22.05

Enhancements

• Add new molecule datatypes (thanks to @muon-spectroscopy-computational-project). Pull Request 12375

• Add DEFERRED datasets to Galaxy (thanks to @jmchilton). Pull Request 12533

• Add Storage dashboard (thanks to @davelopez). Pull Request 13113

• Add built-in converters to tool panel (thanks to @jdavcs). Pull Request 13447

• Enable infinite scrolling / pagination for history and collection items (thanks to @guerler). Pull Request 13477

• Replace SQLAlchemy Migrate with Alembic (thanks to @jdavcs). Pull Request 13513

• Add filtering to new History (thanks to @guerler). Pull Request 13591

• Expose input step order and rework calculation of node position in the workflow editor (thanks to @simonbray). Pull Request 13641

• Focus cursor in text box after clearing search term (thanks to @ahmedhamidawan). Pull Request 13672

• Add 3D PCA visualization (thanks to @xtrojak). Pull Request 13771

• Replace bootstrap-tour.js with popper.js (thanks to @guerler). Pull Request 13778

• Add and update various interactive tools (thanks to @gmauro). Pull Request 13811

• Add more bulk operations to Beta History (thanks to @davelopez). Pull Request 13877

• Update color scheme collection progress bar (thanks to @assuntad23). Pull Request 14031

• Add gulp target for force-rebuild of viz plugins (thanks to @dannon). Pull Request 13370

• Add mzqc datatype (thanks to @bernt-matthias). Pull Request 13564

• Update mypy to 0.942 and fix new mypy errors (thanks to @nsoranzo). Pull Request 13650

• Create data_fetch and set_metadata celery tasks (thanks to @mvdbeek). Pull Request 13655

• Add bigWig to Wig converter (thanks to @gallardoalba). Pull Request 13708

• Replace last use of deprecated imp module (thanks to @nsoranzo). Pull Request 13817

• Add support for gz-compressed gfa1 and gfa2 files (thanks to @gallardoalba). Pull Request 13927

• New Datatype: QIIME 2 (thanks to @ebolyen). Pull Request 14216

• Add scool datatype (thanks to @bernt-matthias). Pull Request 14480

• Add JupyTool, user-configurable interactive Jupyter-based tool (thanks to @blankenberg). Pull Request 13606

• Simplified workflow form runtime options (thanks to @jmchilton). Pull Request 13613

• Selenium tests for much of #13600 (thanks to @jmchilton). Pull Request 13673

• Rework workflow index API for more consistency between deleted/hidden and showing shared workflows (thanks to @jmchilton). Pull Request 13699

• Implement API endpoints and tests for workflow sharing options (thanks to @jmchilton). Pull Request 13719

• Fix workflow file import and enhance UX for workflow imports (thanks to @davelopez). Pull Request 13754

• Implement more useful workflow tagging (thanks to @jmchilton). Pull Request 13786

• Implement initial jest unit tests for WorkflowList.vue (thanks to @jmchilton). Pull Request 13856

• Use an Enum for invocations view (thanks to @jmchilton). Pull Request 13875

• Workflow List Vue Component Improvements (thanks to @jmchilton). Pull Request 13876

• More Workflow List Component Improvements (thanks to @jmchilton). Pull Request 13892

• API workflow index allow ‘searching’ by owner (thanks to @jmchilton). Pull Request 13934

• More Uniform URI Access and Validation (thanks to @jmchilton). Pull Request 13947

• Localize workflow deletion confirmation message (thanks to @jmchilton). Pull Request 13987

• Add workflow deletion selenium tests (thanks to @jmchilton). Pull Request 13994

• Update Client dependency, swap to node 16 (thanks to @dannon). Pull Request 13282

• Run jest tests using node 16 in CI (thanks to @davelopez). Pull Request 13434

• Drop last references to uWSGI (thanks to @nsoranzo). Pull Request 13593

• Add support for gulp build process to use a configurable directory (thanks to @dannon). Pull Request 13657

• Formalize supported browsers, drop transpilation, enforce with eslint (thanks to @dannon). Pull Request 13709

• Swap to vue/recommended eslint (thanks to @dannon). Pull Request 13781

• Citation separation (thanks to @dannon). Pull Request 13847

• Add client build timestamp to application config (thanks to @dannon). Pull Request 13874

• Attach dataset source in model store imports (thanks to @mvdbeek). Pull Request 13560

• Overhaul job metrics (thanks to @jmchilton). Pull Request 13634

• More Python typing around job evaluation code (thanks to @jmchilton). Pull Request 13659

• Migrate jobs index to FastAPI controller (thanks to @jmchilton). Pull Request 13767

• Port api/tools/fetch to FastAPI, add schema, and use __FETCH_DATA__ in most tests (thanks to @mvdbeek). Pull Request 13793

• Jobs Index and Grid Improvements (thanks to @jmchilton). Pull Request 13893

• make maximum number of retries for username validation configurable (thanks to @bernt-matthias). Pull Request 13177

• Workflow invocation pagination (thanks to @mvdbeek). Pull Request 13183

• Menu cleanup (thanks to @dannon). Pull Request 13288

• Add celery and gravity files to .gitignore (thanks to @davebx). Pull Request 13310

• Drop remaining references to uWSGI (thanks to @mvdbeek). Pull Request 13585

• Remove tus uploads during fetch data job (thanks to @mvdbeek). Pull Request 13945

• A few small Gravity updates (thanks to @natefoo). Pull Request 13995

• Add log rotation options and update logging documentation (thanks to @natefoo). Pull Request 14457

• Allow site-specific history default, leave fallback option to legacy (thanks to @dannon). Pull Request 11748

• Check prefix before complete loading when checking yaml and cwl tools (thanks to @bernt-matthias). Pull Request 12604

• Maintain redirect if login is necessary (thanks to @mvdbeek). Pull Request 13274

• Update Python dependencies (thanks to @galaxybot). Pull Request 13312

• Replace data providers and scrolling in new history (thanks to @guerler). Pull Request 13318

• Block workflow invocation if wrong tool versions installed (thanks to @simonbray). Pull Request 13335

