diff --git a/doc/source/releases/24.0.rst b/doc/source/releases/24.0.rst new file mode 100644 index 000000000000..c16120716741 --- /dev/null +++ b/doc/source/releases/24.0.rst @@ -0,0 +1,946 @@ + +.. to_doc + +24.0 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + + +.. feature + +* New Workflow List and Card View + (thanks to `@itisAliRH `__). + `Pull Request 16607`_ +* Add harmonize collections tool (or whatever other name) + (thanks to `@lldelisle `__). + `Pull Request 16662`_ +* Add support for Python 3.12 + (thanks to `@tuncK `__). + `Pull Request 16796`_ +* Support for OIDC API Auth and OIDC integration tests + (thanks to `@nuwang `__). + `Pull Request 16977`_ +* New select component for selecting a large amount of options + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17059`_ +* Qiskit in galaxy + (thanks to `@thepineapplepirate `__). + `Pull Request 17170`_ +* Add accepted extensions to form data input + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17238`_ +* Allow job files to consume TUS uploads + (thanks to `@jmchilton `__). + `Pull Request 17242`_ +* API endpoint that allows "changing" the objectstore for "safe" scenarios. + (thanks to `@jmchilton `__). + `Pull Request 17329`_ +* Allow using tool data bundles as inputs to reference data select parameters + (thanks to `@mvdbeek `__). + `Pull Request 17435`_ +* Tag Autocomplete Rework + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17469`_ +* Add magres datatype + (thanks to `@martenson `__). + `Pull Request 17499`_ +* Add encode ID API endpoint + (thanks to `@mira-miracoli `__). + `Pull Request 17510`_ +* Fixing data_source tools and incrementing tool profile + (thanks to `@wm75 `__). + `Pull Request 17515`_ +* Add npy datatype + (thanks to `@astrovsky01 `__). + `Pull Request 17517`_ +* Add basic TIFF Image visualization + (thanks to `@davelopez `__). + `Pull Request 17553`_ +.. enhancement_tag_viz + +* Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster + (thanks to `@guerler `__). + `Pull Request 17415`_ +* Enhance Avivator display app to support regular Tiffs + (thanks to `@davelopez `__). + `Pull Request 17554`_ +.. enhancement_tag_datatypes + +* Make columns types an empty list for empty tabular data + (thanks to `@bernt-matthias `__). + `Pull Request 13918`_ +* Add support for (fast5.tar).xz binary compressed files + (thanks to `@tuncK `__). + `Pull Request 17106`_ +* Add a3m datatype + (thanks to `@astrovsky01 `__). + `Pull Request 17217`_ +* Add binary datatypes for intermediate output of fastk tools + (thanks to `@astrovsky01 `__). + `Pull Request 17265`_ +* Faster FASTA and FASTQ metadata setting + (thanks to `@bernt-matthias `__). + `Pull Request 17462`_ +* Feature SBOL datatypes + (thanks to `@guillaume-gricourt `__). + `Pull Request 17482`_ +* Better display of estimated line numbers and add number of columns for tabular + (thanks to `@bernt-matthias `__). + `Pull Request 17492`_ +.. enhancement_tag_tools + +* Hide wig_to_bigWig tool + (thanks to `@bernt-matthias `__). + `Pull Request 17328`_ +* Update RStudio GxIT to use the reworked 23.1 image + (thanks to `@natefoo `__). + `Pull Request 17533`_ +.. enhancement_tag_workflows + +* Toward declarative help for Galaxy markdown directives + (thanks to `@jmchilton `__). + `Pull Request 16979`_ +* Add select parameter with options from remote resources + (thanks to `@mvdbeek `__). + `Pull Request 17087`_ +* Expose more tool information / navigability in UI + (thanks to `@jmchilton `__). + `Pull Request 17105`_ +* Overhaul Galaxy Markdown Help + (thanks to `@jmchilton `__). + `Pull Request 17228`_ +* Consider Null inputs + (thanks to `@bernt-matthias `__). + `Pull Request 17271`_ +* Display workflow invocation counts + (thanks to `@jmchilton `__). + `Pull Request 17488`_ +* Filter out subworkflow invocations + (thanks to `@mvdbeek `__). + `Pull Request 17558`_ +* Links to individual invocations + (thanks to `@jmchilton `__). + `Pull Request 17566`_ +* Add help text to workflow invocation states + (thanks to `@jmchilton `__). + `Pull Request 17569`_ +.. enhancement_tag_ui + +.. enhancement_tag_jobs + +* Enable job resubmissions in k8s runner + (thanks to `@nuwang `__). + `Pull Request 17324`_ +.. enhancement_tag_admin + +* Proxy Access-Control-* headers when using x-accel-redirect + (thanks to `@mvdbeek `__). + `Pull Request 17842`_ +* Add docs for tool panel and panel view administration + (thanks to `@bernt-matthias `__). + `Pull Request 17078`_ +* Convert sample object store configuration to YAML and support configuring inline + (thanks to `@natefoo `__). + `Pull Request 17222`_ +* Add documentation on how to use vault keys in file sources + (thanks to `@bernt-matthias `__). + `Pull Request 17498`_ +.. enhancement + +* Allow admin to sharpen language about selected object stores + (thanks to `@jmchilton `__). + `Pull Request 17806`_ +* Fix activity bar unreachable in some pages + (thanks to `@davelopez `__). + `Pull Request 17860`_ +* Record missing outputs as test errors + (thanks to `@bernt-matthias `__). + `Pull Request 17874`_ +* Moves archived histories from Masthead to Histories Grid + (thanks to `@guerler `__). + `Pull Request 17649`_ +* Change user-facing language from "object store" to "storage location" + (thanks to `@martenson `__). + `Pull Request 17763`_ +* Restore histories API behavior for `keys` query parameter + (thanks to `@davelopez `__). + `Pull Request 17779`_ +* Prompt user to change default history permissions + (thanks to `@jmchilton `__). + `Pull Request 17782`_ +* Fix datasets API custom keys encoding + (thanks to `@davelopez `__). + `Pull Request 17793`_ +* Improved error messages for runtime sharing problems + (thanks to `@jmchilton `__). + `Pull Request 17794`_ +* build_mulled: also use namespace for building singularity images + (thanks to `@bernt-matthias `__). + `Pull Request 15657`_ +* Implement Galaxy Markdown directive history_dataset_as_table + (thanks to `@jmchilton `__). + `Pull Request 16681`_ +* Add test and doc showing how dynamic selects are used + (thanks to `@bernt-matthias `__). + `Pull Request 16885`_ +* Dataset Display : force reload on subsequent clicks + (thanks to `@dannon `__). + `Pull Request 16982`_ +* Extend regex groups in stdio regex matches + (thanks to `@bernt-matthias `__). + `Pull Request 17016`_ +* Add Ahmed as a committer + (thanks to `@dannon `__). + `Pull Request 17017`_ +* Vueify Admin User Grid + (thanks to `@guerler `__). + `Pull Request 17030`_ +* Migrate ItemTags API to FastAPI + (thanks to `@arash77 `__). + `Pull Request 17064`_ +* Use eventbus to emit route request in grid list + (thanks to `@guerler `__). + `Pull Request 17070`_ +* Split linters in separate classes + (thanks to `@bernt-matthias `__). + `Pull Request 17081`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17084`_ +* Enhance Notification Broadcasts Admin Panel + (thanks to `@davelopez `__). + `Pull Request 17090`_ +* Make notification message input multi-line + (thanks to `@davelopez `__). + `Pull Request 17091`_ +* Make flex panel drag handle more obvious + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17113`_ +* Vueify Admin Roles Grid + (thanks to `@guerler `__). + `Pull Request 17118`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17123`_ +* Vueify Admin Groups Grid + (thanks to `@guerler `__). + `Pull Request 17126`_ +* Vueify Admin Forms and Quota grids + (thanks to `@guerler `__). + `Pull Request 17141`_ +* Create pydantic model for the return of show operation - get: `/api/jobs/{job_id}` + (thanks to `@heisner-tillman `__). + `Pull Request 17153`_ +* Adding object store plugin for Rucio + (thanks to `@SergeyYakubov `__). + `Pull Request 17156`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17157`_ +* Don't require admin user to list ``/api/tool_data`` + (thanks to `@jozh2008 `__). + `Pull Request 17161`_ +* Much simpler default dataset permissions for typical users + (thanks to `@jmchilton `__). + `Pull Request 17166`_ +* Add future=True flag to SA engine + (thanks to `@jdavcs `__). + `Pull Request 17174`_ +* Add future=True flag to SA session + (thanks to `@jdavcs `__). + `Pull Request 17179`_ +* Clarify the meaning of lexical sorting of discovered datasets + (thanks to `@bernt-matthias `__). + `Pull Request 17190`_ +* Accept any number of arguments to the secret decoder ring + (thanks to `@natefoo `__). + `Pull Request 17191`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17201`_ +* Vueifiy History Grids + (thanks to `@guerler `__). + `Pull Request 17219`_ +* Improve links to Hub, Matrix and WGs in ``CONTRIBUTING.md`` + (thanks to `@nsoranzo `__). + `Pull Request 17221`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17230`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17235`_ +* Workflow node connector improvements + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17240`_ +* Workflow node connector improvements followup + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17244`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17247`_ +* Add History Multiview activity+panel, add "Show Recent" mode to multiview + (thanks to `@ahmedhamidawan `__). + `Pull Request 17251`_ +* Add OIDC backend configuration schema and validation + (thanks to `@uwwint `__). + `Pull Request 17274`_ +* Adds delete, purge and undelete batch operations to History Grid + (thanks to `@guerler `__). + `Pull Request 17282`_ +* Fix any type for tool_data_file_path + (thanks to `@mvdbeek `__). + `Pull Request 17293`_ +* Add ``__KEEP_SUCCESS_DATASETS__`` + (thanks to `@lldelisle `__). + `Pull Request 17294`_ +* Make Workflow Editor Toolbar Toggleable + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17297`_ +* Adjust Flex Panel Drag Handle and Collapse Button + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17298`_ +* New Activity bar - Notifications + (thanks to `@itisAliRH `__). + `Pull Request 17300`_ +* Fix s3fs templating + (thanks to `@bgruening `__). + `Pull Request 17311`_ +* Document SQLAlchemy session lifespan + (thanks to `@mvdbeek `__). + `Pull Request 17322`_ +* Add documentation for data source tool + (thanks to `@PlushZ `__). + `Pull Request 17327`_ +* Custom Multiselect + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17331`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17333`_ +* Unify continuous polling with composable + (thanks to `@davelopez `__). + `Pull Request 17355`_ +* Add element_identifier and ext to inputs config file export + (thanks to `@bernt-matthias `__). + `Pull Request 17357`_ +* Add name_eq and genome_build_eq filters to HistoryFilters + (thanks to `@ahmedhamidawan `__). + `Pull Request 17389`_ +* Cancel all active jobs when the user is deleted + (thanks to `@davelopez `__). + `Pull Request 17390`_ +* Some additional typing for test interactor stuff + (thanks to `@jmchilton `__). + `Pull Request 17398`_ +* Allow removing last value from multi select field + (thanks to `@guerler `__). + `Pull Request 17403`_ +* Enable comments in package dag file + (thanks to `@jdavcs `__). + `Pull Request 17408`_ +* Purge `groups` and `roles` from DB (for real) + (thanks to `@davelopez `__). + `Pull Request 17411`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17420`_ +* Add signpost to training material + (thanks to `@nuwang `__). + `Pull Request 17421`_ +* UI for "relocating" a dataset to a new object store (when safe) + (thanks to `@jmchilton `__). + `Pull Request 17437`_ +* Freeze (make sticky) header row in tabular files + (thanks to `@hujambo-dunia `__). + `Pull Request 17455`_ +* Move Activity Bar Settings to Activity + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17457`_ +* Move Visualizations Activity to Side Panel + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17458`_ +* Allow filtering history datasets by object store ID and quota source + (thanks to `@jmchilton `__). + `Pull Request 17460`_ +* Update release process documentation + (thanks to `@mvdbeek `__). + `Pull Request 17461`_ +* Use short link for TPV shared database + (thanks to `@nuwang `__). + `Pull Request 17467`_ +* `data_column` parameter: use `column_names` metadata if present + (thanks to `@bernt-matthias `__). + `Pull Request 17478`_ +* Type annotation and refactoring of tests + (thanks to `@nsoranzo `__). + `Pull Request 17484`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17486`_ +* Consolidate resource grids into tab views + (thanks to `@guerler `__). + `Pull Request 17487`_ +* Update k8s docker python to 3.12 + (thanks to `@nuwang `__). + `Pull Request 17494`_ +* Add multiple drag/drop and keyboard accessible selection to `HistoryPanel` items + (thanks to `@ahmedhamidawan `__). + `Pull Request 17502`_ +* Add gxadmin to docker and update branch + (thanks to `@nuwang `__). + `Pull Request 17521`_ +* Enable workflow buttons right click + (thanks to `@itisAliRH `__). + `Pull Request 17529`_ +* Workflow list