diff --git a/doc/source/releases/23.0_announce.rst b/doc/source/releases/23.0_announce.rst index bc4658b19e29..966e50be8a95 100644 --- a/doc/source/releases/23.0_announce.rst +++ b/doc/source/releases/23.0_announce.rst @@ -159,7 +159,7 @@ The following files are new, or recently converted to yaml - ``config/themes_conf.yml.sample`` -Deprecation Notice +Deprecation Notices =========================================================== Trackster is deprecated and will be removed in the next release. This functionality will be provided by other visualization plugins (IGV.js, JBrowse). diff --git a/doc/source/releases/23.1.rst b/doc/source/releases/23.1.rst new file mode 100644 index 000000000000..c9b49a079b73 --- /dev/null +++ b/doc/source/releases/23.1.rst @@ -0,0 +1,1120 @@ + +.. to_doc + +23.1 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + + +.. feature + +* Empower Users to Select Storage Destination + (thanks to `@jmchilton `__). + `Pull Request 14073`_ +* Introducing the Activity Bar, initial concept and layout + (thanks to `@guerler `__). + `Pull Request 14802`_ +* Beacon integration + (thanks to `@Paprikant `__). + `Pull Request 15131`_ +* OIDC tokens + (thanks to `@SergeyYakubov `__). + `Pull Request 15300`_ +* Expose additional beaker caching backends + (thanks to `@claudiofr `__). + `Pull Request 15349`_ +* Add support for visualizing HDF5 datasets + (thanks to `@jarrah42 `__). + `Pull Request 15394`_ +* Unify url handling with filesources + (thanks to `@nuwang `__). + `Pull Request 15497`_ +* Move TS to Alembic + (thanks to `@jdavcs `__). + `Pull Request 15509`_ +* Explore tool remote test data + (thanks to `@davelopez `__). + `Pull Request 15510`_ +* Phylocanvas rebuild + (thanks to `@dannon `__). + `Pull Request 15521`_ +* Add Galaxy Notification System + (thanks to `@davelopez `__). + `Pull Request 15663`_ +* Adding fuzzy search functionality to front end search + (thanks to `@tcollins2011 `__). + `Pull Request 15855`_ +* FITS data format + (thanks to `@volodymyrss `__). + `Pull Request 15905`_ +* Emit filterText to HistoryPanel from historyStore + (thanks to `@ahmedhamidawan `__). + `Pull Request 15926`_ +* Add WorkflowBox to Activity bar Side Panel + (thanks to `@ahmedhamidawan `__). + `Pull Request 15944`_ +* Add option to create list for all datasets in a history to dropdown + (thanks to `@assuntad23 `__). + `Pull Request 15947`_ +* Add History Archival feature + (thanks to `@davelopez `__). + `Pull Request 16003`_ +* Add carbon emissions reporting to job information page + (thanks to `@Renni771 `__). + `Pull Request 16155`_ +* Add Processing for Custom Icons + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16157`_ +* Add zipped mongodb and genenotebook datatypes + (thanks to `@abretaud `__). + `Pull Request 16173`_ +* FITS file visualization plugin + (thanks to `@francoismg `__). + `Pull Request 16187`_ +* bring grids for (published) pages on par with workflows + (thanks to `@martenson `__). + `Pull Request 16209`_ +* Add Visium datatype for squidpy and spatialomics tools + (thanks to `@astrovsky01 `__). + `Pull Request 16255`_ +* Display Tags in Workflow Editor + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16282`_ +* Fix tool remote test data + (thanks to `@davelopez `__). + `Pull Request 16311`_ +.. enhancement_tag_viz + +* Small test decorator improvements + (thanks to `@jmchilton `__). + `Pull Request 16220`_ +.. enhancement_tag_datatypes + +* Improve display chunk generation for BAMs + (thanks to `@wm75 `__). + `Pull Request 15972`_ +* Code cleanups from ruff and pyupgrade + (thanks to `@nsoranzo `__). + `Pull Request 16035`_ +* Dataset chunking tests (and small fixes) + (thanks to `@jmchilton `__). + `Pull Request 16069`_ +* Add hdf4 datatype + (thanks to `@TheoMathurin `__). + `Pull Request 16105`_ +.. enhancement_tag_tools + +* Allow pending inputs in some collection operation tools + (thanks to `@mvdbeek `__). + `Pull Request 15892`_ +* Updates MGnify interactive tool to v1.1.0 + (thanks to `@SandyRogers `__). + `Pull Request 16179`_ +.. enhancement_tag_workflows + +* Include workflow invocations in default activity + (thanks to `@mvdbeek `__). + `Pull Request 16338`_ +* Improve help text for conditional workflow step + (thanks to `@mvdbeek `__). + `Pull Request 16355`_ +* Hide conditionally skipped output + (thanks to `@mvdbeek `__). + `Pull Request 16356`_ +* e2e test for workflow license selector + (thanks to `@jmchilton `__). + `Pull Request 16243`_ +.. enhancement_tag_ui + +* Disable console instead of dropping + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16372`_ +* Stricter typescript config + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15311`_ +* Updating build-related dependencies, static cleanup + (thanks to `@dannon `__). + `Pull Request 15527`_ +* Allow typescript unit testing with navigation YAML + (thanks to `@jmchilton `__). + `Pull Request 15784`_ +* Vueify Select field + (thanks to `@guerler `__). + `Pull Request 16010`_ +* Mock fetcher followup + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16011`_ +* New history selector with quick actions + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16040`_ +* Refactor a few client object store components + (thanks to `@jmchilton `__). + `Pull Request 16051`_ +* Fix font-awesome library types + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16068`_ +* TypeScript 5 + (thanks to `@dannon `__). + `Pull Request 16167`_ +* Makefile-based setting of NODE_OPTIONS for client build + (thanks to `@dannon `__). + `Pull Request 16324`_ +.. enhancement_tag_jobs + +* Record input datasets and collections at full parameter path + (thanks to `@mvdbeek `__). + `Pull Request 15978`_ +.. enhancement_tag_admin + +* Add slack error reporting plugin + (thanks to `@hexylena `__). + `Pull Request 15025`_ +* Container resolvers: add docs, typing and tests + (thanks to `@bernt-matthias `__). + `Pull Request 15614`_ +* Add suggested Training material to Tool Form + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15628`_ +* More object store documentation + (thanks to `@jmchilton `__). + `Pull Request 15707`_ +* Migrate to MyST-Parser for Markdown docs + (thanks to `@nsoranzo `__). + `Pull Request 15844`_ +* Export tool citations configurable message + (thanks to `@minh-biocommons `__). + `Pull Request 15998`_ +* implement admin jobs filtering + (thanks to `@martenson `__). + `Pull Request 16020`_ +* unify workflows grid components + (thanks to `@martenson `__). + `Pull Request 16045`_ +.. enhancement + +* Add message showing console