Fix ``preferred_object_store_id`` not respected for discovered outputs with extended metadata by @mvdbeek in #22056

Fix dataset permissions set when upload and discovery jobs finish by @mvdbeek in #24233

Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557

Implement Sample Sheets by @jmchilton in #19305

Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424

Clean up code from pyupgrade by @nsoranzo in #20642

Add support for picking from_work_dir directory by @mvdbeek in #20916

Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749

Fix bug: tool output file may be overwritten by Runner’s multi work t… by @jianzuoyi in #20639

Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650

Create rucio.cfg from inside Rucio objectstore by @SergeyYakubov in #19863

Use lower case extension for setting datatype in data discovery by @bernt-matthias in #19954

Remove transaction helper by @jdavcs in #19407

Format code with black 25.1.0 by @nsoranzo in #19625

Type annotation improvements by @nsoranzo in #19642

Define simple models for job messages. by @jmchilton in #19688

Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852

Create working dir output outside of tool evaluator by @mvdbeek in #20153

Don’t collect unnamed outputs twice in extended metadata mode by @mvdbeek in #19868

Use materialized datasets in pulsar job runner by @mvdbeek in #19807

Fixes for errors reported by mypy 1.11.0 by @nsoranzo in #18608

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

Retry container monitor POST if it fails (don’t assume it succeeded) by @natefoo in #18863

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

Retry container monitor POST if it fails (don’t assume it succeeded) by @natefoo in #18863

Retry container monitor POST if it fails (don’t assume it succeeded) by @natefoo in #18863

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

Enable warn_unused_ignores mypy option by @nsoranzo in #17991

Add galaxy to user agent by @mvdbeek in #18003

Refactor galaxy.files plugin loading + config handling. by @jmchilton in #18049

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

Update Python dependencies by @galaxybot in #18063

Include traceback when logging email PJA exception by @mvdbeek in #18122

Don’t commit in DeleteIntermediatesAction by @mvdbeek in #18131

Don’t fail metadata if we only have an extra output files dir by @mvdbeek in #18179

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

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

Fixes for output discovery by @bernt-matthias in #17266

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

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

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

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

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

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

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

optimize object store cache operations by @SergeyYakubov in #17025

Fix library import from path linking files by @davelopez in #16919

Don’t store job in JobIO instance attributes by @mvdbeek in #16965

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

Fix tags ownership by @davelopez in #16339

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 ItemOwnerShipException in tag removal by @mvdbeek in #16773

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

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

Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421

Unify url handling with filesources by @nuwang in #15497

Handle “email_from” config option consistently, as per schema description by @jdavcs in #15557

Record input datasets and collections at full parameter path by @mvdbeek in #15978

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

Improved Cache Monitoring for Object Stores by @jmchilton in #16110

Remove various fallback behaviors by @mvdbeek in #16199

Fix extra files path handling by @mvdbeek in #16541

Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569

Fixes for extra files handling and cached object stores by @mvdbeek in #16595