small tweaks + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17538`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17541`_ +* Remove virtual scroller from History + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17546`_ +* Add `image_diff` comparison method for test output verification using images + (thanks to `@kostrykin `__). + `Pull Request 17556`_ +* Add shm_size based on ShmSize + (thanks to `@richard-burhans `__). + `Pull Request 17565`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 17580`_ +* Add migrations revision identifier for 24.0 + (thanks to `@jdavcs `__). + `Pull Request 17589`_ +.. small_enhancement + +* Drop release notes webhook + (thanks to `@dannon `__). + `Pull Request 17675`_ +* Port invocation API to fastapi + (thanks to `@martenson `__). + `Pull Request 16707`_ +* SQLAlchemy 2.0 upgrades (part 5) + (thanks to `@jdavcs `__). + `Pull Request 16932`_ +* Python 3.8 as minimum + (thanks to `@mr-c `__). + `Pull Request 16954`_ +* Migrate groups API to fastAPI + (thanks to `@arash77 `__). + `Pull Request 17051`_ +* Remove web framework dependency from tools + (thanks to `@davelopez `__). + `Pull Request 17058`_ +* Migrate job destination parameters store to Pinia + (thanks to `@davelopez `__). + `Pull Request 17119`_ +* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" + (thanks to `@jdavcs `__). + `Pull Request 17122`_ +* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning + (thanks to `@jdavcs `__). + `Pull Request 17132`_ +* Migrate dataset extra files store to Pinia + (thanks to `@davelopez `__). + `Pull Request 17145`_ +* Add simpleKeyStore composable + (thanks to `@davelopez `__). + `Pull Request 17148`_ +* Remove legacy tool versions list from admin panel + (thanks to `@guerler `__). + `Pull Request 17155`_ +* Convert dataset path destination store to composable + (thanks to `@davelopez `__). + `Pull Request 17175`_ +* Replace discouraged Mambaforge with Miniforge3 + (thanks to `@nsoranzo `__). + `Pull Request 17177`_ +* Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter + (thanks to `@jdavcs `__). + `Pull Request 17184`_ +* Migrate workflow invocation store to Pinia + (thanks to `@davelopez `__). + `Pull Request 17203`_ +* Vendorize fastapi-utls.cbv + (thanks to `@jdavcs `__). + `Pull Request 17205`_ +* Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 + (thanks to `@jdavcs `__). + `Pull Request 17216`_ +* Reuse test instance during non-integration tests + (thanks to `@mvdbeek `__). + `Pull Request 17234`_ +* Refactor two of the missing invocation routes to FastAPI + (thanks to `@heisner-tillman `__). + `Pull Request 17237`_ +* Build and cache galaxy client for selenium and startup tests + (thanks to `@mvdbeek `__). + `Pull Request 17239`_ +* Migrate models to pydantic 2 + (thanks to `@mvdbeek `__). + `Pull Request 17262`_ +* Improve ModelManager type hints + (thanks to `@mvdbeek `__). + `Pull Request 17299`_ +* Scoped Store Refactor and Store Composition Refactor + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17304`_ +* Port HistoryPanel component to composition API and typescript + (thanks to `@Renni771 `__). + `Pull Request 17318`_ +* Remove remaining Vuex stores and dependencies + (thanks to `@davelopez `__). + `Pull Request 17348`_ +* History refactors + (thanks to `@itisAliRH `__). + `Pull Request 17353`_ +* Convert entryPointStore to composition API + TS + (thanks to `@davelopez `__). + `Pull Request 17356`_ +* Remove unused statements in job search function + (thanks to `@mvdbeek `__). + `Pull Request 17361`_ +* Enable ``warn_unreachable`` mypy option + (thanks to `@mvdbeek `__). + `Pull Request 17365`_ +* Fix type annotation of code using XML etree + (thanks to `@nsoranzo `__). + `Pull Request 17367`_ +* Combines legacy qv-pattern and advanced filter pattern in history index endpoint + (thanks to `@guerler `__). + `Pull Request 17368`_ +* Add explicit cache_ok attribute to JSONType subclass + (thanks to `@mvdbeek `__). + `Pull Request 17376`_ +* More specific type annotation for ``BaseJobExec.parse_status()`` + (thanks to `@nsoranzo `__). + `Pull Request 17381`_ +* Update to black 2024 stable style + (thanks to `@nsoranzo `__). + `Pull Request 17391`_ +* Refactor MarkdownDialog.vue to ts+composition + (thanks to `@jmchilton `__). + `Pull Request 17399`_ +* Update current version to 24.0.dev0 + (thanks to `@jdavcs `__). + `Pull Request 17402`_ +* Removes outdated Grid controller and backbone modules + (thanks to `@guerler `__). + `Pull Request 17434`_ +* Modernize bits and pieces of storage display + (thanks to `@jmchilton `__). + `Pull Request 17436`_ +* Refactor Common components + (thanks to `@itisAliRH `__). + `Pull Request 17441`_ +* Adds published histories to grid list + (thanks to `@guerler `__). + `Pull Request 17449`_ +* Refactor Workflow API routes - Part 1 + (thanks to `@heisner-tillman `__). + `Pull Request 17463`_ +* Citation refactors + (thanks to `@itisAliRH `__). + `Pull Request 17483`_ +* Refactor Workflow Import components + (thanks to `@itisAliRH `__). + `Pull Request 17495`_ +* Removes legacy history xml makos + (thanks to `@guerler `__). + `Pull Request 17505`_ +* Remove legacy phyloviz, circster and sweepster artifacts + (thanks to `@guerler `__). + `Pull Request 17573`_ + + +Fixes +------------------------------- + +.. major_bug + + +.. bug_tag_viz + +* Fix for fits_image_viewer visualization plugin + (thanks to `@francoismg `__). + `Pull Request 17002`_ +.. bug_tag_datatypes + +* Fix for converter tests + (thanks to `@bernt-matthias `__). + `Pull Request 17188`_ +* Correct dbkey for minerva display app + (thanks to `@hexylena `__). + `Pull Request 17196`_ +.. bug_tag_tools + +.. bug_tag_workflows + +* Make WorkflowInput label, value and uuid optional + (thanks to `@mvdbeek `__). + `Pull Request 17638`_ +* Prevent 500 for anon /api/invocations + (thanks to `@mvdbeek `__). + `Pull Request 17640`_ +* Fix step type serialization for StoredWorkflowDetailed models + (thanks to `@mvdbeek `__). + `Pull Request 17716`_ +* Fix input parameter step type + (thanks to `@mvdbeek `__). + `Pull Request 17767`_ +* Fix ``include_nested_invocations`` parameter use + (thanks to `@mvdbeek `__). + `Pull Request 17768`_ +* Fix change_datatype PJA for dynamic collections + (thanks to `@mvdbeek `__). + `Pull Request 17803`_ +* Render Useful Markdown Components for Mapped Over Steps + (thanks to `@jmchilton `__). + `Pull Request 17198`_ +* Fix