disable/enable, along with instructions o… + (thanks to `@dannon `__). + `Pull Request 16401`_ +* Add missing archived filter in saved histories + (thanks to `@davelopez `__). + `Pull Request 16475`_ +* Bump bx-python to 0.10.0 + (thanks to `@mvdbeek `__). + `Pull Request 16484`_ +* Add Storage Dashboard visualizations for histories + (thanks to `@davelopez `__). + `Pull Request 14820`_ +* Install singularity in the integration GitHub workflow + (thanks to `@nsoranzo `__). + `Pull Request 14922`_ +* External Login Flow: Redirect users if account already exists + (thanks to `@ahmedhamidawan `__). + `Pull Request 15019`_ +* Decompress history data for testing assertions + (thanks to `@bernt-matthias `__). + `Pull Request 15085`_ +* Migrate history store to pinia + (thanks to `@itisAliRH `__). + `Pull Request 15108`_ +* Documents use of k8s_extra_job_envs in job_conf sample advanced + (thanks to `@pcm32 `__). + `Pull Request 15110`_ +* Upgraded to new multiselect Tags component for Workflows, DatasetList, Attributes + (thanks to `@hujambo-dunia `__). + `Pull Request 15225`_ +* Add Storage Management API + (thanks to `@davelopez `__). + `Pull Request 15295`_ +* vueify formUpload with composition API + (thanks to `@assuntad23 `__). + `Pull Request 15409`_ +* Outline Deployment Tests + (thanks to `@jmchilton `__). + `Pull Request 15420`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 15435`_ +* Fix for new style conda packages + (thanks to `@bernt-matthias `__). + `Pull Request 15446`_ +* Protection against problematic boolean parameters + (thanks to `@jmchilton `__). + `Pull Request 15493`_ +* Implement initial tool/wf test assertions module for JSON data + (thanks to `@jmchilton `__). + `Pull Request 15494`_ +* xsd: add multiple to the list of attributes for all parameter types deriving from select + (thanks to `@bernt-matthias `__). + `Pull Request 15534`_ +* Add basic selenium test for shared histories + (thanks to `@davelopez `__). + `Pull Request 15538`_ +* Add new release tags to manage_toolshed_db.sh script + (thanks to `@jdavcs `__). + `Pull Request 15542`_ +* Use sentry-fastapi integration, expose sampling rate + (thanks to `@mvdbeek `__). + `Pull Request 15550`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 15564`_ +* Changes to match latest playbook + (thanks to `@nuwang `__). + `Pull Request 15647`_ +* Minor hid display tweak + (thanks to `@dannon `__). + `Pull Request 15662`_ +* Unpin Beaker requirement + (thanks to `@nsoranzo `__). + `Pull Request 15665`_ +* update the admin activation docs + (thanks to `@martenson `__). + `Pull Request 15670`_ +* Verify that activation and reset emails are properly generated + (thanks to `@guerler `__). + `Pull Request 15681`_ +* Use chevrons instead of eye for showing expandable/collapsible sections + (thanks to `@dannon `__). + `Pull Request 15688`_ +* Mention OpenAPI docs in Galaxy API Documentation + (thanks to `@bernt-matthias `__). + `Pull Request 15713`_ +* Add selenium test for history Related filter + (thanks to `@ahmedhamidawan `__). + `Pull Request 15720`_ +* Fix/Enhance recalculate disk usage API endpoint + (thanks to `@davelopez `__). + `Pull Request 15739`_ +* Add StatesInfo component + (thanks to `@ahmedhamidawan `__). + `Pull Request 15745`_ +* Add Laila as a committer + (thanks to `@dannon `__). + `Pull Request 15789`_ +* Remove jxtx from committers list + (thanks to `@dannon `__). + `Pull Request 15790`_ +* Initial end-to-end tests for separate quota sources per object store + (thanks to `@jmchilton `__). + `Pull Request 15800`_ +* 12875/form drilldown vue conversion + (thanks to `@assuntad23 `__). + `Pull Request 15813`_ +* Add ensureDefined assertion utility + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15834`_ +* Adding onFocus and onBlur functionality to editing the history name + (thanks to `@assuntad23 `__). + `Pull Request 15853`_ +* Show backend search errors in hist panel + (thanks to `@ahmedhamidawan `__). + `Pull Request 15874`_ +* Enable per-destination ``container_resolver_config_file`` + (thanks to `@bernt-matthias `__). + `Pull Request 15884`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 15890`_ +* Exclude tests from TypeScript compilation + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15900`_ +* Allow importing a workflow from a shared URL + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15903`_ +* Advanced tool search result tweaks + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15908`_ +* Summarize long Workflow annotations in WorkflowList + (thanks to `@ahmedhamidawan `__). + `Pull Request 15925`_ +* Updated doc and tests for attribute value filter + (thanks to `@tuncK `__). + `Pull Request 15929`_ +* Convert legacy side panels to flex-compatible panels + (thanks to `@guerler `__). + `Pull Request 15935`_ +* Migrate user and user flags stores to Pinia + (thanks to `@itisAliRH `__). + `Pull Request 15938`_ +* Update release notes footer + (thanks to `@nsoranzo `__). + `Pull Request 15941`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 15942`_ +* Make container builders use mamba + (thanks to `@bernt-matthias `__). + `Pull Request 15953`_ +* Build container with nodejs + (thanks to `@ksuderman `__). + `Pull Request 15979`_ +* Fetcher Mock utility + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15992`_ +* Drop `UserHistories` provider + (thanks to `@itisAliRH `__). + `Pull Request 15993`_ +* reorganize user menu for consistency + (thanks to `@martenson `__). + `Pull Request 15994`_ +* remove inherited title from masthead dropdown items + (thanks to `@martenson `__). + `Pull Request 15995`_ +* Use Filtering class to get and set filter texts + (thanks to `@ahmedhamidawan `__). + `Pull Request 15996`_ +* Add alter_column migration utility + (thanks to `@jdavcs `__). + `Pull Request 16009`_ +* minor tooltip and UI client changes + (thanks to `@martenson `__). + `Pull Request 16017`_ +* Rename object stores in config + (thanks to `@jmchilton `__). + `Pull Request 16029`_ +* Add missing fields to HistorySummary schema model + (thanks to `@davelopez `__). + `Pull Request 16041`_ +* Change release note icon + (thanks to `@itisAliRH `__). + `Pull Request 16049`_ +* Add Repository owner field to ToolSearch + (thanks to `@ahmedhamidawan `__). + `Pull Request 16061`_ +* Add count support for listing filters + (thanks to `@davelopez `__). + `Pull Request 16075`_ +* Add create_foreign_key migration utility + (thanks to `@jdavcs `__). + `Pull Request 16077`_ +* Paginate History Store + (thanks to `@ahmedhamidawan `__). + `Pull Request 