- read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in #15596
- Fix some drs handling issues by @nuwang in #15777
- Fix filesource file url support by @nuwang in #15794
- Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811
- Change confusing pulsar logs message by @kysrpex in #16038
- Fix and test startup with Python 3.11 on macOS by @nsoranzo in #16082
- Fix : Ignore error messages for admin created accounts by @jvanbraekel in #16132
- Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207
- Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by @jdavcs in #16208
- Fix ordering of data libraries from API by @martenson in #16300
- qualify querying for an api-key by @martenson in #16320
- Fix tags ownership by @davelopez in #16339
- Job cache fixes for DCEs by @mvdbeek in #16384
- Fix histories count by @davelopez in #16400
- Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in #16421
- Fix up unit tests for local use by @mvdbeek in #16483
- Run through tmp_dir_creation_statement only once by @mvdbeek in #16529
- Fix double-encoding notification content by @mvdbeek in #16530
- Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537
- Fix multiple remote test data by @davelopez in #16542
- Ignore errors with user-set job resources by @mvdbeek in #16579
- Fix replacement parameters for subworkflows. by @jmchilton in #16592
- make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in #16594
- Bump minimum tpv version to 2.3.2 by @mvdbeek in #16597
- Backport tool mem fixes by @mvdbeek in #16601
- Reload toolbox after forking when using --preload by @mvdbeek in #16620
- Account for expires/expires_in when refreshing token by @mvdbeek in #16621
- Fixes for conditional subworkflow steps by @mvdbeek in #16632
- Fix nested conditional workflow steps by @mvdbeek in #16641
- Ensure Job belongs to current SA session by @mvdbeek in #16655
- Fix expression evaluation for nested state by @mvdbeek in #16656
- Make sort_collection tool require terminal datasets by @mvdbeek in #16661
- Push to object store even if
set_metafails by @mvdbeek in #16667 - Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in #16678
- Fix regex validation for global inline flags by @mvdbeek in #16683
- Fix closed transaction error on galaxy startup/check jobs by @jdavcs in #16687
- Add missing join condition in job search by @mvdbeek in #16710
- Fix job search query by @mvdbeek in #16714
- Copy the collection contents by default when copying a collection by @mvdbeek in #16717
- Fix collection id encoding by @davelopez in #16718
- Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728
- move the email and username redacting from the role loop by @martenson in #16820
- Fix parameter display in job info page for tools with sections by @mvdbeek in #16821
- Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in #16829
- Fix up local tool version handling by @mvdbeek in #16836
- Fix and prevent persisting null file_size by @mvdbeek in #16855
- Allow referring to steps by label only in markdown editor by @mvdbeek in #16861
- Fix safe update version handling in run form by @mvdbeek in #16865
- Remove more flushes in database operation tools by @mvdbeek in #16875
- Fix tag ownership check by @mvdbeek in #16877
- Empower Users to Select Storage Destination by @jmchilton in #14073
- External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019
- Add slack error reporting plugin by @hexylena in #15025
- Various Tool Shed Cleanup by @jmchilton in #15247
- Add Storage Management API by @davelopez in #15295
- OIDC tokens by @SergeyYakubov in #15300
- Expose additional beaker caching backends by @claudiofr in #15349
- Add support for visualizing HDF5 datasets. by @jarrah42 in #15394
- Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421
- Update Python dependencies by @galaxybot in #15435
- Fix for new style conda packages by @bernt-matthias in #15446
- Move database access code out of tool_util by @jdavcs in #15467
- Protection against problematic boolean parameters. by @jmchilton in #15493
- Use connection instead of session for ItemGrabber by @jdavcs in #15496
- Unify url handling with filesources by @nuwang in #15497
- Move TS to Alembic by @jdavcs in #15509
- Explore tool remote test data by @davelopez in #15510
- Handle "email_from" config option consistently, as per schema description by @jdavcs in #15557
- Update Python dependencies by @galaxybot in #15564
- Drop workflow exports to myexperiment.org by @dannon in #15576
- Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
- Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628
- Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643
- Add Galaxy Notification System by @davelopez in #15663
- Unpin Beaker requirement by @nsoranzo in #15665
- Add transactional state to JobHandlerStopQueue by @jdavcs in #15671
- Verify that activation and reset emails are properly generated by @guerler in #15681
- Add transactional state to workflow scheduling manager by @jdavcs in #15683