invocation serialization if no state was set + (thanks to `@mvdbeek `__). + `Pull Request 17278`_ +* Fix workflow report markdown editor toolbox becoming non-responsive + (thanks to `@jmchilton `__). + `Pull Request 17427`_ +* Workflow anonymous user buttons + (thanks to `@itisAliRH `__). + `Pull Request 17537`_ +.. bug_tag_ui + +* Fix typescript warning for grid list operation + (thanks to `@guerler `__). + `Pull Request 17065`_ +* Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 17115`_ +* Bump yaml from 2.1.1 to 2.3.4 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 17125`_ +* Bump follow-redirects from 1.15.1 to 1.15.4 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 17260`_ +* Bump undici from 5.26.5 to 5.28.3 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 17485`_ +.. bug_tag_jobs + +* Also set extension and metadata on copies of job outputs when finishing job + (thanks to `@mvdbeek `__). + `Pull Request 17777`_ +.. bug_tag_admin + +* Optional Reply-to SMTP header in tool error reports + (thanks to `@neoformit `__). + `Pull Request 17243`_ +.. bug + +* Minor refactor of query building logic for readability + (thanks to `@jdavcs `__). + `Pull Request 17835`_ +* Fix help forum integration uses long ID + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17844`_ +* Embed fix + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17852`_ +* Embed download fix + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17861`_ +* Wait for config to load with user prefs options + (thanks to `@martenson `__). + `Pull Request 17865`_ +* Fix bugs relating to history keyboard navigation + (thanks to `@ahmedhamidawan `__). + `Pull Request 17587`_ +* Fix ``test_oidc_login_existing_user`` test + (thanks to `@nsoranzo `__). + `Pull Request 17612`_ +* Increase ContentItem clickable area + (thanks to `@ahmedhamidawan `__). + `Pull Request 17621`_ +* Do not link to invocations for workflow that has never run + (thanks to `@martenson `__). + `Pull Request 17626`_ +* Add basic model import attribute validation + (thanks to `@mvdbeek `__). + `Pull Request 17628`_ +* Make latest_workflow_uuid optional + (thanks to `@mvdbeek `__). + `Pull Request 17629`_ +* More efficient change_state queries, maybe fix deadlock + (thanks to `@mvdbeek `__). + `Pull Request 17632`_ +* Fix tool panel workflow and favorites button bugs + (thanks to `@ahmedhamidawan `__). + `Pull Request 17634`_ +* Default sort all grid histories the same + (thanks to `@martenson `__). + `Pull Request 17635`_ +* Fix workflow person validation + (thanks to `@dannon `__). + `Pull Request 17636`_ +* Fix DataResult type + (thanks to `@mvdbeek `__). + `Pull Request 17639`_ +* Don't fail for anon /api/users request + (thanks to `@mvdbeek `__). + `Pull Request 17645`_ +* Don't index tasks without task_uuid + (thanks to `@mvdbeek `__). + `Pull Request 17646`_ +* Fix history panel arrow navigate by id bug, add `HistoryOperations` to `HistoryView` and prevent item selection in unowned histories + (thanks to `@ahmedhamidawan `__). + `Pull Request 17648`_ +* Fix shared item details and initial filters + (thanks to `@martenson `__). + `Pull Request 17651`_ +* Fix history filters taking up space in `GridList` + (thanks to `@ahmedhamidawan `__). + `Pull Request 17652`_ +* Fix syntax for SA2.0 + (thanks to `@jdavcs `__). + `Pull Request 17663`_ +* Grid filtering bug fixes + (thanks to `@ahmedhamidawan `__). + `Pull Request 17684`_ +* Purge history from history panel + (thanks to `@ahmedhamidawan `__). + `Pull Request 17685`_ +* Fix contentitem display routing. + (thanks to `@dannon `__). + `Pull Request 17687`_ +* Workflow Comment Indexing + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17700`_ +* Fix incorrect history item count in histories lists + (thanks to `@davelopez `__). + `Pull Request 17714`_ +* Improve published histories listing performance in UI + (thanks to `@davelopez `__). + `Pull Request 17717`_ +* Fix archived histories tab anonymous access + (thanks to `@davelopez `__). + `Pull Request 17719`_ +* Fix Collection Scrolling not showing all items + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17720`_ +* Fix Workflow Name Display in `WorkflowCard` to Prevent Bleeding Over Borders + (thanks to `@itisAliRH `__). + `Pull Request 17721`_ +* Always display grid pagination on the right + (thanks to `@guerler `__). + `Pull Request 17722`_ +* Fix histories API index_query serialization + (thanks to `@davelopez `__). + `Pull Request 17726`_ +* Fix source history update_time being updated when importing a public history + (thanks to `@jmchilton `__). + `Pull Request 17728`_ +* Handle missing indexer for a dataset + (thanks to `@ahmedhamidawan `__). + `Pull Request 17736`_ +* Fix overflowing and hiding of storage popovers + (thanks to `@martenson `__). + `Pull Request 17742`_ +* Revise language around non-private object stores + (thanks to `@martenson `__). + `Pull Request 17744`_ +* Fix tag sorting + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17753`_ +* Datasets list anonymous access and history link fixes + (thanks to `@dannon `__). + `Pull Request 17756`_ +* Fix usage of DISTINCT + (thanks to `@jdavcs `__). + `Pull Request 17759`_ +* Prevent dragover for item from same history in history panel + (thanks to `@ahmedhamidawan `__). + `Pull Request 17761`_ +* Improve Shift+Click select in history panel and add it for `ContentItem` selector checkboxes as well + (thanks to `@ahmedhamidawan `__). + `Pull Request 17762`_ +* Don't require history to calculate anon disk usage + (thanks to `@mvdbeek `__). + `Pull Request 17765`_ +* Fix anon user values again + (thanks to `@mvdbeek `__). + `Pull Request 17772`_ +* Add missing fields in histories listings + (thanks to `@davelopez `__). + `Pull Request 17775`_ +* Fix anonymous user create, run and import workflows + (thanks to `@itisAliRH `__). + `Pull Request 17776`_ +* Use ``hg clone --stream`` to clone repos + (thanks to `@mvdbeek `__). + `Pull Request 17786`_ +* Avoid showing a shareable URL with the default slug/username + (thanks to `@dannon `__). + `Pull Request 17788`_ +* Swap history dropdown from using the tiny caret to faBars. + (thanks to `@dannon `__). + `Pull Request 17791`_ +* Fix visualization activity plugin list images + (thanks to `@dannon `__). + `Pull Request 17792`_ +* Defer job attributes that are usually not needed + (thanks to `@mvdbeek `__). + `Pull Request 17795`_ +* Fix new default history