galaxy-app 24.1.4

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

Fix dropped when_expression on step upgrade by @mvdbeek in #18446

Improve workflow-related exception reporting by @mvdbeek in #18447

Fix subwofklow tags serialization type by @arash77 in #18456

by @laperlej in #18459

Add input extra files to get_input_fnames by @mvdbeek in #18462

Return generic message for password reset email by @ahmedhamidawan in #18479

Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

Don’t call job_runner.stop_job on jobs in new state by @mvdbeek in #18495

Prevent job submission if input collection element is deleted by @mvdbeek in #18517

Strip unicode null from tool stdio by @mvdbeek in #18527

Fix map over calculation for runtime inputs by @mvdbeek in #18535

Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

Set minimum weasyprint version by @mvdbeek in #18606

Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

Make sure we set file size also for purged outputs by @mvdbeek in #18681

File source and object store instance api fixes by @mvdbeek in #18685

Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

Fill in missing help for cross product tools. by @jmchilton in #18698

Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

Fix directory get or create logic by @mvdbeek in #18752

Fix job summary for optional unset job data inputs by @mvdbeek in #18754

Allow to change only the description of a quota by @bernt-matthias in #18775

Fix wrong extension on pick data output by @mvdbeek in #18798

Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

Fix named cursor is not valid anymore by @mvdbeek in #18825

Tighten TRS url check by @mvdbeek in #18841

Fix Workflow index bookmark filter by @itisAliRH in #18842

Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

Extend on disk checks to running, queued and error states by @mvdbeek in #18846

Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

Fix data_column ref to nested collection by @mvdbeek in #18875

Fix loading very old workflows with data inputs by @mvdbeek in #18876

Access tool data table filters in workflow building mode by @mvdbeek in #18900

Fix username used in invocation report by @mvdbeek in #18932

Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

Fix job search statement building by @mvdbeek in #19010

Put cached jobs back into queue on handler restart by @mvdbeek in #19012

Fix various invocation export issues by @mvdbeek in #19215

Create harmonized collections from correct tool outputs by @wm75 in #19222

Include workflow invocation id in exception logs by @mvdbeek in #18594

Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Collect job metrics also when job failed by @mvdbeek in #18809

prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

Fix dropped when_expression on step upgrade by @mvdbeek in #18446

Improve workflow-related exception reporting by @mvdbeek in #18447

Fix subwofklow tags serialization type by @arash77 in #18456

by @laperlej in #18459

Add input extra files to get_input_fnames by @mvdbeek in #18462

Return generic message for password reset email by @ahmedhamidawan in #18479

Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

Prevent job submission if input collection element is deleted by @mvdbeek in #18517

Strip unicode null from tool stdio by @mvdbeek in #18527

Fix map over calculation for runtime inputs by @mvdbeek in #18535

Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

Set minimum weasyprint version by @mvdbeek in #18606

Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

Make sure we set file size also for purged outputs by @mvdbeek in #18681

File source and object store instance api fixes by @mvdbeek in #18685

Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

Fill in missing help for cross product tools. by @jmchilton in #18698

Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

Fix directory get or create logic by @mvdbeek in #18752

Fix job summary for optional unset job data inputs by @mvdbeek in #18754

Allow to change only the description of a quota by @bernt-matthias in #18775

Fix wrong extension on pick data output by @mvdbeek in #18798

Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

Fix named cursor is not valid anymore by @mvdbeek in #18825

Tighten TRS url check by @mvdbeek in #18841

Fix Workflow index bookmark filter by @itisAliRH in #18842

Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

Extend on disk checks to running, queued and error states by @mvdbeek in #18846

Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

Fix data_column ref to nested collection by @mvdbeek in #18875

Fix loading very old workflows with data inputs by @mvdbeek in #18876

Access tool data table filters in workflow building mode by @mvdbeek in #18900

Fix username used in invocation report by @mvdbeek in #18932

Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

Fix job search statement building by @mvdbeek in #19010

Put cached jobs back into queue on handler restart by @mvdbeek in #19012

Include workflow invocation id in exception logs by @mvdbeek in #18594

Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Collect job metrics also when job failed by @mvdbeek in #18809

prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

Return generic message for password reset email by @ahmedhamidawan in #18479

Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

Prevent job submission if input collection element is deleted by @mvdbeek in #18517