• Report code coverage (for pytest test suites) (thanks to @mvdbeek). Pull Request 13358

• Feature/hujambo dunia/issue 12022/20220211 workflows node overlap enhancement (thanks to @hujambo-dunia). Pull Request 13361

• Update Python dependencies (thanks to @galaxybot). Pull Request 13364

• Split loading current history from loading all histories (thanks to @mvdbeek). Pull Request 13367

• Add source_metadata attribute for workflows imported using TRS ID or via URL (thanks to @simonbray). Pull Request 13376

• Allow legacy EDAM mappings (thanks to @jmchilton). Pull Request 13413

• Add sorting function to Saved Rules Selector (thanks to @assuntad23). Pull Request 13427

• Add tooltip preview for rules in SavedRulesSelector (thanks to @assuntad23). Pull Request 13438

• Update Python dependencies (thanks to @galaxybot). Pull Request 13449

• let linter check for duplicated names/labels (thanks to @bernt-matthias). Pull Request 13459

• Small enhancements from the deferred data branch (thanks to @jmchilton). Pull Request 13475

• Various Celery Framework Enhancements (thanks to @jmchilton). Pull Request 13488

• Update Python dependencies (thanks to @galaxybot). Pull Request 13490

• Run tests with metadata_strategy: extended on weekly schedule (thanks to @mvdbeek). Pull Request 13503

• Integration end-to-end test for PDF export (thanks to @jmchilton). Pull Request 13504

• Add API endpoint to recalculate user disk usage (thanks to @davelopez). Pull Request 13508

• Add retries to test_github_search (thanks to @davelopez). Pull Request 13509

• More small atomic enhancements from the deferred data branch (thanks to @jmchilton). Pull Request 13517

• Disable implicit optional types (thanks to @jmchilton). Pull Request 13519

• Update Python dependencies (thanks to @galaxybot). Pull Request 13530

• Enable automatically loading webhook based on url (thanks to @hexylena). Pull Request 13535

• Card expansion animation in new history (thanks to @dannon). Pull Request 13545

• History bulk operations (thanks to @davelopez). Pull Request 13555

• Allow setting a workflow as (un)importable via the API (thanks to @simonbray). Pull Request 13571

• Add nonce mismatch hint to exception msg (thanks to @afgane). Pull Request 13572

• Add legacy routes to openapi schema (thanks to @mvdbeek). Pull Request 13579

• Add pre-commit config (thanks to @mvdbeek). Pull Request 13580

• linter: allow setting output format with actions (thanks to @bernt-matthias). Pull Request 13583

• Expose TRS id of imported workflows in the UI (thanks to @simonbray). Pull Request 13600

• Improve matching reliability, add test cases (thanks to @guerler). Pull Request 13623

• Update Python dependencies (thanks to @galaxybot). Pull Request 13625

• Add advanced filtering panel to history, align appearance of panels (thanks to @guerler). Pull Request 13626

• Feature for #13517: Workflow Editor - Scroll Wheel Zoom feature (thanks to @ahmedhamidawan). Pull Request 13630

• Add optional dependency on total-perspective-vortex (thanks to @nuwang). Pull Request 13636

• Decouple legacy model from new history proxy, consolidate history stores (thanks to @guerler). Pull Request 13646

• Porting undocumented API: ‘/api/groups/{encoded_group_id}/users’ to FastAPI (thanks to @shivani-sangwan). Pull Request 13648

• Adjust new history navigation header (thanks to @guerler). Pull Request 13649

• Speed up sniffers by using lru_cache on ffprobe, skip binary sniffers on text files (thanks to @mvdbeek). Pull Request 13654

• Update Python dependencies (thanks to @galaxybot). Pull Request 13661

• Disable implicitly attaching HDAs to histories (thanks to @jmchilton). Pull Request 13670

• Use authenticated git protocol in pre-commit repo (thanks to @davelopez). Pull Request 13680

• Use API link to download datasets (thanks to @davelopez). Pull Request 13681

• Add OIDC PKCE parameter support (thanks to @gecage952). Pull Request 13683

• Infrastructure for building dynamic files for download asynchronously (thanks to @jmchilton). Pull Request 13691

• Update irods client (thanks to @kxk302). Pull Request 13694

• Update Python dependencies (thanks to @galaxybot). Pull Request 13702

• Display History Selection Status in Operations (thanks to @guerler). Pull Request 13705

• Update migrations documentation (inline + readme) (thanks to @jdavcs). Pull Request 13710

• Add more type annotations to test populators (thanks to @nsoranzo). Pull Request 13716

• Watch changes to history object instead of changed history items (thanks to @guerler). Pull Request 13721

• Anonymous user history menu fixes (thanks to @dannon). Pull Request 13724

• Implement pagination of workflows grid (thanks to @jmchilton). Pull Request 13725

• Workflow index API fix and testing (thanks to @jmchilton). Pull Request 13733

• Update Python dependencies (thanks to @galaxybot). Pull Request 13735

• Add history component tests (thanks to @guerler). Pull Request 13739

• Highlight Inputs for a given dataset/collection in the history (thanks to @ahmedhamidawan). Pull Request 13740

• Add Number of Hidden/Deleted Datasets to History Details (thanks to @ahmedhamidawan). Pull Request 13752

• Respect conda channels in mulled docker container building (thanks to @bernt-matthias). Pull Request 13755

• Process pasted content with tus (thanks to @jdavcs). Pull Request 13770

• Restore homogeneous dataset collection indicator (thanks to @davelopez). Pull Request 13772

• Adjust tours and tour tests to new history (thanks to @guerler). Pull Request 13777

• Switch workflow sharing to common Vue component (thanks to @jmchilton). Pull Request 13780

• Replace 2 uses of deprecated imp module (thanks to @nsoranzo). Pull Request 13784

• Fix slow download of large files (thanks to @mvdbeek). Pull Request 13789

• Update committers list (thanks to @jdavcs). Pull Request 13791

• Allow users to view invocations only for a particular workflow (thanks to @jmchilton). Pull Request 13792

