History ------- .. to_doc --------- 26.1.dev0 --------- ------------------- 25.1.2 (2026-03-09) ------------------- ========= Bug fixes ========= * Properly parse build info from requirement info by `@bernt-matthias `_ in `#21481 `_ * Fix loading non-tool files from watched tool directories by `@mvdbeek `_ in `#21880 `_ ------------------- 25.1.1 (2026-02-03) ------------------- ========= Bug fixes ========= * Fix data manager .loc file selection logic by `@jdavcs `_ in `#21664 `_ ============ Enhancements ============ * Document security considerations for using secrets by `@bernt-matthias `_ in `#21654 `_ ============= Other changes ============= * Improve tempdir cleanup in integration tests by `@mvdbeek `_ in `#21520 `_ ------------------- 25.1.0 (2025-12-12) ------------------- ========= Bug fixes ========= * Check for ``format="input"`` as well as ``format="auto"`` in datatype linter by `@bernt-matthias `_ in `#20177 `_ * Test and fix CORS on exceptions by `@mvdbeek `_ in `#21105 `_ * Apply tool test timeout only once by `@bernt-matthias `_ in `#21246 `_ * Update the mulled.py script to check json output by `@nilchia `_ in `#21276 `_ * Use anaconda API to find package download URL by `@nsoranzo `_ in `#21360 `_ ============ Enhancements ============ * Support credentials(secrets/variables) in tool requirements by `@arash77 `_ in `#19084 `_ * Implement Sample Sheets by `@jmchilton `_ in `#19305 `_ * Prepare ``ToolBox.dynamic_tool_to_tool()`` for CWL formats by `@nsoranzo `_ in `#20364 `_ * Type annotation fixes for mypy 1.16.0 by `@nsoranzo `_ in `#20424 `_ * Remove deprecated tool document cache by `@nsoranzo `_ in `#20510 `_ * Implement Data Landing Requests by `@jmchilton `_ in `#20592 `_ * Clean up code from pyupgrade by `@nsoranzo `_ in `#20642 `_ * Add markdown hint to schema by `@bgruening `_ in `#20654 `_ * Add configfiles support and various enhancements for user defined tools by `@mvdbeek `_ in `#20761 `_ * Add support for hierarchical module systems in lmod + module dependency resolvers by `@t1mk1k `_ in `#20866 `_ * Small cleanup of tool execution code. by `@jmchilton `_ in `#20899 `_ * Add support for picking ``from_work_dir`` directory by `@mvdbeek `_ in `#20916 `_ * Allow addressing user defined tools in job config by `@mvdbeek `_ in `#20932 `_ * Wire up and test resource requirement via tpv by `@mvdbeek `_ in `#20936 `_ * Allow specifying a command for determining a docker host port by `@natefoo `_ in `#20953 `_ * Use workflow-style payload in data landing request by `@mvdbeek `_ in `#21107 `_ * Update tool profile version for credentials by `@davelopez `_ in `#21273 `_ ============= Other changes ============= * Merge `release_25.0` into `dev` by `@davelopez `_ in `#20484 `_ ------------------- 25.0.4 (2025-11-18) ------------------- ========= Bug fixes ========= * Fix has_size assertion by `@bernt-matthias `_ in `#21081 `_ * Fix workflow run form input restrictions by `@mvdbeek `_ in `#21095 `_ * Fix direct tool execution not using the latest version by `@jmchilton `_ in `#21240 `_ ------------------- 25.0.3 (2025-09-23) ------------------- ========= Bug fixes ========= * Fix collection element sorting in extended_metadata by `@mvdbeek `_ in `#20928 `_ ------------------- 25.0.2 (2025-08-13) ------------------- ========= Bug fixes ========= * Fix restricting user defined tool input datasets extensions by `@mvdbeek `_ in `#20545 `_ * Don't fail volume mount construction for tools without tool directory by `@mvdbeek `_ in `#20593 `_ * Input linter: add missing attribute to `sort_by` by `@bernt-matthias `_ in `#20693 `_ * Fix ``test_base_image_for_targets`` mulled test to use mzmine by `@nsoranzo `_ in `#20713 `_ ------------------- 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.