creation when in remote or single user mode + (thanks to `@dannon `__). + `Pull Request 17796`_ +* Return published histories first in display_by_username_and_slug + (thanks to `@mvdbeek `__). + `Pull Request 17808`_ +* Show full Data menu when in single user mode + (thanks to `@dannon `__). + `Pull Request 17815`_ +* Remove link to non existent page from Data menu + (thanks to `@martenson `__). + `Pull Request 17816`_ +* Simplify nested collection joins + (thanks to `@mvdbeek `__). + `Pull Request 17817`_ +* Fix very slow user data table query + (thanks to `@mvdbeek `__). + `Pull Request 17830`_ +* Fix optional types in Help Forum API + (thanks to `@davelopez `__). + `Pull Request 17832`_ +* Update db revision 24.0 release tags + (thanks to `@jdavcs `__). + `Pull Request 17834`_ +* Update tour testing selector usage + (thanks to `@jmchilton `__). + `Pull Request 14005`_ +* Enhance Global Drag-and-Drop feature for Upload component + (thanks to `@hujambo-dunia `__). + `Pull Request 16995`_ +* Add history items display state for collections/lists with failed or new populated_state + (thanks to `@ahmedhamidawan `__). + `Pull Request 16996`_ +* Enhancement to Tool Form page, Repeating form fields implement parameter instructions + (thanks to `@hujambo-dunia `__). + `Pull Request 17018`_ +* Prevent excessive `api/tool_panels` calls by keeping views in store + (thanks to `@ahmedhamidawan `__). + `Pull Request 17039`_ +* Allow relative URLs in broadcasts action links + (thanks to `@davelopez `__). + `Pull Request 17042`_ +* xsd: reorder choices for permissive boolean + (thanks to `@bernt-matthias `__). + `Pull Request 17187`_ +* Update DatasetError.vue to fix broken link + (thanks to `@jennaj `__). + `Pull Request 17193`_ +* Reload built-in converters on toolbox reload + (thanks to `@bernt-matthias `__). + `Pull Request 17209`_ +* tus wants a json response from v2.0.0 + (thanks to `@mira-miracoli `__). + `Pull Request 17246`_ +* Add missing re-usable commit-id output + (thanks to `@mvdbeek `__). + `Pull Request 17248`_ +* Allow for upper case container tags + (thanks to `@bernt-matthias `__). + `Pull Request 17254`_ +* Fixes for output discovery + (thanks to `@bernt-matthias `__). + `Pull Request 17266`_ +* Fix Workflow Comment Model for Pydantic 2 + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17296`_ +* Package tests fixes + (thanks to `@nsoranzo `__). + `Pull Request 17301`_ +* Follow-up on `#17274 `__ and `#17262 `__ + (thanks to `@nsoranzo `__). + `Pull Request 17302`_ +* LDAP3 fix for attributes returned as strings + (thanks to `@bernt-matthias `__). + `Pull Request 17305`_ +* Fix quotas ID encoding + (thanks to `@davelopez `__). + `Pull Request 17335`_ +* Fixes for flake8-bugbear 24.1.17 + (thanks to `@nsoranzo `__). + `Pull Request 17340`_ +* Fix model store exports that include implicit conversions. + (thanks to `@jmchilton `__). + `Pull Request 17346`_ +* Escape pipe character in tool XSD docs + (thanks to `@neoformit `__). + `Pull Request 17359`_ +* XSD schema doc building: quote pipe characters in attribute tables + (thanks to `@bernt-matthias `__). + `Pull Request 17364`_ +* Fix minor oidc_backends_config comment bug + (thanks to `@ahmedhamidawan `__). + `Pull Request 17385`_ +* Fix activity-settings hidden behind left side panel bug + (thanks to `@ahmedhamidawan `__). + `Pull Request 17392`_ +* Fix z-index in BroadcastContainer.vue + (thanks to `@davelopez `__). + `Pull Request 17401`_ +* Fix IUC best practices links, mention data_source_async in XSD + (thanks to `@wm75 `__). + `Pull Request 17409`_ +* Fix data_source and data_source_async bugs + (thanks to `@wm75 `__). + `Pull Request 17422`_ +* Only check access permissions in ``/api/{history_dataset_collection_id}/contents/{dataset_collection_id}`` + (thanks to `@ahmedhamidawan `__). + `Pull Request 17444`_ +* More defensive access of extra props in filesources + (thanks to `@nuwang `__). + `Pull Request 17445`_ +* Fix `datasetStore.saveDatasets` bug + (thanks to `@ahmedhamidawan `__). + `Pull Request 17448`_ +* Fix text to match options in HistoryStorageOverview + (thanks to `@jmchilton `__). + `Pull Request 17450`_ +* Add tool XML schema documention for outputs - collection - data + (thanks to `@bernt-matthias `__). + `Pull Request 17465`_ +* Fix for a regression change - auto-select/highlight file name text + (thanks to `@hujambo-dunia `__). + `Pull Request 17466`_ +* Exclude password reset link from login form where users don't have the ability to manage accounts + (thanks to `@dannon `__). + `Pull Request 17473`_ +* has_size assertion: implement size (as synonym for value) + (thanks to `@bernt-matthias `__). + `Pull Request 17490`_ +* Stringify cgroups metrics formatted value return + (thanks to `@dannon `__). + `Pull Request 17520`_ +* Fix ``test_index_advanced_filter`` API test re-running + (thanks to `@nsoranzo `__). + `Pull Request 17547`_ +* Change default milestone to target 24.1 + (thanks to `@jdavcs `__). + `Pull Request 17549`_ +* Drop plugin-based new user welcome + (thanks to `@dannon `__). + `Pull Request 17568`_ +* Apply default theme to theme selector + (thanks to `@ElectronicBlueberry `__). + `Pull Request 17583`_ + +.. include:: 24.0_prs.rst + diff --git a/doc/source/releases/24.0_announce.rst b/doc/source/releases/24.0_announce.rst index d6ef5449d037..34c63d9757dd 100644 --- a/doc/source/releases/24.0_announce.rst +++ b/doc/source/releases/24.0_announce.rst @@ -1,12 +1,102 @@ -:orphan: +=========================================================== +24.0 Galaxy Release (March 2024) +=========================================================== + +.. include:: _header.rst + +Highlights +=========================================================== + +**New Workflow List and Card View.** As part of our ongoing efforts to enhance user experience, we are proud to announce several new improvements to the workflows user interface, including workflow list view, workflow card view and workflow quick view. These improvements also include new tabs for "My workflows" (owned by the user), "Shared with me" (shared by other users) and "Published workflows" (publicly accessible workflows). + +**New select component for selecting a large amount of options.