21.01

Enhancements

• Galaxy Markdown enhancements including integration of visualizations - allow embedding visualizations in Galaxy Markdown (workflow invocation reports and pages) with Markdown editor support and allow exporting workflow reports directly to Galaxy Pages. Pull Request 10241, Pull Request 10288, Pull Request 10404

• Add workflow invocation detail component. Pull Request 10976

• History panel rewrite (available in the UI as a beta option). Pull Request 8441, Pull Request 11071, Pull Request 10971

• Allow organizing the panel via EDAM ontology annotations. (thanks to @hexylena). Pull Request 10592

• Large overhaul over history import and export - including improved user experience, APIs, and allowing importing and exporting to file sources plugins (including FTP). Pull Request 11054, Pull Request 10993

• Various substantial improvements to data library user interface and performance (thanks to @OlegZharkov). Pull Request 10204, Pull Request 11099, Pull Request 10557, Pull Request 10558, Pull Request 10807

• Script for finding missing db indexes Pull Request 10350

• Implement Galaxy database model schema rendering script. Pull Request 10571

• Allow configuration of activation email message. Pull Request 10959

• UI & API for Supporting Best Practice Workflows Pull Request 10988, Pull Request 11025

• Implement edit & upgrade subworkflow buttons in workflow editor. Pull Request 11032

• Implement user-facing objectstore metadata. Pull Request 10233

• Fixes and improvements to favorited tools in the tool panel. Pull Request 10955, Pull Request 9873

• Move upload button below Tool panel header, increase size, add label. Pull Request 10499, Pull Request 10696

• Fix upload button tooltip. (thanks to @OlegZharkov). Pull Request 11541

• Fix markdown tag for history dataset collections. Pull Request 11587

• Add author and license metadata and corresponding web microdata annotations for tools and workflows. Pull Request 10408

• iRODS data migration script (thanks to @kxk302). Pull Request 10125

• Integrate NORA’s image viewer - a medical image viewer and annotation tool. (thanks to @bgruening). Pull Request 11035

• Add the OpenSeadragon viewer and extend datatypes for deep zoom images (thanks to @gregvonkuster). Pull Request 10756, Pull Request 11017, Pull Request 10546

• Add gfa2 datatype (thanks to @bernt-matthias). Pull Request 10270

• Add nifti1 and nifti2 datatype (thanks to @bgruening). Pull Request 11020

• Add tck and trk datatype (thanks to @bgruening). Pull Request 11021

• Add gifti datatype (thanks to @bgruening). Pull Request 11028

• Add cmap datatype (thanks to @jaidevjoshi83). Pull Request 11471

• Expand image formats for viewing in OpenSeadragon (thanks to @gregvonkuster). Pull Request 11017

• add ome.tiff datatype (thanks to @qiagu). Pull Request 10349

• Add datatype converters for various MD filetypes (thanks to @simonbray). Pull Request 10757

• Add Apache Parquet datatype Pull Request 11047

• Add msf datatype (thanks to @nsoranzo). Pull Request 11084

• Allow the “Apply Rules” tool to attach tags to output datasets. Pull Request 10382

• Implement mypy type checking for the Galaxy Python backend. Pull Request 11009, Pull Request 11037, Pull Request 11022, Pull Request 11007, Pull Request 11027, Pull Request 11039, Pull Request 11000, Pull Request 10992, Pull Request 11013, Pull Request 11019

• Allow setting file download filename_pattern by client. Pull Request 11108

• Add FastAPI migration of licenses endpoints (thanks to @davelopez). Pull Request 11056

• Improvements to workflow imports from GA4GH TRS servers (thanks to @OlegZharkov). Pull Request 10805, Pull Request 10619

• Major enhancements for the galaxy-tool-test script (installed as part of the PyPI package galaxy-tool-util). Pull Request 10620, Pull Request 10779, Pull Request 10908, Pull Request 10879, Pull Request 10725, Pull Request 10735 Pull Request 10767

• Add ffindex and ffdata database file types Pull Request 11218

• Add compressed paf datatype (thanks to @astrovsky01). Pull Request 11567

• Speedup xml replacement Pull Request 10804

• Allow build_list tool inputs to be optional Pull Request 10871 (thanks to @abretaud). Pull Request 10878

