galaxy-data 23.2.1

Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in #16553

MINERVA display application: enable cors, add for tabular by @hexylena in #16737

Use AlignedSegment.to_string by @mvdbeek in #16803

Ruff and flake8 fixes by @nsoranzo in #16884

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

Fix cardinality violation error: subquery returns multiple results by @jdavcs in #17224

Fix Display Application link generation by @mvdbeek in #17227

Display application fixes and tests by @mvdbeek in #17233

Rollback invalidated transaction by @jdavcs in #17280

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

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

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

Display beginning of non-text files as text instead of triggering a download by @SergeyYakubov in #15447

Tool Shed 2.0 by @jmchilton in #15639

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 #16409

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

Implement datatype upload warnings by @jmchilton in #16564

Support new genome browser chain file format by @claudiofr in #16576

Workflow Comments 💬 by @ElectronicBlueberry in #16612

Bump samtools converters by @bernt-matthias in #16668

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

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

Migrate collection elements store to Pinia by @davelopez in #16725

Reset autocommit to False by @jdavcs in #16745

Drop legacy server-side search by @jdavcs in #16755

Optimize iteration in DatasetInstance model + SA2.0 fix by @jdavcs in #16776

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

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

Allow partial matches in workflow name tag search and search all tags for unquoted query by @ahmedhamidawan in #16860

Vueify Visualizations Grid by @guerler in #16892

Standardize to W3C naming for color. by @dannon in #16949

Move and re-use persist_extra_files by @mvdbeek in #16955

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

optimize object store cache operations by @SergeyYakubov in #17025

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

Add magres datatype by @martenson in #17499

Merge 23.1 into dev by @mvdbeek in #16534

Merge release_23.1 into dev by @mvdbeek in #16768

Create db head merge revision. by @dannon in #16838

merge release_23.1 into dev by @martenson in #16933

Minor clarification/typo fix in datatypes.data by @dannon in #16993

Fix .file_name access in merge forward by @mvdbeek in #17097

Backport model store fixes by @mvdbeek in #17439

Fix succces typo by @mvdbeek in #17481

Fix User.current_galaxy_session by @mvdbeek in #17232

Backport #17188: Fix for converter tests by @mvdbeek in #17231

Skip change_datatype things if we’re not actually changing the extension by @mvdbeek in #16931

Fix copying metadata to copied job outputs by @mvdbeek in #17007

Update tar_to_directory dependency by @mvdbeek in #17009

Assert that DatasetCollectioElement has an associated object by @mvdbeek in #17071

Fix input dates in notifications: consider timezone offset by @davelopez in #17088

Allow relative URLs in broadcasts action links by @davelopez in #17093

Improve invocation error reporting by @mvdbeek in #16917

Add support for larch datatypes by @patrick-austin in #17080

Fix bad auto-merge of dev. by @jmchilton in #15386

Merge conflicting db migration branches into one by @jdavcs in #15771

Enable strict_equality mypy option by @nsoranzo in #15808

Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811

Fix anonymous user uploads when vault is configured by @tchaussepiedifb in #15858

Fix nullable deleted column in API Keys table by @davelopez in #15956

Attempt to fix mypy check by @davelopez in #16103

Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207

Reset autocommit to True (temporarily) by @jdavcs in #16283

Update 23.1 release tags for migration scripts by @jdavcs in #16294

Fix form builder value handling by @guerler in #16304

Fix tags ownership by @davelopez in #16339

Fix disk usage recalculation for distributed object stores by @mvdbeek in #16380

Job cache fixes for DCEs by @mvdbeek in #16384

Fix histories count by @davelopez in #16400

Fix double-encoding notification content by @mvdbeek in #16530

Optimize getting current user session by @mvdbeek in #16604

Fixes for conditional subworkflow steps by @mvdbeek in #16632

Copy the collection contents by default when copying a collection by @mvdbeek in #16717

Fix allowlist deserialization in file sources by @mvdbeek in #16729

Fix workflow output display without label by @mvdbeek in #16749

Fix and prevent persisting null file_size by @mvdbeek in #16855

Fix workflow import losing tool_version by @mvdbeek in #16869

Remove more flushes in database operation tools by @mvdbeek in #16875

Fix join condition for nested collection query by @mvdbeek in #16880

Empower Users to Select Storage Destination by @jmchilton in #14073

Add Storage Dashboard visualizations for histories by @davelopez in #14820

Towards decoupling datatypes and model by @jdavcs in #15186

Add Storage Management API by @davelopez in #15295

OIDC tokens by @SergeyYakubov in #15300

Expose additional beaker caching backends by @claudiofr in #15349

Follow up to #15186 by @jdavcs in #15388

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

Unify url handling with filesources by @nuwang in #15497

Move TS to Alembic by @jdavcs in #15509

Update Python dependencies by @galaxybot in #15564

Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611

Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in #15633

Add Galaxy Notification System by @davelopez in #15663

Drop model mapping unit tests by @jdavcs in #15669

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

Drop database views by @jdavcs in #15876

Update Python dependencies by @galaxybot in #15890

FITS data format by @volodymyrss in #15905

Improve display chunk generation for BAMs by @wm75 in #15972

Add History Archival feature by @davelopez in #16003

Add alter_column migration utility by @jdavcs in #16009

Code cleanups from ruff and pyupgrade by @nsoranzo in #16035

Add missing fields to HistorySummary schema model by @davelopez in #16041

Dataset chunking tests (and small fixes) by @jmchilton in #16069

Add create_foreign_key migration utility by @jdavcs in #16077

Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in #16080

Use automated naming convention to generate indexes and constraints in database by @jdavcs in #16089

Add zipped mongodb and genenotebook datatypes by @abretaud in #16173

Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198

bring grids for (published) pages on par with workflows by @martenson in #16209

Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in #16255

Filter deleted keys from api_keys relationship by @dannon in #16321

Increase CustosAuthnzToken.external_user_id column size by @davelopez in #16818

Follow up on object store selection PR. by @jmchilton in #15654

Fix Enums in API docs by @davelopez in #15740

merge release_23.0 into dev by @martenson in #15830

Fix linting of FITS datatype code by @mvdbeek in #16169

backport of pysam tostring by @martenson in #16822