23.0

Enhancements

• Add AWS Batch runner (thanks to @qiagu). Pull Request 13466

• Implement initial GA4GH DRS Support (thanks to @jmchilton). Pull Request 13949

• Add support for sorting contents in data libraries (thanks to @davelopez). Pull Request 14300

• Feature: Advanced Tool Search Menu (thanks to @ahmedhamidawan). Pull Request 14391

• Add “Datatypes” Page (thanks to @ElectronicBlueberry). Pull Request 14464

• A replacement for manage_db.sh + rewrite of migration system documentation (thanks to @jdavcs). Pull Request 14537

• Adding Bulk Datatype Change to Collection Edit (thanks to @assuntad23). Pull Request 14646

• History drag and drop (thanks to @itisAliRH). Pull Request 14659

• Enable fine-grained celery configuration (thanks to @jdavcs). Pull Request 14708

• visjs-based transition system visualization (thanks to @xtrojak). Pull Request 14766

• feat: mamba support for mulled-build (thanks to @johanneskoester). Pull Request 14770

• implement undeleting a workflow (thanks to @martenson). Pull Request 14794

• 6493/feature/undelete workflows (thanks to @assuntad23). Pull Request 14816

• Add task-based history export tracking (thanks to @davelopez). Pull Request 14839

• Implement conditional workflow steps (thanks to @mvdbeek). Pull Request 14846

• Add global drag and drop upload (thanks to @ElectronicBlueberry). Pull Request 14905

• Add interactive tool for Mgnify Jupyter lab (thanks to @bebatut). Pull Request 14950

• Fix subworkflow map-over (thanks to @mvdbeek). Pull Request 14954

• pinia-based store for active IT entry points (thanks to @martenson). Pull Request 15030

• Add interactive tool for Pavian

(thanks to @bebatut). Pull Request 15068

• Add autogenerated typescript API client & use it (thanks to @mvdbeek). Pull Request 15106

• Filter Inputs and Outputs in HistoryPanel (thanks to @ahmedhamidawan). Pull Request 15210

• Add Theme support (thanks to @ElectronicBlueberry). Pull Request 15252

• Modernize workflow editor state handling (thanks to @mvdbeek). Pull Request 15268

• Implement conditional workflow editor UI, optional connections, track and display invalid connections (thanks to @mvdbeek). Pull Request 15328

• Fix x-accel-redirect handling and implement byte-range handling (thanks to @mvdbeek). Pull Request 14990

• Enable conversion of bz2 files to gz in converter (thanks to @mvdbeek). Pull Request 15590

• Replace pysam in converters by command line tools (thanks to @bernt-matthias). Pull Request 13411

• Add datatypes for Sybila tools (thanks to @xtrojak). Pull Request 14362

• Add CASTEP datatypes (thanks to @mvdbeek). Pull Request 14504

• Remove legacy tool shed datatype handling (thanks to @jmchilton). Pull Request 14617

• Add support for the PSL data format (thanks to @gregvonkuster). Pull Request 14813

• Add ludwig report datatype (thanks to @qiagu). Pull Request 14903

• Display model diagram for h5mlm datatype (thanks to @qiagu). Pull Request 14992

• Enable Tabix download + New datatype JuicerMediumTabix in 22.05 (thanks to @lldelisle). Pull Request 15024

• Type hints for datatypes (thanks to @jdavcs). Pull Request 15052

• Add wiff2 composite/tar datatypes (thanks to @neoformit). Pull Request 15249

• Add linting with ruff (thanks to @nsoranzo). Pull Request 15315

• Add ecology type section + hdr and bil datatypes (thanks to @yvanlebras). Pull Request 15337

• add xsd datatype (thanks to @bernt-matthias). Pull Request 15344

• Update interactivetool_ml_jupyter_notebook.xml (thanks to @anuprulez). Pull Request 15297

• Support empty compressed dataset in filter_empty_datasets tool (thanks to @mvdbeek). Pull Request 14360

• Type annotations for base toolbox functionality. (thanks to @jmchilton). Pull Request 14629

• Improve performance for rendering and changing large workflows (thanks to @mvdbeek). Pull Request 15776

• Display dialog when saving workflow with invalid connections (thanks to @mvdbeek). Pull Request 15817

• Find correct collection type if collection_type_source points at input of “any” collection type (thanks to @mvdbeek). Pull Request 15823

• Mark disconnected required inputs in editor (thanks to @mvdbeek). Pull Request 15357

• Add workflow invocations link to email template (thanks to @hujambo-dunia). Pull Request 14062

• Add Workflow Invocation Tabs (thanks to @davelopez). Pull Request 14069

• Add some type annotations (thanks to @nsoranzo). Pull Request 14356

• Implement RO Crate export of Galaxy histories and invocations (thanks to @jmchilton). Pull Request 14595

• Bring BioCompute exports under invocation export framework (thanks to @jmchilton). Pull Request 14620

• Enable simplified workflow with optional disconnected data inputs (thanks to @mvdbeek). Pull Request 14643

• Add some type annotations to workflow-related code (thanks to @nsoranzo). Pull Request 14717

• TRS import via URL (thanks to @fbacall). Pull Request 14927

• Order steps relation of workflow_invocation by order_index (thanks to @jmchilton). Pull Request 14946

• Fix all B027 errors reported by new flake8-bugbear (thanks to @nsoranzo). Pull Request 14952

• Improve type annotations for model store (thanks to @nsoranzo). Pull Request 15081

• Misc fixes 202301 (thanks to @nsoranzo). Pull Request 15275

• Client build performance tweak backport (thanks to @dannon). Pull Request 15911

• Allow configuring webpack devserver port (thanks to @mvdbeek). Pull Request 15379

• Client README updates, watch/serve tweaks (thanks to @dannon). Pull Request 15380

• Convert Client to Single Page application (thanks to @guerler). Pull Request 13984

• Upgrade to Vue2.7 (thanks to @dannon). Pull Request 14250

• Better tabular/csv file splitting (thanks to @dannon). Pull Request 14396

• Add and document make target for skipping the client build (thanks to @ElectronicBlueberry). Pull Request 14404

• Add “About this Galaxy” page (thanks to @dannon). Pull Request 14461

• Tool form improvements (thanks to @ElectronicBlueberry). Pull Request 14549

• Use hsluv to generate colors instead of hsl (thanks to @ElectronicBlueberry). Pull Request 14587

• Upgrade vue2-jest to 29.1.0 (thanks to @ElectronicBlueberry). Pull Request 14623

• Add minimal tsconfig for type completion (thanks to @ElectronicBlueberry). Pull Request 14741

• Test upgrade to bootstrap-vue 2.23 (thanks to @dannon). Pull Request 14850

• New nodejs LTS - 18 (thanks to @dannon). Pull Request 14901

• Upgrade vue-router to latest 3x series for composition api usage (thanks to @dannon). Pull Request 14916

• Pinia history store init (thanks to @itisAliRH). Pull Request 15049

• Set accessible default font (thanks to @ElectronicBlueberry). Pull Request 15062

• Typescript configuration updates, integration with vue and the primary app (thanks to @dannon). Pull Request 15097

• TS config and linting tweaks (thanks to @dannon). Pull Request 15121

• Upgrade Jest from v27 to v29 (thanks to @dannon). Pull Request 15126

• Standardize local package imports with @ alias in TypeScript (thanks to @dannon). Pull Request 15169

• Properly annotate model_class fields as const and required in openAPI schema (thanks to @mvdbeek). Pull Request 15173

• Bump json5 from 1.0.1 to 1.0.2 in /client (thanks to @galaxyproject). Pull Request 15270

• Increase memory limit of dev server (thanks to @ElectronicBlueberry). Pull Request 15334

• Update prettier (thanks to @ElectronicBlueberry). Pull Request 15335

• Preliminary prebuilt client support (thanks to @dannon). Pull Request 15339

• Adding GPU support to Galaxy (thanks to @gulsumgudukbay). Pull Request 12775

• Improved logging for some flakey integration tests (thanks to @jmchilton). Pull Request 14117

• Add some integration tests for the job files API (thanks to @jmchilton). Pull Request 14137

• Deprecate cluster_files_directory and store DRMAA job template and PBS shell, error and out files in job working directory (thanks to @bernt-matthias). Pull Request 14430