Strip unicode null from tool stdio by @mvdbeek in #18527

Fix map over calculation for runtime inputs by @mvdbeek in #18535

Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

Set minimum weasyprint version by @mvdbeek in #18606

Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

Make sure we set file size also for purged outputs by @mvdbeek in #18681

File source and object store instance api fixes by @mvdbeek in #18685

Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

Fill in missing help for cross product tools. by @jmchilton in #18698

Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

Fix directory get or create logic by @mvdbeek in #18752

Fix job summary for optional unset job data inputs by @mvdbeek in #18754

Allow to change only the description of a quota by @bernt-matthias in #18775

Fix wrong extension on pick data output by @mvdbeek in #18798

Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

Fix named cursor is not valid anymore by @mvdbeek in #18825

Tighten TRS url check by @mvdbeek in #18841

Fix Workflow index bookmark filter by @itisAliRH in #18842

Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

Extend on disk checks to running, queued and error states by @mvdbeek in #18846

Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

Fix data_column ref to nested collection by @mvdbeek in #18875

Fix loading very old workflows with data inputs by @mvdbeek in #18876

Include workflow invocation id in exception logs by @mvdbeek in #18594

Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Collect job metrics also when job failed by @mvdbeek in #18809

prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

Unpin social-auth-core dependency by @nsoranzo in #17607

Dynamic tool fixes by @dcore94 in #18085

Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106

Revert some requests import changes by @nsoranzo in #18199

Small bug fixes for user data plugins by @jmchilton in #18246

Fix handler: access to result row items changed in SA2.0 by @jdavcs in #18274

Fix various packages’ issues by @nsoranzo in #18301

Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in #18305

Fix empty usernames in database + bug in username generation by @jdavcs in #18379

Add TypedDict for JobsSummary by @mvdbeek in #18418

Pin pydantic to >=2.7.4 by @nsoranzo in #18423

Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

Fix dropped when_expression on step upgrade by @mvdbeek in #18446

Improve workflow-related exception reporting by @mvdbeek in #18447

Fix subwofklow tags serialization type by @arash77 in #18456

Disable password reset for deleted users [GCC2024_COFEST] by @laperlej in #18459

Add input extra files to get_input_fnames by @mvdbeek in #18462

Only include tool stdout/stderr in HDA info by @natefoo in #16730

Adding object store plugin for Rucio by @SergeyYakubov in #17156

Enable all-vs-all collection analysis patterns. by @jmchilton in #17366

Add onedata objectstore by @bwalkowi in #17540

Type annotation improvements by @nsoranzo in #17601

Type annotation and CWL-related improvements by @nsoranzo in #17630

Update Python dependencies by @galaxybot in #17653

Code cleanups from ruff and pyupgrade by @nsoranzo in #17654

Update Python dependencies by @galaxybot in #17764

SQLAlchemy 2.0 by @jdavcs in #17778

Update Python dependencies by @galaxybot in #17819

Update Python dependencies by @galaxybot in #17870

Add email notifications channel by @davelopez in #17914

Model edits and bug fixes by @jdavcs in #17922

Update Python dependencies by @galaxybot in #17923

Model typing and SA2.0 follow-up by @jdavcs in #17958

Error reporting unit tests by @jmchilton in #17968

Make urgent notifications mandatory by @davelopez in #17975

Update Python dependencies by @galaxybot in #17982

Enable warn_unused_ignores mypy option by @nsoranzo in #17991

Add galaxy to user agent by @mvdbeek in #18003

Add Zenodo integration by @davelopez in #18022

Update Python dependencies by @galaxybot in #18035

Add stronger type annotations in file sources + refactoring by @davelopez in #18050

Add pagination support to Files Source plugins by @davelopez in #18059

Update Python dependencies by @galaxybot in #18063

Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067

Ensure history update_time is set when exporting by @davelopez in #18086

Overhaul Azure storage infrastructure. by @jmchilton in #18087

Update Python dependencies by @galaxybot in #18095

Update Python dependencies by @galaxybot in #18125

Revises handling of warnings in the workflow run form by @guerler in #18126

Empower users to bring their own storage and file sources by @jmchilton in #18127