• Revise tool inputs to allow nested parameters and allow build_for_rerun and other (thanks to @simonbray). Pull Request 11332, Pull Request 10720

• Allow empty file uploads (thanks to @bernt-matthias). Pull Request 11079

• Convert collection creator user interface components to Vue. Pull Request 10240

• Disable dataset edit button after the dataset has been deleted (thanks to @simonbray). Pull Request 10589

• update the cellxgene IT container (thanks to @bgruening). Pull Request 11546

• Implement expression tool for picking non-null values for CWL-style merging of conditional branches in native Galaxy workflows. Pull Request 10712

• Add and document API for publishing and tagging workflows (thanks to @simonbray). Pull Request 10748

• Allow relative paths when staging jobs (e.g. with planemo run) (thanks to @simonbray). Pull Request 10886

• Various small cleanups and improvements to the workflow editor and migrations toward Vue. Pull Request 10999, Pull Request 11001, Pull Request 11024, Pull Request 10769, Pull Request 11036, Pull Request 11042, Pull Request 11041, Pull Request 10580, Pull Request 11046

• Add FastAPI as backend and start porting backend to an ASGI webapp to enable modern programming features such a message queues and web sockets. Pull Request 10823, Pull Request 11074

• Follow-up on best practice workflow linting user interface component Pull Request 11140

• Bug fix - cannot set dbkeys in workflow tests. Pull Request 11543

• Replace StreamBall, replace tarballs with zip Pull Request 10919

• Move upload button below Tool panel header, increase size, add label. Pull Request 10499

• Convert dataset and job information displays to Vue (thanks to @OlegZharkov). Pull Request 10327, Pull Request 10353, Pull Request 10980

• Simpler API for getting user API key. Pull Request 10522

• Add S3 plugin for remote files browser. Pull Request 10523

• Fixed sync between legacy galaxy variable and Vuex current history Pull Request 11172

• Set undesired execution hosts to avoid in LSF (thanks to @pcm32). Pull Request 10260

• Limit CPUs used in docker containers (thanks to @bernt-matthias). Pull Request 10373

• Adding nodeSelector to K8S runner job pod spec (thanks to @almahmoud). Pull Request 10380

• Cache container resolution during job execution Pull Request 10451

• Support stopping Interactive Tools without deleting their outputs Pull Request 10497

• Override some k8s runner params with destination params (thanks to @almahmoud). Pull Request 10520

• Improve database operation job submission performance Pull Request 10539

• Don’t specify default bind type for singularity (thanks to @bernt-matthias). Pull Request 10625

• Allow extra job metadata to be specified for k8s (thanks to @nuwang). Pull Request 11078

• Implement backend quota interface - with better logic isolation and unit tests. Pull Request 10212

• When compiling dynamic installation tool conf files, ensure location is actually writeable. Pull Request 10387

• Display minutes in admin jobs cutoff (thanks to @OlegZharkov). Pull Request 10493

• Display user disk usage in admin user panel. Pull Request 10666

• Allow GA4GH TRS servers configuration to not be undefined/empty (thanks to @selten). Pull Request 10817

• Drop legacy_eager_objectstore_initialization config option. Pull Request 10828

• Clarify master_api_key intended use (thanks to @nsoranzo). Pull Request 11067

• Allow InteractiveTools to use path-based proxying when requires_domain=False. Pull Request 8596

• Add setting that lets admins enable/disable the tool document cache Pull Request 11186

• Add warning for non-existing tool versions on tool form (thanks to @OlegZharkov). Pull Request 10139

• Add default dbkey when collecting builds. Pull Request 10667

• Fix running subworkflows with parameter input steps. Pull Request 10722

• Fix workflow runs with data_column runtime parameter changes. Pull Request 11596

• Various fixes for copying workflow nodes. Pull Request 11602

• Fix optional workflow parameter inputs not recovered when setting step outputs. Pull Request 11626

• Drop API Key listings from admin user list. Pull Request 10745

• Render OpenEBench link in new consolidated tool metadata. Pull Request 10789

• Rework arguments to a couple model security operations to allow greater reuse. Pull Request 10835

• Add cancel option to workflow create form. Pull Request 10953

• Cleanup client unit test removing jquery and mocking ajax calls. Pull Request 10904

• Add tooltip to workflow node output checkbox. Pull Request 10957

• More structured workflow create and update parameter handling. Pull Request 11016