• Refactor dynamic destination mapper (thanks to @qiagu). Pull Request 14472

• Misc fixes 202208 (thanks to @nsoranzo). Pull Request 14524

• Configurable get IP method for container monitor (thanks to @natefoo). Pull Request 14695

• Update pulsar-galaxy-lib to 0.14.16 (thanks to @jmchilton). Pull Request 14748

• Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes (thanks to @jmchilton). Pull Request 14777

• Allow LSF Cli submission to detect walltime reached (thanks to @selten). Pull Request 14917

• Replace XML job conf sample with YAML (thanks to @natefoo). Pull Request 15018

• Use sentry-fastapi integration, expose sampling rate (thanks to @mvdbeek). Pull Request 15553

• Add documentation how to avoid data modification by tools (thanks to @bernt-matthias). Pull Request 14239

• Update docs on adding Python dependencies (thanks to @nsoranzo). Pull Request 14593

• Allow path-based interactive tools using nginx proxy (thanks to @sveinugu). Pull Request 14694

• Extend security docs (thanks to @bernt-matthias). Pull Request 14740

• Dev html email (thanks to @neoformit). Pull Request 14825

• Add LDAP authenticator variant using ldap3 package (thanks to @mahendrapaipuri). Pull Request 14849

• Updated docs with nginx config for upstream proxy of path-based Interactive tools (thanks to @sveinugu). Pull Request 15227

• Move theme selector to user preferences (thanks to @guerler). Pull Request 15256

• Fix history annotation filtering: make it case insensitive (thanks to @davelopez). Pull Request 15897

• Backport - Use Animation Frame in Workflow Editor (thanks to @ElectronicBlueberry). Pull Request 15751

• Workflow Editor Minimap Performance (thanks to @ElectronicBlueberry). Pull Request 15754

• Add option to disable the fetch_data celery task (thanks to @jdavcs). Pull Request 15767

• Dataset Counts Toggle (thanks to @dannon). Pull Request 15810

• Fix Invocation RO-Crate metadata (thanks to @pauldg). Pull Request 15841

• Make options text clear for datasets list (thanks to @davelopez). Pull Request 15410

• Reduce workflow tool form request frequency (thanks to @guerler). Pull Request 15426

• Workflow editor minimap rework (thanks to @ElectronicBlueberry). Pull Request 15463

• More comfortable initial pan for workflow editor (thanks to @dannon). Pull Request 15466

• Test validators for optional parameters (thanks to @ElectronicBlueberry). Pull Request 15491

• More responsive clientside search (thanks to @dannon). Pull Request 15545

• Automatically sort tools in sections by name (thanks to @dannon). Pull Request 12288

• Add duplicate_file_to_collection tool (thanks to @simonbray). Pull Request 12999

• Report resolution cache miss for galaxy.tool_util.deps.container_reso… (thanks to @brinkmanlab). Pull Request 13608

• expect_test_failure: also test if no failure was found (thanks to @bernt-matthias). Pull Request 13815

• Drop nose (thanks to @nsoranzo). Pull Request 13909

• Allow any as value for boolean default parameters in filter text (thanks to @guerler). Pull Request 13973

• Implement initial tool shed API tests (thanks to @jmchilton). Pull Request 13977

• New history multiple view (thanks to @itisAliRH). Pull Request 13985

• Refactor uses_shed.py so test_base doesn’t depend on galaxy-app (thanks to @jmchilton). Pull Request 14010

• Rename samples_tool_conf to sample_tool_conf (thanks to @dannon). Pull Request 14035

• Slightly modernized and standardized API error handling (thanks to @jmchilton). Pull Request 14118

• Combine Convert and Datatypes forms (thanks to @hujambo-dunia). Pull Request 14159

• Decouple galaxy-app and galaxy-selenium (thanks to @jmchilton). Pull Request 14188

• Update Python dependencies (thanks to @galaxybot). Pull Request 14195

• Upgrade to Selenium 4.3.0 (thanks to @jmchilton). Pull Request 14207

• Enhance history ContentItem buttons appearance (thanks to @ahmedhamidawan). Pull Request 14222

• Enhance library folder contents search API (thanks to @davelopez). Pull Request 14236

• Improve robustness of tus upload and calculation of progress (thanks to @mvdbeek). Pull Request 14246

• add doc and linting for test output compare attribute (thanks to @bernt-matthias). Pull Request 14247

• Relocate dynamic outputs for CWL jobs (thanks to @nsoranzo). Pull Request 14254

• Replace CoC with link to new webpage (thanks to @nsoranzo). Pull Request 14327

• Update WorkflowInvocationExportOptions.vue (thanks to @biocompute-objects). Pull Request 14333

• Try fixing Gitpod configuration? (thanks to @jmchilton). Pull Request 14350

• Add bio.tools ids for 2000 tools (thanks to @astrovsky01). Pull Request 14366

• Mark galaxy packages as containing typing information (thanks to @mr-c). Pull Request 14367

• type hints that cwltool used to carry (thanks to @mr-c). Pull Request 14368

• BCODB submit form (thanks to @biocompute-objects). Pull Request 14374

• Remove schema-salad pin (thanks to @mr-c). Pull Request 14379

• Update Python dependencies (thanks to @galaxybot). Pull Request 14385

• Allow sort order for sort_by to be reversed (thanks to @pvanheus). Pull Request 14389

• Data Libraries - Change “Export to History” to “Send to History” (thanks to @ahmedhamidawan). Pull Request 14393

• Warn users if History is not being watched (thanks to @ahmedhamidawan). Pull Request 14397

• Update Python dependencies (thanks to @galaxybot). Pull Request 14409

• Remove Button Morphing during Tool Installation (thanks to @ElectronicBlueberry). Pull Request 14413

• Present unavailable options to logged-out users (thanks to @ElectronicBlueberry). Pull Request 14419

• Improve dynamic option filter efficiency (thanks to @qiagu). Pull Request 14439

• Update Python dependencies (thanks to @galaxybot). Pull Request 14448

• Hide Disabled Installation Actions for Tool Installations (thanks to @ElectronicBlueberry). Pull Request 14474

• Primary analysis interface a11y fixes (thanks to @dannon). Pull Request 14481

• API key enhancements (thanks to @itisAliRH). Pull Request 14489

• Update Python dependencies (thanks to @galaxybot). Pull Request 14490

• Register admin routes in vue router (thanks to @guerler). Pull Request 14499

• Place security policy in canonical location (thanks to @mvdbeek). Pull Request 14503

• Various small Python typing improvements and fixes (thanks to @jmchilton). Pull Request 14508

• Update Python dependencies (thanks to @galaxybot). Pull Request 14521

• Revise masthead route handling and component (thanks to @guerler). Pull Request 14523

• Frontend tool search bug fix (thanks to @hujambo-dunia). Pull Request 14529

• Report that (text) datatype test files need to have a final newline (thanks to @mvdbeek). Pull Request 14532

• Re-license under MIT all work from 2021-04-07 onwards (thanks to @nsoranzo). Pull Request 14540

• Implement keyedColorScheme for all tags, not only nametags (thanks to @ahmedhamidawan). Pull Request 14542

• Remove more dead code from tool shed (thanks to @jmchilton). Pull Request 14551

• Include HID count in quick history menu switcher (thanks to @ahmedhamidawan). Pull Request 14552

• More API tests for the tool shed (thanks to @jmchilton). Pull Request 14553

• Use active attribute for some dropdown menus (thanks to @ElectronicBlueberry). Pull Request 14561

• Remove broken tool shed API endpoint (thanks to @jmchilton). Pull Request 14562

• Update Python dependencies (thanks to @galaxybot). Pull Request 14567

• Add config option for post logout redirect url (thanks to @guerler). Pull Request 14570

• Drop GitHub workflow for legacy history Selenium tests (thanks to @nsoranzo). Pull Request 14571

• Implement API endpoint for calculating dataset hashes asynchronously (thanks to @jmchilton). Pull Request 14576

• Some additional typing for galaxy.util.path (thanks to @jmchilton). Pull Request 14598

• Update Python dependencies (thanks to @galaxybot). Pull Request 14599

• linter: check for inputs with duplicated names (thanks to @bernt-matthias). Pull Request 14604