16084`_ +* Selenium test for displaying workflows with problems in pages + (thanks to `@jmchilton `__). + `Pull Request 16085`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 16086`_ +* Use automated naming convention to generate indexes and constraints in database + (thanks to `@jdavcs `__). + `Pull Request 16089`_ +* Workflow Editor Infinite Grid with Landmark-Lines + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16097`_ +* Expand query selector list to encompass 'a' + (thanks to `@hexylena `__). + `Pull Request 16100`_ +* Workflow Connections Dynamic Radius + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16102`_ +* Improved Cache Monitoring for Object Stores + (thanks to `@jmchilton `__). + `Pull Request 16110`_ +* De-duplication and improvements to the in-process object store cache monitor + (thanks to `@jmchilton `__). + `Pull Request 16111`_ +* Allow HEAD request for requesting metadata files + (thanks to `@martenson `__). + `Pull Request 16113`_ +* Integrate accessibility testing into Selenium testing + (thanks to `@jmchilton `__). + `Pull Request 16122`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 16123`_ +* Add option to see invocations related to a history + (thanks to `@martenson `__). + `Pull Request 16136`_ +* Improve histories and datasets immutability checks + (thanks to `@davelopez `__). + `Pull Request 16143`_ +* When writing test error debug directories, create a 'latest' symlink. + (thanks to `@jmchilton `__). + `Pull Request 16148`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 16153`_ +* Migrate display applications API to Fast API + (thanks to `@heisner-tillman `__). + `Pull Request 16156`_ +* End-to-end tests for new user welcome + (thanks to `@jmchilton `__). + `Pull Request 16158`_ +* Axe-detected accessibility fixes for some history-related things + (thanks to `@jmchilton `__). + `Pull Request 16159`_ +* adjust grid sharing indicators + (thanks to `@martenson `__). + `Pull Request 16163`_ +* Fix and Improve Workflow Editor Panning + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16178`_ +* Merge ``Target`` class with ``CondaTarget`` + (thanks to `@nsoranzo `__). + `Pull Request 16181`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 16182`_ +* Allow user customization of the activity bar + (thanks to `@guerler `__). + `Pull Request 16184`_ +* Update carbon emissions calculations explanation page styling + (thanks to `@Renni771 `__). + `Pull Request 16192`_ +* Allow users to create new activity bar items + (thanks to `@guerler `__). + `Pull Request 16196`_ +* Initial e2e test for history storage + (thanks to `@jmchilton `__). + `Pull Request 16221`_ +* Selenium test for page history links + (thanks to `@jmchilton `__). + `Pull Request 16222`_ +* tool_util: switch to mambaforge on non-32bit; add arm64 support + (thanks to `@mr-c `__). + `Pull Request 16223`_ +* E2E Tests for Edit Dataset Attributes Page + (thanks to `@jmchilton `__). + `Pull Request 16224`_ +* Show search in `HistoryView` + (thanks to `@ahmedhamidawan `__). + `Pull Request 16225`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 16227`_ +* Selenium type fixes and annotations + (thanks to `@jmchilton `__). + `Pull Request 16242`_ +* Refine activity bar dragging behavior + (thanks to `@guerler `__). + `Pull Request 16245`_ +* Marginally more storage management selenium coverage + (thanks to `@jmchilton `__). + `Pull Request 16263`_ +* Adjust notifications activity item + (thanks to `@guerler `__). + `Pull Request 16265`_ +* Add interactive tools activity + (thanks to `@guerler `__). + `Pull Request 16266`_ +* Update Python dependencies + (thanks to `@galaxybot `__). + `Pull Request 16267`_ +* Set Initial Filter for Paired List Collection Creator Based on Initial Elements + (thanks to `@assuntad23 `__). + `Pull Request 16279`_ +* Fix Storage Dashboard missing archived histories + (thanks to `@davelopez `__). + `Pull Request 16473`_ +.. small_enhancement + +* Filter deleted keys from api_keys relationship + (thanks to `@dannon `__). + `Pull Request 16321`_ +* Drop expunge_all() call in WebTransactionRequest + (thanks to `@mvdbeek `__). + `Pull Request 16606`_ +* Towards decoupling datatypes and model + (thanks to `@jdavcs `__). + `Pull Request 15186`_ +* Various Tool Shed Cleanup + (thanks to `@jmchilton `__). + `Pull Request 15247`_ +* Follow up to `#15186 `__ + (thanks to `@jdavcs `__). + `Pull Request 15388`_ +* Towards SQLAlchemy 2.0: drop session autocommit setting + (thanks to `@jdavcs `__). + `Pull Request 15421`_ +* Prettier targeting refinements + (thanks to `@dannon `__). + `Pull Request 15449`_ +* QUnit elimination + (thanks to `@dannon `__). + `Pull Request 15452`_ +* Move database access code out of tool_util + (thanks to `@jdavcs `__). + `Pull Request 15467`_ +* Use connection instead of session for ItemGrabber + (thanks to `@jdavcs `__). + `Pull Request 15496`_ +* Update browserslist and exclusions, linting + (thanks to `@dannon `__). + `Pull Request 15524`_ +* Another round of easy tool shed cleanup + (thanks to `@jmchilton `__). + `Pull Request 15540`_ +* Handle "email_from" config option consistently, as per schema description + (thanks to `@jdavcs `__). + `Pull Request 15557`_ +* Drop workflow exports to myexperiment.org + (thanks to `@dannon `__). + `Pull Request 15576`_ +* Update database_heartbeat for SA 2.0 compatibility + (thanks to `@jdavcs `__). + `Pull Request 15611`_ +* Update supports_skip_locked, supports_returning for SA 2.0 compatibility + (thanks to `@jdavcs `__). + `Pull Request 15633`_ +* Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) + (thanks to `@jdavcs `__). + `Pull Request 15643`_ +* Deprecate tools/evolution + (thanks to `@bernt-matthias `__). + `Pull Request 15656`_ +* Drop model mapping unit tests + (thanks to `@jdavcs `__). + `Pull Request 15669`_ +* Add transactional state to JobHandlerStopQueue + (thanks to `@jdavcs `__). + `Pull Request 15671`_ +* Add transactional state to workflow scheduling manager + (thanks to `@jdavcs `__). + `Pull Request 15683`_ +* Remove DELETED_NEW job state from code base + (thanks to `@jdavcs `__). + `Pull Request 15690`_ +* Convert utilities to typescript + (thanks to `@dannon `__). + `Pull Request 15718`_ +* Use Animation Frame in Workflow Editor + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15725`_ +* Add API test and refactor code for related:hid history filter + (thanks to `@ahmedhamidawan `__). + `Pull Request 15786`_ +* Utils refactor + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15837`_ +* Enable no-throw-literal eslint