** This new tool form component improves selecting many options at once. The elements interface features a table based layout which can be filtered using plain-text or regular expressions. Options can be added individually, in bulk via the filter value, or by highlighting a range. It appears when there are many options available in a multi-select field, but can also be switched to/from and can be set as a default directly from within the tool form. + +**Multiple item drag and drop and keyboard navigation.** This new feature allows users to select multiple history items and drag and drop them into other histories or even tool forms! Users can also navigate their history using the arrow keys; multiple history items can be selected with the Shift + ArrowUp/ArrowDown key combination. + +**image_diff.** For tool developers, image_diff, a new comparison method for test output verification using images has been added. Unlike previously used comparison methods, image_diff is specifically tailored for single-channel and multi-channel image data (e.g. RGB). The difference of a pair of images is quantified as the pixel-wise distance between the images, for which different metrics can be used. A pair of images is considered to be equal in terms of the specified metric, if the distance between the images computed with respect to the metric is not above a given threshold. For more details, see `the original pull request `__). + +Other notable improvements include consolidating resource grids for histories, visualizations and pages into tab views; the addition of a new UI feature for "relocating" a dataset to a new object store; and, for tool developers, a new comparison method for test output verification using images. Check out the `24.0 user release notes <24.0_announce_user.html>`__ 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: + .. code-block:: shell + + $ git clone -b release_24.0 https://github.com/galaxyproject/galaxy.git + +To update an existing Galaxy repository run: + .. code-block:: shell + + $ git fetch origin && git checkout release_24.0 && git pull --ff-only origin release_24.0 +See the `community hub `__ for additional details on source code locations. + +Administration Notes =========================================================== -24.0 Galaxy Release (Early 2024) + +* A new built-in tool has been added: "Harmonize two collections". It takes two collections as input. Outputs are two collections with the same identifiers, with identifiers that are specific to one or the other removed. The tool creates new history datasets from the collection, but the user's quota usage does not increase. ( #16662) +* A new object store plugin for the Rucio data management system has been added. (#17156) +* The wig_to_bigWig tool removed; replaced by Wigbigwig. (#17328) +* Notification Broadcasts Admin Panel has been enhanced. (#17090) +* Setting dataset permissions for typical users has been simplified. (#17166) +* When a user is deleted, all active user jobs will be canceled. (#17390) +* Job resubmissions have been enabled in the k8s runner. (#17324) +* Documentation has been added for tool panel and panel view administration. (#17078) +* Documentation has been added on how to use vault keys in file sources. (#17498) +* The release notes webhook has been dropped in favor of utilizing the notification system. (#17675) +* Python 3.8 is now a minimum requirement. (#16954) +* Python 3.12 is now supported. (#16796) + +Configuration Changes =========================================================== +Added +----- + +The following configuration options are new + +config/galaxy.yml.sample:galaxy +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- mapping.galaxy.mapping.object_store_config +- mapping.galaxy.mapping.oidc_scope_prefix +- mapping.galaxy.mapping.tus_upload_store_job_files + + +Changed +------- + +The following configuration options have been changed -Schedule +config/galaxy.yml.sample:galaxy +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- mapping.galaxy.mapping.tus_upload_store.desc has changed from + + :: + + The upload store is a temporary directory in which files uploaded by the + tus middleware or server will be placed. + Defaults to new_file_path if not set. + + to + + :: + + The upload store is a temporary directory in which files uploaded by the + tus middleware or server for user uploads will be placed. + Defaults to new_file_path if not set. + +Release Notes =========================================================== - * Planned Freeze Date: 2024-02-05 - * Planned Release Date: 2024-02-26 + +.. include:: 24.0.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/24.0_announce_user.rst b/doc/source/releases/24.0_announce_user.rst new file mode 100644 index 000000000000..362067299fab --- /dev/null +++ b/doc/source/releases/24.0_announce_user.rst @@ -0,0 +1,191 @@ + +=========================================================== +24.0 Galaxy Release (March 2024) +=========================================================== + +.. include:: _header.rst + +Highlights +=========================================================== + +New Workflow List and Card View +----------------------------------------------------------- + +As part of our ongoing efforts to enhance user experience, we are proud to announce several new improvements to the workflows user interface, including workflow list view, workflow card view and workflow quick view. These improvements also include new tabs for "My workflows" (owned by the user), "Shared with me" (shared by other users) and "Published workflows" (publicly accessible workflows). + +.. raw:: html + + + +My workflows: card view + +.. figure:: images/24.0-wf-cardview.png + :alt: Workflow card view. + +My workflows: list view + +.. figure:: images/24.0-wf-listview.png + :alt: Workflow list view. + +New select component for selecting a large amount of options +----------------------------------------------------------- + +This new component addresses the need of selecting a very large number of options at once. The component features a list based layout which can be filtered using plain-text or a regular expression. Options can be added individually, in bulk via the filter value, or by first highlighting a range. + +The component is fully keyboard accessible. All methods of selection and highlighting work via keyboard. The options are not selectable individually with tab, but can be scrolled through using the arrow-keys. The hover hint adapts when a keyboard is used. + +The size of the table can be increased to allow for seeing more options at once.The options in the list are limited to 1000 