• Adapt invocation export UI for plugins (thanks to @davelopez). Pull Request 14606

• Remove unused tool shed functions (thanks to @jmchilton). Pull Request 14612

• More tool shed API tests (+fixes) (thanks to @jmchilton). Pull Request 14616

• Headings Changes and Heading Component (thanks to @ElectronicBlueberry). Pull Request 14622

• Improvements to mypy setup (thanks to @jmchilton). Pull Request 14626

• Update Python dependencies (thanks to @galaxybot). Pull Request 14650

• indicate history name in collection navigation (thanks to @itisAliRH). Pull Request 14655

• ToolShedApp for more correct typing in tool shed code (thanks to @jmchilton). Pull Request 14656

• Some more typing for test populators (thanks to @jmchilton). Pull Request 14657

• Cleanup Tool Shed Tests (thanks to @jmchilton). Pull Request 14662

• add scroll shadow on the right and left sides (thanks to @itisAliRH). Pull Request 14665

• More cleanup of tool shed tests (thanks to @jmchilton). Pull Request 14672

• Replace unittest.TestCase with pytest-based partial re-implementation (thanks to @nsoranzo). Pull Request 14679

• More typing and unit testing for tool test verification functions (thanks to @jmchilton). Pull Request 14691

• Migrate more tool shed functional testing to Galaxy API (thanks to @jmchilton). Pull Request 14693

• Update Python dependencies (thanks to @galaxybot). Pull Request 14696

• Removed unnecessary page reload on the workflow list page (thanks to @shubham4315). Pull Request 14699

• Prevent number inputs (in tool forms) from binding wheel events. (thanks to @dannon). Pull Request 14704

• Change ToolPanel search to client side and Advanced search to backend (thanks to @ahmedhamidawan). Pull Request 14707

• Outline modernizing tool shed repositories API (thanks to @jmchilton). Pull Request 14719

• Disable multi-view create hook hiding toolbox. (thanks to @dannon). Pull Request 14729

• Migrate index and show tool shed repositories endpoints to Pydantic and FastAPI (thanks to @jmchilton). Pull Request 14736

• Update Python dependencies (thanks to @galaxybot). Pull Request 14745

• Make HTTP request object available to AuthManager (thanks to @mahendrapaipuri). Pull Request 14776

• Skip 2 unit tests if bio.tools is down (thanks to @nsoranzo). Pull Request 14782

• Update tool recommendation API using transformers (neural network) (thanks to @anuprulez). Pull Request 14791

• Make connect_args for SQLAlchemy’s engine configurable (thanks to @jdavcs). Pull Request 14792

• Update Python dependencies (thanks to @galaxybot). Pull Request 14800

• Disable integrity check for CWL relocate script (thanks to @nsoranzo). Pull Request 14804

• Replace set-output commands with $GITHUB_OUTPUT environment file in GitHub workflows (thanks to @nsoranzo). Pull Request 14806

• Move base tool data infrastructure into tool_util package (thanks to @jmchilton). Pull Request 14822

• Add client tests for login components (thanks to @guerler). Pull Request 14842

• Update Python dependencies (thanks to @galaxybot). Pull Request 14844

• Fix tool linting with comments (thanks to @davelopez). Pull Request 14845

• Add type annotations to config_manage.py (thanks to @nsoranzo). Pull Request 14847

• Visible marker to distinguish required/optional tool params (thanks to @ElectronicBlueberry). Pull Request 14861

• bugfix and UX enh. for tool form footer (thanks to @martenson). Pull Request 14865

• Visually show which parameters belong to a conditional (thanks to @ElectronicBlueberry). Pull Request 14866

• Update release-next to 23.0 (thanks to @dannon). Pull Request 14867

• Move model/mapping utils into packaged code for reuse by the tool shed (thanks to @jmchilton). Pull Request 14881

• Install latest miniconda and conda. Enable libmamba solver (thanks to @nsoranzo). Pull Request 14882

• Update Python dependencies (thanks to @galaxybot). Pull Request 14888

• Simplify and speed up converter testing (thanks to @mvdbeek). Pull Request 14891

• i18n of login and register forms (thanks to @martenson). Pull Request 14921

• Add automated tests for presenting unavailable options to logged-out users (thanks to @ElectronicBlueberry). Pull Request 14925

• Create traceback.txt when external metadata fails (thanks to @mvdbeek). Pull Request 14932

• New Tag component based on VueMultiselect (thanks to @ElectronicBlueberry). Pull Request 14936

• Fix deprecation of ProcessPool.schedule() since pebble 5.0 (thanks to @nsoranzo). Pull Request 14944

• Add types to galaxy/util/zipstream.py (thanks to @jmchilton). Pull Request 14945

• Small change to job runner docs to state more explicitly what check_watched_item() should return (thanks to @simonbray). Pull Request 14947

• lint for coexisting expect_num_outputs and expect_failure (thanks to @bernt-matthias). Pull Request 14959

• Type annotations and refactorings of input staging (thanks to @nsoranzo). Pull Request 14963

• Update cwltool pin (thanks to @nsoranzo). Pull Request 14964

• bonus Python typing (thanks to @mr-c). Pull Request 14971

• Vuetify published histories (thanks to @itisAliRH). Pull Request 14985

• Use TypeScript for rule specification tests (thanks to @jmchilton). Pull Request 15001

• add GH private reporting option to security policy (thanks to @galaxyproject). Pull Request 15003

• Run mypy on a fully loaded galaxy venv for stricter type checking (thanks to @jdavcs). Pull Request 15004

• Add composable confirmation dialog (thanks to @davelopez). Pull Request 15008

• Unify Composable Naming and add Documentation (thanks to @ElectronicBlueberry). Pull Request 15012

• Update Gravity version to 1.0.0 pre-release (thanks to @natefoo). Pull Request 15017

• Use APITestCase class to run framework tool tests (thanks to @mvdbeek). Pull Request 15028

• Infrastructure for indicating Galaxy features being used by tests (thanks to @jmchilton). Pull Request 15031

• Update Python dependencies (thanks to @galaxybot). Pull Request 15033

• Prefill bug reports with current user’s email (thanks to @hujambo-dunia). Pull Request 15042

• Typing and other small improvements to tool plumbing (thanks to @jmchilton). Pull Request 15051

• Convert Checkbox component to Vue (thanks to @hujambo-dunia). Pull Request 15054

• Address some of the new mypy notes about unchecked annotations (thanks to @jmchilton). Pull Request 15069

• Type some of tool test parsing code (thanks to @jmchilton). Pull Request 15079

• Bring Multi History Shadows to Front and Adjust Content Item Color (thanks to @ElectronicBlueberry). Pull Request 15092

• Add pkce to dev/test requirements (thanks to @nsoranzo). Pull Request 15095

• Fix broken resubmission_job_conf.xml reference in documentation (thanks to @abueg). Pull Request 15096

• Sort library folders by name by default (thanks to @davelopez). Pull Request 15099

• Enhance RO-Crate export of Galaxy invocations (thanks to @davelopez). Pull Request 15101

• Update Python dependencies (thanks to @galaxybot). Pull Request 15104

• Implement tool data bundles (thanks to @jmchilton). Pull Request 15129

• Advanced tool search results page design changes (thanks to @ElectronicBlueberry). Pull Request 15134

• Warning when importing published history by URL (thanks to @ElectronicBlueberry). Pull Request 15149

• Build package script, reset package versions (thanks to @mvdbeek). Pull Request 15150

• Add Front-End Styleguide (thanks to @ElectronicBlueberry). Pull Request 15154

• Security policy update – using github advisories (thanks to @dannon). Pull Request 15158

• Update Python dependencies (thanks to @galaxybot). Pull Request 15166

• Make weasyprint requirements a bit clearer (thanks to @wm75). Pull Request 15175

• Fixup types surrounding workflow refactoring testing (thanks to @jmchilton). Pull Request 15177

• Improve typing in galaxy.tool_util.data (thanks to @jmchilton). Pull Request 15179

• Convert multiple view to composition API except MultipleViewList (thanks to @itisAliRH). Pull Request 15182

• Fix various issues with OpenAPI schema conformance, add linting (thanks to @mvdbeek). Pull Request 15183

