galaxy-job-execution 25.1.2

Galaxy job execution runtime utilities

Overview

The Galaxy job execution runtime module.

• Code: https://github.com/galaxyproject/galaxy

History

25.1.2 (2026-03-09)

No recorded changes since last release

25.1.1 (2026-02-03)

Bug fixes

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

25.1.0 (2025-12-12)

Enhancements

• 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

Other changes

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

25.0.4 (2025-11-18)

No recorded changes since last release

25.0.3 (2025-09-23)

No recorded changes since last release

25.0.2 (2025-08-13)

Bug fixes

• 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

25.0.1 (2025-06-20)

No recorded changes since last release

25.0.0 (2025-06-18)

Bug fixes

• 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

Enhancements

• 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

24.2.4 (2025-06-17)

Bug fixes

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

24.2.3 (2025-03-16)

Bug fixes

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

24.2.2 (2025-03-08)

No recorded changes since last release

24.2.1 (2025-02-28)

No recorded changes since last release

24.2.0 (2025-02-11)

Bug fixes

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

24.1.4 (2024-12-11)

Bug fixes

• 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

24.1.3 (2024-10-25)

Bug fixes

• 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

24.1.2 (2024-09-25)

Bug fixes

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

24.1.1 (2024-07-02)

Bug fixes

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

Enhancements

• 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

24.0.3 (2024-06-28)

Bug fixes

• 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

24.0.2 (2024-05-07)

No recorded changes since last release

24.0.1 (2024-05-02)

No recorded changes since last release

24.0.0 (2024-04-02)

Bug fixes

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

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

Enhancements

• 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

23.2.1 (2024-02-21)

Enhancements

• 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

23.1.4 (2024-01-04)

No recorded changes since last release

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

• 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

23.1.1 (2023-10-23)

Bug fixes

• 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

Enhancements

• 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

23.0.6 (2023-10-23)

Bug fixes

• 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

23.0.5 (2023-07-29)

No recorded changes since last release

23.0.4 (2023-06-30)

No recorded changes since last release

23.0.3 (2023-06-26)

No recorded changes since last release

23.0.2 (2023-06-13)

No recorded changes since last release

23.0.1 (2023-06-08)

No recorded changes since last release

20.9.0 (2020-10-15)

• First release from the 20.09 branch of Galaxy.

20.5.0 (2020-07-04)

• First release from the 20.05 branch of Galaxy.