for performance reasons, but this can be temporarily increased in steps of 500, when reaching the end of a list. + +.. figure:: images/24.0-selectview.png + :alt: Using the new select component. + +The component can be chosen when multiple options are available; a local preference for which component to choose can be set. If no preference is set, the component will be used if there are more than 15 options selected, or more than 500 options are available. + +.. figure:: images/24.0-selectdropdown.png + :alt: Choosing the new select component. + +Multiple item drag and drop and keyboard navigation +----------------------------------------------------------- + +This new feature allows users to select multiple history items and drag and drop them into other histories or even tool forms! Users can also navigate their history using the arrow keys; multiple history items can be selected with the Shift + ArrowUp/ArrowDown key combination. + +Drag and drop: + +.. raw:: html + + + +Keyboard navigation and selection: + +.. raw:: html + + + +Resource grids have been consolidated into tab views +----------------------------------------------------------- + +Your histories, visualisations, and pages are now consolidated into an easier to use interface. Switch between your results and published results easily. + +.. raw:: html + + + +Move datasets between storage locations +----------------------------------------------------------- + +Relocate a dataset to a new object store with ease using this new UI feature! The example below uses an instance with four object stores defined, but only three of them declaring the same "device" ID. Clicking on the dataset information and scrolling to storage details has a "Relocate" option if the dataset is "safe" to relocate and there are valid targets to relocate it to. The UI utilizes the same visual language used for describing attributes of the storage and exposing admin provided details. This example also shows what the buttons look like with quota enabled object stores and object stores without quota enabled. + +.. raw:: html + + + +Visualizations +=========================================================== + +.. visualizations +* Fix for fits_image_viewer visualization plugin + (thanks to `@francoismg `__). + `Pull Request 17002`_ +* Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster + (thanks to `@guerler `__). + `Pull Request 17415`_ +* Add basic TIFF Image visualization + (thanks to `@davelopez `__). + `Pull Request 17553`_ +* Enhance Avivator display app to support regular Tiffs + (thanks to `@davelopez `__). + `Pull Request 17554`_ +* Remove legacy phyloviz, circster and sweepster artifacts + (thanks to `@guerler `__). + `Pull Request 17573`_ + +Datatypes +=========================================================== + +.. datatypes +* Make columns types an empty list for empty tabular data + (thanks to `@bernt-matthias `__). + `Pull Request 13918`_ +* Python 3.8 as minimum + (thanks to `@mr-c `__). + `Pull Request 16954`_ +* Add support for (fast5.tar).xz binary compressed files + (thanks to `@tuncK `__). + `Pull Request 17106`_ +* Fix for converter tests + (thanks to `@bernt-matthias `__). + `Pull Request 17188`_ +* correct dbkey for minerva display app + (thanks to `@hexylena `__). + `Pull Request 17196`_ +* Add a3m datatype + (thanks to `@astrovsky01 `__). + `Pull Request 17217`_ +* Add binary datatypes for intermediate output of fastk tools + (thanks to `@astrovsky01 `__). + `Pull Request 17265`_ +* Enable ``warn_unreachable`` mypy option + (thanks to `@mvdbeek `__). + `Pull Request 17365`_ +* Fix type annotation of code using XML etree + (thanks to `@nsoranzo `__). + `Pull Request 17367`_ +* Update to black 2024 stable style + (thanks to `@nsoranzo `__). + `Pull Request 17391`_ +* Allow using tool data bundles as inputs to reference data select parameters + (thanks to `@mvdbeek `__). + `Pull Request 17435`_ +* Faster FASTA and FASTQ metadata setting + (thanks to `@bernt-matthias `__). + `Pull Request 17462`_ +* Feature SBOL datatypes + (thanks to `@guillaume-gricourt `__). + `Pull Request 17482`_ +* Better display of estimated line numbers and add number of columns for tabular + (thanks to `@bernt-matthias `__). + `Pull Request 17492`_ +* Add magres datatype + (thanks to `@martenson `__). + `Pull Request 17499`_ +* Add npy datatype + (thanks to `@astrovsky01 `__). + `Pull Request 17517`_ + +Builtin Tool Updates +=========================================================== + +.. tools +* Qiskit in galaxy + (thanks to `@thepineapplepirate `__). + `Pull Request 17170`_ +* Hide wig_to_bigWig tool + (thanks to `@bernt-matthias `__). + `Pull Request 17328`_ +* Update to black 2024 stable style + (thanks to `@nsoranzo `__). + `Pull Request 17391`_ +* Update RStudio GxIT to use the reworked 23.1 image + (thanks to `@natefoo `__). + `Pull Request 17533`_ + +Release Testing Team +=========================================================== + +A special thanks to the release testing team: + +* `Ahmed Awan `__ +* `Amirhossein Naghsh Nilchi `__ +* `David López `__ +* `Jennifer Hillman-Jackson `__ +* `John Davis `__ +* `Tyler Collins `__ + +Release Notes +=========================================================== + +Please see the :doc:`full release notes <24.0_announce>` for more details. + +.. include:: 24.0_prs.rst + +.. include:: _thanks.rst diff --git a/doc/source/releases/24.0_prs.rst b/doc/source/releases/24.0_prs.rst new file mode 100644 index 000000000000..63674154fe6c --- /dev/null +++ b/doc/source/releases/24.0_prs.rst @@ -0,0 +1,311 @@ + +.. github_links +.. _Pull Request 17806: https://github.com/galaxyproject/galaxy/pull/17806 +.. _Pull Request 17835: https://github.com/galaxyproject/galaxy/pull/17835 +.. _Pull Request 17842: https://github.com/galaxyproject/galaxy/pull/17842 +.. _Pull Request 17844: https://github.com/galaxyproject/galaxy/pull/17844 +.. _Pull Request 17851: https://github.com/galaxyproject/galaxy/pull/17851 +.. _Pull Request 17852: https://github.com/galaxyproject/galaxy/pull/17852 +.. _Pull Request 17860: https://github.com/galaxyproject/galaxy/pull/17860 +.. _Pull Request 17861: https://github.com/galaxyproject/galaxy/pull/17861 +.. _Pull Request 17865: https://github.com/galaxyproject/galaxy/pull/17865 +.. _Pull Request 17874: https://github.com/galaxyproject/galaxy/pull/17874 +.. _Pull Request 17587: https://github.com/galaxyproject/galaxy/pull/17587 +.. _Pull