23.0 Galaxy Release (April 2023)

Highlights

This release includes significant user interface changes enhancing accessibility and usability. This includes a new tool search, modernized multi-history view, new tag displays, theme support, and better drag and drop handling across the application. There are also brand new ‘Datatypes’ and ‘About This Galaxy’ interfaces. Interactive Tools are more seamlessly integrated into the user interface and Galaxy also comes with a new MGnify Notebook IT. The workflow editor has been completely overhauled with significant improvements to usability and extensibility, including new conditional workflow step functionality.

Check out the 23.0 user release notes for all the details. Are you an admin? See the Administration Notes below, and check out some admin relevant PRs.

Get Galaxy

The code lives at GitHub and you should have Git to obtain it.

To get a new Galaxy repository run:

$ git clone -b release_23.0 https://github.com/galaxyproject/galaxy.git

To update an existing Galaxy repository run:

$ git fetch origin && git checkout release_23.0 && git pull --ff-only origin release_23.0

See the community hub for additional details on source code locations.

Administration Notes

Dependencies for various built-in converter tools have been changed from pysam to samtools. Please make sure you install these dependencies through the admin panel or manually. See more details on the PR here.

Configuration default values are no longer read from the sample files – they now come directly from the config schema. If you are relying on local changes to sample files, be aware that you will need to adjust your configuration. See more details on configuration changes on the PR here.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample

• gravity

config/galaxy.yml.sample:galaxy

• mapping.tool_shed.mapping.bootstrap_admin_api_key

• mapping.tool_shed.mapping.sentry_traces_sample_rate

Changed

The following configuration options have been changed

config/galaxy.yml.sample:galaxy

• mapping.galaxy.mapping.job_config_file.default has changed from

  job_conf.xml
  

  to

  job_conf.yml
  

• mapping.galaxy.mapping.logo_src.default has changed from

  /static/favicon.png
  

  to

  /static/favicon.svg
  

• mapping.galaxy.mapping.tool_recommendation_model_path.default has changed from

  https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5
  

  to

  https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model_v_0.2.hdf5
  

• mapping.galaxy.mapping.topk_recommendations.default has changed from

  10
  

  to

  20
  

Removed

The following configuration options have been completely removed

config/galaxy.yml.sample:galaxy

• mapping.reports.mapping.debug

• mapping.reports.mapping.use_lint

• mapping.reports.mapping.use_profile

New Configuration Files

The following files are new, or recently converted to yaml

• config/themes_conf.yml.sample

Deprecation Notices

Trackster is deprecated and will be removed in the next release. This functionality will be provided by other visualization plugins (IGV.js, JBrowse).

Workflow exports to myexperiment.org are deprecated and will be removed in the next release.

Release Notes

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

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