Create version 24.1.0

lib/galaxy/version.py

@@ -1,3 +1,3 @@
-VERSION_MAJOR = "24.2"
-VERSION_MINOR = "dev0"
+VERSION_MAJOR = "24.1"
+VERSION_MINOR = "0"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")

packages/app/HISTORY.rst

@@ -3,11 +3,116 @@ History
 
 .. to_doc
 
----------
-24.1.dev0
----------
+-------------------
+24.1.0 (2024-06-20)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Unpin social-auth-core dependency by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17607 <https://github.com/galaxyproject/galaxy/pull/17607>`_
+* Dynamic tool fixes by `@dcore94 <https://github.com/dcore94>`_ in `#18085 <https://github.com/galaxyproject/galaxy/pull/18085>`_
+* Raise exception if collection elements missing during download by `@jdavcs <https://github.com/jdavcs>`_ in `#18094 <https://github.com/galaxyproject/galaxy/pull/18094>`_
+* Allow purge query param, deprecate purge body param by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18105 <https://github.com/galaxyproject/galaxy/pull/18105>`_
+* Fix for unexpected OIDC XML validation error by `@Edmontosaurus <https://github.com/Edmontosaurus>`_ in `#18106 <https://github.com/galaxyproject/galaxy/pull/18106>`_
+* Don't log exception if cancelled slurm job doesn't have stderr file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18121 <https://github.com/galaxyproject/galaxy/pull/18121>`_
+* Downgrade missing output file in working directory to warning for failed jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18123 <https://github.com/galaxyproject/galaxy/pull/18123>`_
+* Fix data default values not getting added to history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18132 <https://github.com/galaxyproject/galaxy/pull/18132>`_
+* Drop redundant error message by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18156 <https://github.com/galaxyproject/galaxy/pull/18156>`_
+* Emit warning when user-cancelled job already complete by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18178 <https://github.com/galaxyproject/galaxy/pull/18178>`_
+* Avoid object store path lookup when constructing JobState object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18190 <https://github.com/galaxyproject/galaxy/pull/18190>`_
+* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
+* Revert some requests import changes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18199 <https://github.com/galaxyproject/galaxy/pull/18199>`_
+* Add string cast for dbkey / genome_build by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18207 <https://github.com/galaxyproject/galaxy/pull/18207>`_
+* Check dataset state when attempting to acces dataset contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18214 <https://github.com/galaxyproject/galaxy/pull/18214>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Small bug fixes for user data plugins by `@jmchilton <https://github.com/jmchilton>`_ in `#18246 <https://github.com/galaxyproject/galaxy/pull/18246>`_
+* Raise exception when extracting dataset from collection without datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18249 <https://github.com/galaxyproject/galaxy/pull/18249>`_
+* Skip tests if toolshed, dx.doi not responding by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18250 <https://github.com/galaxyproject/galaxy/pull/18250>`_
+* Fix handler: access to result row items changed in SA2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#18274 <https://github.com/galaxyproject/galaxy/pull/18274>`_
+* Don't attempt to download purged datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18278 <https://github.com/galaxyproject/galaxy/pull/18278>`_
+* Check various preconditions in FeatureLocationIndexDataProvider by `@davelopez <https://github.com/davelopez>`_ in `#18283 <https://github.com/galaxyproject/galaxy/pull/18283>`_
+* Fix various packages' issues by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18301 <https://github.com/galaxyproject/galaxy/pull/18301>`_
+* Adapt Tool prediction API to Transformer-based deep learning architecture by `@anuprulez <https://github.com/anuprulez>`_ in `#18305 <https://github.com/galaxyproject/galaxy/pull/18305>`_
+* Don't serialize display application links for deleted datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18307 <https://github.com/galaxyproject/galaxy/pull/18307>`_
+* Downgrade doi fetch error to debug by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18330 <https://github.com/galaxyproject/galaxy/pull/18330>`_
+* Fix authentication error for anonymous users querying jobs by `@davelopez <https://github.com/davelopez>`_ in `#18333 <https://github.com/galaxyproject/galaxy/pull/18333>`_
+* Fix seek in slurm memory check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18338 <https://github.com/galaxyproject/galaxy/pull/18338>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+* Kill pulsar job if job stopped on galaxy side by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18348 <https://github.com/galaxyproject/galaxy/pull/18348>`_
+* Allow DCE as outer input to to_cwl by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18349 <https://github.com/galaxyproject/galaxy/pull/18349>`_
+* Fix anonymous user job retrieval logic by `@davelopez <https://github.com/davelopez>`_ in `#18358 <https://github.com/galaxyproject/galaxy/pull/18358>`_
+* Fix update group API payload model by `@davelopez <https://github.com/davelopez>`_ in `#18374 <https://github.com/galaxyproject/galaxy/pull/18374>`_
+* Fix empty usernames in database + bug in username generation by `@jdavcs <https://github.com/jdavcs>`_ in `#18379 <https://github.com/galaxyproject/galaxy/pull/18379>`_
+* Fix user's private role can be missing by `@davelopez <https://github.com/davelopez>`_ in `#18381 <https://github.com/galaxyproject/galaxy/pull/18381>`_
+* Fix null inputs in database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18385 <https://github.com/galaxyproject/galaxy/pull/18385>`_
+* Assign default ``data`` extension on discovered collection output  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18389 <https://github.com/galaxyproject/galaxy/pull/18389>`_
+* Fix ``get_accessible_job`` if called without session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18400 <https://github.com/galaxyproject/galaxy/pull/18400>`_
+* Fix invocation step_job_summary for new collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18402 <https://github.com/galaxyproject/galaxy/pull/18402>`_
+* Really allow in-range validator for txt by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#18411 <https://github.com/galaxyproject/galaxy/pull/18411>`_
+* Fix collection map over status for dragged collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18416 <https://github.com/galaxyproject/galaxy/pull/18416>`_
+* Add TypedDict for JobsSummary by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18418 <https://github.com/galaxyproject/galaxy/pull/18418>`_
+* Serialize purged flag for datasets in collections by `@davelopez <https://github.com/davelopez>`_ in `#18420 <https://github.com/galaxyproject/galaxy/pull/18420>`_
+* Pin pydantic to >=2.7.4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18423 <https://github.com/galaxyproject/galaxy/pull/18423>`_
 
