galaxy-app 23.1.3

Fix unbound runner variable when there is an error in the job config by @mvdbeek in #16906

Fix discarded dataset ordering in Storage Dashboard by @davelopez in #16929

Include owner’s annotation when exporting workflow by @dannon in #16930

Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in #16937

Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961

Prevent workflow submission with missing input values by @mvdbeek in #17048

Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in #17067

Remove rollback from __check_jobs_at_startup by @mvdbeek in #17085

Improve invocation error reporting by @mvdbeek in #16917

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_meta fails 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.LegacyVersion by @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

Update pulsar client library to 0.15.5 by @mvdbeek in #16701

Bump galaxy-release-util version to 0.1.2 by @mvdbeek in #16241

When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

Forward port of slugify username received from oidc by @nuwang in #16271

Fix Text File Busy errors at the source by @mvdbeek in #16212

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

Startup fix when tool removed between reboot by @mvdbeek in #16175