• Drop temporary hacks for upgrading export jobs from Galaxy 19.01 to 19.05. Pull Request 10990

• Make Selenium BibTeX rendering test more robust. (thanks to @OlegZharkov). Pull Request 10809

• Implement select all box on admin “Manage Dependencies” page. (thanks to @OlegZharkov). Pull Request 10758

• Add link to view dataset in dataset params. (thanks to @simonbray). Pull Request 10752

• Set up confirmation page for new Custos/oidc users. Pull Request 10198, Pull Request 10952

• Add script to diff two release config files. (thanks to @hexylena). Pull Request 10258

• Small optimization for uploads. Pull Request 10316

• More convenient syntax for configuring file source plugins. Pull Request 10326

• Allow planemo run to stage in existing datasets without re-uploading (thanks to @simonbray). Pull Request 10334

• Auto-focus upload name in upload dialog. Pull Request 10487

• Revise style of radio button groups to improve visibility. Pull Request 10489

• Add update time to workflow version selector in workflow editor. Pull Request 10492

• Update authnz to include Azure as IDP (thanks to @cginmn). Pull Request 10413

• Let python-irodsclient session manage connections. Pull Request 10437

• Document workflow model classes (thanks to @innovate-invent). Pull Request 10471

• Update link for Galaxy configuration file in Galaxy debug document. Pull Request 10488

• Add missing documentation for macro elements in XSD (thanks to @davelopez). Pull Request 10495

• Update developer guidelines with instructions for proper commit messages. Pull Request 10498

• Use dataset selector in rules input dialog. Pull Request 10505

• List tool functionality/compatiblity changes with profile version in tool schema (thanks to @bernt-matthias). Pull Request 10798

• Add enumeration restriction to detect_errors in tool XML schema (thanks to @davelopez). Pull Request 10510

• More informative error message for /api/authenticate/baseauth (thanks to @OlegZharkov). Pull Request 10524

• Add more tags to Github. Pull Request 10525

• More comments for rapid testing optional galaxy.files stuff. Pull Request 10526

• Add copy to clipboard button to datasets (thanks to @OlegZharkov). Pull Request 10529

• Add awesome-galaxy repo link to docs (thanks to @innovate-invent). Pull Request 10530

• Generate path resolution note for sample file, docs. Pull Request 10537

• Allow admins to add an additional custom logo to the masthead Pull Request 10540

• Improve performance of copying HDAs and HDCAs. Pull Request 10549

• Update to new LTS nodejs version. Pull Request 10565

• Document data manager repository layout (thanks to @innovate-invent). Pull Request 10573

• Set uwsgi’s honour-stdin option when in debug mode. Pull Request 10577

• Make primary extract workflow action button more visible (thanks to @hexylena). Pull Request 10583

• Allow pgcleanup to redirect logging to stdout (thanks to @gmauro). Pull Request 10594

• Remove IUC conda channel from default configuration (thanks to @bernt-matthias). Pull Request 10608

• Document toolshed repository response object (thanks to @innovate-invent). Pull Request 10633

• Full Python dependencies update (thanks to @nsoranzo). Pull Request 10660

• Rev Python cwltool dependency to 3.0.20201109103151. Pull Request 10658

• Add AnVILFS conditional dependency. (thanks to @almahmoud). Pull Request 11569

• Migrate API tests to GitHub workflow (thanks to @nsoranzo). Pull Request 10674

• Fix metadata_bcf framework test (thanks to @nsoranzo). Pull Request 11603

• Added dockerfile [biohackathon] (thanks to @nuwang). Pull Request 10681

• Harden, formalize ‘null’ handling around boolean tool parameters Pull Request 10694

• Allow expression tools to output copies of input HDAs. Pull Request 10700

• Update ftp document for rounds=100000 (thanks to @linnil1). Pull Request 10701

• Implement and test proper null handling and optional values for integers, floats, and text parameters in tools and workflows. Pull Request 10703

• Re-sync galaxy.tool_util.cwl with CWL branch of Galaxy. Pull Request 10716

• Upgrade syntax using pyupgrade --py36-plus (thanks to @nsoranzo). Pull Request 10751

• Revision of sharing component, adds url copy to clipboard feature Pull Request 10754