+============
+Enhancements
+============
+
+* Only include tool stdout/stderr in HDA info by `@natefoo <https://github.com/natefoo>`_ in `#16730 <https://github.com/galaxyproject/galaxy/pull/16730>`_
+* Adding object store plugin for Rucio by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17156 <https://github.com/galaxyproject/galaxy/pull/17156>`_
+* Enable all-vs-all collection analysis patterns. by `@jmchilton <https://github.com/jmchilton>`_ in `#17366 <https://github.com/galaxyproject/galaxy/pull/17366>`_
+* Add onedata objectstore by `@bwalkowi <https://github.com/bwalkowi>`_ in `#17540 <https://github.com/galaxyproject/galaxy/pull/17540>`_
+* Type annotation improvements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17601 <https://github.com/galaxyproject/galaxy/pull/17601>`_
+* Type annotation and CWL-related improvements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17630 <https://github.com/galaxyproject/galaxy/pull/17630>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17653 <https://github.com/galaxyproject/galaxy/pull/17653>`_
+* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17654 <https://github.com/galaxyproject/galaxy/pull/17654>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17764 <https://github.com/galaxyproject/galaxy/pull/17764>`_
+* SQLAlchemy 2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17778 <https://github.com/galaxyproject/galaxy/pull/17778>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17819 <https://github.com/galaxyproject/galaxy/pull/17819>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17870 <https://github.com/galaxyproject/galaxy/pull/17870>`_
+* Add `email` notifications channel by `@davelopez <https://github.com/davelopez>`_ in `#17914 <https://github.com/galaxyproject/galaxy/pull/17914>`_
+* Model edits and bug fixes by `@jdavcs <https://github.com/jdavcs>`_ in `#17922 <https://github.com/galaxyproject/galaxy/pull/17922>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17923 <https://github.com/galaxyproject/galaxy/pull/17923>`_
+* Model typing and SA2.0 follow-up by `@jdavcs <https://github.com/jdavcs>`_ in `#17958 <https://github.com/galaxyproject/galaxy/pull/17958>`_
+* Error reporting unit tests by `@jmchilton <https://github.com/jmchilton>`_ in `#17968 <https://github.com/galaxyproject/galaxy/pull/17968>`_
+* Make urgent notifications mandatory by `@davelopez <https://github.com/davelopez>`_ in `#17975 <https://github.com/galaxyproject/galaxy/pull/17975>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17982 <https://github.com/galaxyproject/galaxy/pull/17982>`_
+* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17991 <https://github.com/galaxyproject/galaxy/pull/17991>`_
+* Add galaxy to user agent by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18003 <https://github.com/galaxyproject/galaxy/pull/18003>`_
+* Add Zenodo integration by `@davelopez <https://github.com/davelopez>`_ in `#18022 <https://github.com/galaxyproject/galaxy/pull/18022>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18035 <https://github.com/galaxyproject/galaxy/pull/18035>`_
+* Add stronger type annotations in file sources + refactoring by `@davelopez <https://github.com/davelopez>`_ in `#18050 <https://github.com/galaxyproject/galaxy/pull/18050>`_
+* Add pagination support to Files Source plugins by `@davelopez <https://github.com/davelopez>`_ in `#18059 <https://github.com/galaxyproject/galaxy/pull/18059>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18063 <https://github.com/galaxyproject/galaxy/pull/18063>`_
+* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18067 <https://github.com/galaxyproject/galaxy/pull/18067>`_
+* Ensure history `update_time` is set when exporting by `@davelopez <https://github.com/davelopez>`_ in `#18086 <https://github.com/galaxyproject/galaxy/pull/18086>`_
+* Overhaul Azure storage infrastructure. by `@jmchilton <https://github.com/jmchilton>`_ in `#18087 <https://github.com/galaxyproject/galaxy/pull/18087>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18095 <https://github.com/galaxyproject/galaxy/pull/18095>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18125 <https://github.com/galaxyproject/galaxy/pull/18125>`_
+* Revises handling of warnings in the workflow run form by `@guerler <https://github.com/guerler>`_ in `#18126 <https://github.com/galaxyproject/galaxy/pull/18126>`_
+* Empower users to bring their own storage and file sources by `@jmchilton <https://github.com/jmchilton>`_ in `#18127 <https://github.com/galaxyproject/galaxy/pull/18127>`_
+* Update s3fs dependency. by `@jmchilton <https://github.com/jmchilton>`_ in `#18135 <https://github.com/galaxyproject/galaxy/pull/18135>`_
+* More unit testing for object store stuff. by `@jmchilton <https://github.com/jmchilton>`_ in `#18136 <https://github.com/galaxyproject/galaxy/pull/18136>`_
+* Harden User Object Store and File Source Creation by `@jmchilton <https://github.com/jmchilton>`_ in `#18172 <https://github.com/galaxyproject/galaxy/pull/18172>`_
+* Fix boto3-stubs typecheck dependency by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18173 <https://github.com/galaxyproject/galaxy/pull/18173>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18226 <https://github.com/galaxyproject/galaxy/pull/18226>`_
+* More structured indexing for user data objects. by `@jmchilton <https://github.com/jmchilton>`_ in `#18291 <https://github.com/galaxyproject/galaxy/pull/18291>`_
+* More data access tests, some refactoring and cleanup by `@jdavcs <https://github.com/jdavcs>`_ in `#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`_
+* Onedada object store and files source stability fixes by `@bwalkowi <https://github.com/bwalkowi>`_ in `#18372 <https://github.com/galaxyproject/galaxy/pull/18372>`_
+* Allow running and editing workflows for specific versions by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18378 <https://github.com/galaxyproject/galaxy/pull/18378>`_
+
+=============
+Other changes
+=============
 