• Update Python dependencies (thanks to @galaxybot). Pull Request 13797

• Adjustments to hidden/deleted history links (thanks to @guerler). Pull Request 13802

• Highlight filter textfield when populated (thanks to @ahmedhamidawan). Pull Request 13806

• Limit Custos SDK logging from showing up in Galaxy (thanks to @afgane). Pull Request 13808

• Use load_app_properties() to load Galaxy config file (thanks to @nsoranzo). Pull Request 13809

• Improve assert error for transient citation rendering test issue (thanks to @jmchilton). Pull Request 13814

• Add allowance for members changing their own name… (thanks to @dannon). Pull Request 13819

• Populate filterSettings when filterText changes (thanks to @ahmedhamidawan). Pull Request 13821

• Custos Login Ambiguity enhancement (thanks to @ahmedhamidawan). Pull Request 13829

• Update Python dependencies (thanks to @galaxybot). Pull Request 13836

• Beta History: display ‘processing’ message while running bulk operations (thanks to @davelopez). Pull Request 13844

• Typing fixes from deferred data branch (thanks to @jmchilton). Pull Request 13845

• Beta History: display global history bulk operations only when necessary (thanks to @davelopez). Pull Request 13846

• Beta History: notify query selection break (thanks to @davelopez). Pull Request 13850

• Improved typing of Galaxy model store related stuff (thanks to @jmchilton). Pull Request 13861

• galaxy-tool-util: better link in the README (thanks to @mr-c). Pull Request 13863

• Various CI fixes and enhancements (thanks to @nsoranzo). Pull Request 13864

• Workflow Index Fixes and Improvements (thanks to @jmchilton). Pull Request 13867

• Pages Index API Improvements (thanks to @jmchilton). Pull Request 13870

• Don’t reprint a traceback that has already been printed at the end of galaxy-tool-test (thanks to @natefoo). Pull Request 13872

• Infrastructure for Jest Testing of Localization (thanks to @jmchilton). Pull Request 13880

• Decompose History Export UI (thanks to @jmchilton). Pull Request 13908

• Advanced filter menu enhancements (thanks to @ahmedhamidawan). Pull Request 13910

• Beta History: handle bulk operation errors (thanks to @davelopez). Pull Request 13911

• Drop uncredit pull requestor list (thanks to @nsoranzo). Pull Request 13915

• Replace scratchbook with window manager (thanks to @guerler). Pull Request 13922

• Assorted Python typing. (thanks to @jmchilton). Pull Request 13932

• More explicit History Import button (thanks to @ahmedhamidawan). Pull Request 13946

• Update Python dependencies (thanks to @galaxybot). Pull Request 13948

• Recommend rebasing PRs over merging the target branch (thanks to @nsoranzo). Pull Request 13961

• More remove legacy tool dependencies handling in tool shed (thanks to @jmchilton). Pull Request 13966

• Refactor authenticate controller into a services layer (thanks to @jmchilton). Pull Request 13967

• Use colon symbol instead of equal sign in history filters (thanks to @guerler). Pull Request 13971

• Remove can_eliminate_tool_dependency from tool shed code (thanks to @jmchilton). Pull Request 13975

• Update Python dependencies (thanks to @galaxybot). Pull Request 13981

• Run CI on test_base so we can catch issues with packaging (thanks to @jmchilton). Pull Request 13983

• Add history update time to Beta History (thanks to @ahmedhamidawan). Pull Request 13989

• More workflow Jest tests (thanks to @jmchilton). Pull Request 13993

• Small tour tweaks (thanks to @jmchilton). Pull Request 13996

• Add text to history import/switch buttons (thanks to @ahmedhamidawan). Pull Request 14001

• Script to validate tours structure (thanks to @jmchilton). Pull Request 14003

• Cleaner, More Robust Workflow Creation Form Testing Logic (thanks to @jmchilton). Pull Request 14004

• Add galaxy-test-driver to CI package tests (thanks to @jmchilton). Pull Request 14011

• Bring galaxy-test-api under CI also (thanks to @jmchilton). Pull Request 14012

• Update Python dependencies (thanks to @galaxybot). Pull Request 14016

• Use setuptools custom package discovery instead of explicit listing (thanks to @nsoranzo). Pull Request 14022

• Add a tour for deferred datasets (thanks to @jmchilton). Pull Request 14036

• Add tour requirements (thanks to @jmchilton). Pull Request 14037

• Enable change datatype in bulk (thanks to @davelopez). Pull Request 14042

• Updated _generate_invocation_bco to output a valid IEEE-2791-2020 object (thanks to @biocompute-objects). Pull Request 14048

• Swap new hidden icon from ‘lock’ to ‘eye-slash’ (thanks to @dannon). Pull Request 14052

• Restore section and repeat block help in forms (thanks to @guerler). Pull Request 14064

• Update Mercurial to 6.1.4 (thanks to @natefoo). Pull Request 14075

• Prefer venv module over virtualenv (thanks to @nsoranzo). Pull Request 14077

• Update Python dependencies (thanks to @galaxybot). Pull Request 14104

• Rephrase ‘updated’ to ‘refreshed’ in history counter (thanks to @simonbray). Pull Request 14113

• Support bulk dbkey and datatype collection changes (thanks to @mvdbeek). Pull Request 14172

• Add release tag to client-submitted sentry events (thanks to @dannon). Pull Request 14205

• Add selenium tests for uploads (thanks to @jdavcs). Pull Request 14232

• Only serialize history if changed since last check (thanks to @mvdbeek). Pull Request 14251

• Add purged dataset badge (thanks to @davelopez). Pull Request 14252

• Add Deleted histories plugin for DiskUsage dashboard (thanks to @dannon). Pull Request 14253

• Small speedup by using cache_ok on MetadataType (thanks to @mvdbeek). Pull Request 14255

• Improve handling of non-existent or uninitialized database when running upgrade script (thanks to @jdavcs). Pull Request 14329

• Optimize active counts query (thanks to @mvdbeek). Pull Request 14338

• Include auth in openAPI schema (thanks to @mvdbeek). Pull Request 14345

• Optimize History watcher to request detailed information only for expanded items (thanks to @davelopez). Pull Request 14375