• Don’t cancel other selenium steps, if one step fails (thanks to @OlegZharkov). Pull Request 10801

• Extension lookup with lower case extension (thanks to @bernt-matthias). Pull Request 10803

• Retry failing selenium test once Pull Request 10806

• Add GitHub workflow to build docs (thanks to @nsoranzo). Pull Request 10811

• Maintainance Bot with GithubActions (thanks to @OlegZharkov). Pull Request 10813

• document optional default for multiple in xsd (thanks to @bernt-matthias). Pull Request 10819

• Implement read-only conda resolver (alternative) Pull Request 10822

• Improved error handling in API Interactor Pull Request 10833

• Add <filter> inline python example for select type in tool schema docs (thanks to @tensionhead). Pull Request 10838

• Use github-script action for maintenance_bot job too (thanks to @nsoranzo). Pull Request 10844

• Unit testing and optimization for creating private roles and dataset sharing. Pull Request 10845

• Always expand tool about section if metadata is available Pull Request 10847

• Fix tag image in UI for consistency. Pull Request 10853

• Run CI labeler on reopened PRs, but skip if area labels are present (thanks to @nsoranzo). Pull Request 10861

• Allow build_list tool inputs to be optional (thanks to @innovate-invent). Pull Request 10863, Pull Request 10871

• Allow selecting dynamic select parameters by name in the API and tool tests (thanks to @bernt-matthias). Pull Request 10880

• Add screenshot decorators to selenium tests (thanks to @OlegZharkov). Pull Request 10911

• Add version tab which links to release notes to help tab. (thanks to @astrovsky01). Pull Request 10960

• Update locale.js (thanks to @shenweiyan). Pull Request 11011

• Document how parameters in sections are referenced (thanks to @bernt-matthias). Pull Request 11026

• Upload test results as artifact in case of failure (thanks to @nsoranzo). Pull Request 11030

• Remove migration logic that will never be used now. Pull Request 11038

• Support complex markers in run_tests.sh (thanks to @nsoranzo). Pull Request 11045

• Optimized binary datatype sniffing for various binary datatypes. Pull Request 11049

• Move framework tests to GitHub workflows + lint test tools (thanks to @nsoranzo). Pull Request 11055

• Allow setting filename_pattern by client (thanks to @brinkmanlab). Pull Request 11058

• Add validation for tool data_collection parameters (thanks to @bernt-matthias). Pull Request 11063

• Verify behavior of non-existent from_work_dir outputs. Pull Request 11073

• Show OpenAPI documentation for API tags (thanks to @davelopez). Pull Request 11083

• Major overhaul and expansion of documentation for writing tests in Galaxy. Pull Request 11088, Pull Request 11102, Pull Request 11104

• Parallelize client and server builds in dockerfile (thanks to @nuwang). Pull Request 11161

• add more markers for screenshooting (thanks to @OlegZharkov). Pull Request 11171

• Don’t flush for each failed output dataset Pull Request 11282

• Don’t check if item is in list, use set subtraction Pull Request 11284

• Persist scroll/url information for GTN webhook (thanks to @hexylena). Pull Request 11290

• Add tracking code to webhook for GTN stats (thanks to @hexylena). Pull Request 11387

• Sort tool versions from newest to oldest in tool form (thanks to @cat-bro). Pull Request 11490

• Improve API test for changing datatype (thanks to @simonbray). Pull Request 10272

• Various datatype code structure improvements (thanks to @nsoranzo). Pull Request 10279

• Drop unnecessary list casting in Anndata datatype. Pull Request 10296

• Drop unused helpers in web.framework.helpers Pull Request 10345

• Drop support for retired Python 3.5 (thanks to @nsoranzo). Pull Request 10368

• Make MetadataCollection a proper mapping (thanks to @nsoranzo). Pull Request 10374

• Typos and semantic fixes for iRODS object store (thanks to @trel). Pull Request 10423

• Fix K8s job runner typo (thanks to @almahmoud). Pull Request 10501

• Drop communication server. Pull Request 10514

• Add workflow tests for some newer workflow features. Pull Request 10478, Pull Request 10669

• Various small changes to test helper code. Pull Request 10668, Pull Request 10783

• Refactor logic for workflow_step.input_type into model. Pull Request 10657

• Rename flake8 ignorelist. Pull Request 10702

• Rely on emails to determine GitLab users. (thanks to @selten). Pull Request 10830

