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Create version 24.0.0
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jdavcs committed Apr 2, 2024
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2 changes: 1 addition & 1 deletion lib/galaxy/version.py
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@@ -1,3 +1,3 @@
VERSION_MAJOR = "24.0"
VERSION_MINOR = "0.dev0"
VERSION_MINOR = "0"
VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "")
102 changes: 98 additions & 4 deletions packages/app/HISTORY.rst
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.. to_doc
---------
24.0.dev0
---------
-------------------
24.0.0 (2024-04-02)
-------------------


=========
Bug fixes
=========

* Reload built-in converters on toolbox reload by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17209 <https://github.com/galaxyproject/galaxy/pull/17209>`_
* Optional Reply-to SMTP header in tool error reports by `@neoformit <https://github.com/neoformit>`_ in `#17243 <https://github.com/galaxyproject/galaxy/pull/17243>`_
* Package tests fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17301 <https://github.com/galaxyproject/galaxy/pull/17301>`_
* Follow-up on #17274 and #17262 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17302 <https://github.com/galaxyproject/galaxy/pull/17302>`_
* Rollback invalidated transaction: catch them earlier by `@jdavcs <https://github.com/jdavcs>`_ in `#17312 <https://github.com/galaxyproject/galaxy/pull/17312>`_
* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17340 <https://github.com/galaxyproject/galaxy/pull/17340>`_
* Fix data_source and data_source_async bugs by `@wm75 <https://github.com/wm75>`_ in `#17422 <https://github.com/galaxyproject/galaxy/pull/17422>`_
* More efficient change_state queries, maybe fix deadlock by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17632 <https://github.com/galaxyproject/galaxy/pull/17632>`_
* Don't index tasks without task_uuid by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17646 <https://github.com/galaxyproject/galaxy/pull/17646>`_
* Separate `ConnectedValue` from `RuntimeValue` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17678 <https://github.com/galaxyproject/galaxy/pull/17678>`_
* Fix step type serialization for StoredWorkflowDetailed models by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17716 <https://github.com/galaxyproject/galaxy/pull/17716>`_
* Fix usage of DISTINCT by `@jdavcs <https://github.com/jdavcs>`_ in `#17759 <https://github.com/galaxyproject/galaxy/pull/17759>`_
* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17777 <https://github.com/galaxyproject/galaxy/pull/17777>`_
* Use ``hg clone --stream`` to clone repos by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17786 <https://github.com/galaxyproject/galaxy/pull/17786>`_
* Defer job attributes that are usually not needed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17795 <https://github.com/galaxyproject/galaxy/pull/17795>`_
* Fix change_datatype PJA for dynamic collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17803 <https://github.com/galaxyproject/galaxy/pull/17803>`_
* Fix archived histories mixing with active in histories list by `@davelopez <https://github.com/davelopez>`_ in `#17856 <https://github.com/galaxyproject/galaxy/pull/17856>`_
* Normalize extensions when loading tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17868 <https://github.com/galaxyproject/galaxy/pull/17868>`_
* Ignore user data table errors for now by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17880 <https://github.com/galaxyproject/galaxy/pull/17880>`_