• Support quoted strings in bool expressions (thanks to @davelopez). Pull Request 14406

• Docker k8s ansible fixes (thanks to @nuwang). Pull Request 14449

• Disable translogger middleware by default (thanks to @natefoo). Pull Request 14467

• Fix Jobs API index to accept query parameters as lists (thanks to @davelopez). Pull Request 14482

• Python code formatting standard, automatic (thanks to @dannon). Pull Request 11162

• Remove uWSGI / WSGI support (thanks to @mvdbeek). Pull Request 13071

• Remove custom serialization views for new history, strip unused visualization details (thanks to @guerler). Pull Request 13355

• Touch up framework dependency documentation (thanks to @mvdbeek). Pull Request 13379

• Refactor client tests to use await for mutations (thanks to @davelopez). Pull Request 13408

• Relax checks for test_github_search (thanks to @davelopez). Pull Request 13410

• Disable implicit re-imports across the project (thanks to @jmchilton). Pull Request 13476

• Update logging configuration documentation (thanks to @jdavcs). Pull Request 13481

• Upgrade syntax to Python 3.7 (thanks to @nsoranzo). Pull Request 13500

• Use Vuex for new History (thanks to @guerler). Pull Request 13512

• Add link to issue to error message (thanks to @jdavcs). Pull Request 13529

• Add source_metadata column to workflow table as alembic revision (thanks to @jdavcs). Pull Request 13541

• Misc. SQLAlchemy 2.0 upgrades (thanks to @jdavcs). Pull Request 13562

• Drop redundant legacy API endpoints (thanks to @mvdbeek). Pull Request 13582

• Refactor model/mapping/migrations unit testing infrastructure (thanks to @jdavcs). Pull Request 13588

• Drop unused code (GIE, Swarm, workflow controller methods) (thanks to @mvdbeek). Pull Request 13601

• Fix mypy error on bool expressions (thanks to @davelopez). Pull Request 13712

• Rework admin job tables into reusable Galaxy job table component (thanks to @jmchilton). Pull Request 13769

• Unused client dependency purge (thanks to @dannon). Pull Request 13785

• Separate content item options into component (thanks to @guerler). Pull Request 13798

• Elminate client (direct) dependency on moment.js (thanks to @dannon). Pull Request 13800

• Move some imports on top (thanks to @nsoranzo). Pull Request 13818

• Map Dataset declaratively (thanks to @jdavcs). Pull Request 13833

• Duplicates removed from filtering.js (thanks to @ahmedhamidawan). Pull Request 13835

• ToolSourceDisplay dynamic import for shared libs bundle size improvement (thanks to @dannon). Pull Request 13837

• Refactor toward invocations service layer (thanks to @jmchilton). Pull Request 13862

• Update committer login name (thanks to @jdavcs). Pull Request 13883

• Refactor bulk operation processing (thanks to @guerler). Pull Request 13890

• Beta History Collections: set default visible and deleted state in ContentOptions (thanks to @davelopez). Pull Request 13939

• Small code cleanup fixes to galaxy.model.store related code (thanks to @jmchilton). Pull Request 13944

• Drop update_time from JobStateHistory (thanks to @jdavcs). Pull Request 13997

• Misc client eslint warning fixes (thanks to @dannon). Pull Request 14024

• Move mypy configuration to mypy.ini (thanks to @nsoranzo). Pull Request 14034

• Modernise build of packages (thanks to @nsoranzo). Pull Request 14040

• Update tpv rule module name and constrain version (thanks to @nuwang). Pull Request 14072

• Move Show Histories Side-by-Side menu entry below histories count (thanks to @davelopez). Pull Request 14214

• Avoid loading expensive properties for all histories (thanks to @davelopez). Pull Request 14347

• remove debug statements from tool search (thanks to @bgruening). Pull Request 14386

Fixes

• Properly initialize chart settings for new visualizations (thanks to @guerler). Pull Request 13561

• Point to GTN tutorial in visualizations readme (thanks to @beatrizserrano). Pull Request 13616

• Support phylocanvas autobuild (thanks to @dannon). Pull Request 14023

• Fix a bug in PCA artifact staging that prevents a plugin rebuild (thanks to @dannon). Pull Request 14148

• Visualization fix for MSA (thanks to @dannon). Pull Request 14263

• Tighten sniffers (thanks to @mvdbeek). Pull Request 13959

• Don’t create a BGZF index when running the compressing converter (thanks to @nsoranzo). Pull Request 13969

• Fix bug: set creation_date on dataset.metadata, not dataset (thanks to @jdavcs). Pull Request 14039

• Fix composite datatypes with substitute_name_with_metadata (thanks to @mvdbeek). Pull Request 14053

• Enable generating urls for WSGI routes within FastAPI routes (thanks to @mvdbeek). Pull Request 14066

• Fix collection download for BAM native files (thanks to @mvdbeek). Pull Request 14162

• Make Agp set_meta more lenient (thanks to @astrovsky01). Pull Request 14277

• Deleted, discarded and deferred file not found tweaks (thanks to @mvdbeek). Pull Request 14296

• Fix xml deprecation warning in parse_requirements_from_xml (thanks to @bernt-matthias). Pull Request 14483

• Fix David URL (thanks to @hexylena). Pull Request 13666

• Bump ncb-datasets-cli dependency to 13.14.0 (thanks to @mvdbeek). Pull Request 13853

• Fixes for JupyTool, and overlapping versions with jupyter (thanks to @blankenberg). Pull Request 14309

• Grep1 tool: fix keep_header option (thanks to @jancrichter). Pull Request 14475

• Fix workflow index API boolean parameters (thanks to @jmchilton). Pull Request 13698

• More robust workflow grid selenium tests (thanks to @jmchilton). Pull Request 13855

• Fix workflow bookmarking API (thanks to @jmchilton). Pull Request 13857

• Fix showing invocations for a particular workflow (thanks to @jmchilton). Pull Request 14102

• Fix effective datatype in workflow editor node terminals (thanks to @mvdbeek). Pull Request 14473

• Bump karma from 6.3.13 to 6.3.14 in /client (thanks to @galaxyproject). Pull Request 13357