• Convert datasets.set_edit to modern decorator, reuse manager. Pull Request 10854

• Make model somewhat compatible with sqlalchemy-1.4. Pull Request 10856

• Run maintenance bot only once (thanks to @OlegZharkov). Pull Request 10858

• Replace usage of mkstemp with NamedTemporaryFile. Pull Request 10862

• Small edits objectstore code. Pull Request 10867

• Remove trans from stream_dataset_collection() Pull Request 10907

• Use email_from value from schema for tool error report email. Pull Request 10956

• Drop migration hack for htcondor. (thanks to @bgruening). Pull Request 10991

• Remove unused tag_outputs workflow controller action. Pull Request 11040

• Fix workflow terminals not updating appropriately. Pull Request 11542

Fixes

• Hide purged datasets from visualizations (thanks to @OlegZharkov). Pull Request 10483

• Fix reference error in MVP client application (thanks to @tmcgowan). Pull Request 10782

• Nora visualization version bump incorporating a few upstream bugfixes. Pull Request 11475

• Cleanup the supported filestypes for Nora. (thanks to @bgruening). Pull Request 11544

• Fix for GTF sniffer (thanks to @mtekman). Pull Request 10588

• Fix AnnData datatype peek (thanks to @mtekman). Pull Request 10986

• Remove mutatable arguments from Pythn function calls (thanks to @bgruening). Pull Request 10998, Pull Request 11003, Pull Request 11006

• Fix mtx unbound error. Pull Request 11368

• Fix sniffers of interval datatypes for files starting with many comments (thanks to @nsoranzo). Pull Request 11416

• Avoid false positives in Phylip sniffer. Pull Request 11595

• Add display_in_upload for protobuf datatypes. Pull Request 11555

• Don’t display obs_names in select list. Pull Request 11574

• Disable tool cache if there is a problem. Pull Request 10808

• Put new toolshed tools in existing tool panel sections if the ID matches. Pull Request 10984

• Make hash selection mandatory in hash tool. Pull Request 11427

• Various Pyiron interactive tool fixes. (thanks to @bgruening). Pull Request 11545

• Allow using Openrefine without data inputs. (thanks to @bgruening). Pull Request 11547

• Set $HOME for interactive tools that require a specific directory. (thanks to @abretaud). Pull Request 11577

• Add checks to workflow toolbox, avoid displaying empty sections. Pull Request 10363

• Filter duplicate workflow output labels when initializing workflow step outputs. Pull Request 10432

• Properly scale workflow node coordinates before saving workflow. Pull Request 10511

• Fix changing versions in workflow editor. Pull Request 10516

• Fix currently failing Selenium tests, move to GitHub workflow. Pull Request 10755

• Don’t preload editor mako with hidden workflows. Pull Request 10759

• Fix generation of BCO object_id and etag (thanks to @nsoranzo). Pull Request 10964

• Record invocation_step outputs as appropriate. Pull Request 10970

• Fix workflow parameter text value restriction when connected to select and text parameter. Pull Request 10975

• Convert deprecated log.warn()` calls to log.warning() (thanks to @bgruening). Pull Request 10996

• Misc fixes (thanks to @nsoranzo). Pull Request 11029

• Maintain expanded state of JobStep during polling Pull Request 11144

• Fix tool version switch in workflow editor. Pull Request 11257

• Fix populated state for empty collections. Pull Request 11312

• Fix Workflow report markdown lost upon renaming the workflow. (thanks to @davelopez). Pull Request 11317

• Fix TypeError in WorkflowsAPIController.get_versions() (thanks to @rikeshi). Pull Request 11373

• Wrap core of workflow monitor thread in try/except. Pull Request 11434

• Fix random-ish workflow error with maximum_workflow_jobs_per_scheduling_iteration. Pull Request 11513

• Mark workflow as changed when editing step label or annotation. Pull Request 11533

• Add input step data label when extracting workflow. Pull Request 11532

• Fix saving FileSource parameter in a workflow. (thanks to @OlegZharkov). Pull Request 11605

• Fix collection mapping over filtered output problem. Pull Request 11621

• Bump client axios dependency from 0.19.2 to 0.21.1. Pull Request 11053

• Improved exception handling for missing job parameter field. Pull Request 10298