============
Enhancements
============

* Add harmonize collections tool (or whatever other name) by `@lldelisle <https://github.com/lldelisle>`_ in `#16662 <https://github.com/galaxyproject/galaxy/pull/16662>`_
* Add support for Python 3.12 by `@tuncK <https://github.com/tuncK>`_ in `#16796 <https://github.com/galaxyproject/galaxy/pull/16796>`_
* 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>`_
* Support for OIDC API Auth and OIDC integration tests by `@nuwang <https://github.com/nuwang>`_ in `#16977 <https://github.com/galaxyproject/galaxy/pull/16977>`_
* Toward declarative help for Galaxy markdown directives. by `@jmchilton <https://github.com/jmchilton>`_ in `#16979 <https://github.com/galaxyproject/galaxy/pull/16979>`_
* Extend regex groups in stdio regex matches by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17016 <https://github.com/galaxyproject/galaxy/pull/17016>`_
* 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>`_
* 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>`_
* Vueify Admin Groups Grid by `@guerler <https://github.com/guerler>`_ in `#17126 <https://github.com/galaxyproject/galaxy/pull/17126>`_
* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs <https://github.com/jdavcs>`_ in `#17132 <https://github.com/galaxyproject/galaxy/pull/17132>`_
* Vueify Admin Forms and Quota grids by `@guerler <https://github.com/guerler>`_ in `#17141 <https://github.com/galaxyproject/galaxy/pull/17141>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17157 <https://github.com/galaxyproject/galaxy/pull/17157>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17201 <https://github.com/galaxyproject/galaxy/pull/17201>`_
* Vendorize fastapi-utls.cbv by `@jdavcs <https://github.com/jdavcs>`_ in `#17205 <https://github.com/galaxyproject/galaxy/pull/17205>`_
* Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by `@jdavcs <https://github.com/jdavcs>`_ in `#17216 <https://github.com/galaxyproject/galaxy/pull/17216>`_
* Vueifiy History Grids by `@guerler <https://github.com/guerler>`_ in `#17219 <https://github.com/galaxyproject/galaxy/pull/17219>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17230 <https://github.com/galaxyproject/galaxy/pull/17230>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17235 <https://github.com/galaxyproject/galaxy/pull/17235>`_
* Allow job files to consume TUS uploads by `@jmchilton <https://github.com/jmchilton>`_ in `#17242 <https://github.com/galaxyproject/galaxy/pull/17242>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17247 <https://github.com/galaxyproject/galaxy/pull/17247>`_
* Migrate models to pydantic 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17262 <https://github.com/galaxyproject/galaxy/pull/17262>`_
* Consider Null inputs by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17271 <https://github.com/galaxyproject/galaxy/pull/17271>`_
* Add OIDC backend configuration schema and validation by `@uwwint <https://github.com/uwwint>`_ in `#17274 <https://github.com/galaxyproject/galaxy/pull/17274>`_
* Adds delete, purge and undelete batch operations to History Grid by `@guerler <https://github.com/guerler>`_ in `#17282 <https://github.com/galaxyproject/galaxy/pull/17282>`_
* Add ``__KEEP_SUCCESS_DATASETS__`` by `@lldelisle <https://github.com/lldelisle>`_ in `#17294 <https://github.com/galaxyproject/galaxy/pull/17294>`_
* Improve ModelManager type hints by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17299 <https://github.com/galaxyproject/galaxy/pull/17299>`_
* API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton <https://github.com/jmchilton>`_ in `#17329 <https://github.com/galaxyproject/galaxy/pull/17329>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17333 <https://github.com/galaxyproject/galaxy/pull/17333>`_
* Add element_identifier and ext to inputs config file export by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17357 <https://github.com/galaxyproject/galaxy/pull/17357>`_
* Remove unused statements in job search function by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17361 <https://github.com/galaxyproject/galaxy/pull/17361>`_
* Enable ``warn_unreachable`` mypy option by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17365 <https://github.com/galaxyproject/galaxy/pull/17365>`_
* Fix type annotation of code using XML etree by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17367 <https://github.com/galaxyproject/galaxy/pull/17367>`_
* More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17381 <https://github.com/galaxyproject/galaxy/pull/17381>`_
* Cancel all active jobs when the user is deleted by `@davelopez <https://github.com/davelopez>`_ in `#17390 <https://github.com/galaxyproject/galaxy/pull/17390>`_
* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_
* Purge `groups` and `roles` from DB (for real) by `@davelopez <https://github.com/davelopez>`_ in `#17411 <https://github.com/galaxyproject/galaxy/pull/17411>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17420 <https://github.com/galaxyproject/galaxy/pull/17420>`_
* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17435 <https://github.com/galaxyproject/galaxy/pull/17435>`_
* Adds published histories to grid list by `@guerler <https://github.com/guerler>`_ in `#17449 <https://github.com/galaxyproject/galaxy/pull/17449>`_
* Allow filtering history datasets by object store ID and quota source. by `@jmchilton <https://github.com/jmchilton>`_ in `#17460 <https://github.com/galaxyproject/galaxy/pull/17460>`_
* `data_column` parameter: use `column_names` metadata if present by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17478 <https://github.com/galaxyproject/galaxy/pull/17478>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17486 <https://github.com/galaxyproject/galaxy/pull/17486>`_
* Consolidate resource grids into tab views by `@guerler <https://github.com/guerler>`_ in `#17487 <https://github.com/galaxyproject/galaxy/pull/17487>`_
* Update k8s docker python to 3.12 by `@nuwang <https://github.com/nuwang>`_ in `#17494 <https://github.com/galaxyproject/galaxy/pull/17494>`_
* add encode ID API endpoint by `@mira-miracoli <https://github.com/mira-miracoli>`_ in `#17510 <https://github.com/galaxyproject/galaxy/pull/17510>`_
* Fixing data_source tools and incrementing tool profile by `@wm75 <https://github.com/wm75>`_ in `#17515 <https://github.com/galaxyproject/galaxy/pull/17515>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17541 <https://github.com/galaxyproject/galaxy/pull/17541>`_
* Add `image_diff` comparison method for test output verification using images by `@kostrykin <https://github.com/kostrykin>`_ in `#17556 <https://github.com/galaxyproject/galaxy/pull/17556>`_
* Filter out subworkflow invocations by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17558 <https://github.com/galaxyproject/galaxy/pull/17558>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17580 <https://github.com/galaxyproject/galaxy/pull/17580>`_
* Restore histories API behavior for `keys` query parameter by `@davelopez <https://github.com/davelopez>`_ in `#17779 <https://github.com/galaxyproject/galaxy/pull/17779>`_
* Fix datasets API custom keys encoding by `@davelopez <https://github.com/davelopez>`_ in `#17793 <https://github.com/galaxyproject/galaxy/pull/17793>`_
* Improved error messages for runtime sharing problems. by `@jmchilton <https://github.com/jmchilton>`_ in `#17794 <https://github.com/galaxyproject/galaxy/pull/17794>`_
* Allow admin to sharpen language about selected object stores. by `@jmchilton <https://github.com/jmchilton>`_ in `#17806 <https://github.com/galaxyproject/galaxy/pull/17806>`_