• Bump follow-redirects from 1.14.7 to 1.14.8 in /client (thanks to @galaxyproject). Pull Request 13365

• Fix UnhandledPromiseRejection in client tests (thanks to @davelopez). Pull Request 13435

• Bump prismjs from 1.26.0 to 1.27.0 in /client (thanks to @galaxyproject). Pull Request 13448

• Bump url-parse from 1.5.4 to 1.5.10 in /client (thanks to @galaxyproject). Pull Request 13450

• Bump karma from 6.3.14 to 6.3.16 in /client (thanks to @galaxyproject). Pull Request 13471

• Update to new @galaxyproject/bootstrap-tour to fix tour anchor selection (thanks to @dannon). Pull Request 13539

• Bump node-forge from 1.2.1 to 1.3.0 in /client (thanks to @galaxyproject). Pull Request 13596

• Bump minimist from 1.2.5 to 1.2.6 in /client (thanks to @galaxyproject). Pull Request 13614

• Fix toolshed style loading (thanks to @dannon). Pull Request 13668

• Fix a broken code block in clientREADME.md (thanks to @NicholasWeiner). Pull Request 13671

• Bump moment from 2.29.1 to 2.29.2 in /client (thanks to @galaxyproject). Pull Request 13703

• Bump async from 2.6.3 to 2.6.4 in /client (thanks to @galaxyproject). Pull Request 13761

• Once committed to a plugin rebuild, stage old hash… (thanks to @dannon). Pull Request 14153

• Update yarn.lock file (thanks to @nsoranzo). Pull Request 14337

• Fix for uploading metadata to remote object store (thanks to @mvdbeek). Pull Request 13348

• SLURM: check first if stopped for cancelled jobs (thanks to @bernt-matthias). Pull Request 13453

• Fix extended_metadata jobs with dce inputs (thanks to @mvdbeek). Pull Request 13553

• Write to exit code file before running metadata script (thanks to @mvdbeek). Pull Request 13557

• Only stream stdout/stderr on kubernetes (thanks to @nsoranzo). Pull Request 13642

• Improve error handling for CLI job runner (thanks to @jmchilton). Pull Request 13759

• Fix error when getting destinations by tag (thanks to @abretaud). Pull Request 13790

• Redirect stderr of trap cleanup (thanks to @mvdbeek). Pull Request 13905

• Redirect stderr of trap cleanup (thanks to @bgruening). Pull Request 13913

• Remove some unused code and fix some typos (thanks to @nuwang). Pull Request 14017

• Fix exception handling in pulsar job runner (thanks to @mvdbeek). Pull Request 14046

• Fix deleting jobs when deleting datasets (thanks to @mvdbeek). Pull Request 14108

• Put revoke for canceling upload task behind enable_celery_tasks flag (thanks to @mvdbeek). Pull Request 14219

• Specify time as datetime object in job queries (thanks to @simonbray). Pull Request 14281

• Drop uWSGI from Galaxy Reports documentation (thanks to @jdavcs). Pull Request 13406

• Fix FormElement: doesn’t populate options for parameters (thanks to @davelopez). Pull Request 13639

• Fix persistent mulled cache unused for repo_has_name (thanks to @mvdbeek). Pull Request 13718

• Fix up configuration for STS. Can’t rebuild config without this (thanks to @dannon). Pull Request 13834

• Misc fixes 2022-05 (thanks to @nsoranzo). Pull Request 13878

• Fix a small error in job doc (thanks to @qiagu). Pull Request 14013

• Interactivetool doc/sample tweaks (thanks to @dannon). Pull Request 14025

• Decrease log level for tool not found (thanks to @mvdbeek). Pull Request 14204

• Drop extension from config_exception (thanks to @mvdbeek). Pull Request 14320

• Fix first startup when only python3 is on PATH (thanks to @mvdbeek). Pull Request 14414

• Pass --cleanenv by default to singularity command (thanks to @mvdbeek). Pull Request 14429

• Doc fixes (thanks to @nsoranzo). Pull Request 14488

• fix drill_down parameters (thanks to @bernt-matthias). Pull Request 12232

• Trim spaces from around email addresses and usernames when registering (thanks to @natefoo). Pull Request 12482

• Fix a bug in username minimum length transformation and set minimum length to 1 (thanks to @bernt-matthias). Pull Request 13195

• Use dev version of Gravity temporarily (thanks to @natefoo). Pull Request 13262

• Update locale.js (thanks to @shenweiyan). Pull Request 13323

• Update Favorite Icon Style (Fixes #12622) (thanks to @ahmedhamidawan). Pull Request 13332

• Bump tensorflow from 2.5.2 to 2.5.3 in /lib/galaxy/dependencies (thanks to @galaxyproject). Pull Request 13345

• Remove node_modules when upgrading Node (thanks to @natefoo). Pull Request 13371

• Fix make diff-format (thanks to @nsoranzo). Pull Request 13397

• Test the webapps package (thanks to @nsoranzo). Pull Request 13402

• Remove uwsgi mention from debug config option (thanks to @jdavcs). Pull Request 13426

• Update config docs (uwsgi >> gunicorn) (thanks to @jdavcs). Pull Request 13456

• Progress towards SQLAlchemy 2.0 (backref_cascade issue) (thanks to @jdavcs). Pull Request 13458

• Fix copy tool id (thanks to @itisAliRH). Pull Request 13463

• Make test_user_library_permissions.py more robust (thanks to @jmchilton). Pull Request 13487

• Expand input parameter workflow steps in workflow run form (thanks to @guerler). Pull Request 13496

• More backref_cascade fixes (SQLAlchemy 2.0) (thanks to @jdavcs). Pull Request 13498

• Fixes for mulled search (thanks to @nsoranzo). Pull Request 13532

• Fix for configfiles examples in galaxy.xsd (thanks to @galaxyproject). Pull Request 13563

• Fix tool shed bootstrapping (thanks to @mvdbeek). Pull Request 13573

• Fix model discovery unit tests (thanks to @nsoranzo). Pull Request 13576

• Fix test_callback_nonce_validation_with_bad_nonce unit test (thanks to @nsoranzo). Pull Request 13577