rule + (thanks to `@ElectronicBlueberry `__). + `Pull Request 15849`_ +* Drop use_legacy_history from config + (thanks to `@dannon `__). + `Pull Request 15861`_ +* Fix WorkflowDisplay error message handling + (thanks to `@dannon `__). + `Pull Request 15865`_ +* Drop database views + (thanks to `@jdavcs `__). + `Pull Request 15876`_ +* ci: show test classes with non standard names + (thanks to `@bernt-matthias `__). + `Pull Request 15886`_ +* Remove legacy form fields from parameter factory + (thanks to `@guerler `__). + `Pull Request 15983`_ +* Refactor badge parsing/serialization/typing for reuse + (thanks to `@jmchilton `__). + `Pull Request 15987`_ +* Migrate job metrics store and component to use pinia and composition api + (thanks to `@Renni771 `__). + `Pull Request 16056`_ +* Vendorise ``packaging.versions.LegacyVersion`` + (thanks to `@nsoranzo `__). + `Pull Request 16058`_ +* Use jsdom-worker instead of mock + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16064`_ +* Refactor models enums to eliminate schema dependency on model layer + (thanks to `@jmchilton `__). + `Pull Request 16080`_ +* Use `_.+` for unused variables + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16098`_ +* De-duplicate code around object store caches. + (thanks to `@jmchilton `__). + `Pull Request 16108`_ +* Refactor caching object stores ahead of adding task-based store + (thanks to `@jmchilton `__). + `Pull Request 16144`_ +* Remove involucro, add to .gitignore + (thanks to `@jdavcs `__). + `Pull Request 16176`_ +* Drop workarounds for old ro-crate-py and docutils versions + (thanks to `@mvdbeek `__). + `Pull Request 16198`_ +* Remove various fallback behaviors + (thanks to `@mvdbeek `__). + `Pull Request 16199`_ +* Drop TS unit mapping tests + (thanks to `@jdavcs `__). + `Pull Request 16206`_ +* Replace bootstrap_history.py with galaxy-release-util + (thanks to `@mvdbeek `__). + `Pull Request 16231`_ +* Don't error on missing parameters or unused parameters in UI controllers + (thanks to `@mvdbeek `__). + `Pull Request 16246`_ +* Prepare Uploader Vueification by removing jQuery + (thanks to `@guerler `__). + `Pull Request 16408`_ + + +Fixes +------------------------------- + +.. major_bug + +* Copy the collection contents by default when copying a collection + (thanks to `@mvdbeek `__). + `Pull Request 16717`_ + +.. bug_tag_viz + +* H5web updates + (thanks to `@dannon `__). + `Pull Request 16509`_ +* Update galaxyproject/charts utilizing visualizations + (thanks to `@dannon `__). + `Pull Request 16674`_ +* Fixes the parcel2 build for hdf5 viz when using node18. + (thanks to `@dannon `__). + `Pull Request 16047`_ +.. bug_tag_datatypes + +* Enable ``strict_equality`` mypy option + (thanks to `@nsoranzo `__). + `Pull Request 15808`_ +* Improve robustness of collection edit E2E test + (thanks to `@jmchilton `__). + `Pull Request 16092`_ +.. bug_tag_tools + +* Remove render.py script from iSEE + (thanks to `@neoformit `__). + `Pull Request 16616`_ +* FileInput no longer accept 'U' in the file mode + (thanks to `@bgruening `__). + `Pull Request 16704`_ +.. bug_tag_workflows + +* Fixes for conditional subworkflow steps + (thanks to `@mvdbeek `__). + `Pull Request 16632`_ +* Fix invocation progress bar for skipped and deleted jobs + (thanks to `@mvdbeek `__). + `Pull Request 16365`_ +* Fix workflow invocation detail reactivity + (thanks to `@mvdbeek `__). + `Pull Request 16369`_ +* Fix replacement parameters for subworkflows + (thanks to `@jmchilton `__). + `Pull Request 16592`_ +* Backport tool mem fixes + (thanks to `@mvdbeek `__). + `Pull Request 16601`_ +* Fix expression evaluation for nested state + (thanks to `@mvdbeek `__). + `Pull Request 16656`_ +* Push to object store even if ``set_meta`` fails + (thanks to `@mvdbeek `__). + `Pull Request 16667`_ +* Add missing join condition in job search + (thanks to `@mvdbeek `__). + `Pull Request 16710`_ +* Fix job search query + (thanks to `@mvdbeek `__). + `Pull Request 16714`_ +* Fix "database is locked" error (occurring in the context of workflow testing under SQLite) + (thanks to `@jdavcs `__). + `Pull Request 16208`_ +* Fix default when statement evaluation + (thanks to `@mvdbeek `__). + `Pull Request 16332`_ +.. bug_tag_ui + +* Fix dataset create time convert + (thanks to `@itisAliRH `__). + `Pull Request 15329`_ +* Bump undici from 5.14.0 to 5.19.1 in /client + (thanks to `@dependabot[bot] `__). + `Pull Request 15609`_ +* Fix eslint / ts overrides + (thanks to `@dannon `__). + `Pull Request 16166`_ +.. bug_tag_jobs + +* Workaround for XML nodes of job resource parameters losing their children + (thanks to `@kysrpex `__). + `Pull Request 16728`_ +* Add missing singularity_no_mount prop parsing + (thanks to `@mvdbeek `__). + `Pull Request 16367`_ +* Job cache fixes for DCEs + (thanks to `@mvdbeek `__). + `Pull Request 16384`_ +* Run through tmp_dir_creation_statement only once + (thanks to `@mvdbeek `__). + `Pull Request 16529`_ +* Ignore errors with user-set job resources + (thanks to `@mvdbeek `__). + `Pull Request 16579`_ +* make sure that TMP, TEMP, and TMPDIR are set + (thanks to `@bernt-matthias `__). + `Pull Request 16594`_ +* Ensure Job belongs to current SA session + (thanks to `@mvdbeek `__). + `Pull Request 16655`_ +* Fix metadata setting in extended metadata + outputs_to_working_directory mode + (thanks to `@mvdbeek `__). + `Pull Request 16678`_ +* Fix closed transaction error on galaxy startup/check jobs + (thanks to `@jdavcs `__). + `Pull Request 16687`_ +* read job_conf directly from `config_dir` instead of computing it again from `config_file` + (thanks to `@bernt-matthias `__). + `Pull Request 15596`_ +* Change confusing pulsar logs message + (thanks to `@kysrpex `__). + `Pull Request 16038`_ +* Fix job failure handling when condor indicates job failure + (thanks to `@mvdbeek `__). + `Pull Request 16096`_ +.. bug_tag_admin + +* Reload toolbox after forking when using `--preload` + (thanks to `@mvdbeek `__). + `Pull Request 16620`_ +* Improve container resolver documentation + (thanks to `@mvdbeek `__). + `Pull Request 16280`_ +.. bug + +* Fix unittest mocks to support us checking geturl() + (thanks to `@dannon `__). + `Pull Request 16726`_ +* Fix allowlist deserialization in file sources + (thanks to `@mvdbeek `__). + `Pull Request 16729`_ +* force wrap long parameter names in the workflow form + (thanks to `@martenson `__). + `Pull Request 16731`_ +* force wrap long parameter names in the workflow form + (thanks to `@martenson `__). + `Pull Request 16732`_ +* prevent toolbox scrollbar + (thanks