=============
Other changes
=============

* consistently compare profile versions by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16492 <https://github.com/galaxyproject/galaxy/pull/16492>`_

-------------------
23.2.1 (2024-02-21)
Expand Down Expand Up @@ -87,7 +181,7 @@ Enhancements
* Galaxy Markdown - add workflow image and license to Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16672 <https://github.com/galaxyproject/galaxy/pull/16672>`_
* Implement instance URLs in Galaxy markdown. by `@jmchilton <https://github.com/jmchilton>`_ in `#16675 <https://github.com/galaxyproject/galaxy/pull/16675>`_
* Change Sentry error reporting plug-in by `@kysrpex <https://github.com/kysrpex>`_ in `#16686 <https://github.com/galaxyproject/galaxy/pull/16686>`_
* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola <https://github.com/lopiola>`_ in `#16690 <https://github.com/galaxyproject/galaxy/pull/16690>`_
* Use fs.onedatarestfs for Onedata files source plugin implementation by `@lopiola <https://github.com/lopiola>`_ in `#16690 <https://github.com/galaxyproject/galaxy/pull/16690>`_
* Enhance task monitor composable by `@davelopez <https://github.com/davelopez>`_ in `#16695 <https://github.com/galaxyproject/galaxy/pull/16695>`_
* 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>`_
Expand Down
4 changes: 2 additions & 2 deletions packages/app/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -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 = 24.0.0

[options]
include_package_data = True
Expand Down Expand Up @@ -85,4 +85,4 @@ console_scripts =
[options.packages.find]
exclude =
galaxy.tools.bundled*
tests*
tests*
18 changes: 15 additions & 3 deletions packages/auth/HISTORY.rst
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Expand Up @@ -3,11 +3,23 @@ History

.. to_doc
---------
24.0.dev0
---------
-------------------
24.0.0 (2024-04-02)
-------------------


=========
Bug fixes
=========

* LDAP3 fix for attributes returned as strings by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17305 <https://github.com/galaxyproject/galaxy/pull/17305>`_

============
Enhancements
============

* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_

-------------------
23.2.1 (2024-02-21)
Expand Down
4 changes: 2 additions & 2 deletions packages/auth/setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -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 = 24.0.0

[options]
include_package_data = True
Expand All @@ -39,4 +39,4 @@ python_requires = >=3.8

[options.packages.find]
exclude =
tests*
tests*
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