galaxy-tool-util 23.2.dev0

Galaxy tool and tool dependency utilities

Overview

The Galaxy tool utilities.

• Code: https://github.com/galaxyproject/galaxy/tree/dev/packages/tool_util

History

23.2rc1

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

• Change log level for duplicate data table entries to warning by @mvdbeek in #16988

• Upgrade minimum conda to be compatible with latest conda-build by @bernt-matthias in #17013

• Fix duplicated tools in tool panel view section copying by @jmchilton in #17036

Enhancements

• Adds biii as supported xref reference type by @kostrykin in #16952

23.1.1 (2023-10-23)

Bug fixes

• Fixes for two framework test tools by @bernt-matthias in #15483

• add missing f for f-string by @bernt-matthias in #15584

• Fix call to docker_cached_container_description by @bernt-matthias in #15598

• Fix log message by @bernt-matthias in #15838

• add required_files to the tag list for linting by @bernt-matthias in #16129

• Handle appending to a results file that does not exists. by @ksuderman in #16233

• Improve container resolver documentation by @mvdbeek in #16280

• Add missing singularity_no_mount prop parsing by @mvdbeek in #16367

• Restore resolution of Conda environments generated from non-lowercase package names by @nsoranzo in #16474

• Fix up unit tests for local use by @mvdbeek in #16483

• Fix multiple remote test data by @davelopez in #16542

• Don’t use docker run –user flag on OSX by @mvdbeek in #16573

• Backport tool mem fixes by @mvdbeek in #16601

• xsd: allow name attribute of test collections by @bernt-matthias in #16663

• Fix short ids in tool panel views. by @jmchilton in #16800

• Fix tool panel views for versionless tool ids by @mvdbeek in #16809

Enhancements

• Decompress history data for testing assertions by @bernt-matthias in #15085

• OIDC tokens by @SergeyYakubov in #15300

• Fix for new style conda packages by @bernt-matthias in #15446

• Move database access code out of tool_util by @jdavcs in #15467

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

• Implement initial tool/wf test assertions module for JSON data. by @jmchilton in #15494

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

• xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in #15534

• Update Python dependencies by @galaxybot in #15564

• Container resolvers: add docs, typing and tests by @bernt-matthias in #15614

• Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844

• Enable per-destination container_resolver_config_file by @bernt-matthias in #15884

• Updated doc and tests for attribute value filter by @tuncK in #15929

• Make container builders use mamba by @bernt-matthias in #15953

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

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

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

• Small test decorator improvements. by @jmchilton in #16220

• tool_util: switch to mambaforge on non-32bit; add arm64 support by @mr-c in #16223

• Fix tool remote test data by @davelopez in #16311

Other changes

• Restore tmp mounting by @mvdbeek in #16533

23.0.6 (2023-10-23)

Bug fixes

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

• Fix create/install commands for conda 23.9.0 by @nsoranzo in #16831

23.0.5 (2023-07-29)

Bug fixes

• Allow duplicate labels in linter if outputs contain filters by @bernt-matthias in #15933

• Fix parsing tool metadata from bio.tools by @kysrpex in #16449

• Linter: fix regex for profile version by @bernt-matthias in #16480

• Adjust test_data_download method in GalaxyInteractorApi so an admin user is not required by @simonbray in #16482

23.0.4 (2023-06-30)

No recorded changes since last release

23.0.3 (2023-06-26)

Bug fixes

• xsd: add missing sep attribute for has_n_columns by @bernt-matthias in #16262

• Missing init prevents models.py being bundled into tool_util by @nuwang in #16308

Enhancements

• When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

23.0.2 (2023-06-13)

Bug fixes

• Don’t fail CWL tool parsing when Cheetah not installed by @mvdbeek in #16219

• Allow skipping expect_num_outputs when expect_failure is set in tool test by @bernt-matthias in #16237

23.0.1 (2023-06-08)

Bug fixes

• Fix assertion linting to not fail on byte suffixes by @bernt-matthias in #15873

• Fix get_test_from_anaconda() and base_image_for_targets() functions by @nsoranzo in #16125

• Fix test search for mulled container hashes by @mvdbeek in #16170

Enhancements

• Allow setting auto_decompress property in staging interface by @mvdbeek in #16014

22.1.5 (2022-11-14)

• Set test status to success on expected failure

22.1.4 (2022-10-28)

• Add missing unittest_utils package to galaxy-tool-util

22.1.3 (2022-10-27)

• Pin minimum pyopenssl version when installing Conda

• Add --strict-channel-priority to conda create/install commands if using conda >=4.7.5

22.1.2 (2022-08-29)

• Fix lint context error level

• Pin galaxy-util to >= 22.1

• Fix biocontainer resolution without beaker cache

22.1.1 (2022-08-22)

• First release from the 22.01 branch of Galaxy

21.9.2 (2021-11-23)

• Fix linting of multiple="true" select inputs.

21.9.1 (2021-11-03)

• Fix tool linting.

21.9.0 (2021-11-03)

• First release from the 21.09 branch of Galaxy.

21.1.2 (2021-06-23)

21.1.1 (2021-05-21)

21.1.0 (2021-03-19)

• First release from the 21.01 branch of Galaxy.

20.9.1 (2020-10-28)

• Bugfixes to work around & annotate expected tool test failures.

20.9.0 (2020-10-28)

• First release from the 20.09 branch of Galaxy.

20.9.0.dev2 (2020-08-02)

• First release from the 20.09 branch of Galaxy.

20.5.0 (2020-07-04)

• First release from the 20.05 branch of Galaxy.

20.1.0 (2020-07-04)

• First release from the 20.01 branch of Galaxy.

19.9.1 (2019-12-28)

• Fix declared dependency problem with package.

19.9.0 (2019-12-16)

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