galaxy-tool-util 25.0.1

Galaxy tool and tool dependency utilities

Overview

The Galaxy tool utilities.

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

History

25.0.1 (2025-06-20)

Bug fixes

• Fix single data element identifier to be a regular string by @mvdbeek in #20438

• Relax validation of XML test assertion parsing by @mvdbeek in #20511

• Fix import of galaxy.tool_util.cwl module by @nsoranzo in #20529

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

• Alternative format_source fix by @mvdbeek in #19395

• Fix test_mulled_build.py::test_mulled_build_files_cli with use_mamba=True by @kysrpex in #19545

• Fix incorrect type in tool_util.deps and fix package structure. by @jmchilton in #19702

• Add linter argument to linter report function calls by @bernt-matthias in #19708

• Fix linting with markdown in tool help by @bgruening in #20058

• Yaml parser fixes part2 by @mvdbeek in #20162

• Fix conda_link to use platform.machine() for architecture detection by @chrisagrams in #20381

• Add job config variable for singularity –contain by @bernt-matthias in #20400

Enhancements

• Dynamic options: add data table filter by @bernt-matthias in #12941

• Isolate singularity containers more thoroughly for better reproducibility. by @rhpvorderman in #18628

• Implement tool markdown reports. by @jmchilton in #19054

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

• Misc fixes 202412 by @nsoranzo in #19341

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

• Make conditional discriminators literals instead of generic string/bool by @mvdbeek in #19374

• 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

• Allow controlling strict channel priority in mulled-build by @bernt-matthias in #19425

• Document $__user_name__ by @bernt-matthias in #19433

• Add User-Defined Tools by @mvdbeek in #19434

• Type annotations improvements by @nsoranzo in #19442

• Type annotation improvements by @nsoranzo in #19485

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

• Mention default values for truevalue and falsevalue by @pvanheus in #19657

• Refactor dependencies for tool output actions. by @jmchilton in #19662

• Define simple models for job messages. by @jmchilton in #19688

• Add forgotten linter test by @bernt-matthias in #19690

• Speedup mulled build test by @bernt-matthias in #19712

• ToolShed2 - Add more context when navigating between tools an repositories. by @jmchilton in #19738

• Improvements to package decomposition. by @jmchilton in #19759

• Rename tool “Citations” to “References” by @nsoranzo in #19770

• Allow overriding datatypes for planemo lint by @selten in #19780

• xsd: use CollectionType for collections in tests by @bernt-matthias in #19802

• Add basic support for icons in tools by @davelopez in #19850

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

• Improve docs for output filters by @bernt-matthias in #19904

• Fix local import in __resolvers_dict by @mvdbeek in #19944

• Update Python dependencies by @galaxybot in #19964

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

• Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008

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

• Yaml parser fixes and improvements (part 1) by @mvdbeek in #20158

• Add more descriptions to custom tool source schema by @mvdbeek in #20266

24.2.4 (2025-06-17)

Bug fixes

• Fix #19515 - invalid citation handling changed with 24.2. by @jmchilton in #19716

• Drop unused alembic-utils from galaxy-data package requirements by @nsoranzo in #19896

• Report TestCaseValidation as linter error for 24.2 and above by @bernt-matthias in #19928

• Fix various parameter validation issues. by @jmchilton in #19949

• Fix mulled-search –destination quay, add index reuse by @natefoo in #20107

• Fix DataCollectionParameterModel factory by @mvdbeek in #20164

• Fix mull_targets() with mamba 2.x by @nsoranzo in #20416

24.2.3 (2025-03-16)

Bug fixes

• Fix parameter model constructions with leading underscores, fixes converter linting by @mvdbeek in #19790

24.2.2 (2025-03-08)

Bug fixes

• add missing linter name argument to linter report function calls by @bernt-matthias in #19707

• Assertion linter fixes by @jmchilton in #19715

• Fix dataypes linter: allow auto for output tags by @bernt-matthias in #19757

Enhancements

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

24.2.1 (2025-02-28)

Bug fixes

• Fix mulled tests by @nsoranzo in #19626

• xsd: fix format by @bernt-matthias in #19683

• Fix validation of required floats specified as empty strings in tool XML. by @jmchilton in #19701

• Fix container building by @bernt-matthias in #19714

24.2.0 (2025-02-11)

Bug fixes

• Fix some deprecations by @nsoranzo in #18433

• Fix handling of v2 hashes by @bernt-matthias in #18522

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

• Handle output parsing when tool is not available for tool-centric API. by @jmchilton in #18643