• Tweak OpenAPI schema (thanks to @mvdbeek). Pull Request 15189

• Typing for tool test plumbing code (thanks to @jmchilton). Pull Request 15192

• Do not OpenAPI schema lint for operation-4xx-response (thanks to @jmchilton). Pull Request 15193

• Update API schema generation to be explicit about unsecured endpoints (thanks to @jmchilton). Pull Request 15194

• Include spell checking in API schema linting. (thanks to @jmchilton). Pull Request 15195

• A bit more typing in interactor.py (thanks to @jmchilton). Pull Request 15203

• Migrate baseauth endpoint to FastAPI (thanks to @jmchilton). Pull Request 15214

• replace the png logo with svg version (thanks to @martenson). Pull Request 15246

• Apply all linters to data managers (which are applied to tools) (thanks to @bernt-matthias). Pull Request 15254

• Upgrade TPV to v2.0.0 (thanks to @nuwang). Pull Request 15259

• Enable collapsing markdown elements (thanks to @guerler). Pull Request 15260

• Update Python dependencies (thanks to @galaxybot). Pull Request 15264

• Update Python dependencies (thanks to @galaxybot). Pull Request 15281

• add HTML description meta tag (thanks to @neoformit). Pull Request 15288

• Update Python dependencies (thanks to @galaxybot). Pull Request 15308

• doc accept_default as deprecated (thanks to @bernt-matthias). Pull Request 15338

• Update Python dependencies (thanks to @galaxybot). Pull Request 15346

• Fix attribute error on base models (thanks to @davelopez). Pull Request 15731

• Add 2 indexes to WorkflowRequest* tables on the workflow_invocation_id field (thanks to @jdavcs). Pull Request 15733

• Fix typo in docstring (thanks to @jdavcs). Pull Request 15793

• Remove some IDs from error messages (thanks to @davelopez). Pull Request 15882

• Update default GALAXY_URL for webpack-dev-server (thanks to @dannon). Pull Request 15391

• Refactor _FieldText to vue.js (thanks to @neoformit). Pull Request 13375

• Remove new shed datatypes (thanks to @jmchilton). Pull Request 13976

• Decompose UserPreferences for reuse (thanks to @jmchilton). Pull Request 14109

• Combine “as” imports with other “from” imports (thanks to @nsoranzo). Pull Request 14119

• save one call to datatype_by_extension (thanks to @bernt-matthias). Pull Request 14209

• Migrate library folder contents API to FastAPI (thanks to @davelopez). Pull Request 14223

• Update lists of non-passing CWL conformance tests (thanks to @nsoranzo). Pull Request 14258

• Fix B023 warnings from flake8-bugbear 22.7.1 (thanks to @nsoranzo). Pull Request 14260

• Rename GenomeProvider to DbKeyProvider (thanks to @davelopez). Pull Request 14262

• Rename test to accurately describe the code it tests [improves content of new tutorial] (thanks to @jdavcs). Pull Request 14285

• Drop root controller methods (thanks to @mvdbeek). Pull Request 14290

• Code cleanups from pyupgrade (thanks to @nsoranzo). Pull Request 14313

• Extend docs and tests for conditional output actions (thanks to @bernt-matthias). Pull Request 14314

• Eslint upgrade and fixes (thanks to @dannon). Pull Request 14384

• Refactor history contents API ID encoding (thanks to @davelopez). Pull Request 14392

• Vueify Quota-Meter (thanks to @ElectronicBlueberry). Pull Request 14435

• Refactor pydantic id handling (thanks to @davelopez). Pull Request 14436

• Remove legacy page and panel builders (thanks to @guerler). Pull Request 14505

• RxJS cleanup; removing cruft we no longer use (thanks to @dannon). Pull Request 14506

• Separate unsorted styles from base file (thanks to @guerler). Pull Request 14520

• Panel init template cleanup (thanks to @dannon). Pull Request 14535

• Remove no longer useful API endpoint in the toolshed (thanks to @jmchilton). Pull Request 14554

• Unit tests and type fixes for tool data tables code (thanks to @jmchilton). Pull Request 14582

• Multipanel cleanup, remove dead code (thanks to @dannon). Pull Request 14608

• Place Toolshed JS modules into separate bundle (thanks to @guerler). Pull Request 14609

• Remove mypy exceptions for deleted files (thanks to @jmchilton). Pull Request 14613

• More Tool Shed Cleanup (thanks to @jmchilton). Pull Request 14615

• Cleanup update_repository_manager in Galaxy repository install code (thanks to @jmchilton). Pull Request 14628

• Remove outdated display structured history view (thanks to @guerler). Pull Request 14630

• Remove legacy history usage from js-modules (thanks to @guerler). Pull Request 14638

• Refactor tool shed registry into utility code (thanks to @jmchilton). Pull Request 14642

• Eliminate configuresgalaxymixin (thanks to @jmchilton). Pull Request 14645

• Drop unnecessary config tests (thanks to @jdavcs). Pull Request 14648

• Remove repository review functionality from tool shed (thanks to @jmchilton). Pull Request 14649

• Eliminated JQuery from PluginList (thanks to @shubham4315). Pull Request 14653

• Remove legacy history from code base (thanks to @guerler). Pull Request 14660

• Remove now redundant base class (thanks to @nsoranzo). Pull Request 14663

• Cleanup tool_util.py (thanks to @jmchilton). Pull Request 14668

• Various unsorted tool shed code cleanup. (thanks to @jmchilton). Pull Request 14669

• Packaging and configurability for the container monitor script (thanks to @natefoo). Pull Request 14673

• Replace self.assert*() method calls with plain asserts (thanks to @nsoranzo). Pull Request 14674

• Generate somewhat valid SafeStringWrapper-wrapped class names (thanks to @mvdbeek). Pull Request 14675

• Tool Shed and Tool Utility Cleanup (thanks to @jmchilton). Pull Request 14681

• More typing for tool shed install and relevant utility code (thanks to @jmchilton). Pull Request 14682

• Add type hints for galaxy.workflow.{run, run_request} (thanks to @mvdbeek). Pull Request 14683

• Remove is_beta_history flag from selenium tests (thanks to @guerler). Pull Request 14686

• Remove legacy base panel makos (thanks to @guerler). Pull Request 14687

• Storing selected histories in multiple view into local storage (thanks to @itisAliRH). Pull Request 14703

• Fixed typo for quota default change (thanks to @abueg). Pull Request 14706

• Minor reformatting of verification error (thanks to @bernt-matthias). Pull Request 14712

• Remove workflow export mako (thanks to @guerler). Pull Request 14716

• Cleanup hack in job files API for very old versions of Galaxy (thanks to @jmchilton). Pull Request 14720

• Simplify tool shed tests (thanks to @jmchilton). Pull Request 14735

• Drop ToolsView (thanks to @dannon). Pull Request 14737

• Replace unittest.TestCase in API, framework, performance, Selenium and ToolShed tests (thanks to @nsoranzo). Pull Request 14739

• Small cleanups to shed package dependency structures (thanks to @jmchilton). Pull Request 14744

• Cleanup installed_repository_manager.py and related code a bit more (thanks to @jmchilton). Pull Request 14746

• Update history size tooltip (thanks to @dannon). Pull Request 14749

• Align url handling for more consistency (thanks to @guerler). Pull Request 14752

• Migrate workflow import to composition API (thanks to @itisAliRH). Pull Request 14775

• Cleanup More Tool Shed Admin Controllers and Makos (thanks to @jmchilton). Pull Request 14793

• Point to new documentation instead of github issue (thanks to @jdavcs). Pull Request 14796

• Rename FooBarTestCase test classes as TestFooBar (thanks to @nsoranzo). Pull Request 14797

• Add avatar to published item components (thanks to @guerler). Pull Request 14803

• More tool shed dependency and dead code cleanup (thanks to @jmchilton). Pull Request 14810

• Remove legacy reinstall endpoint from admin_toolshed.py (thanks to @jmchilton). Pull Request 14811

• Misc. fixes to datatypes modules (thanks to @jdavcs). Pull Request 14817

• Move ToolShedRepositoryCache into galaxy.tool_shed (thanks to @jmchilton). Pull Request 14824

• Remove legacy dependency manager mako (thanks to @guerler). Pull Request 14826

• Fix tool help headings and sizes (thanks to @ElectronicBlueberry). Pull Request 14830