• Fixes #13542: Click targets for folder explorer seem off (thanks to @ahmedhamidawan). Pull Request 13590

• Fix bug in setting check_migrate_databases config value (thanks to @jdavcs). Pull Request 13594

• Wrap update statement in revision to silence safe error (thanks to @jdavcs). Pull Request 13595

• Fix config file generation if name and filename are given (thanks to @bernt-matthias). Pull Request 13602

• New History: Break item’s name to fit and show completely (thanks to @itisAliRH). Pull Request 13604

• Handle missing error response in failed upload (thanks to @guerler). Pull Request 13611

• Fix bug to enable alembic’s stamp command: revision can be a list of revisions (thanks to @jdavcs). Pull Request 13618

• Check if column exists before executing upgrade/downgrade operations in select revisions (thanks to @jdavcs). Pull Request 13624

• Fix allow admin to use private datasets (thanks to @davelopez). Pull Request 13628

• update beta history from legacy grid-view.js (thanks to @itisAliRH). Pull Request 13629

• Minor tweak to language in history dropdown in beta history (thanks to @dannon). Pull Request 13631

• Potentially fix flakey rename test with beta history (thanks to @jmchilton). Pull Request 13633

• Limit tool parameter value to show only 20 lines with overflow scrolling (thanks to @itisAliRH). Pull Request 13635

• Forward type annotation of depends (thanks to @mvdbeek). Pull Request 13643

• Fix package CI for pysam errors (thanks to @jmchilton). Pull Request 13644

• Fix unselect file in FTP uploader popup (thanks to @itisAliRH). Pull Request 13652

• Correct data fetch API call in the client (thanks to @jmchilton). Pull Request 13669

• Update supervisor config when starting galaxy via run.sh (thanks to @mvdbeek). Pull Request 13674

• Misc fixes (thanks to @nsoranzo). Pull Request 13676

• Fix apache upload config, update gunicorn_extra_args (thanks to @mvdbeek). Pull Request 13682

• Respect GRAVITY_STATE_DIR when activating venv (thanks to @nsoranzo). Pull Request 13685

• Re-add announce_start label to 22.01 release notes (thanks to @nsoranzo). Pull Request 13686

• Fix sorting of recursively discovered datasets (thanks to @bernt-matthias). Pull Request 13688

• Fix download collection button in history panel (thanks to @jmchilton). Pull Request 13690

• Two small fixes to testing infrastructure (thanks to @jmchilton). Pull Request 13693

• Raise a more appropriate error when there’s no version table (thanks to @jdavcs). Pull Request 13695

• Treat db with kombu tables same as empty; adjust tests (thanks to @jdavcs). Pull Request 13700

• Drop symlink to removed file (thanks to @jdavcs). Pull Request 13701

• Better test for kombu-only tables in database (thanks to @nsoranzo). Pull Request 13706

• Fix histories API index filter query params (thanks to @davelopez). Pull Request 13713

• Miscellaneous Histories API fixes (thanks to @davelopez). Pull Request 13717

• Simplify some selenium upload tests to respect either history properly (thanks to @jmchilton). Pull Request 13726

• Converge testing and classes for history options across new and old history panel (thanks to @jmchilton). Pull Request 13727

• Eliminate dependency of legacy history for history sharing tests (thanks to @jmchilton). Pull Request 13729

• Unquote url before using it (thanks to @jdavcs). Pull Request 13730

• Fix test_navigates_galaxy.py for beta history panel (thanks to @jmchilton). Pull Request 13732

• Fix tests for simple_constructs.yml (thanks to @jmchilton). Pull Request 13758

• More robust is_beta_history() testing check (thanks to @jmchilton). Pull Request 13762

• Add an option to disable searching for distributed object store datasets that don’t have an object_store_id (thanks to @natefoo). Pull Request 13764

• Fix race condition in object store dir creation (thanks to @kxk302). Pull Request 13768

• Added exist_ok flag to other object stores (thanks to @kxk302). Pull Request 13773

• Do not store toolbox on ToolPanelViewSearch (thanks to @cat-bro). Pull Request 13776

• Fixes for sharing component error handling (thanks to @jmchilton). Pull Request 13779

• Beta History: fix history query counts synchronization (thanks to @davelopez). Pull Request 13783

• SelectionStatus component/test fixes (thanks to @dannon). Pull Request 13787

• Fix thread accumulation in testing (thanks to @mvdbeek). Pull Request 13788

• Potential fix for certain kind of transient Selenium library errors (thanks to @jmchilton). Pull Request 13794

• Pulsar fix for tools that use chromosome len files (thanks to @gregvonkuster). Pull Request 13803

• Raise RequestValidationError in as_form decorator (thanks to @mvdbeek). Pull Request 13810

• History animation method change, constrained info box (thanks to @dannon). Pull Request 13827

• Trigger scroller refresh when history changes (thanks to @guerler). Pull Request 13832

• Handle fixes in the latest version of mypy. (thanks to @jmchilton). Pull Request 13843

• Improve name tag display in New History (thanks to @ahmedhamidawan). Pull Request 13848

• Beta History: selection and operations small fixes (thanks to @davelopez). Pull Request 13858

• Move TusMiddleware so XForwardedMiddleware runs first (thanks to @mvdbeek). Pull Request 13860

• Fix download of composite files via API (thanks to @mvdbeek). Pull Request 13871

• Update gravity, fixes celery-beat in privsep setup (thanks to @mvdbeek). Pull Request 13879

• Fix flaky user histories providers test (thanks to @guerler). Pull Request 13881

• replace encodestring with encodebytes (thanks to @bgruening). Pull Request 13884

• Allow disabling default history filters (thanks to @guerler). Pull Request 13891

• Backport: Respect GRAVITY_STATE_DIR when activating venv (thanks to @mvdbeek). Pull Request 13897

• Fix typing for unpinned request dependency (thanks to @jmchilton). Pull Request 13898

• Expand/collapse history dataset display content (thanks to @itisAliRH). Pull Request 13899