Request 17612: https://github.com/galaxyproject/galaxy/pull/17612 +.. _Pull Request 17621: https://github.com/galaxyproject/galaxy/pull/17621 +.. _Pull Request 17626: https://github.com/galaxyproject/galaxy/pull/17626 +.. _Pull Request 17628: https://github.com/galaxyproject/galaxy/pull/17628 +.. _Pull Request 17629: https://github.com/galaxyproject/galaxy/pull/17629 +.. _Pull Request 17632: https://github.com/galaxyproject/galaxy/pull/17632 +.. _Pull Request 17634: https://github.com/galaxyproject/galaxy/pull/17634 +.. _Pull Request 17635: https://github.com/galaxyproject/galaxy/pull/17635 +.. _Pull Request 17636: https://github.com/galaxyproject/galaxy/pull/17636 +.. _Pull Request 17638: https://github.com/galaxyproject/galaxy/pull/17638 +.. _Pull Request 17639: https://github.com/galaxyproject/galaxy/pull/17639 +.. _Pull Request 17640: https://github.com/galaxyproject/galaxy/pull/17640 +.. _Pull Request 17644: https://github.com/galaxyproject/galaxy/pull/17644 +.. _Pull Request 17645: https://github.com/galaxyproject/galaxy/pull/17645 +.. _Pull Request 17646: https://github.com/galaxyproject/galaxy/pull/17646 +.. _Pull Request 17648: https://github.com/galaxyproject/galaxy/pull/17648 +.. _Pull Request 17649: https://github.com/galaxyproject/galaxy/pull/17649 +.. _Pull Request 17651: https://github.com/galaxyproject/galaxy/pull/17651 +.. _Pull Request 17652: https://github.com/galaxyproject/galaxy/pull/17652 +.. _Pull Request 17663: https://github.com/galaxyproject/galaxy/pull/17663 +.. _Pull Request 17675: https://github.com/galaxyproject/galaxy/pull/17675 +.. _Pull Request 17684: https://github.com/galaxyproject/galaxy/pull/17684 +.. _Pull Request 17685: https://github.com/galaxyproject/galaxy/pull/17685 +.. _Pull Request 17687: https://github.com/galaxyproject/galaxy/pull/17687 +.. _Pull Request 17700: https://github.com/galaxyproject/galaxy/pull/17700 +.. _Pull Request 17714: https://github.com/galaxyproject/galaxy/pull/17714 +.. _Pull Request 17716: https://github.com/galaxyproject/galaxy/pull/17716 +.. _Pull Request 17717: https://github.com/galaxyproject/galaxy/pull/17717 +.. _Pull Request 17719: https://github.com/galaxyproject/galaxy/pull/17719 +.. _Pull Request 17720: https://github.com/galaxyproject/galaxy/pull/17720 +.. _Pull Request 17721: https://github.com/galaxyproject/galaxy/pull/17721 +.. _Pull Request 17722: https://github.com/galaxyproject/galaxy/pull/17722 +.. _Pull Request 17724: https://github.com/galaxyproject/galaxy/pull/17724 +.. _Pull Request 17726: https://github.com/galaxyproject/galaxy/pull/17726 +.. _Pull Request 17728: https://github.com/galaxyproject/galaxy/pull/17728 +.. _Pull Request 17736: https://github.com/galaxyproject/galaxy/pull/17736 +.. _Pull Request 17742: https://github.com/galaxyproject/galaxy/pull/17742 +.. _Pull Request 17744: https://github.com/galaxyproject/galaxy/pull/17744 +.. _Pull Request 17753: https://github.com/galaxyproject/galaxy/pull/17753 +.. _Pull Request 17756: https://github.com/galaxyproject/galaxy/pull/17756 +.. _Pull Request 17759: https://github.com/galaxyproject/galaxy/pull/17759 +.. _Pull Request 17761: https://github.com/galaxyproject/galaxy/pull/17761 +.. _Pull Request 17762: https://github.com/galaxyproject/galaxy/pull/17762 +.. _Pull Request 17763: https://github.com/galaxyproject/galaxy/pull/17763 +.. _Pull Request 17765: https://github.com/galaxyproject/galaxy/pull/17765 +.. _Pull Request 17767: https://github.com/galaxyproject/galaxy/pull/17767 +.. _Pull Request 17768: https://github.com/galaxyproject/galaxy/pull/17768 +.. _Pull Request 17772: https://github.com/galaxyproject/galaxy/pull/17772 +.. _Pull Request 17775: https://github.com/galaxyproject/galaxy/pull/17775 +.. _Pull Request 17776: https://github.com/galaxyproject/galaxy/pull/17776 +.. _Pull Request 17777: https://github.com/galaxyproject/galaxy/pull/17777 +.. _Pull Request 17779: https://github.com/galaxyproject/galaxy/pull/17779 +.. _Pull Request 17782: https://github.com/galaxyproject/galaxy/pull/17782 +.. _Pull Request 17786: https://github.com/galaxyproject/galaxy/pull/17786 +.. _Pull Request 17788: https://github.com/galaxyproject/galaxy/pull/17788 +.. _Pull Request 17789: https://github.com/galaxyproject/galaxy/pull/17789 +.. _Pull Request 17790: https://github.com/galaxyproject/galaxy/pull/17790 +.. _Pull Request 17791: https://github.com/galaxyproject/galaxy/pull/17791 +.. _Pull Request 17792: https://github.com/galaxyproject/galaxy/pull/17792 +.. _Pull Request 17793: https://github.com/galaxyproject/galaxy/pull/17793 +.. _Pull Request 17794: https://github.com/galaxyproject/galaxy/pull/17794 +.. _Pull Request 17795: https://github.com/galaxyproject/galaxy/pull/17795 +.. _Pull Request 17796: https://github.com/galaxyproject/galaxy/pull/17796 +.. _Pull Request 17803: https://github.com/galaxyproject/galaxy/pull/17803 +.. _Pull Request 17808: https://github.com/galaxyproject/galaxy/pull/17808 +.. _Pull Request 17815: https://github.com/galaxyproject/galaxy/pull/17815 +.. _Pull Request 17816: https://github.com/galaxyproject/galaxy/pull/17816 +.. _Pull Request 17817: https://github.com/galaxyproject/galaxy/pull/17817 +.. _Pull Request 17830: https://github.com/galaxyproject/galaxy/pull/17830 +.. _Pull Request 17832: https://github.com/galaxyproject/galaxy/pull/17832 +.. _Pull Request 17834: https://github.com/galaxyproject/galaxy/pull/17834 +.. _Pull Request 13918: https://github.com/galaxyproject/galaxy/pull/13918 +.. _Pull Request 14005: https://github.com/galaxyproject/galaxy/pull/14005 +.. _Pull Request 15657: https://github.com/galaxyproject/galaxy/pull/15657 +.. _Pull Request 16492: https://github.com/galaxyproject/galaxy/pull/16492 +.. _Pull Request 16607: https://github.com/galaxyproject/galaxy/pull/16607 +.. _Pull Request 16662: https://github.com/galaxyproject/galaxy/pull/16662 +.. _Pull Request 16681: https://github.com/galaxyproject/galaxy/pull/16681 +.. _Pull Request 16707: https://github.com/galaxyproject/galaxy/pull/16707 +.. _Pull Request 16796: https://github.com/galaxyproject/galaxy/pull/16796 +.. _Pull Request 16885: https://github.com/galaxyproject/galaxy/pull/16885 +.. _Pull Request 16932: https://github.com/galaxyproject/galaxy/pull/16932 +.. _Pull Request 16954: https://github.com/galaxyproject/galaxy/pull/16954 +.. _Pull Request 16977: https://github.com/galaxyproject/galaxy/pull/16977 +.. _Pull Request 16979: 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