• Remove redirect mako from tool runner controller (thanks to @guerler). Pull Request 14831

• Remove legacy js mount-helpers for makos (thanks to @guerler). Pull Request 14832

• Refactor markdownHelp (thanks to @ElectronicBlueberry). Pull Request 14838

• Workflow API refactor and porting to fastAPI (thanks to @martenson). Pull Request 14843

• Vueify Rules Edit (thanks to @ElectronicBlueberry). Pull Request 14878

• Remove ability to delete individual files from tool shed (thanks to @jmchilton). Pull Request 14909

• Update interactivetool_ml_jupyter_notebook.xml (thanks to @anuprulez). Pull Request 14910

• Vueify Toast (thanks to @ElectronicBlueberry). Pull Request 14935

• Remove old WSGI middleware that is no longer useful (thanks to @jmchilton). Pull Request 14965

• Refactor, add type hints to get_chunk() in datatypes (thanks to @jdavcs). Pull Request 14993

• Upgrade FastAPI to 0.87.0, drop old workarounds (thanks to @mvdbeek). Pull Request 14996

• Bump loader-utils from 1.4.0 to 1.4.2 in /client (thanks to @galaxyproject). Pull Request 14997

• Pinia addition and initial conversion from vuex for a few basic stores (thanks to @dannon). Pull Request 14999

• Use galaxy_directory() util function to check if code is running from root or from packages (thanks to @jdavcs). Pull Request 15010

• Convert radio button to vue (thanks to @guerler). Pull Request 15016

• Eslint upgrades, rule tweaks (thanks to @dannon). Pull Request 15026

• Update .pre-commit-config.yml.sample (thanks to @mvdbeek). Pull Request 15050

• Remove leftover log message (thanks to @bernt-matthias). Pull Request 15066

• Use Galaxy logo instead of Logo/Text combo, refactor masthead to composition api (thanks to @guerler). Pull Request 15082

• Move JavaScript linting to GitHub workflows (thanks to @nsoranzo). Pull Request 15102

• Convert UtcDate from options to composition+ts (thanks to @dannon). Pull Request 15116

• Fix and Convert composables to TypeScript (thanks to @ElectronicBlueberry). Pull Request 15119

• Update to 2022 NAR paper (thanks to @mschatz). Pull Request 15123

• New Filtering class (thanks to @itisAliRH). Pull Request 15153

• Drop beta contents near endpoint (thanks to @mvdbeek). Pull Request 15171

• Day 1 Typeathon (thanks to @ElectronicBlueberry). Pull Request 15180

• Convert localization from old amd module (thanks to @dannon). Pull Request 15181

• Migrate Storage Dashboard to TS + Composition API (thanks to @davelopez). Pull Request 15184

• Small mypy improvements. (thanks to @jmchilton). Pull Request 15185

• Pinia-fy historyItemsStore (thanks to @ahmedhamidawan). Pull Request 15190

• Mark method parameter as meant to be used only for testing (thanks to @jmchilton). Pull Request 15199

• Convert Admin/JobLock to composition+ts+apiclient (thanks to @dannon). Pull Request 15200

• Extract list of packages ordered by dependency dag for reuse (thanks to @nsoranzo). Pull Request 15209

• Fix url in group user API (thanks to @davelopez). Pull Request 15217

• Drop unused run_tests.sh options (thanks to @mvdbeek). Pull Request 15233

• Typeathon Day-2 (thanks to @ElectronicBlueberry). Pull Request 15234

• Show Workflow Import Message (thanks to @ElectronicBlueberry). Pull Request 15235

• Tabular dataset display component (thanks to @dannon). Pull Request 15285

• Annotate utils/redirect, rename safePath (thanks to @dannon). Pull Request 15298

• Avoid legacy API routes increase (thanks to @davelopez). Pull Request 15312

• Towards SQLAlchemy 2.0: use model attributes instead of strings (thanks to @jdavcs). Pull Request 15340

Fixes

• Fix path for history contents API request (thanks to @reid-wagner). Pull Request 14437

• Prepend Galaxy root to dataset download URLs in visualization plugins (thanks to @mahendrapaipuri). Pull Request 15064

• Visualization mounting fix & test (thanks to @dannon). Pull Request 15332

• Avoid passing headers argument twice in datatypes display - take 2 (thanks to @wm75). Pull Request 15766

• Account for charge and spin in den_fmt sniffer (thanks to @muon-spectroscopy-computational-project). Pull Request 15797

• Do not pass dataset keyword parameter into datatype.display_data (thanks to @mvdbeek). Pull Request 15695

• Format Python code with black 23.1.0 (thanks to @nsoranzo). Pull Request 15488

• Fix large_file.mako arguments (thanks to @mvdbeek). Pull Request 15503

• do not split “.” but the path (thanks to @bernt-matthias). Pull Request 14760

• Fix indentation level on SnpSiftDbNSFP.set_peek() (thanks to @jdavcs). Pull Request 14953

• fix interval_to_bgzip for sub gff classes (thanks to @lldelisle). Pull Request 15053

• Fix wrong tool converter names (thanks to @mvdbeek). Pull Request 15579

• Fix unbound local error in sort collection tool (thanks to @mvdbeek). Pull Request 15583

• interval2maf remove from unversioned or deprecate (thanks to @bernt-matthias). Pull Request 14573

• Misc fixes 202209 (thanks to @nsoranzo). Pull Request 14592

• Simplify head wrapper - same functionality, no pipe (thanks to @wm75). Pull Request 14895

• Fix add value tool, bump linter level for format="input" to error (thanks to @mvdbeek). Pull Request 15304

• Make dragImage transparent in workflow editor (thanks to @mvdbeek). Pull Request 15593

• Don’t include output name in css classes for node outputs (thanks to @mvdbeek). Pull Request 15782

• Fix overly strict map over constraints (thanks to @mvdbeek). Pull Request 15818

• Fix saving workflow with conditional subworkflow step (thanks to @mvdbeek). Pull Request 15649

• Fix anonymous workflow preview (thanks to @mvdbeek). Pull Request 15679

• Adding more directive to the Invalid Input tooltip (thanks to @assuntad23). Pull Request 15406

• Fix node input map over status (thanks to @mvdbeek). Pull Request 15408

• Resolve collection_type_source in workflow editor (thanks to @mvdbeek). Pull Request 15430

• Fix data_column and empty_file filters when DCE is passed (thanks to @mvdbeek). Pull Request 15465

• Fix multi-input connection handling in workflow editor (thanks to @mvdbeek). Pull Request 15472

• Fix incorrect warning for workflow output duplicate label (thanks to @davelopez). Pull Request 15475

• Fix inserting inputs through repeats (thanks to @mvdbeek). Pull Request 15500

• Fix refactor action dropping outputs on subworkflow connection (thanks to @mvdbeek). Pull Request 14494

• Always call strip() on data_column column values (thanks to @mvdbeek). Pull Request 14518

• Fix post job action getting lost when node is made active (thanks to @mvdbeek). Pull Request 14539

• Fix workflow parameter connectability (thanks to @mvdbeek). Pull Request 14563

• Fix delayed optional data input handling (thanks to @mvdbeek). Pull Request 14641

• Fix loading subworkflows from editor interface (thanks to @mvdbeek). Pull Request 14870

• Fix restricted values for parameter connected to subworkflow input (thanks to @mvdbeek). Pull Request 14873

• Remove incorrect references to datasets instead of dataset instances in run_request.py (thanks to @jmchilton). Pull Request 14943

• Make workflow cycle test side-effect free (thanks to @mvdbeek). Pull Request 14986

• Backport #14643: Enable simplified workflow with optional disconnected data inputs (thanks to @mvdbeek). Pull Request 14987

• Ensure tool_id is null for subworkflow steps (thanks to @mvdbeek). Pull Request 15310

• Fix workflow mako rendering (thanks to @mvdbeek). Pull Request 15343

• Fix plugin framework build compatibility with node 16 (thanks to @dannon). Pull Request 15756

• Webpack dependency updates to address dependabot alert (thanks to @dannon). Pull Request 15806

• Data Libraries Sanitization (thanks to @dannon). Pull Request 15706

• Provide d3@3 for older visualization compatibility (thanks to @dannon). Pull Request 15462