• Misc fixes 2022-05-11 (thanks to @nsoranzo). Pull Request 13901

• Set default celery app for all threads (thanks to @mvdbeek). Pull Request 13904

• Allow anonymous users to import published histories (thanks to @davelopez). Pull Request 13906

• Fix date handling in workflow editor attributes panel (thanks to @hujambo-dunia). Pull Request 13912

• Beta History: fix reset selection (thanks to @davelopez). Pull Request 13914

• Fix currently failing client tests (thanks to @guerler). Pull Request 13923

• fix two bugs in mulled container building (thanks to @bernt-matthias). Pull Request 13925

• Bulk operations: more API tests & fixes (thanks to @davelopez). Pull Request 13935

• Beta History: allow search datasets by name tag using # (thanks to @davelopez). Pull Request 13952

• Fix job metrics route is missing (thanks to @qiagu). Pull Request 13953

• Bump tensorflow from 2.5.3 to 2.6.4 in /lib/galaxy/dependencies (thanks to @galaxyproject). Pull Request 13954

• Update/restore collection progress bar/13743 (thanks to @assuntad23). Pull Request 13956

• Use INFO log level for irods (thanks to @mvdbeek). Pull Request 13957

• Fix padding in history content items (thanks to @guerler). Pull Request 13962

• Refactoring and testing of workflow parameter handling (thanks to @guerler). Pull Request 13965

• Restore Tour List View as Vue Component [PR for issue #13796] (thanks to @hujambo-dunia). Pull Request 13968

• Bump tensorflow from 2.6.4 to 2.7.2 in /lib/galaxy/dependencies (thanks to @galaxyproject). Pull Request 13972

• Fix tag search non finding non-nametags (thanks to @ahmedhamidawan). Pull Request 13979

• Fix job cancellation on delete dataset (thanks to @davelopez). Pull Request 13986

• Fix the swift integration tests that are using some minio container (thanks to @bgruening). Pull Request 14008

• Only set job state if state is not None (thanks to @mvdbeek). Pull Request 14009

• Fix jest test warnings for saved rules and markdown test (thanks to @guerler). Pull Request 14015

• Add missing webapp to webapp package (thanks to @nuwang). Pull Request 14018

• Fix missing biotools package (thanks to @nuwang). Pull Request 14020

• Remove fabric as a dependency for Galaxy (thanks to @jmchilton). Pull Request 14030

• Add sessioncookie with SameSite=None; secure for tool_runner path (thanks to @mvdbeek). Pull Request 14038

• Job Outputs only appear after they load (thanks to @ahmedhamidawan). Pull Request 14049

• Beta History: Display history counter always (thanks to @davelopez). Pull Request 14070

• Fix test_application_stack_post_fork unit test (thanks to @nsoranzo). Pull Request 14074

• Prevent user from closing the rule builder modal when clicking outside of it (thanks to @assuntad23). Pull Request 14076

• Fix overlapping method/var name in domain validation (thanks to @natefoo). Pull Request 14080

• Fix disable change datatype bulk without celery (thanks to @davelopez). Pull Request 14085

• Fix rule builder input with integer values (thanks to @mvdbeek). Pull Request 14086

• Clear history refresh timeout for snappier operations in new history (thanks to @mvdbeek). Pull Request 14088

• Fix unlimited quota display in Storage Dashboard (thanks to @davelopez). Pull Request 14090

• Update window manager margin (thanks to @simonbray). Pull Request 14091

• Fix minor empty History Filter bug (thanks to @ahmedhamidawan). Pull Request 14092

• Write temporary files created within celery tasks to working directory (thanks to @mvdbeek). Pull Request 14100

• Fix contains_collection check for empty root collections (thanks to @mvdbeek). Pull Request 14103

• Improve robustness of test_exit_code_127 k8s test (thanks to @mvdbeek). Pull Request 14105

• Adjust history store operations when switching between histories (thanks to @guerler). Pull Request 14110

• Mark openPBS integration test cases as xfail (thanks to @mvdbeek). Pull Request 14114

• Fix bulk operations visibility (thanks to @davelopez). Pull Request 14115

• Reduce bulk operations drop-down cutting off (thanks to @davelopez). Pull Request 14116

• Allow downloading individual metadata files in History (thanks to @guerler). Pull Request 14124

• Fix: make tag filtering case insensitive (thanks to @davelopez). Pull Request 14127

• Place progressbar below collection name, allow full width (thanks to @guerler). Pull Request 14138

• Start counting collection elements at 1 (thanks to @guerler). Pull Request 14142

• Add queued as acceptable state for collection states (thanks to @guerler). Pull Request 14143

• Fix: skip setting metadata on deferred datasets when changing datatype in bulk (thanks to @davelopez). Pull Request 14149

• Eliminate dependency on selenium in core galaxy (thanks to @mvdbeek). Pull Request 14150

• Adapt byte content for StreamingResponse (thanks to @mvdbeek). Pull Request 14157

• Fix set_user function (thanks to @mvdbeek). Pull Request 14158

• Fix sqlalchemy error (thanks to @jdavcs). Pull Request 14164

• Fix importing whole folders as datasets (thanks to @mvdbeek). Pull Request 14167

• Drop history context menu purge command (thanks to @dannon). Pull Request 14170

• History edit attributes tweaks (thanks to @dannon). Pull Request 14171

• Fix dataset link copy (thanks to @dannon). Pull Request 14176

• Fix draggable source for content items (thanks to @dannon). Pull Request 14179

• Deferred data fixes (thanks to @mvdbeek). Pull Request 14181

• Show job progress bar while there are non-terminal jobs, declutter text (thanks to @assuntad23). Pull Request 14182

• Switch History Modal: fix pagination (thanks to @davelopez). Pull Request 14183

• Fix histories API URL building (thanks to @davelopez). Pull Request 14186

• Fix logic around tool favorites for anonymous users (thanks to @jmchilton). Pull Request 14189

• Fix FilesDialog navigation back when a file source shows an error (thanks to @davelopez). Pull Request 14190

• Send composite datasets directly to tusUpload (thanks to @jdavcs). Pull Request 14191