Update s3fs dependency. by @jmchilton in #18135

More unit testing for object store stuff. by @jmchilton in #18136

Harden User Object Store and File Source Creation by @jmchilton in #18172

Fix boto3-stubs typecheck dependency by @nsoranzo in #18173

More structured indexing for user data objects. by @jmchilton in #18291

Onedada object store and files source stability fixes by @bwalkowi in #18372

Allow running and editing workflows for specific versions by @ahmedhamidawan in #18378

Chore: remove repetitive words by @tianzedavid in #18076

Fix #18316 (anonymous file sources) by @jmchilton in #18352

Merge 24.0 into 24.1 by @jdavcs in #18353

Merge 24.0 into 24.1 by @jdavcs in #18365

Raise exception if collection elements missing during download by @jdavcs in #18094

Allow purge query param, deprecate purge body param by @mvdbeek in #18105

Backport OIDC schema fix by @mvdbeek in #18111

Don’t log exception if cancelled slurm job doesn’t have stderr file by @mvdbeek in #18121

Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123

Fix data default values not getting added to history by @mvdbeek in #18132

Drop redundant error message by @mvdbeek in #18156

Emit warning when user-cancelled job already complete by @mvdbeek in #18178

Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190

Add string cast for dbkey / genome_build by @mvdbeek in #18207

Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214

Don’t set dataset peek for errored jobs by @mvdbeek in #18231

Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249

Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250

Don’t attempt to download purged datasets by @mvdbeek in #18278

Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283

Don’t serialize display application links for deleted datasets by @mvdbeek in #18307

Downgrade doi fetch error to debug by @mvdbeek in #18330

Fix authentication error for anonymous users querying jobs by @davelopez in #18333

Fix seek in slurm memory check by @mvdbeek in #18338

Do not copy purged outputs to object store by @mvdbeek in #18342

Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348

Allow DCE as outer input to to_cwl by @mvdbeek in #18349

Fix anonymous user job retrieval logic by @davelopez in #18358

Fix update group API payload model by @davelopez in #18374

Fix user’s private role can be missing by @davelopez in #18381

Fix null inputs in database operation tools by @mvdbeek in #18385

Assign default data extension on discovered collection output by @mvdbeek in #18389

Fix get_accessible_job if called without session by @mvdbeek in #18400

Fix invocation step_job_summary for new collections by @mvdbeek in #18402

Really allow in-range validator for txt by @bernt-matthias in #18411

Fix collection map over status for dragged collections by @mvdbeek in #18416

Serialize purged flag for datasets in collections by @davelopez in #18420

Minor linting cleanup by @mvdbeek in #18421

Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Fix tool version switch in editor by @mvdbeek in #17858

Fix workflow run form failing on certain histories by @mvdbeek in #17869

Always serialize element_count and populated when listing contents by @mvdbeek in #17890

Fix saving workflows with freehand_comments only by @mvdbeek in #17901

Always discard session after __handle_waiting_jobs is done by @mvdbeek in #17913

Fix workflow run form for workflows with null rename PJA by @mvdbeek in #17929

Revert unnecessary error change by @mvdbeek in #17948

Fix missing implicit conversion for mapped over jobs by @mvdbeek in #17952

Fix get_content_as_text for compressed text datatypes by @mvdbeek in #17976

Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in #17981

Fix LengthValidator if no value passed by @mvdbeek in #17983

Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in #17985

Don’t attempt to commit in dry_run mode by @mvdbeek in #17987

Don’t fail if reporting invalid parameter values by @mvdbeek in #18002

Include exception info when something goes wrong while refreshing tokens by @mvdbeek in #18008

Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in #18011

Don’t commit without having set a hid by @mvdbeek in #18014

Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in #18023

Fix tag regex pattern by @jdavcs in #18025

Fix History Dataset Association creation so that hid is always set by @mvdbeek in #18036

Change wrong quota_source value from KeyError to ValueError by @mvdbeek in #18040

Check database connection to issue a rollback if no connection by @jdavcs in #18070

Fix remote files sources error handling by @davelopez in #18027

Drop left-over debug statement by @mvdbeek in #17939

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