• Ensure requirements in a DependenciesDescription is a ToolRequirements (thanks to @nsoranzo). Pull Request 11044

• Allow specifying remote Pulsar app configuration external to job destination attributes to prevent persisting connection secrets. Pull Request 11254, Pull Request 11256, Pull Request 11261

• Fix history import job done before import complete. Pull Request 11170

• Allow specifying remote pulsar app config by path. Pull Request 11191

• Fix jobs finishing after update to 21.01 Pull Request 11330

• Add server name, PID and thread name to each handler log message. (thanks to @nsoranzo). Pull Request 11609, Pull Request 11598

• Don’t log handled exceptions when filling cheetah template. Pull Request 11355

• Update Pulsar client to 0.14.2 Pull Request 11381

• Always mount a writable $_JOB_TMP_DIR when running tools in containers. (thanks to @bernt-matthias). Pull Request 11448

• Restore the ability to pull containers from admin menu. Pull Request 10814

• Fix error in admin panel when creating new quota (thanks to @davelopez). Pull Request 11277

• Fix error on Admin panel when creating or editing Forms (thanks to @davelopez). Pull Request 11388

• Fix DefaultQuotaAssociation access to Enum values (thanks to @davelopez). Pull Request 11511

• Add logging if installable tool config file not found Pull Request 11515

• Fix ToolShed link in Admin->Local Data (thanks to @davelopez). Pull Request 11548

• Properly log out of oidc on galaxy logout (thanks to @juleengraham). Pull Request 10108

• Fix quota meter style. Pull Request 10299

• Fix pytest breakage in package testing. Pull Request 10320

• Update documentation for proftpd configuration (thanks to @FredericBGA). Pull Request 10351

• Add test for data_column parameter referring to non-tabular data (bed) and fix bug. (thanks to @bernt-matthias). Pull Request 10365

• Fix assigning default value to variables in run_test_wrapper.sh (thanks to @nsoranzo). Pull Request 10381

• Fix issues with copying tags and collections. Pull Request 10761

• Fix various style issues with rule builder. Pull Request 10766

• Fix certain classes of workflow extraction on copied objects. Pull Request 11151

• Fix Pulsar client to add tool environment variables to remote jobs. Pull Request 11349

• Fix workflow preview for tool repeat blocks without title. Pull Request 10851

• Fix various issues with the sharing user interface component. Pull Request 11305

• Fix various issues with the admin jobs user interface component. Pull Request 11205

• Fix handling of collection element identifiers in history panel. Pull Request 10427

• Fix report’s library function call in dataset_info.mako. Pull Request 10476

• Fix drag and drop highlighting in tool form for data inputs. Pull Request 10494

• Display consistent format for job runtime (thanks to @kxk302). Pull Request 10504

• Modified list-of-pairs to copy datasets as hidden (thanks to @assuntad23). Pull Request 10508

• Fix search info popup to become hidden on click away (thanks to @astrovsky01). Pull Request 10512

• Disable upload option in default data dialog since history panel is not always available Pull Request 10533

• Fix ObjectUploadTarget handling in tool util staging code. Pull Request 10650

• Fix link to job config sample in docs (thanks to @galaxyproject). Pull Request 10673

• Produce a clean list of dataset instances if not datasets in collection. Pull Request 10676

• Add refresh_time to iRODS configuration, so that connections older than refresh_time are re-created. (thanks to @kxk302). Pull Request 10698

• Fix typo in filter_failed_collection help section Pull Request 10717

• Cleanup announce samples. Pull Request 10762

• Fix admin job configuration example links (thanks to @RichardJActon). Pull Request 10771

• Fix collectl plugin for Python 3. Pull Request 10775

• Improve update handling for switches, use es6 and listento functions. Pull Request 10785

• Fix list of cached Docker images not getting updated. Pull Request 10796

• Small fixes to history panel. Pull Request 10802

• Fix vue-unit test in toolsview.test.js (thanks to @OlegZharkov). Pull Request 10812

• Various bugfixes for reloading the toolbox. Pull Request 10818

• Cast ncores to str for subprocess.call() (thanks to @nsoranzo). Pull Request 10825

• Test cases and fix for config option new_user_dataset_access_role_default_private. Pull Request 10834

• Fix label verifier in Github Maintenance Bot (thanks to @OlegZharkov). Pull Request 10836