• Fix new flake8-bugbear B039 and mypy type-var errors by @nsoranzo in #18755

• Fix commas that shouldn’t be in biotools_mappings.tsv by @jmchilton in #18919

• Allow modes z and Z for docker volumes by @bernt-matthias in #18998

• Add requirement/resource to schema docs by @bernt-matthias in #19172

• Fix mulled_hash by @bernt-matthias in #19199

• Outputs filter linter fixes by @bernt-matthias in #19208

• Replace mambaforge Docker image with miniforge3 by @nsoranzo in #19327

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

• Backport fix for test_singularity_container_test test by @nsoranzo in #19349

• Remove unnecessary quoting in conda package specification by @nsoranzo in #19382

• Fix timeout handling for planemo / galaxy-tool-util by @mvdbeek in #19384

• Fix for empty string in regex validator message. by @jmchilton in #19387

• mulled-build-tool fix for packages wo version by @bernt-matthias in #19450

• Fix parsing of validators with inf limits by @mvdbeek in #19459

• Remove print statement by @bernt-matthias in #19469

• Downgrade ‘InteractiveTools are not enabled’ to warning by @mvdbeek in #19518

Enhancements

• Add linters for datatypes by @bernt-matthias in #17600

• Update Python dependencies by @galaxybot in #18406

• Stray small changes from structured_tool_state branch. by @jmchilton in #18453

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

• Mixed enhancements from CWL branch by @nsoranzo in #18539

• Implement Declarative Testing for Workflow Behaviors by @jmchilton in #18542

• Improvements to Tool Test Parsing by @jmchilton in #18560

• More tool test typing. by @jmchilton in #18590

• Parameter Model Improvements by @jmchilton in #18641

• Another round of parameter model improvements. by @jmchilton in #18673

• De-couple XML from tool interface for test collections. by @jmchilton in #18676

• Another round of parameter model enhancements and tool tests by @jmchilton in #18678

• Dynamic Models for Tool Test Validation by @jmchilton in #18679

• Improvements to help terms & tool help. by @jmchilton in #18722

• Implement tool upgrade assistant. by @jmchilton in #18728

• Improvements to parameter models for test case inputs by @jmchilton in #18743

• Remove defaults channel for conda usage by @bernt-matthias in #18757

• Modelling for Test Assertions by @jmchilton in #18787

• Workflow Landing Requests by @jmchilton in #18807

• Add docs on indexing for filter column by @bernt-matthias in #18844

• Implement Pydantic model for workflow test format. by @jmchilton in #18884

• Improvements to Planemo test format based on feedback/discussions. by @jmchilton in #18889

• Add support for arbitrarily ordered image axes in image content assertions by @kostrykin in #18891

• Remove some unused dynamic drill down options. by @jmchilton in #18892

• Type annotations and fixes by @nsoranzo in #18911

• Add filter null collection operation tool by @mvdbeek in #18928

• Assert that data_column parameters have a valid data_ref by @bernt-matthias in #18949

• More concise, readable tool execution testing. by @jmchilton in #18977

• Workflow landing improvements by @mvdbeek in #18979

• Add hint to the tool schema about runtime conditional changes by @martenson in #18996

• A variety of improvements around tool parameter modeling (second try) by @jmchilton in #19027

• Better logging around tool loading by @jmchilton in #19029

• Update Python dependencies by @galaxybot in #19031

• Integrate Tool Parameter Modeling into Linting (for Planemo) by @jmchilton in #19073

• Allow deferred datasets to behave as URIs by @davelopez in #19077

• Implement workflow parameter validators. by @jmchilton in #19092

• Enable specifying dataset hash in test jobs by @mvdbeek in #19113

• Add linter to check validity of output filters by @bernt-matthias in #19114

• Also use miniforge docker for container building by @bernt-matthias in #19128

• Fix default value handling for parameters connected to required parameters by @mvdbeek in #19219

24.1.4 (2024-12-11)

Bug fixes

• Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510

• xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605

• Remove defaults channel for conda usage by @bernt-matthias in #18859

• Don’t check availability of shellescape by @nsoranzo in #18954

• Backport 2 CI fixes by @nsoranzo in #18973

• Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

• Fix extra call to test_data_path that requires an admin key by @jmchilton in #19011

• flip default value for use_mamba to false by @bgruening in #19295

• Linter: allow dynamic option definition by from_url by @bernt-matthias in #19300

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

24.1.3 (2024-10-25)

Bug fixes

• Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510

• xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605

• Remove defaults channel for conda usage by @bernt-matthias in #18859

• Don’t check availability of shellescape by @nsoranzo in #18954

• Backport 2 CI fixes by @nsoranzo in #18973

• Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

• Fix extra call to test_data_path that requires an admin key by @jmchilton in #19011

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

24.1.2 (2024-09-25)

Bug fixes

• Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510

• xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

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.