• Support stop_job param in query string (thanks to @mvdbeek). Pull Request 14194

• Replace release note videos with youtube links (thanks to @hexylena). Pull Request 14201

• Add SuppressNoResponseReturnedMiddleware (thanks to @mvdbeek). Pull Request 14202

• Shift ‘queued’ state lower in priority in collection status (thanks to @dannon). Pull Request 14217

• Generate the headers handson table uses to avoid missing header issue (thanks to @assuntad23). Pull Request 14218

• Fixes for the tus resumable upload command line script (thanks to @natefoo). Pull Request 14221

• HistoryFilters datepicker fix: date now shows up in field (thanks to @ahmedhamidawan). Pull Request 14226

• Citation link decoding fix (thanks to @dannon). Pull Request 14231

• Place watchHistory logic in try/catch/finally (thanks to @mvdbeek). Pull Request 14233

• Fix validation of nested element fetch data payloads (thanks to @mvdbeek). Pull Request 14245

• History watch throttling – relax when backgrounded (thanks to @dannon). Pull Request 14264

• Fix History dataset database entry overflow (thanks to @ahmedhamidawan). Pull Request 14266

• Allow delete option when history items are shown outside of panel (thanks to @guerler). Pull Request 14269

• Replace old storage FAQ in preferences (thanks to @davelopez). Pull Request 14270

• Fix ReviewCleanupDialog state in Storage Dashboard (thanks to @davelopez). Pull Request 14271

• Drop exception catching when querying db for session (thanks to @mvdbeek). Pull Request 14274

• Small tour fixes (thanks to @jmchilton). Pull Request 14280

• Fix encoding Decimal values and inf/-inf (thanks to @mvdbeek). Pull Request 14284

• Drop dataset error controller method (thanks to @mvdbeek). Pull Request 14287

• Fix tag autocomplete for strings that need url encoding (thanks to @mvdbeek). Pull Request 14288

• Fix display_as with authz_method=rbac (thanks to @mvdbeek). Pull Request 14289

• Check for app_name and link_name before unquoting (thanks to @mvdbeek). Pull Request 14291

• Avoid race condition in disk object store delete (thanks to @mvdbeek). Pull Request 14292

• Increase contrast of Beta label (accessibility) in Storage Dashboard (thanks to @davelopez). Pull Request 14302

• Sort histories in history switcher by most recently updated (thanks to @davelopez). Pull Request 14307

• Fix jobs API not allowing dates for date_range_min and date_range_max (thanks to @nsoranzo). Pull Request 14315

• Prevent iframe from interfering with drop events (thanks to @guerler). Pull Request 14318

• Fix local version switching (thanks to @mvdbeek). Pull Request 14319

• Add HREF links to some history item actions (thanks to @davelopez). Pull Request 14325

• Attempt to use epoch of client build time for cache busting (thanks to @mvdbeek). Pull Request 14328

• Fix filtering by an extension list in dataset API (thanks to @nsoranzo). Pull Request 14330

• fix startswith attribute of <options> (thanks to @bernt-matthias). Pull Request 14332

• Drop serverside i18n (thanks to @dannon). Pull Request 14334

• Upgrade FastAPI to 0.79.0 (thanks to @mvdbeek). Pull Request 14335

• Avoid FileNotFoundError when Dataset is purged, but HDA is not (thanks to @mvdbeek). Pull Request 14336

• Don’t hit object store when getting size (thanks to @mvdbeek). Pull Request 14340

• Fix GET /api/whoami when last_password_change is NULL (thanks to @nsoranzo). Pull Request 14342

• Fix oldstyle dataset display (thanks to @dannon). Pull Request 14343

• Reload histories when the user ‘really’ changes (thanks to @davelopez). Pull Request 14349

• Workflow download API: check if a workflow is importable (not published) (thanks to @nsoranzo). Pull Request 14355

• Keep current history details on list of histories update (thanks to @davelopez). Pull Request 14357

• Fix handling + encoding of spaces in tool names (thanks to @hexylena). Pull Request 14358

• Fix enable_account_interface option hiding too much (thanks to @davelopez). Pull Request 14363

• Fix tool search config defaults (thanks to @dannon). Pull Request 14364

• Fixed tool_utils types & schema-salad pin (thanks to @mr-c). Pull Request 14371

• Tool search backend bug fixes (thanks to @neoformit). Pull Request 14372

• Fix incorrect history swapping in some cases where we swap on the client but the server is never notified (thanks to @dannon). Pull Request 14376

• Fix unhashable type in history contents API (thanks to @davelopez). Pull Request 14388

• Fix validation issue for dataset_details (thanks to @davelopez). Pull Request 14395

• Always allow ‘copy datasets’ action in history, even when empty (thanks to @dannon). Pull Request 14402

• Calculate CRC32 for files in size between 1444 and 1459 bytes (thanks to @mvdbeek). Pull Request 14417

• Fix additional errors when requesting dataset details in history contents (thanks to @davelopez). Pull Request 14418

• Fix number of jobs submitted display in tool success (thanks to @dannon). Pull Request 14420

• Fix workflow direct step insertion in workflow editor (thanks to @dannon). Pull Request 14424

• Make history contents filter with contains case insensitive (thanks to @davelopez). Pull Request 14426

• Update pylibmagic and gravity (thanks to @mvdbeek). Pull Request 14428

• Fix cache image singularity resolver if path contains uppercase chars (thanks to @mvdbeek). Pull Request 14431

• Revert startswith of tool parameter options (thanks to @qiagu). Pull Request 14440

• Fix console errors when stored workflow id hasn’t been fetched yet (thanks to @mvdbeek). Pull Request 14444

• Register trailing slashes in API routes (thanks to @mvdbeek). Pull Request 14452

• Fix data_range_{min,max} parsing (thanks to @mvdbeek). Pull Request 14456

• Fix doc versioning banner and other doc fixes (thanks to @nsoranzo). Pull Request 14466

• Bump Gravity version to 0.13.3 (thanks to @natefoo). Pull Request 14471

• Update error message when building ucsc_build_sites.txt fails (thanks to @mvdbeek). Pull Request 14479