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galaxy/packages/util/HISTORY.rst
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mvdbeek c6b2a34916 Merge branch 'release_24.2' into dev 
# Conflicts:
#	lib/galaxy/version.py
#	packages/app/HISTORY.rst
#	packages/app/setup.cfg
#	packages/auth/HISTORY.rst
#	packages/auth/setup.cfg
#	packages/config/HISTORY.rst
#	packages/config/setup.cfg
#	packages/data/HISTORY.rst
#	packages/data/setup.cfg
#	packages/files/HISTORY.rst
#	packages/files/setup.cfg
#	packages/job_execution/HISTORY.rst
#	packages/job_execution/setup.cfg
#	packages/job_metrics/HISTORY.rst
#	packages/job_metrics/setup.cfg
#	packages/navigation/HISTORY.rst
#	packages/navigation/setup.cfg
#	packages/objectstore/HISTORY.rst
#	packages/objectstore/setup.cfg
#	packages/schema/HISTORY.rst
#	packages/schema/setup.cfg
#	packages/selenium/HISTORY.rst
#	packages/selenium/setup.cfg
#	packages/test_api/HISTORY.rst
#	packages/test_api/setup.cfg
#	packages/test_base/HISTORY.rst
#	packages/test_base/setup.cfg
#	packages/test_driver/HISTORY.rst
#	packages/test_driver/setup.cfg
#	packages/tool_shed/HISTORY.rst
#	packages/tool_shed/setup.cfg
#	packages/tool_util/HISTORY.rst
#	packages/tool_util/setup.cfg
#	packages/tours/HISTORY.rst
#	packages/tours/setup.cfg
#	packages/util/HISTORY.rst
#	packages/util/setup.cfg
#	packages/web_apps/HISTORY.rst
#	packages/web_apps/setup.cfg
#	packages/web_framework/HISTORY.rst
#	packages/web_framework/setup.cfg
#	packages/web_stack/HISTORY.rst
#	packages/web_stack/setup.cfg
2025-03-16 11:38:19 +01:00

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History
-------
.. to_doc
---------
25.0.dev0
---------
-------------------
24.2.3 (2025-03-16)
-------------------
No recorded changes since last release
-------------------
24.2.2 (2025-03-08)
-------------------
============
Enhancements
============
* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
-------------------
24.2.1 (2025-02-28)
-------------------
No recorded changes since last release
-------------------
24.2.0 (2025-02-11)
-------------------
=========
Bug fixes
=========
* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
* Fix numerous issues with tool input format "21.01" by `@jmchilton <https://github.com/jmchilton>`_ in `#19030 <https://github.com/galaxyproject/galaxy/pull/19030>`_
* Partial backport of #19331 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19342 <https://github.com/galaxyproject/galaxy/pull/19342>`_
* Fix config template validation for file sources and object store templates by `@davelopez <https://github.com/davelopez>`_ in `#19414 <https://github.com/galaxyproject/galaxy/pull/19414>`_
* Serialize message exceptions on execution error by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19483 <https://github.com/galaxyproject/galaxy/pull/19483>`_
============
Enhancements
============
* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
* Add Python 3.13 support by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18449 <https://github.com/galaxyproject/galaxy/pull/18449>`_
* Add Tool-Centric APIs to the Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18524 <https://github.com/galaxyproject/galaxy/pull/18524>`_
* Rip repository_registry out of tool shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#18647 <https://github.com/galaxyproject/galaxy/pull/18647>`_
* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
* Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18811 <https://github.com/galaxyproject/galaxy/pull/18811>`_
* Raise exception if CompressedFile used on incompatible file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18888 <https://github.com/galaxyproject/galaxy/pull/18888>`_
* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
* Enhance UTF-8 support for filename handling in downloads by `@arash77 <https://github.com/arash77>`_ in `#19161 <https://github.com/galaxyproject/galaxy/pull/19161>`_
-------------------
24.1.4 (2024-12-11)
-------------------
=========
Bug fixes
=========
* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
============
Enhancements
============
* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
-------------------
24.1.3 (2024-10-25)
-------------------
=========
Bug fixes
=========
* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
============
Enhancements
============
* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
-------------------
24.1.2 (2024-09-25)
-------------------
=========
Bug fixes
=========
* Fix Archive header encoding by `@arash77 <https://github.com/arash77>`_ in `#18583 <https://github.com/galaxyproject/galaxy/pull/18583>`_
* File source and object store instance api fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18685 <https://github.com/galaxyproject/galaxy/pull/18685>`_
============
Enhancements
============
* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18805 <https://github.com/galaxyproject/galaxy/pull/18805>`_