to `@martenson `__). + `Pull Request 16734`_ +* Update 23.1 release tags for migration scripts + (thanks to `@jdavcs `__). + `Pull Request 16294`_ +* Remove pin on ``packaging`` in packages + (thanks to `@nsoranzo `__). + `Pull Request 16322`_ +* Fix 'news' webhook to account for the RC one more time. + (thanks to `@dannon `__). + `Pull Request 16328`_ +* Fix disk usage recalculation for distributed object stores + (thanks to `@mvdbeek `__). + `Pull Request 16380`_ +* Fix histories count + (thanks to `@davelopez `__). + `Pull Request 16400`_ +* Fix toolform creator + (thanks to `@dannon `__). + `Pull Request 16419`_ +* For display (only) allow control+click for new window opening + (thanks to `@dannon `__). + `Pull Request 16432`_ +* Swap datatype&convert tab to a static 'datatypes' tab. + (thanks to `@dannon `__). + `Pull Request 16466`_ +* Fix tagging component for anonymous users + (thanks to `@mvdbeek `__). + `Pull Request 16481`_ +* Fix up unit tests for local use + (thanks to `@mvdbeek `__). + `Pull Request 16483`_ +* Fix history item states help display to apply same styling attributes + (thanks to `@dannon `__). + `Pull Request 16500`_ +* fix font-weight disparity between browsers + (thanks to `@hujambo-dunia `__). + `Pull Request 16515`_ +* Fix for Accessibility, on Workflows List page Tooltip + (thanks to `@hujambo-dunia `__). + `Pull Request 16520`_ +* Fix double-encoding notification content + (thanks to `@mvdbeek `__). + `Pull Request 16530`_ +* Exclude selenium version with broken type hints + (thanks to `@mvdbeek `__). + `Pull Request 16531`_ +* Limit tool document cache to tool configs with explicit cache path + (thanks to `@mvdbeek `__). + `Pull Request 16537`_ +* Fix `multiple` remote test data + (thanks to `@davelopez `__). + `Pull Request 16542`_ +* Don't use ``docker run`` --user flag on OSX + (thanks to `@mvdbeek `__). + `Pull Request 16573`_ +* Fix shared item notification link + (thanks to `@davelopez `__). + `Pull Request 16581`_ +* Make datatype edit default value a string instead of list of strings + (thanks to `@mvdbeek `__). + `Pull Request 16591`_ +* Bump minimum tpv version to 2.3.2 + (thanks to `@mvdbeek `__). + `Pull Request 16597`_ +* Optimize getting current user session + (thanks to `@mvdbeek `__). + `Pull Request 16604`_ +* Drop RecursiveMiddleware + (thanks to `@mvdbeek `__). + `Pull Request 16605`_ +* Only reindex tool search once after forking + (thanks to `@mvdbeek `__). + `Pull Request 16611`_ +* Account for expires/expires_in when refreshing token + (thanks to `@mvdbeek `__). + `Pull Request 16621`_ +* Fix nested conditional workflow steps + (thanks to `@mvdbeek `__). + `Pull Request 16641`_ +* Login/Register fixes + (thanks to `@dannon `__). + `Pull Request 16652`_ +* Make sort_collection tool require terminal datasets + (thanks to `@mvdbeek `__). + `Pull Request 16661`_ +* xsd: allow name attribute of test collections + (thanks to `@bernt-matthias `__). + `Pull Request 16663`_ +* Only show 'edit' on published pages when viewer is the owner. + (thanks to `@dannon `__). + `Pull Request 16680`_ +* Fix regex validation for global inline flags + (thanks to `@mvdbeek `__). + `Pull Request 16683`_ +* Fix legend not scrollable in storage overview charts + (thanks to `@davelopez `__). + `Pull Request 16703`_ +* List extra files only for terminal datasets + (thanks to `@mvdbeek `__). + `Pull Request 16705`_ +* Fix collection id encoding + (thanks to `@davelopez `__). + `Pull Request 16718`_ +* linter: allow options elements in data params + (thanks to `@bernt-matthias `__). + `Pull Request 14572`_ +* Fix resetting metadata on many repositories at once via the shed API + (thanks to `@jmchilton `__). + `Pull Request 14906`_ +* Fixes for two framework test tools + (thanks to `@bernt-matthias `__). + `Pull Request 15483`_ +* Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance + (thanks to `@hujambo-dunia `__). + `Pull Request 15517`_ +* add missing f for f-string + (thanks to `@bernt-matthias `__). + `Pull Request 15584`_ +* Fix jest tests run on CI + (thanks to `@davelopez `__). + `Pull Request 15588`_ +* Fix call to `docker_cached_container_description` + (thanks to `@bernt-matthias `__). + `Pull Request 15598`_ +* Fix masthead element padding and improve brand text contrast + (thanks to `@guerler `__). + `Pull Request 15689`_ +* Update selenium hid text assertion + (thanks to `@dannon `__). + `Pull Request 15691`_ +* Fix occasional package problems related to dependencies. + (thanks to `@jmchilton `__). + `Pull Request 15734`_ +* Merge conflicting db migration branches into one + (thanks to `@jdavcs `__). + `Pull Request 15771`_ +* Fix some drs handling issues + (thanks to `@nuwang `__). + `Pull Request 15777`_ +* Fix filesource file url support + (thanks to `@nuwang `__). + `Pull Request 15794`_ +* Fix revision scripts, run migrations in CI, add repair option, improve migrations utils + (thanks to `@jdavcs `__). + `Pull Request 15811`_ +* Fix log message + (thanks to `@bernt-matthias `__). + `Pull Request 15838`_ +* Fix tool recommendations shown in a d3 js tree + (thanks to `@anuprulez `__). + `Pull Request 15852`_ +* Fix anonymous user uploads when vault is configured + (thanks to `@tchaussepiedifb `__). + `Pull Request 15858`_ +* Fix information popovers when displaying object stores for selection + (thanks to `@jmchilton `__). + `Pull Request 15867`_ +* Fix Multi-History infinite loading loop + (thanks to `@dannon `__). + `Pull Request 15931`_ +* Fix nullable deleted column in API Keys table + (thanks to `@davelopez `__). + `Pull Request 15956`_ +* Update locale.js + (thanks to `@undergone2345 `__). + `Pull Request 15963`_ +* Add text-break to wrap long published titles + (thanks to `@guerler `__). + `Pull Request 15980`_ +* Fix backbone-based data selector to materialize consistent attribute set + (thanks to `@guerler `__). + `Pull Request 15981`_ +* Fix Activity Bar toggle reactivity + (thanks to `@davelopez `__). + `Pull Request 15988`_ +* Fix for link pop-up window/toaster after Data Library to History import + (thanks to `@hujambo-dunia `__). + `Pull Request 16008`_ +* Fix pasting file fails if text starts with `file ` + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16023`_ +* Ensure that unselected checkbox inputs emit null instead of an empty array + (thanks to `@guerler `__). + `Pull Request 16059`_ +* Fix and test startup with Python 3.11 on macOS + (thanks to `@nsoranzo `__). + `Pull Request 16082`_ +* Improve robustness of collection upload tests + (thanks to `@jmchilton `__). + `Pull