galaxy-tool-util 24.1.1

Galaxy tool and tool dependency utilities

Overview

The Galaxy tool utilities.

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

History

24.1.1 (2024-07-02)

Bug fixes

• Fix bug in galaxy.xsd by @kostrykin in #17752

• Fix bug in assert_has_image_n_labels by @kostrykin in #17754

• Remove linter for unstripped text content for tool xml leaves by @bernt-matthias in #18252

Enhancements

• Add test and doc showing how dynamic selects are used by @bernt-matthias in #16885

• Add content assertion XML tags for test output verification using images by @kostrykin in #17581

• Set minimal metadata also for empty bed datasets by @wm75 in #17586

• Automatically bind galaxy_data_manager_data_path in containers by @bernt-matthias in #17596

• Type annotation improvements by @nsoranzo in #17601

• Type annotation and CWL-related improvements by @nsoranzo in #17630

• Update Python dependencies by @galaxybot in #17653

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

• Tool linter: check for valid bio.tools entries by @bernt-matthias in #17655

• Tool linter: check for leaf nodes with unstripped text content by @bernt-matthias in #17656

• Issue #17631: Make it possible to use custom invfile.lua if needed by @martin-g in #17693

• SQLAlchemy 2.0 by @jdavcs in #17778

• Add support for floating point TIFF files in verification of image-based tool outputs by @kostrykin in #17797

• Add tool linting for valid EDAM terms by @bernt-matthias in #17839

• Add pin_labels attribute for image_diff comparison method by @kostrykin in #17866

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

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

• Document syntax for accessing nested parameters in change_format - when tags by @bernt-matthias in #18018

• Update Python dependencies by @galaxybot in #18063

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

24.0.3 (2024-06-28)

Bug fixes

• Allow purge query param, deprecate purge body param by @mvdbeek in #18105

• Make sure that all Linter subclasses are imported for listing them by @bernt-matthias in #18339

• Assign default data extension on discovered collection output by @mvdbeek in #18389

• Allow in_range validator for selects by @bernt-matthias in #18403

24.0.2 (2024-05-07)

Bug fixes

• Tool linters: allow to skip by old linter names (by allowing to skip linter modules) by @bernt-matthias in #18091

• tool linters: output filters should only consider child filter nodes by @bernt-matthias in #18096

24.0.1 (2024-05-02)

Bug fixes

• Fix conditional Image imports by @mvdbeek in #17899

24.0.0 (2024-04-02)

Bug fixes

• xsd: reorder choices for permissive boolean by @bernt-matthias in #17187

• Allow for upper case container tags by @bernt-matthias in #17254

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

• Escape pipe character in tool XSD docs by @neoformit in #17359

• XSD schema doc building: quote pipe characters in attribute tables by @bernt-matthias in #17364

• Fix IUC best practices links, mention data_source_async in XSD by @wm75 in #17409

• Fix data_source and data_source_async bugs by @wm75 in #17422

• Add tool XML schema documention for outputs - collection - data by @bernt-matthias in #17465

• has_size assertion: implement size (as synonym for value) by @bernt-matthias in #17490

• Yaml nested assertions: fix parsing by @bernt-matthias in #17641

Enhancements

• build_mulled: also use namespace for building singularity images by @bernt-matthias in #15657

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

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

• Split linters in separate classes by @bernt-matthias in #17081

• Add select parameter with options from remote resources by @mvdbeek in #17087

• Replace discouraged Mambaforge with Miniforge3 by @nsoranzo in #17177

• Clarify the meaning of lexical sorting of discovered datasets by @bernt-matthias in #17190

• Migrate models to pydantic 2 by @mvdbeek in #17262

• Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357

• 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

• Some additional typing for test interactor stuff. by @jmchilton in #17398

• Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435

• data_column parameter: use column_names metadata if present by @bernt-matthias in #17478

• Fixing data_source tools and incrementing tool profile by @wm75 in #17515

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

• add shm_size based on ShmSize by @richard-burhans in #17565

• Record missing outputs as test errors by @bernt-matthias in #17874

Other changes

• consistently compare profile versions by @bernt-matthias in #16492

23.2.1 (2024-02-21)

Bug fixes

• Never consider _galaxy_ conda env as unused by @bernt-matthias in #16460

• chore: fix typos by @afuetterer in #16851

• Ruff and flake8 fixes by @nsoranzo in #16884

• Quote singularity env parameters by @bernt-matthias in #17055

• Remove duplicates when copying sections for tool panel view by @bernt-matthias in #17117

• Display application fixes and tests by @mvdbeek in #17233

Enhancements

• Implement default locations for data and collection parameters. by @jmchilton in #14955

• Add framework test for profile behavior of format=”input” by @bernt-matthias in #15482

• Tool Shed 2.0 by @jmchilton in #15639

• Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825

• Migrate a part of the users API to Fast API by @heisner-tillman in #16341

• Update Python dependencies by @galaxybot in #16436

• Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536

• Document that required text parameters need a validator by @bernt-matthias in #16538

• Include regex when linting validators by @davelopez in #16684

• Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by @ahmedhamidawan in #16739

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

• 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

• Remove remaining legacy backbone form input elements by @guerler in #16834

• Change api/tool_panel to api/tool_panels/… by @ahmedhamidawan in #16928

• optimize object store cache operations by @SergeyYakubov in #17025

• Enhance xsd schema and allow simpler assertion lists by @mvdbeek in #17134

Other changes

• Merge 23.1 into dev by @mvdbeek in #16534

• Explicitly document default of multiple by @bernt-matthias in #16625

23.1.4 (2024-01-04)

Bug fixes

• Separate collection and non-collection data element by @mvdbeek in #17236

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.