-------------------
24.1.1 (2024-07-02)
-------------------
=========
Bug fixes
=========
* Fix bug in image_util.py by `@kostrykin <https://github.com/kostrykin>`_ in `#17749 <https://github.com/galaxyproject/galaxy/pull/17749>`_
* Revert some requests import changes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18199 <https://github.com/galaxyproject/galaxy/pull/18199>`_
============
Enhancements
============
* Better display of estimated line numbers and add number of columns for tabular by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17492 <https://github.com/galaxyproject/galaxy/pull/17492>`_
* 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>`_
* SQLAlchemy 2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17778 <https://github.com/galaxyproject/galaxy/pull/17778>`_
* Error reporting unit tests by `@jmchilton <https://github.com/jmchilton>`_ in `#17968 <https://github.com/galaxyproject/galaxy/pull/17968>`_
* 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>`_
* 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>`_
* Overhaul Azure storage infrastructure. by `@jmchilton <https://github.com/jmchilton>`_ in `#18087 <https://github.com/galaxyproject/galaxy/pull/18087>`_
* 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>`_
* Harden User Object Store and File Source Creation by `@jmchilton <https://github.com/jmchilton>`_ in `#18172 <https://github.com/galaxyproject/galaxy/pull/18172>`_
-------------------
24.0.3 (2024-06-28)
-------------------
=========
Bug fixes
=========
* Use config_section to distinguish between galaxy and ts or other apps by `@jdavcs <https://github.com/jdavcs>`_ in `#18215 <https://github.com/galaxyproject/galaxy/pull/18215>`_
-------------------
24.0.2 (2024-05-07)
-------------------
=========
Bug fixes
=========
* Adds logging of messageExceptions in the fastapi exception handler. by `@dannon <https://github.com/dannon>`_ in `#18041 <https://github.com/galaxyproject/galaxy/pull/18041>`_
-------------------
24.0.1 (2024-05-02)
-------------------
=========
Bug fixes
=========
* Fix conditional Image imports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17899 <https://github.com/galaxyproject/galaxy/pull/17899>`_
-------------------
24.0.0 (2024-04-02)
-------------------
=========
Bug fixes
=========
* Optional Reply-to SMTP header in tool error reports by `@neoformit <https://github.com/neoformit>`_ in `#17243 <https://github.com/galaxyproject/galaxy/pull/17243>`_
* Follow-up on #17274 and #17262 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17302 <https://github.com/galaxyproject/galaxy/pull/17302>`_
* Fixes for flake8-bugbear 24.1.17 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17340 <https://github.com/galaxyproject/galaxy/pull/17340>`_
============
Enhancements
============
* Add support for Python 3.12 by `@tuncK <https://github.com/tuncK>`_ in `#16796 <https://github.com/galaxyproject/galaxy/pull/16796>`_
* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
* Remove web framework dependency from tools by `@davelopez <https://github.com/davelopez>`_ in `#17058 <https://github.com/galaxyproject/galaxy/pull/17058>`_
* Add support for (fast5.tar).xz binary compressed files by `@tuncK <https://github.com/tuncK>`_ in `#17106 <https://github.com/galaxyproject/galaxy/pull/17106>`_
* Reuse test instance during non-integration tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17234 <https://github.com/galaxyproject/galaxy/pull/17234>`_
* Add OIDC backend configuration schema and validation by `@uwwint <https://github.com/uwwint>`_ in `#17274 <https://github.com/galaxyproject/galaxy/pull/17274>`_
* 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>`_
* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_
* 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>`_
-------------------
23.2.1 (2024-02-21)
-------------------
=========
Bug fixes
=========
* Ruff and flake8 fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16884 <https://github.com/galaxyproject/galaxy/pull/16884>`_
============
Enhancements
============
* Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#15639 <https://github.com/galaxyproject/galaxy/pull/15639>`_
* Move database access code out of ``galaxy.util`` by `@jdavcs <https://github.com/jdavcs>`_ in `#16526 <https://github.com/galaxyproject/galaxy/pull/16526>`_
* 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>`_
* 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>`_
* 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>`_
=============
Other changes
=============
* Merge 23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16534 <https://github.com/galaxyproject/galaxy/pull/16534>`_
-------------------
23.1.4 (2024-01-04)
-------------------
No recorded changes since last release
-------------------
23.1.3 (2023-12-01)
-------------------
No recorded changes since last release
-------------------
23.1.2 (2023-11-29)
