galaxy-app 24.0.0

Reload built-in converters on toolbox reload by @bernt-matthias in #17209

Optional Reply-to SMTP header in tool error reports by @neoformit in #17243

Package tests fixes by @nsoranzo in #17301

Follow-up on #17274 and #17262 by @nsoranzo in #17302

Rollback invalidated transaction: catch them earlier by @jdavcs in #17312

Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340

Fix data_source and data_source_async bugs by @wm75 in #17422

More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632

Don’t index tasks without task_uuid by @mvdbeek in #17646

Separate ConnectedValue from RuntimeValue by @mvdbeek in #17678

Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in #17716

Fix usage of DISTINCT by @jdavcs in #17759

Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777

Use hg clone --stream to clone repos by @mvdbeek in #17786

Defer job attributes that are usually not needed by @mvdbeek in #17795

Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803

Fix archived histories mixing with active in histories list by @davelopez in #17856

Normalize extensions when loading tool by @mvdbeek in #17868

Ignore user data table errors for now by @mvdbeek in #17880

Add harmonize collections tool (or whatever other name) by @lldelisle in #16662

Add support for Python 3.12 by @tuncK in #16796

SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932

Python 3.8 as minimum by @mr-c in #16954

Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977

Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979

Extend regex groups in stdio regex matches by @bernt-matthias in #17016

Vueify Admin User Grid by @guerler in #17030

Remove web framework dependency from tools by @davelopez in #17058

Add select parameter with options from remote resources by @mvdbeek in #17087

Expose more tool information / navigability in UI. by @jmchilton in #17105

Vueify Admin Roles Grid by @guerler in #17118

SA2.0 updates: handling “object is being merged into a Session along the backref cascade path” by @jdavcs in #17122

Update Python dependencies by @galaxybot in #17123

Vueify Admin Groups Grid by @guerler in #17126

Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132

Vueify Admin Forms and Quota grids by @guerler in #17141

Update Python dependencies by @galaxybot in #17157

Update Python dependencies by @galaxybot in #17201

Vendorize fastapi-utls.cbv by @jdavcs in #17205

Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216

Vueifiy History Grids by @guerler in #17219

Update Python dependencies by @galaxybot in #17230

Update Python dependencies by @galaxybot in #17235

Allow job files to consume TUS uploads by @jmchilton in #17242

Update Python dependencies by @galaxybot in #17247

Migrate models to pydantic 2 by @mvdbeek in #17262

Consider Null inputs by @bernt-matthias in #17271

Add OIDC backend configuration schema and validation by @uwwint in #17274

Adds delete, purge and undelete batch operations to History Grid by @guerler in #17282

Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294

Improve ModelManager type hints by @mvdbeek in #17299

API endpoint that allows “changing” the objectstore for “safe” scenarios. by @jmchilton in #17329

Update Python dependencies by @galaxybot in #17333

Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357

Remove unused statements in job search function by @mvdbeek in #17361

Enable warn_unreachable mypy option by @mvdbeek in #17365

Fix type annotation of code using XML etree by @nsoranzo in #17367

More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381

Cancel all active jobs when the user is deleted by @davelopez in #17390

Update to black 2024 stable style by @nsoranzo in #17391

Purge groups and roles from DB (for real) by @davelopez in #17411

Update Python dependencies by @galaxybot in #17420

Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435

Adds published histories to grid list by @guerler in #17449

Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460

data_column parameter: use column_names metadata if present by @bernt-matthias in #17478

Update Python dependencies by @galaxybot in #17486

Consolidate resource grids into tab views by @guerler in #17487

Update k8s docker python to 3.12 by @nuwang in #17494

add encode ID API endpoint by @mira-miracoli in #17510

Fixing data_source tools and incrementing tool profile by @wm75 in #17515

Update Python dependencies by @galaxybot in #17541

Add image_diff comparison method for test output verification using images by @kostrykin in #17556

Filter out subworkflow invocations by @mvdbeek in #17558

Update Python dependencies by @galaxybot in #17580

Restore histories API behavior for keys query parameter by @davelopez in #17779

Fix datasets API custom keys encoding by @davelopez in #17793

Improved error messages for runtime sharing problems. by @jmchilton in #17794

Allow admin to sharpen language about selected object stores. by @jmchilton in #17806

