Fix ToolExpressionOutput.to_model() for boolean type. by @jmchilton in #22038

Fix `base_image_for_targets()` for newer conda search output by @nsoranzo in #23496

Backport mulled cache seeding to fix flaky integration tests by @mvdbeek in #23541

Fix CI failures and flaky tests by @mvdbeek in #24028

Skip Quay search tests on runtime API outages by @mvdbeek in #24432

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

Fix data manager .loc file selection logic by @jdavcs in #21664

Document security considerations for using secrets by @bernt-matthias in #21654

Improve tempdir cleanup in integration tests by @mvdbeek in #21520

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

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

Merge release_25.0 into dev by @davelopez in #20484

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

Fix collection element sorting in extended_metadata by @mvdbeek in #20928

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

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

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

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

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

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

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

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

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

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

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

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

Make default_panel_view a _by_host option by @natefoo in #18471

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

Make default_panel_view a _by_host option by @natefoo in #18471

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

Make default_panel_view a _by_host option by @natefoo in #18471

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

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

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

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

Fix conditional Image imports by @mvdbeek in #17899

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

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

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

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

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

Merge 23.1 into dev by @mvdbeek in #16534

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

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

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

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

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

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

Restore tmp mounting by @mvdbeek in #16533

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

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

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

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

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

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

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