- Remove DELETED_NEW job state from code base by @jdavcs in #15690
- Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
- Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786
- Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844
- Drop use_legacy_history from config by @dannon in #15861
- Drop database views by @jdavcs in #15876
- Update Python dependencies by @galaxybot in #15890
- Allow pending inputs in some collection operation tools by @mvdbeek in #15892
- Updated doc and tests for attribute value filter by @tuncK in #15929
- Update Python dependencies by @galaxybot in #15942
- Record input datasets and collections at full parameter path by @mvdbeek in #15978
- Export tool citations configurable message by @minh-biocommons in #15998
- Add History Archival feature by @davelopez in #16003
- Code cleanups from ruff and pyupgrade by @nsoranzo in #16035
- Add missing fields to HistorySummary schema model by @davelopez in #16041
- Vendorise
packaging.versions.LegacyVersionby @nsoranzo in #16058 - Add Repository owner field to ToolSearch by @ahmedhamidawan in #16061
- Add count support for listing filters by @davelopez in #16075
- Update Python dependencies by @galaxybot in #16086
- Improved Cache Monitoring for Object Stores by @jmchilton in #16110
- Integrate accessibility testing into Selenium testing by @jmchilton in #16122
- Update Python dependencies by @galaxybot in #16123
- Improve histories and datasets immutability checks by @davelopez in #16143
- Update Python dependencies by @galaxybot in #16153
- Migrate display applications API to Fast API by @heisner-tillman in #16156
- adjust grid sharing indicators by @martenson in #16163
- Update Python dependencies by @galaxybot in #16182
- Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198
- Remove various fallback behaviors by @mvdbeek in #16199
- bring grids for (published) pages on par with workflows by @martenson in #16209
- Update Python dependencies by @galaxybot in #16227
- Update Python dependencies by @galaxybot in #16267
- Fix tool remote test data by @davelopez in #16311
- Hide conditionally skipped output by @mvdbeek in #16356
- Fix Storage Dashboard missing archived histories by @davelopez in #16473
- Bump bx-python to 0.10.0 by @mvdbeek in #16484
- Drop expunge_all() call in WebTransactionRequest by @mvdbeek in #16606
- Follow up on object store selection PR. by @jmchilton in #15654
- merge release_23.0 into dev by @martenson in #15830
- Move axe-selenium-python to dev dependencies by @nsoranzo in #16162
- Bump msal version by @mvdbeek in #16285
- Fix error_reports linting by @mvdbeek in #16465
- Fix upload paramfile handling (for real user setups) by @bernt-matthias in #16504
- Fix extra files path handling by @mvdbeek in #16541
- Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569
- Fix conditional step evaluation with datasets in repeats by @mvdbeek in #16584
- Don't read request body into memory by @mvdbeek in #16585
- Fixes for extra files handling and cached object stores by @mvdbeek in #16595
- Lazy load tool data tables in celery worker by @mvdbeek in #16640
- Force __DUPLICATE_FILE_TO_COLLECTION__ 'size' param to integer by @simonbray in #16659
- Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by @bernt-matthias in #16403
- Fix test discovery in vscode by @mvdbeek in #16413
- Fixes for (gitlab) error reporting by @bernt-matthias in #16424
- Fix default when statement evaluation by @mvdbeek in #16332
- Redact private role name and description when purging user by @mvdbeek in #16349
- When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247
- Point release deps fixes and docs by @mvdbeek in #16214
- Use galaxy-release-util to upload python packages by @mvdbeek in #16240
- Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744
- Fix mixed outputs_to_working_directory pulsar destinations by @mvdbeek in #15927
- Update Gravity to 1.0.3 by @natefoo in #15939
- Various fixes to path prefix handling by @mvdbeek in #16033
- Fix case sensitive filtering by name in histories by @davelopez in #16036
- Fix gcsfs test discovery by @mvdbeek in #16039
- Replace httpbin service with pytest-httpserver by @mvdbeek in #16042
- Update pulsar to 0.15.2 by @mvdbeek in #16050
- Anonymous User tool link bug fix by @ahmedhamidawan in #16065
- Fix BCO export by updating gxformat2 by @mvdbeek in #16081
- Fix job failure handling when condor indicates job failure by @mvdbeek in #16096
- Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099
- Extract HDA for code_file validate_input hook by @mvdbeek in #16120
- Fix sort error when re-running job with DCE collection input by @mvdbeek in #16126
- Fix related-hid in bulk contents API by @mvdbeek in #16128
- Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in #16137
- Tool warnings can either be None or a Dictionary but not a String by @guerler in #16183
- Pin minimum tpv version by @mvdbeek in #16201
- First release from the 20.09 branch of Galaxy.
- First release from the 20.05 branch of Galaxy.