• Fix run client dev server in Gitpod (thanks to @itisAliRH). Pull Request 14111

• Bump jquery-ui from 1.13.1 to 1.13.2 in /client (thanks to @galaxyproject). Pull Request 14344

• Bump terser from 5.10.0 to 5.14.2 in /client (thanks to @galaxyproject). Pull Request 14352

• Cleanup noisey warning in JobParameters.test.js (thanks to @jmchilton). Pull Request 14555

• Bump engine.io from 6.2.0 to 6.2.1 in /client (thanks to @galaxyproject). Pull Request 15044

• Fix js linting (thanks to @jdavcs). Pull Request 15048

• Bump decode-uri-component from 0.2.0 to 0.2.1 in /client (thanks to @galaxyproject). Pull Request 15103

• Fix tool stdio on pulsar and implement job stdio (thanks to @mvdbeek). Pull Request 15907

• Fail linked job if task fails (thanks to @mvdbeek). Pull Request 15909

• Fix pulsar error when when home_target is pwd (thanks to @mvdbeek). Pull Request 15914

• Add missing filter in job query (thanks to @mvdbeek). Pull Request 15846

• Fix visible handling for exisiting datasets on discovery (thanks to @mvdbeek). Pull Request 15525

• Fixes for Pulsar 0.15.0 discovered on usegalaxy.org (thanks to @jmchilton). Pull Request 15535

• Cast job_key to string (thanks to @mvdbeek). Pull Request 15578

• Synchronize job runner utils with fixes from and for Pulsar’s version (thanks to @jmchilton). Pull Request 14727

• Synchronize job script module with Pulsar fixes (thanks to @jmchilton). Pull Request 14784

• Drop broken output.parent logic (thanks to @mvdbeek). Pull Request 14862

• Various Pulsar extended metadata fixes (thanks to @jmchilton). Pull Request 14863

• Downgrade exception to warning when job properties files could not be found (thanks to @simonbray). Pull Request 14968

• Disable table sort reset by clicking on unsortable headers (thanks to @itisAliRH). Pull Request 15610

• Change Field Method for Tool Table Columns to a Map (thanks to @assuntad23). Pull Request 15529

• Drop SentryWSGIMiddleware (thanks to @mvdbeek). Pull Request 15548

• Disallow indexing of the /training-materials/ proxy used for “Tutorial Mode” (thanks to @galaxyproject). Pull Request 14283

• Update Gravity to 0.13.4 and document setting env vars on dynamic handlers (thanks to @natefoo). Pull Request 14550

• Bump minimum pip version to 20.3 . Ignore --replace-pip and --no-replace-pip startup options (thanks to @nsoranzo). Pull Request 15322

• Admin interface navguard (thanks to @dannon). Pull Request 15906

• Allow messagebox rich contents (thanks to @dannon). Pull Request 15912

• Fix history RO-crate export with discarded datasets (thanks to @davelopez). Pull Request 15916

• Fix Short Term Storage cleanup when metadata is lost (thanks to @davelopez). Pull Request 15724

• Validate history Related filter in backend (thanks to @ahmedhamidawan). Pull Request 15741

• Fix rule builder table display (thanks to @mvdbeek). Pull Request 15743

• Fix Worflow editor loading issues (thanks to @ElectronicBlueberry). Pull Request 15750

• Fix GTN webhook (thanks to @dannon). Pull Request 15755

• Add missing history export link (thanks to @davelopez). Pull Request 15758

• Remove code left over from debugging (thanks to @jdavcs). Pull Request 15764

• Cast url_for() output to str (thanks to @nsoranzo). Pull Request 15775

• fix premature return in user API (thanks to @martenson). Pull Request 15780

• Bump Gravity to 1.0.1 (thanks to @natefoo). Pull Request 15787

• Allow hyphenated tool-name to be searchable in ToolSearch (thanks to @ahmedhamidawan). Pull Request 15788

• Fix regression in distinguishing between select and text types (thanks to @jmchilton). Pull Request 15792

• Fix loading of job submission success page on route change (thanks to @ahmedhamidawan). Pull Request 15801

• Bump tuswsgi middleware (thanks to @mvdbeek). Pull Request 15803

• Show workflow errors in embedded markdown element (thanks to @guerler). Pull Request 15807

• Fix toggling output visibility (thanks to @mvdbeek). Pull Request 15812

• Fix User Preferences Manage External Identities element v-if (thanks to @ahmedhamidawan). Pull Request 15824

• Fix API for latest FastAPI (0.95) (thanks to @jmchilton). Pull Request 15829

• Fix tool recommendation in the workflow editor (thanks to @ElectronicBlueberry). Pull Request 15842

• Update Gravity to 1.0.2 (thanks to @natefoo). Pull Request 15862

• Don’t set datatype for optional datasets that were not provided (thanks to @mvdbeek). Pull Request 15871

• List tags in /api/dataset_collections/{hdca_id}/contents/{parent_id} (thanks to @mvdbeek). Pull Request 15883

• Fix tool bar on top of pop-ups (thanks to @ElectronicBlueberry). Pull Request 15891

• Fix short term storage archive export extension on download (thanks to @davelopez). Pull Request 15894

• Sync ToolForm and WorkflowRun with history changes (thanks to @ahmedhamidawan). Pull Request 15565

• Fix Filter history inputs and outputs server error (thanks to @ahmedhamidawan). Pull Request 15572

• Fix escaped html in alert regarding login activation (thanks to @dannon). Pull Request 15632

• Fix bioblend GalaxyClient import for mypy (thanks to @nsoranzo). Pull Request 15637

• check for sessionless and userless API access (thanks to @martenson). Pull Request 15659

• Rework collapsible FormCard handling; (thanks to @dannon). Pull Request 15661

• convert activate method substitutions to f-strings (thanks to @martenson). Pull Request 15666

• Ignore spurious mypy error (thanks to @nsoranzo). Pull Request 15667

• Temporarily restore old BCO export mechanism (without Celery) (thanks to @davelopez). Pull Request 15674

• Fix sentry in WSGI/ASGI context (thanks to @mvdbeek). Pull Request 15675

• Fix stock tool URL generation in BCOs (thanks to @davelopez). Pull Request 15685

• Fix run_form=true if trs_url is used (thanks to @mvdbeek). Pull Request 15687

• Use more efficient model properties when serializing histories (thanks to @mvdbeek). Pull Request 15705

• Fix task-based export error handling (thanks to @davelopez). Pull Request 15719

• Fix library bulk selection (thanks to @dannon). Pull Request 15721

• Ensure that tool form is initialized before attempting updates (thanks to @guerler). Pull Request 15325

• Use galaxy.util.download_to_file instead of wget/curl (thanks to @mvdbeek). Pull Request 15356

• Add failed metadata info (thanks to @guerler). Pull Request 15359

• Reset confirmation state when unmounting workflow editor (thanks to @mvdbeek). Pull Request 15378

• Fix history modal selection highlight (thanks to @davelopez). Pull Request 15381

• Fix workflow editing route for workflows created from history (thanks to @guerler). Pull Request 15384

• Fix Datatypes Page (thanks to @ElectronicBlueberry). Pull Request 15398

• Fix Workflow Editor Zoom (thanks to @ElectronicBlueberry). Pull Request 15399

• Redirect anonymous users on histories/list (thanks to @davelopez). Pull Request 15400

• Disable create and switch histories anonymously (thanks to @davelopez). Pull Request 15403

• Sort tool sections in a way that works for both Chrome and Firefox (thanks to @dannon). Pull Request 15419

• Hide metadata auto-detection option if dataset is in improper state (thanks to @guerler). Pull Request 15422

• Move workflow node loading indicator (thanks to @martenson). Pull Request 15423

• Clarify info messages for Collection Edit tabs (thanks to @assuntad23). Pull Request 15431

• ToolBoxWorkflow fix tool compatibility and search (thanks to @ahmedhamidawan). Pull Request 15432

• Add name+description ToolSearch (thanks to @ahmedhamidawan). Pull Request 15434

• fix looks_like_yaml_or_cwl_with_class (thanks to @bernt-matthias). Pull Request 15439