+* Chore: remove repetitive words by `@tianzedavid <https://github.com/tianzedavid>`_ in `#18076 <https://github.com/galaxyproject/galaxy/pull/18076>`_
+* Fix #18316 (anonymous file sources) by `@jmchilton <https://github.com/jmchilton>`_ in `#18352 <https://github.com/galaxyproject/galaxy/pull/18352>`_
+* Merge 24.0 into 24.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#18353 <https://github.com/galaxyproject/galaxy/pull/18353>`_
+* Merge 24.0 into 24.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#18365 <https://github.com/galaxyproject/galaxy/pull/18365>`_
+* Minor linting cleanup by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18421 <https://github.com/galaxyproject/galaxy/pull/18421>`_
 
 -------------------
 24.0.2 (2024-05-07)

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 = 24.1.0
 
 [options]
 include_package_data = True
@@ -85,4 +85,4 @@ console_scripts =
 [options.packages.find]
 exclude =
     galaxy.tools.bundled*
-    tests*
+    tests*

packages/auth/HISTORY.rst

@@ -3,11 +3,17 @@ History
 
 .. to_doc
 
----------
-24.1.dev0
----------
+-------------------
+24.1.0 (2024-06-20)
+-------------------
+
 
+============
+Enhancements
+============
 
+* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17654 <https://github.com/galaxyproject/galaxy/pull/17654>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18063 <https://github.com/galaxyproject/galaxy/pull/18063>`_
 
 -------------------
 24.0.2 (2024-05-07)

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 = 24.1.0
 
 [options]
 include_package_data = True
@@ -39,4 +39,4 @@ python_requires = >=3.8
 
 [options.packages.find]
 exclude =
-    tests*
+    tests*