head merge revision. by `@dannon <https://github.com/dannon>`_ in `#16838 <https://github.com/galaxyproject/galaxy/pull/16838>`_
+* merge release_23.1 into dev by `@martenson <https://github.com/martenson>`_ in `#16933 <https://github.com/galaxyproject/galaxy/pull/16933>`_
+* Minor clarification/typo fix in datatypes.data by `@dannon <https://github.com/dannon>`_ in `#16993 <https://github.com/galaxyproject/galaxy/pull/16993>`_
+* Fix `.file_name` access in merge forward by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17097 <https://github.com/galaxyproject/galaxy/pull/17097>`_
+* Backport model store fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17439 <https://github.com/galaxyproject/galaxy/pull/17439>`_
+* Fix succces typo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17481 <https://github.com/galaxyproject/galaxy/pull/17481>`_
 
 -------------------
 23.1.4 (2024-01-04)

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True
@@ -72,4 +72,4 @@ console_scripts =
 
 [options.packages.find]
 exclude =
-    tests*
+    tests*

packages/files/HISTORY.rst

@@ -3,11 +3,29 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
 
+=========
+Bug fixes
+=========
+
+* pin fs.dropboxfs to >=1 by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16451 <https://github.com/galaxyproject/galaxy/pull/16451>`_
+* Write to a temp filename in posix file source plugin by `@natefoo <https://github.com/natefoo>`_ in `#17350 <https://github.com/galaxyproject/galaxy/pull/17350>`_
+* Set webdav file source to use temp files by default by `@davelopez <https://github.com/davelopez>`_ in `#17388 <https://github.com/galaxyproject/galaxy/pull/17388>`_
+* More defensive access of extra props in filesources by `@nuwang <https://github.com/nuwang>`_ in `#17445 <https://github.com/galaxyproject/galaxy/pull/17445>`_
+
+============
+Enhancements
+============
 
+* Add Invenio RDM repository integration by `@davelopez <https://github.com/davelopez>`_ in `#16381 <https://github.com/galaxyproject/galaxy/pull/16381>`_
+* Refactor FilesDialog + Remote Files API schema improvements by `@davelopez <https://github.com/davelopez>`_ in `#16420 <https://github.com/galaxyproject/galaxy/pull/16420>`_
+*  Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola <https://github.com/lopiola>`_ in `#16690 <https://github.com/galaxyproject/galaxy/pull/16690>`_
+* Remove record access handling for Invenio RDM plugin by `@davelopez <https://github.com/davelopez>`_ in `#16900 <https://github.com/galaxyproject/galaxy/pull/16900>`_
+* Enhance Invenio RDM integration by `@davelopez <https://github.com/davelopez>`_ in `#16964 <https://github.com/galaxyproject/galaxy/pull/16964>`_
 
 -------------------
 23.1.4 (2024-01-04)

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True
@@ -41,4 +41,4 @@ python_requires = >=3.7
 
 [options.packages.find]
 exclude =
-    tests*
+    tests*

packages/job_execution/HISTORY.rst

@@ -3,11 +3,19 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
 
+============
+Enhancements
+============
 
+* Replace file_name property with get_file_name function by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#16783 <https://github.com/galaxyproject/galaxy/pull/16783>`_
+* Enable some flake8-logging-format rules in ruff by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16915 <https://github.com/galaxyproject/galaxy/pull/16915>`_
+* Move and re-use persist_extra_files by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16955 <https://github.com/galaxyproject/galaxy/pull/16955>`_
+* optimize object store cache operations by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17025 <https://github.com/galaxyproject/galaxy/pull/17025>`_
 
 -------------------
 23.1.4 (2024-01-04)

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True

packages/job_metrics/HISTORY.rst

@@ -3,11 +3,22 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Add support for Cgroupsv2 by `@natefoo <https://github.com/natefoo>`_ in `#17169 <https://github.com/galaxyproject/galaxy/pull/17169>`_
 
+============
+Enhancements
+============
 
+* Support configuring job metrics inline, update documentation by `@natefoo <https://github.com/natefoo>`_ in `#17178 <https://github.com/galaxyproject/galaxy/pull/17178>`_
 
 -------------------
 23.1.4 (2024-01-04)

packages/job_metrics/setup.cfg

@@ -27,7 +27,7 @@ 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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True

packages/navigation/HISTORY.rst

@@ -3,11 +3,11 @@ History
 
 .. to_doc
 
----------
-23.2.dev0
----------
-
+-------------------
+23.2.1 (2024-02-21)
+-------------------
 
+No recorded changes since last release
 
 -------------------
 23.1.4 (2024-01-04)

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 = 23.2.dev0
+version = 23.2.1
 
 [options]
 include_package_data = True