-------------------
============
Enhancements
============
* Improve invocation error reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16917 <https://github.com/galaxyproject/galaxy/pull/16917>`_
-------------------
23.1.1 (2023-10-23)
-------------------
=========
Bug fixes
=========
* Fix bad auto-merge of dev. by `@jmchilton <https://github.com/jmchilton>`_ in `#15386 <https://github.com/galaxyproject/galaxy/pull/15386>`_
* Fix some drs handling issues by `@nuwang <https://github.com/nuwang>`_ in `#15777 <https://github.com/galaxyproject/galaxy/pull/15777>`_
* Enable ``strict_equality`` mypy option by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15808 <https://github.com/galaxyproject/galaxy/pull/15808>`_
* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
* Fix form builder value handling by `@guerler <https://github.com/guerler>`_ in `#16304 <https://github.com/galaxyproject/galaxy/pull/16304>`_
* Backport tool mem fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16601 <https://github.com/galaxyproject/galaxy/pull/16601>`_
* Workaround for XML nodes of job resource parameters losing their children by `@kysrpex <https://github.com/kysrpex>`_ in `#16728 <https://github.com/galaxyproject/galaxy/pull/16728>`_
* Fix allowlist deserialization in file sources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16729 <https://github.com/galaxyproject/galaxy/pull/16729>`_
* Exclude on_opened and on_closed from watcher events by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16850 <https://github.com/galaxyproject/galaxy/pull/16850>`_
============
Enhancements
============
* Various Tool Shed Cleanup by `@jmchilton <https://github.com/jmchilton>`_ in `#15247 <https://github.com/galaxyproject/galaxy/pull/15247>`_
* Protection against problematic boolean parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#15493 <https://github.com/galaxyproject/galaxy/pull/15493>`_
* Unify url handling with filesources by `@nuwang <https://github.com/nuwang>`_ in `#15497 <https://github.com/galaxyproject/galaxy/pull/15497>`_
* Explore tool remote test data by `@davelopez <https://github.com/davelopez>`_ in `#15510 <https://github.com/galaxyproject/galaxy/pull/15510>`_
* Drop database views by `@jdavcs <https://github.com/jdavcs>`_ in `#15876 <https://github.com/galaxyproject/galaxy/pull/15876>`_
* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15890 <https://github.com/galaxyproject/galaxy/pull/15890>`_
* Record input datasets and collections at full parameter path by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15978 <https://github.com/galaxyproject/galaxy/pull/15978>`_
* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16035 <https://github.com/galaxyproject/galaxy/pull/16035>`_
* Vendorise ``packaging.versions.LegacyVersion`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16058 <https://github.com/galaxyproject/galaxy/pull/16058>`_
* Improve histories and datasets immutability checks by `@davelopez <https://github.com/davelopez>`_ in `#16143 <https://github.com/galaxyproject/galaxy/pull/16143>`_
* Merge ``Target`` class with ``CondaTarget`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16181 <https://github.com/galaxyproject/galaxy/pull/16181>`_
-------------------
23.0.6 (2023-10-23)
-------------------
No recorded changes since last release
-------------------
23.0.5 (2023-07-29)
-------------------
No recorded changes since last release
-------------------
23.0.4 (2023-06-30)
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No recorded changes since last release
-------------------
23.0.3 (2023-06-26)
-------------------
No recorded changes since last release
-------------------
23.0.2 (2023-06-13)
-------------------
No recorded changes since last release
-------------------
23.0.1 (2023-06-08)
-------------------
=========
Bug fixes
=========
* Replace httpbin service with pytest-httpserver by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16042 <https://github.com/galaxyproject/galaxy/pull/16042>`_
-------------------
22.1.2 (2022-12-08)
-------------------
* Pin packaging dependency to < 22, fixes ``LegacyVersion`` import errors
* Add missing pyparsing dependency
-------------------
22.1.1 (2022-08-22)
-------------------
* First release from the 22.01 branch of Galaxy
-------------------
21.1.0 (2021-03-19)
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* First release from the 21.01 branch of Galaxy.
-------------------
20.9.1 (2020-10-28)
-------------------
-------------------
20.9.0 (2020-10-15)
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* First release from the 20.09 branch of Galaxy.
-------------------
20.5.0 (2020-07-03)
-------------------
* First release from 20.05 branch of Galaxy.
-------------------
19.9.0 (2019-11-21)
-------------------
* Initial import from dev branch of Galaxy during 19.09 development cycle.
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