• Serialize CWL tools via json, not pickle (thanks to @mvdbeek). Pull Request 15441

• Adjust to bleach.ALLOWED_PROTOCOLS being frozenset (thanks to @mvdbeek). Pull Request 15442

• fix password reset url (thanks to @martenson). Pull Request 15453

• Fix workflow toolbox sorting of workflows (thanks to @dannon). Pull Request 15455

• restore rst_invalid function (thanks to @bernt-matthias). Pull Request 15457

• Strip EDAM Quotes (thanks to @ElectronicBlueberry). Pull Request 15474

• Fix workflow output activiting on activating node (thanks to @mvdbeek). Pull Request 15478

• Create ToolSuccess route and refactor component (thanks to @ahmedhamidawan). Pull Request 15484

• ToolSearch trim whitespace in query (thanks to @ahmedhamidawan). Pull Request 15485

• ToolBox remove Expression Tools section (thanks to @ahmedhamidawan). Pull Request 15486

• Add support for Python 3.11 (thanks to @nsoranzo). Pull Request 15487

• Update Collection Element in Collection View (thanks to @ElectronicBlueberry). Pull Request 15501

• Add Database filter to HistoryFilters (thanks to @ahmedhamidawan). Pull Request 15505

• xsd fixes for output actions (thanks to @bernt-matthias). Pull Request 15508

• Fix phyloviz (thanks to @dannon). Pull Request 15516

• Fix webhook backbone view (thanks to @mvdbeek). Pull Request 15522

• Fix histories shared with me navigation (thanks to @davelopez). Pull Request 15531

• prevent leaking decoded ids through markdown error handling (thanks to @martenson). Pull Request 15536

• Fix workflow success banner history target display (thanks to @dannon). Pull Request 15541

• Add new release tags to manage_db.sh script (thanks to @jdavcs). Pull Request 15543

• Refactor and fix file dragging (thanks to @martenson). Pull Request 15544

• Switch to official setup-node action for cache (thanks to @mvdbeek). Pull Request 15547

• Disable invocation export when Celery is disabled (thanks to @davelopez). Pull Request 15556

• fix hostname parsing for newer Docker versions (thanks to @SergeyYakubov). Pull Request 15561

• Fix db migration release tag migration hashes for 23.0 (thanks to @jdavcs). Pull Request 15571

• Update gravity dependency to 1.0 PyPI release (thanks to @nsoranzo). Pull Request 15577

• Fix job completion email from tool form (thanks to @mvdbeek). Pull Request 15585

• Backport of #15517 (thanks to @davelopez). Pull Request 15586

• Allow anonymous access to tool source view (thanks to @dannon). Pull Request 15589

• History scroller fixes (thanks to @ElectronicBlueberry). Pull Request 15595

• Fix masthead/ribbon alerts to use Alert component, update variant (thanks to @dannon). Pull Request 15603

• check only first 64 chars of the activation token (thanks to @martenson). Pull Request 15605

• Fix new user welcome resource loading (thanks to @dannon). Pull Request 15615

• Fix duplicated Copy History dialog in Shared Histories (thanks to @davelopez). Pull Request 15619

• linter: warn if expect_num_outputs is missing (thanks to @bernt-matthias). Pull Request 12975

• column label renaming for clarity (thanks to @hujambo-dunia). Pull Request 14051

• Fix for Preferred Language refresh bug in Localization process related to User Preferences Page [13653] (thanks to @hujambo-dunia). Pull Request 14082

• Fix flaky test_workflow_delete selenium test (thanks to @mvdbeek). Pull Request 14112

• Get last history list offset and restore on return (thanks to @itisAliRH). Pull Request 14139

• Fix parse_requirements_and_containers() for CWL and YAML tools (thanks to @nsoranzo). Pull Request 14144

• Use imports instead of variable assignment for galaxy.util.Element (thanks to @mvdbeek). Pull Request 14197

• Encode history name in tool_util.verify.interactor.get_history (thanks to @cat-bro). Pull Request 14208

• Misc fixes 2022-06-28 (thanks to @nsoranzo). Pull Request 14215

• Fix mypy reexport error for testfixtures (thanks to @nsoranzo). Pull Request 14272

• Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools (thanks to @cat-bro). Pull Request 14373

• Fix dataset list operation to switch between histories (thanks to @guerler). Pull Request 14398

• Fix duplicate Request to CurrentUser (thanks to @ElectronicBlueberry). Pull Request 14441

• Register client library routes in app router (thanks to @guerler). Pull Request 14445

• Disable Dataset Display icon in queued state, and Improve Window Manager tour (thanks to @ahmedhamidawan). Pull Request 14446

• watching historyID for change, if it changes, close the CollectionPanel (thanks to @assuntad23). Pull Request 14493

• Fix dataset operations inconsistent hover styles (thanks to @ElectronicBlueberry). Pull Request 14495

• Release script fixes (thanks to @mvdbeek). Pull Request 14498

• Fix dataset operation highlighting in Safari and dataset error route (thanks to @guerler). Pull Request 14500

• Enable logging for manage_db.sh (thanks to @jdavcs). Pull Request 14507

• Fix setting metadata elements in conditional tool action (thanks to @mvdbeek). Pull Request 14510

• Fix toolshed installation progress overview shows no status (thanks to @ElectronicBlueberry). Pull Request 14516

• Fix dataset visualize action routing (thanks to @dannon). Pull Request 14517

• Fix typos in test linter (thanks to @bernt-matthias). Pull Request 14526

• Fix absolute path generation util (thanks to @dannon). Pull Request 14531

• Fix double nested application when visualizing dataset (without scratchbook) (thanks to @dannon). Pull Request 14534

• Allow changing type of regex rule in RBU (thanks to @assuntad23). Pull Request 14543

• Request extended details when modifying history attributes (thanks to @guerler). Pull Request 14548

• Use url’s database to connect at startup (thanks to @jdavcs). Pull Request 14556

• Fix reference to config option in schema (thanks to @jdavcs). Pull Request 14558

• Don’t query the database when running migrations in offline mode (thanks to @jdavcs). Pull Request 14564

• Fix output_action_change_format framework tests (thanks to @nsoranzo). Pull Request 14565

• Consistently use our now() in the model (thanks to @nsoranzo). Pull Request 14581

• Ensure guid is hexadecimal value (thanks to @mvdbeek). Pull Request 14588

• Include /bin in sample systemd unit path (thanks to @mvdbeek). Pull Request 14590

• Better + additional fix for alembic offline mode (thanks to @jdavcs). Pull Request 14596

• Pin CacheControl to prevent missing dependency (thanks to @nsoranzo). Pull Request 14607

• Change HTTP status code for DeprecatedMethod exception to 410 (thanks to @nsoranzo). Pull Request 14614

• Fix toolbox access in invocation export (thanks to @davelopez). Pull Request 14624

• Fix export RO-crate to file source (thanks to @davelopez). Pull Request 14639

• Bug fix related to collecting invocation jobs (thanks to @jmchilton). Pull Request 14654

• VCF/Tabular display fix (thanks to @dannon). Pull Request 14671

• Fix old style workflow parameter regression in Number entry (thanks to @dannon). Pull Request 14689

• Small test fixes (thanks to @nsoranzo). Pull Request 14711

• Idle connection pool cleaner (thanks to @kxk302). Pull Request 14714

• Allow to force push client routes (thanks to @guerler). Pull Request 14725

• Fix validation_dataset_metadata_in_file framework test (thanks to @nsoranzo). Pull Request 14728

• Fix subworkflow upgrade (thanks to @mvdbeek). Pull Request 14733

• Accessibility issue fixes in workflow list/import interfaces (thanks to @dannon). Pull Request 14747

• Fix tool recommendations display (thanks to @abretaud). Pull Request 14751

• Do not load sample config file; assign correct config paths (thanks to @jdavcs). Pull Request 14755

• Improve galaxy version extra file loading (thanks to @dannon). Pull Request 14758

• improve UX of admin job page (thanks to @martenson). Pull Request 14769

• Fix disappearing right anchor (thanks to @dannon). Pull Request 14778

• Add a utility function that returns first available value for prefix+key set in the environment; fix bug (thanks to @jdavcs). Pull Request 14788

• Fix test_get_alternative_versions unit test (thanks to @nsoranzo). Pull Request 14789

