History ------- .. to_doc --------- 26.1.dev0 --------- ------------------- 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.