• Move new config files samples to lib/galaxy/config/sample/ (thanks to @nsoranzo). Pull Request 10842

• Fix mulled unit test. Pull Request 10857

• Fixes to Github action for building documentation (thanks to @nsoranzo). Pull Request 10866

• Import Mapping from collection.abc (thanks to @nsoranzo). Pull Request 10872

• Update lxml for CVE-2020-27783 (thanks to @nsoranzo). Pull Request 10882

• Update Makefile target and verbiage for Jest. Pull Request 10910

• Allow YAML list format for config options. Pull Request 10945

• Bump tensorflow Python dependency from 2.3.1 to 2.4.0. Pull Request 10946

• Added handler for history options menu webhook (thanks to @kjetilkl). Pull Request 10949

• Various documentation fixes (thanks to @nsoranzo). Pull Request 10963

• Fix tool validation for empty files in certain scenarios. Pull Request 10981

• Overwrite uwsgi default py-call-osafterfork. Pull Request 10983

• Small improvements to package structure to try to get galaxy-app closer to working. Pull Request 11010

• Fix change feed. Pull Request 11018

• Pass job to setup_external_metadata() in SetMetadataToolAction.execute_via_app() (thanks to @nsoranzo). Pull Request 11031

• Document min, max, and optional for data parameters (thanks to @bernt-matthias). Pull Request 11061

• Add empty preferences attribute to BootstrapAdminUser (thanks to @simonbray). Pull Request 11062

• Make YAML tool parser parse expect_failure. Pull Request 11072

• Fix type column in library folder. (thanks to @OlegZharkov). Pull Request 11093

• Fix exporting datasets from library as collection. (thanks to @OlegZharkov). Pull Request 11623, Pull Request 11625

• Fix spurious “Select” button in upload. Pull Request 11096

• Cleanup a variety of sphinx warnings and update lib structure. Pull Request 11097, Pull Request 11103

• Don’t use copy when serializing JSON in safe_dumps. Pull Request 11169

• Reduce authnz exception exposure. Pull Request 11212

• Fix arguments in create_api_key (thanks to @davelopez). Pull Request 11243

• Routing fixes for username path components and username validation fixes. Pull Request 11260

• Decrease verbosity of urllib connectionpool logging Pull Request 11266

• Set correct status code in old history route Pull Request 11269

• Update Python dependency pulsar-galaxy-lib to 0.14.1. Pull Request 11279

• Use nested state tracking with sqlalchemy-mutable Pull Request 11288

• Fix /u/username/* routes. Pull Request 11289

• Raise correct exceptions in MetadataCollection (thanks to @nsoranzo). Pull Request 11293

• Unpin pulsar-galaxy-lib in packages Pull Request 11294 Pull Request 11314

• Multi-character strings shouldn’t be split (thanks to @selten). Pull Request 11341

• Fix command line building when using interpreter (thanks to @nsoranzo). Pull Request 11343

• Fix job_destination display if job has no destination params yet. Pull Request 11354

• Only attempt to resolve loc file fallback if path is relative path. Pull Request 11361

• Fix setCurrentHistoryId in legacy history panel context. Pull Request 11369

• Fix rule-based screenshots. (thanks to @OlegZharkov). Pull Request 11389

• Fix CircleCI unit tests. (thanks to @nsoranzo). Pull Request 11391

• Fix interactivetools_proxy_host typo. (thanks to @almahmoud). Pull Request 11441

• Disable tool document cache by default. Pull Request 11447

• Fix typo in folder search. (thanks to @OlegZharkov). Pull Request 11463

• List most common Galaxy file plugins at the top. Pull Request 11491

• Fix OIDC logout and redirection. Pull Request 11520

• Fix markdown tag visualizations. Pull Request 11534

• Fix unhandled error when creating tags with multiple dots. (thanks to @davelopez). Pull Request 11535

• Allow format attribute in output collections. (thanks to @bernt-matthias). Pull Request 11536

• Fix remote user logout redirect. Pull Request 11540

• Fix various Rule Builder issues. Pull Request 11553

• Fix upload button tooltip blocking tool search field. Pull Request 11572

• Fix name and hid when selecting uploaded datasets. Pull Request 11576

• Improve feedback for remote file listing exceptions. Pull Request 11581