• fix container_resolvers API index and show (thanks to @cat-bro). Pull Request 14807

• 2 bug fixes (thanks to @nsoranzo). Pull Request 14812

• Fixes welcome panel route in login component (thanks to @guerler). Pull Request 14823

• Fix Tool form header overlaps with window manager (thanks to @ElectronicBlueberry). Pull Request 14828

• Fix export history RO-Crate without workflows (thanks to @davelopez). Pull Request 14835

• Fix sample config (thanks to @davelopez). Pull Request 14841

• Fix invocation filtering by stored workflow (thanks to @mvdbeek). Pull Request 14853

• Use dnspython to check specifically for an “MX” DNS record (thanks to @nsoranzo). Pull Request 14854

• Require also a recent pyOpenSSL package when installing conda (thanks to @nsoranzo). Pull Request 14856

• make solo fontawesome elements render attached tooltips properly (thanks to @martenson). Pull Request 14857

• Cherry pick #14807 and add test for /api/container_resolvers/resolve (thanks to @cat-bro). Pull Request 14859

• fix tooltip rendering on icons (thanks to @martenson). Pull Request 14874

• Fix response encoding when getting tool citations via API (thanks to @nsoranzo). Pull Request 14876

• reintroduce decoding for PUT /dataset/set_edit calls (thanks to @martenson). Pull Request 14885

• Fix collection download link (thanks to @dannon). Pull Request 14897

• Do not mask collection download exceptions (thanks to @martenson). Pull Request 14898

• Update cryptography to 38.0.3 (thanks to @natefoo). Pull Request 14904

• Fix displaying named tags (thanks to @itisAliRH). Pull Request 14907

• Fix errors when querying for invalid repos or repos without valid tools (thanks to @mvdbeek). Pull Request 14911

• Mark optional form parameters followup (thanks to @ElectronicBlueberry). Pull Request 14914

• Fix broken subworkflow reordering on workflow import (thanks to @mvdbeek). Pull Request 14918

• Fix conda-build version not compatible (thanks to @nsoranzo). Pull Request 14919

• Fix edit history details button hidden from anonymous users (thanks to @ElectronicBlueberry). Pull Request 14924

• Update tool shed migration instructions (thanks to @jdavcs). Pull Request 14926

• Change Custos url in oidc_backends_config (thanks to @ahmedhamidawan). Pull Request 14929

• Fix download urls in embedded workflow component (thanks to @guerler). Pull Request 14930

• Fix select2 value selection in selenium (thanks to @mvdbeek). Pull Request 14937

• Stabilize test_edit_subworkflow selenium test (thanks to @mvdbeek). Pull Request 14940

• Fix merge forward of #14918 (thanks to @nsoranzo). Pull Request 14941

• Fix typo in CWL representation code (thanks to @jmchilton). Pull Request 14957

• Fix GiHttpMixin by passing API key in request headers (thanks to @nsoranzo). Pull Request 14960

• Make unique resources set in workflows api test unique with uuid suffix (thanks to @mvdbeek). Pull Request 14961

• Fix VCF handling for IGV Viewer (thanks to @guerler). Pull Request 14973

• Fix invalid quota amount (thanks to @davelopez). Pull Request 14981

• Add HEAD route for /api/datasets/{history_content_id}/display (thanks to @mvdbeek). Pull Request 14983

• Fix discarded datasets when importing history from file sources using tasks (thanks to @davelopez). Pull Request 14989

• Fix wrongly skipped test_test_data_null_boolean_inputs API test (thanks to @nsoranzo). Pull Request 14991

• Fix interpolation in NicerConfigParser on Python 3.11 (thanks to @nsoranzo). Pull Request 15002

• Job-based chart UX improvements (thanks to @dannon). Pull Request 15013

• Tool Client Search bug fix and add client tests (thanks to @ahmedhamidawan). Pull Request 15015

• Drop link to celery docs that don’t exist (thanks to @mvdbeek). Pull Request 15029

• use history_id fixture instead of instance variable with the same name (thanks to @mr-c). Pull Request 15037

• Fix metadata setting for discovered datasets with extended metadata (thanks to @mvdbeek). Pull Request 15038

• Mount $TMPDIR, $TMP and $TEMP into container (thanks to @mvdbeek). Pull Request 15039

• Fix display collection error in history items (thanks to @davelopez). Pull Request 15040

• History item color to hsla (thanks to @itisAliRH). Pull Request 15055

• minimal changes for MyPy 0.991 (thanks to @mr-c). Pull Request 15065

• Update routing for collection info display, a11y tweaks (thanks to @dannon). Pull Request 15072

• Use absolute imports (thanks to @jdavcs). Pull Request 15073

• Fix export history to FTP using tasks (thanks to @davelopez). Pull Request 15090

• Various fixes for Short Term Storage API (thanks to @davelopez). Pull Request 15094

• Fix model_class field annotations (thanks to @mvdbeek). Pull Request 15105

• Update gravity to 0.13.6 (thanks to @natefoo). Pull Request 15122

• update the workflow form language (thanks to @galaxyproject). Pull Request 15125

• Install involucro when resolvers are instantiated (thanks to @nsoranzo). Pull Request 15130

• Support for path-based proxying of interactive tools (thanks to @sveinugu). Pull Request 15147

• Fix link to markdown editor (thanks to @guerler). Pull Request 15152

• Add/remove/pin/unpin Python requirements (thanks to @nsoranzo). Pull Request 15159

• Update Vue Virtual Scroll List (thanks to @guerler). Pull Request 15160

• Fix lxml deprecation warning (thanks to @galaxyproject). Pull Request 15161

• Add x-forwarded-proto to middleware (thanks to @nuwang). Pull Request 15167

• Small fixes to YAML export of OpenAPI schema (thanks to @jmchilton). Pull Request 15187

• Fix typo (thanks to @hexylena). Pull Request 15215

• Fix for Workflow Editor Tags Formatting (thanks to @hujambo-dunia). Pull Request 15223

• Watch offset and update_time to fetch historyItems (thanks to @ahmedhamidawan). Pull Request 15226

• Fix type hints for alembic/env.py (thanks to @jdavcs). Pull Request 15236

• Fix UploadModalContent “__v_isRef” is not defined (thanks to @ElectronicBlueberry). Pull Request 15245

• Refine scroll behavior, avoid redundant refresh requests (thanks to @guerler). Pull Request 15248

• Remove duplicated url param separator from dataset services (thanks to @guerler). Pull Request 15251

• Fix test_mulled_build_files_cli mulled unit test (thanks to @nsoranzo). Pull Request 15255

• Fixes #15224 - tools token are created with a size of 10 chars when interactivetools_shorten_url is true (thanks to @Lain-inrae). Pull Request 15265

• Fix boolean parameter handling (thanks to @guerler). Pull Request 15266

• Fix form builder in admin panel (thanks to @guerler). Pull Request 15271

• entrypoints - use timeout instead of interval to prevent stacking requests (thanks to @martenson). Pull Request 15277

• add set_random_password to tool_shed User (thanks to @jhl667). Pull Request 15280

• Bump cwltest requirement and fix import (thanks to @mvdbeek). Pull Request 15287

• Restore toolshed masthead appearance (thanks to @guerler). Pull Request 15293

• Fix Sign Out Selenium test (thanks to @davelopez). Pull Request 15299

• Fix immediate dataset purge in bulk (thanks to @davelopez). Pull Request 15305

• Fix collection drilldown in dataset details view (thanks to @guerler). Pull Request 15309

• Revert check for new legacy API routes (thanks to @davelopez). Pull Request 15320

• Update lists of non-passing CWL conformance tests (thanks to @nsoranzo). Pull Request 15324

• Global drag and drop followup (thanks to @ElectronicBlueberry). Pull Request 15330

• Require selecting a test mode in run_tests.sh (thanks to @nsoranzo). Pull Request 15331

• Fix button alignment and change external icon in Tools List (thanks to @ahmedhamidawan). Pull Request 15333

• Fix view migration for sqlite (thanks to @mvdbeek). Pull Request 15341

• Stabilize mulled integration tests (thanks to @mvdbeek). Pull Request 15347

• Update purge dataset for new testcase-less testing (thanks to @mvdbeek). Pull Request 15348