galaxy-util 25.1.1

Galaxy generic utilities

Overview

The Galaxy utilities module.

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

History

25.1.1 (2026-02-03)

No recorded changes since last release

25.1.0 (2025-12-12)

Bug fixes

• Extract: do not use common prefix dir by @bernt-matthias in #20929

• Test and fix CORS on exceptions by @mvdbeek in #21105

Enhancements

• Implement Sample Sheets by @jmchilton in #19305

• Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288

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

• Remove deprecated tool document cache by @nsoranzo in #20510

• Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728

• Support remote file source hashes by @davelopez in #20853

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

• Prevent importing workflows with invalid step UUID by @davelopez in #20596

• Remove base_dir from zip in make_fast_zipfile by @davelopez in #20739

25.0.1 (2025-06-20)

No recorded changes since last release

25.0.0 (2025-06-18)

Bug fixes

• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331

• Use fissix also when python3-lib2to3 is not installed by @nsoranzo in #19749

• Fix test_in_directory on osx by @mvdbeek in #19943

Enhancements

• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181

• Fix UP031 errors - Part 3 by @nsoranzo in #19218

• Fix UP031 errors - Part 4 by @nsoranzo in #19235

• Fix UP031 errors - Part 5 by @nsoranzo in #19282

• Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372

• Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377

• Set safe default extraction filter for tar archives by @nsoranzo in #19406

• Format code with black 25.1.0 by @nsoranzo in #19625

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

• Allow PathLike parameters in make_fast_zipfile() by @nsoranzo in #19955

• Implement dataset collection support in workflow landing requests by @mvdbeek in #20004

• Add DOI to workflow metadata by @jdavcs in #20033

• Improve type annotation of galaxy.util submodules by @nsoranzo in #20104

• Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in #20150

24.2.4 (2025-06-17)

Bug fixes

• Use make_fast_zipfile directly by @mvdbeek in #19947

24.2.3 (2025-03-16)

No recorded changes since last release

24.2.2 (2025-03-08)

Enhancements

• Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

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

• Fix numerous issues with tool input format “21.01” by @jmchilton in #19030

• Partial backport of #19331 by @nsoranzo in #19342

• Fix config template validation for file sources and object store templates by @davelopez in #19414

• Serialize message exceptions on execution error by @mvdbeek in #19483

Enhancements

• Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by @jmchilton in #18272

• Add Python 3.13 support by @nsoranzo in #18449

• Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in #18524

• Rip repository_registry out of tool shed 2.0 by @jmchilton in #18647

• Workflow Landing Requests by @jmchilton in #18807

• Update Mypy to 1.11.2 and fix new signature override errors by @nsoranzo in #18811

• Raise exception if CompressedFile used on incompatible file by @mvdbeek in #18888

• Type annotations and fixes by @nsoranzo in #18911

• Workflow landing improvements by @mvdbeek in #18979

• Run installed Galaxy with no config and a simplified entry point by @natefoo in #19050

• Enhance UTF-8 support for filename handling in downloads by @arash77 in #19161

24.1.4 (2024-12-11)

Bug fixes

• Fix Archive header encoding by @arash77 in #18583

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

Enhancements

• Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805

24.1.3 (2024-10-25)

Bug fixes

• Fix Archive header encoding by @arash77 in #18583

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

Enhancements

• Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805

24.1.2 (2024-09-25)

Bug fixes

• Fix Archive header encoding by @arash77 in #18583

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

Enhancements

• Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805

24.1.1 (2024-07-02)

Bug fixes

• Fix bug in image_util.py by @kostrykin in #17749

• Revert some requests import changes by @nsoranzo in #18199

Enhancements

• Better display of estimated line numbers and add number of columns for tabular by @bernt-matthias in #17492

• Update Python dependencies by @galaxybot in #17653

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

• SQLAlchemy 2.0 by @jdavcs in #17778

• Error reporting unit tests by @jmchilton in #17968

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

• Add galaxy to user agent by @mvdbeek in #18003

• Update Python dependencies by @galaxybot in #18063

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

• Overhaul Azure storage infrastructure. by @jmchilton in #18087

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

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

24.0.3 (2024-06-28)

Bug fixes

• Use config_section to distinguish between galaxy and ts or other apps by @jdavcs in #18215

24.0.2 (2024-05-07)

Bug fixes

• Adds logging of messageExceptions in the fastapi exception handler. by @dannon in #18041

24.0.1 (2024-05-02)

Bug fixes

• Fix conditional Image imports by @mvdbeek in #17899

24.0.0 (2024-04-02)

Bug fixes

• Optional Reply-to SMTP header in tool error reports by @neoformit in #17243

• Follow-up on #17274 and #17262 by @nsoranzo in #17302

• Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340

Enhancements

• Add support for Python 3.12 by @tuncK in #16796

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

• Remove web framework dependency from tools by @davelopez in #17058

• Add support for (fast5.tar).xz binary compressed files by @tuncK in #17106

• Reuse test instance during non-integration tests by @mvdbeek in #17234

• Add OIDC backend configuration schema and validation by @uwwint in #17274

• Enable warn_unreachable mypy option by @mvdbeek in #17365

• Fix type annotation of code using XML etree by @nsoranzo in #17367

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

• Add image_diff comparison method for test output verification using images by @kostrykin in #17556

23.2.1 (2024-02-21)

Bug fixes

• Ruff and flake8 fixes by @nsoranzo in #16884

Enhancements

• Tool Shed 2.0 by @jmchilton in #15639

• 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

• 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

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

Other changes

• Merge 23.1 into dev by @mvdbeek in #16534

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)

Enhancements

• Improve invocation error reporting by @mvdbeek in #16917

23.1.1 (2023-10-23)

Bug fixes

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

• Fix some drs handling issues by @nuwang in #15777

• Enable strict_equality mypy option by @nsoranzo in #15808

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

• Fix form builder value handling by @guerler in #16304

• Backport tool mem fixes by @mvdbeek in #16601

• Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728

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

• Exclude on_opened and on_closed from watcher events by @mvdbeek in #16850

Enhancements

• Various Tool Shed Cleanup by @jmchilton in #15247

• Protection against problematic boolean parameters. by @jmchilton in #15493

• Unify url handling with filesources by @nuwang in #15497

• Explore tool remote test data by @davelopez in #15510

• Drop database views by @jdavcs in #15876

• Update Python dependencies by @galaxybot in #15890

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

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

• Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058

• Improve histories and datasets immutability checks by @davelopez in #16143

• Merge Target class with CondaTarget by @nsoranzo in #16181

23.0.6 (2023-10-23)

No recorded changes since last release

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)

Bug fixes

• Replace httpbin service with pytest-httpserver by @mvdbeek in #16042

22.1.2 (2022-12-08)

• Pin packaging dependency to < 22, fixes LegacyVersion import errors

• Add missing pyparsing dependency

22.1.1 (2022-08-22)

• First release from the 22.01 branch of Galaxy

21.1.0 (2021-03-19)

• First release from the 21.01 branch of Galaxy.

20.9.1 (2020-10-28)

20.9.0 (2020-10-15)

• First release from the 20.09 branch of Galaxy.

20.5.0 (2020-07-03)

• First release from 20.05 branch of Galaxy.

19.9.0 (2019-11-21)

• Initial import from dev branch of Galaxy during 19.09 development cycle.