consistently compare profile versions by @bernt-matthias in #16492

pin fs.dropboxfs to >=1 by @bernt-matthias in #16451

Remove unnecessary check: item cannot be None by @jdavcs in #16550

Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561

Fix dependency update GitHub workflow by @nsoranzo in #16639

Ensure Job belongs to current SA session by @jdavcs in #16647

Account for shared usage between TS and galaxy apps by @jdavcs in #16746

move the email and username redacting from the role loop by @martenson in #16805

Fix shed unit test by @mvdbeek in #16811

chore: fix typos by @afuetterer in #16851

Fix bug in SQLAlchemy statement by @jdavcs in #16881

Ruff and flake8 fixes by @nsoranzo in #16884

Update help in relabel_from_file.xml by @lldelisle in #16891

Fix subtle bug in listify function + simplify list munging by @jdavcs in #16904

prep for updated h5py and typos by @mr-c in #16963

Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in #17018

Expose file_name property in DatasetFilenameWrapper by @jdavcs in #17107

Fix to_cwl for nested collections by @mvdbeek in #17276

Rollback invalidated transaction by @jdavcs in #17280

Install newer celery on python 3.8+ by @mvdbeek in #17309

Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in #17315

Discard sqlalchemy session after task completion by @mvdbeek in #17317

Scope session for job runner monitor loop by @mvdbeek in #17319

Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in #17384

Update python-multipart to 0.0.7 by @nsoranzo in #17429

Build param dict before creating entrypoint by @mvdbeek in #17440

Fix bug: true >> True by @jdavcs in #17446

Set metadata states on dataset association, not dataset by @mvdbeek in #17474

Remove two print statements by @bernt-matthias in #17480

Provide working routes.url_for every ASGI request by @mvdbeek in #17497

Implement default locations for data and collection parameters. by @jmchilton in #14955

Enable job resubmissions in k8s runner by @pcm32 in #15238

Add parameter name to validation errors by @bernt-matthias in #15440

Tool Shed 2.0 by @jmchilton in #15639

Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825

Limit number of celery task executions per second per user by @claudiofr in #16232

Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in #16252

Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264

Update Python dependencies by @galaxybot in #16305

Add carbon emissions admin configuration options by @Renni771 in #16307

Migrate a part of the users API to Fast API by @heisner-tillman in #16341

Update Python dependencies by @galaxybot in #16360

Add Invenio RDM repository integration by @davelopez in #16381

Update Python dependencies by @galaxybot in #16389

Update Python dependencies by @galaxybot in #16409

Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420

Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431

SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in #16434

Update Python dependencies by @galaxybot in #16436

Update Python dependencies by @galaxybot in #16485

Rename MetadataEqualsValidator by @bernt-matthias in #16489

Add support for CILogon deployments in different regions than the US by @uwwint in #16490

Refactor/OIDC custos by @uwwint in #16497

Update Python dependencies by @galaxybot in #16521

Move database access code out of galaxy.util by @jdavcs in #16526

Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536

Update Python dependencies by @galaxybot in #16577

Vueify Tool Form Data Selector by @guerler in #16578

Workflow Comments 💬 by @ElectronicBlueberry in #16612

Switch out conditional requirement parser by @mvdbeek in #16636

Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642

Bump samtools converters by @bernt-matthias in #16668

Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in #16672

Implement instance URLs in Galaxy markdown. by @jmchilton in #16675

Change Sentry error reporting plug-in by @kysrpex in #16686

Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690

Enhance task monitor composable by @davelopez in #16695

Misc. edits/refactorings to session handling by @jdavcs in #16712

SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in #16724

Update Python dependencies by @galaxybot in #16735

Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in #16758

Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762

Update Python dependencies by @galaxybot in #16770

Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778

Add EGI Check-in as OIDC authentication option by @enolfc in #16782

Replace file_name property with get_file_name function by @SergeyYakubov in #16783

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 in #16795

Galaxy help forum integration by @ElectronicBlueberry in #16798

Update Python dependencies by @galaxybot in #16807

Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in #16833

Remove remaining legacy backbone form input elements by @guerler in #16834

SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in #16852

Update Python dependencies by @galaxybot in #16853

Drop unused HistoryContentManager code and related tests by @jdavcs in #16882

Vueify Visualizations Grid by @guerler in #16892

Update Python dependencies by @galaxybot in #16896

Enable some flake8-logging-format rules in ruff by @nsoranzo in #16915

Remove “Create Workflow” form and allow workflow creation in editor by @ahmedhamidawan in #16938

Update Python dependencies by @galaxybot in #16939

Add helper to get dataset or collection via src and id by @mr-c in #16953

Allow non-optional integer/float params without value attribute by @nsoranzo in #16966

Update Python dependencies by @galaxybot in #16978

Fix invocation report to target correct workflow version. by @jmchilton in #17008

Update Python dependencies by @galaxybot in #17011

Upgrade job manager’s index_query method to SA2.0 by @jdavcs in #17020

optimize object store cache operations by @SergeyYakubov in #17025

Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in #17038

Update Python dependencies by @galaxybot in #17050

Migrate groups API to fastAPI by @arash77 in #17051

Migrate ItemTags API to FastAPI by @arash77 in #17064

Update Python dependencies by @galaxybot in #17084

Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342

Merge 23.1 into dev by @mvdbeek in #16534

Revert “[23.1] Enable job resubmissions in k8s runner” by @nuwang in #17323

Fix succces typo by @mvdbeek in #17481

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