Request 16093`_ +* Fix minor Switch to History bug in `HistoryView` + (thanks to `@ahmedhamidawan `__). + `Pull Request 16095`_ +* Attempt to fix mypy check + (thanks to `@davelopez `__). + `Pull Request 16103`_ +* Place admin panel section data into computed prop + (thanks to `@guerler `__). + `Pull Request 16115`_ +* add required_files to the tag list for linting + (thanks to `@bernt-matthias `__). + `Pull Request 16129`_ +* Fix : Ignore error messages for admin created accounts + (thanks to `@jvanbraekel `__). + `Pull Request 16132`_ +* Scope pinned histories by user ID + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16142`_ +* Accessibility fixes for workflows, login, and registration + (thanks to `@jmchilton `__). + `Pull Request 16146`_ +* Disable invalid link for anonymous users + (thanks to `@jmchilton `__). + `Pull Request 16147`_ +* Raise configuration error if connection URL is unparseable + (thanks to `@jdavcs `__). + `Pull Request 16152`_ +* Fix transiently failing published histories test + (thanks to `@jmchilton `__). + `Pull Request 16172`_ +* Hide Activity Bar for anonymous users + (thanks to `@ahmedhamidawan `__). + `Pull Request 16200`_ +* Verify existence of default value attribute for user forms fields + (thanks to `@guerler `__). + `Pull Request 16205`_ +* Ensure session is request-scoped for legacy endpoints + (thanks to `@jdavcs `__). + `Pull Request 16207`_ +* Fixes initial state of select all checkbox + (thanks to `@guerler `__). + `Pull Request 16217`_ +* allow anon access for api/datasets/get_content_as_text + (thanks to `@martenson `__). + `Pull Request 16226`_ +* Handle appending to a results file that does not exists + (thanks to `@ksuderman `__). + `Pull Request 16233`_ +* Fix dropbox import to support newer versions + (thanks to `@nuwang `__). + `Pull Request 16239`_ +* Reset autocommit to True (temporarily) + (thanks to `@jdavcs `__). + `Pull Request 16283`_ +* Open latest version of tool from tool panel link + (thanks to `@mvdbeek `__). + `Pull Request 16290`_ +* use router instead of hard links for certain page urls + (thanks to `@martenson `__). + `Pull Request 16297`_ +* Fix ordering of data libraries from API + (thanks to `@martenson `__). + `Pull Request 16300`_ +* handle prefix in dataset contents properly + (thanks to `@martenson `__). + `Pull Request 16301`_ +* Fix form builder value handling + (thanks to `@guerler `__). + `Pull Request 16304`_ +* qualify querying for an api-key + (thanks to `@martenson `__). + `Pull Request 16320`_ +* Refactor workflow store to be more reliable + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16334`_ +* Fix tags ownership + (thanks to `@davelopez `__). + `Pull Request 16339`_ +* Make tags in public histories read-only + (thanks to `@davelopez `__). + `Pull Request 16348`_ +* Sanitize substring in matchingTerm + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16351`_ +* Fix Nested Tool Panel Labels + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16376`_ +* Fix select statement syntax for SQLAlchemy 2.0 + (thanks to `@jdavcs `__). + `Pull Request 16421`_ +* Fix multi-broadcast overlap + (thanks to `@davelopez `__). + `Pull Request 16444`_ +* Fix webhook release note seen pin + (thanks to `@dannon `__). + `Pull Request 16446`_ +* Fix parsing tool metadata from bio.tools + (thanks to `@kysrpex `__). + `Pull Request 16449`_ +* Fix history items repeated search bug + (thanks to `@ahmedhamidawan `__). + `Pull Request 16452`_ +* Bump version of chromedriver setup action + (thanks to `@mvdbeek `__). + `Pull Request 16461`_ +* Remove blinking animation from icons + (thanks to `@itisAliRH `__). + `Pull Request 16471`_ +* Restore resolution of Conda environments generated from non-lowercase package names + (thanks to `@nsoranzo `__). + `Pull Request 16474`_ +* Linter: fix regex for profile version + (thanks to `@bernt-matthias `__). + `Pull Request 16480`_ +* Fix `ToolBoxWorkflow` search delay bug + (thanks to `@ahmedhamidawan `__). + `Pull Request 16505`_ +* Make ToolBox v-b-tooltip.hover directives noninteractive + (thanks to `@ahmedhamidawan `__). + `Pull Request 16506`_ +* Fix Published Pages and Pages view showing same content + (thanks to `@ahmedhamidawan `__). + `Pull Request 16614`_ + +.. include:: 23.1_prs.rst + diff --git a/doc/source/releases/23.1_announce.rst b/doc/source/releases/23.1_announce.rst index 61d5b308afdc..e93689b11036 100644 --- a/doc/source/releases/23.1_announce.rst +++ b/doc/source/releases/23.1_announce.rst @@ -1,12 +1,209 @@ -:orphan: - =========================================================== Mid 2023 Galaxy Release (v 23.1) =========================================================== +.. include:: _header.rst -Schedule +Highlights =========================================================== - * Planned Freeze Date: 2023-05-15 - * Planned Release Date: 2023-06-30 + + +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_23.1 https://github.com/galaxyproject/galaxy.git + +To update an existing Galaxy repository run: + .. code-block:: shell + + $ git fetch origin && git checkout release_23.1 && git pull --ff-only origin release_23.1 + +See the `community hub `__ for additional details on source code locations. + +Administration Notes +==================== + + +Configuration Changes +===================== + +Added +----- + +The following configuration options are new + +config/galaxy.yml.sample:galaxy +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- mapping.tool_shed.mapping.citation_cache_schema_name +- mapping.tool_shed.mapping.citation_cache_table_name +- mapping.tool_shed.mapping.citation_cache_url + + +Changed +------- + +The following configuration options have been changed + +config/file_sources_conf.yml.sample +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- has changed from + + :: + + {'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'accessToken': "${user.preferences['dropbox|access_token']}"} + {'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}"} + {'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'} + {'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'} + {'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21} + {'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21} + {'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21} + {'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222} + {'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'} + {'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True} + {'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True} + {'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True} + {'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True} + {'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True} + {'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True} + {'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True} + {'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True} + {'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True} + {'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True} + {'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True} + {'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True} + + to + + :: + + {'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'accessToken': "${user.preferences['dropbox|access_token']}"} + {'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}"} + {'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'} + {'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'} + {'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21} + {'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21} + {'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21} + {'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222} + {'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'} + {'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True} + {'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True} + {'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True} + {'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True} + {'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True} + {'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True} + {'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True} + {'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True} + {'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True} + {'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True} + {'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True} + {'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True} + {'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'} + {'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'} + {'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'} + {'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'} + + + +config/galaxy.yml.sample:galaxy +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- mapping.galaxy.mapping.cache_dir.desc has changed from + + :: + + Top level cache directory. Any other cache directories (tool_cache_data_dir, + template_cache_path, etc.) should be subdirectories. + + to + + :: + + Top level cache directory. Any other cache directories + (template_cache_path, etc.) should be subdirectories. + + +- mapping.galaxy.mapping.container_resolvers_config_file.desc has changed from + + :: + + Container resolvers configuration. Set up a file describing + container resolvers to use when discovering containers for Galaxy. If + this is set to None, the default container resolvers loaded is + determined by enable_mulled_containers. + For available options see config/container_resolvers_conf.xml.sample. + + to + + :: + + Container resolvers configuration. Set up a file describing + container resolvers to use when discovering containers for Galaxy. If + this is set to None, the default container resolvers loaded is + determined by enable_mulled_containers. + For available options see https://docs.galaxyproject.org/en/master/admin/container_resolvers.html + + +- mapping.galaxy.mapping.enable_tool_document_cache.desc has changed from + + :: + + Whether to enable the tool document cache. This cache stores + expanded XML strings. Enabling the tool cache results in slightly faster startup + times. The tool cache is backed by a SQLite database, which cannot + be stored on certain network disks. The cache location is configurable + using the ``tool_cache_data_dir`` setting, but can be disabled completely here. + + to + + :: + + Whether to enable the tool document cache. This cache stores + expanded XML strings. Enabling the tool cache results in slightly faster startup + times. The tool cache is backed by a SQLite database, which cannot + be stored on certain network disks. The cache location is configurable + with the ``tool_cache_data_dir`` tag in tool config files. + + + + +Removed +------- + +The following configuration options have been completely removed + +config/galaxy.yml.sample:galaxy +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- mapping.galaxy.mapping.delay_tool_initialization +- mapping.galaxy.mapping.myexperiment_target_url +- mapping.galaxy.mapping.tool_cache_data_dir +- mapping.galaxy.mapping.use_legacy_history + + +New Configuration Files +----------------------- + +The following files are new, or recently converted to yaml + +- ``config/container_resolvers.yml.sample`` + +Deprecation Notices +=========================================================== + +The first Galaxy release of 2024 (24.0) will drop support for Python 3.7, which has already reached end of life (EOL). + +Release Notes +=========================================================== + +.. include:: 23.1.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/23.1_announce_user.rst b/doc/source/releases/23.1_announce_user.rst new file mode 100644 index 000000000000..277aaeb395ae --- /dev/null +++ b/doc/source/releases/23.1_announce_user.rst @@ -0,0 +1,192 @@ + +=========================================================== +June 2023 Galaxy Release (v 23.1) +=========================================================== + +.. include:: _header.rst + +Highlights +=========================================================== + +Activity Bar Interface +-------------------------- + +23.1 introduces the Activity Bar, a new customizable interface element designed +for swift navigation through various sections of the application. The feature is +currently opt-in, and you can try it today by enabling it in User Preferences. +Upcoming releases will enable this by default for all users, and will extend +functionality with new activities and by allowing users to drag items such as +datasets and workflows directly from the UI into the activity bar component. + +.. figure:: images/23.1-activity-bar.png + :alt: Screenshot of the new activity bar interface showing several options for navigation. + +Carbon Emissions Reporting +--------------------------- + +Monitor your environmental impact with our new Carbon Emissions Reporting +feature. This feature is available on the job information page, allowing users +to track their carbon footprint in real-time. The calculations assume global +average values for carbon intensity and power usage effectiveness. Monitor your +carbon footprint and become inspired to better your relationship with the +environment! + +.. figure:: images/23.1-carbon-footprint.png + :alt: Screenshot of the new carbon emissions reporting feature. + +History Archival Feature +------------------------- +The history menu has a new option to move a history out of your active histories +and into an archive. When archiving a history, you will be presented with two +options: either to “Keep the Storage Space” or to “Free the Storage Space” taken +up by the history. Keeping the storage space will keep the contents of the +history where they are, allowing them to be restored at any moment, but will +prevent the UI from allowing certain operations on the history. Freeing the +storage space will prompt you to package and export the history to a permanent +remote source as a backup snapshot, and then will purge the history and its +contents to free up storage space. There will be a simple list, titled Archived +Histories, for you to explore your archived histories and restore and reimport +them, as needed! + +Visualize HDF5 Datasets +------------------------ + +Users can now visualize their HDF5 datasets directly in Galaxy, thanks to the +integration of the h5web visualizer (https://h5web.panosc.eu/)! + +.. figure:: images/23.1-hdf5.png + :alt: Screenshot of the new HDF5 visualization plugin. + +Galaxy Notification Framework +----------------------------- +Galaxy now contains a universal notification framework. This will facilitate +sending notifications about a wide variety of scenarios like job completion, +artifact sharing, server updates, and more. Users have control over their +notifications, including the option to subscribe/unsubscribe from certain types +of notifications. The new notification system also supports broadcast +notifications, allowing administrators to send server-wide announcements, such +as server maintenance or downtime notifications. + + +New Visualizations +=========================================================== + +.. visualizations +* H5web updates + (thanks to `@dannon `__). + `Pull Request 16509`_ +* Update galaxyproject/charts utilizing visualizations + (thanks to `@dannon `__). + `Pull Request 16674`_ +* Add support for visualizing HDF5 datasets + (thanks to `@jarrah42 `__). + `Pull Request 15394`_ +* Phylocanvas rebuild + (thanks to `@dannon `__). + `Pull Request 15521`_ +* Gitignore update + (thanks to `@ElectronicBlueberry `__). + `Pull Request 16046`_ +* Fixes the parcel2 build for hdf5 viz when using node18. + (thanks to `@dannon `__). + `Pull Request 16047`_ +* FITS file visualization plugin + (thanks to `@francoismg `__). + `Pull Request 16187`_ +* Small test decorator improvements + (thanks to `@jmchilton `__). + `Pull Request 16220`_ + +New Datatypes +=========================================================== + +.. datatypes +* Fix bad auto-merge of dev + (thanks to `@jmchilton `__). + `Pull Request 15386`_ +* Follow up to `#15186 `__ + (thanks to `@jdavcs `__). + `Pull Request 15388`_ +* Add support for visualizing HDF5 datasets + (thanks to `@jarrah42 `__). + `Pull Request 15394`_ +* Merge 23.0 into dev + (thanks to `@mvdbeek `__). + `Pull Request 15594`_ +* Enable ``strict_equality`` mypy option + (thanks to `@nsoranzo `__). + `Pull Request 15808`_ +* FITS data format + (thanks to `@volodymyrss `__). + `Pull Request 15905`_ +* Improve display chunk generation for BAMs + (thanks to `@wm75 `__). + `Pull Request 15972`_ +* Code cleanups from ruff and pyupgrade + (thanks to `@nsoranzo `__). + `Pull Request 16035`_ +* Dataset chunking tests (and small fixes) + (thanks to `@jmchilton `__). + `Pull Request 16069`_ +* Merge release_23.0 into dev + (thanks to `@nsoranzo `__). + `Pull Request 16088`_ +* Improve robustness of collection edit E2E test + (thanks to `@jmchilton `__). + `Pull Request 16092`_ +* Add hdf4 datatype + (thanks to `@TheoMathurin `__). + `Pull Request 16105`_ +* Fix linting of FITS datatype code + (thanks to `@mvdbeek `__). + `Pull Request 16169`_ +* Add zipped mongodb and genenotebook datatypes + (thanks to `@abretaud `__). + `Pull Request 16173`_ +* Add Visium datatype for squidpy and spatialomics tools + (thanks to `@astrovsky01 `__). + `Pull Request 16255`_ + +Builtin Tool Updates +=========================================================== + +.. tools +* Remove render.py script from iSEE + (thanks to `@neoformit `__). + `Pull Request 16616`_ +* FileInput no longer accept 'U' in the file mode + (thanks to `@bgruening `__). + `Pull Request 16704`_ +* Deprecate tools/evolution + (thanks to `@bernt-matthias `__). + `Pull Request 15656`_ +* Allow pending inputs in some collection operation tools + (thanks to `@mvdbeek `__). + `Pull Request 15892`_ +* Updates MGnify interactive tool to v1.1.0 + (thanks to `@SandyRogers `__). + `Pull Request 16179`_ +* Remove various fallback behaviors + (thanks to `@mvdbeek `__). + `Pull Request 16199`_ + +Release Testing Team +=========================================================== + +A special thanks to the release testing team for testing many of the new features: + +* `Jennifer Hillman-Jackson `__ +* `John Davis `__ +* `Luke Sargent `__ +* `Martin Cech `__ +* `Michelle Savage `__ +* `Stephen Mosher `__ + +Release Notes +=========================================================== + +Please see the :doc:`full release notes <23.1_announce>` for more details. + +.. include:: 23.1_prs.rst + +.. include:: _thanks.rst diff --git a/doc/source/releases/23.1_prs.rst b/doc/source/releases/23.1_prs.rst new file mode 100644 index 000000000000..2d21a2c7ebe7 --- /dev/null +++ b/doc/source/releases/23.1_prs.rst @@ -0,0 +1,384 @@ + +.. github_links +.. _Pull Request 16717: https://github.com/galaxyproject/galaxy/pull/16717 +.. _Pull Request 16726: https://github.com/galaxyproject/galaxy/pull/16726 +.. _Pull Request 16728: https://github.com/galaxyproject/galaxy/pull/16728 +.. _Pull Request 16729: https://github.com/galaxyproject/galaxy/pull/16729 +.. _Pull Request 16731: https://github.com/galaxyproject/galaxy/pull/16731 +.. _Pull Request 16732: https://github.com/galaxyproject/galaxy/pull/16732 +.. _Pull Request 16734: https://github.com/galaxyproject/galaxy/pull/16734 +.. _Pull Request 16632: https://github.com/galaxyproject/galaxy/pull/16632 +.. _Pull Request 16294: https://github.com/galaxyproject/galaxy/pull/16294 +.. _Pull Request 16299: https://github.com/galaxyproject/galaxy/pull/16299 +.. _Pull Request 16321: https://github.com/galaxyproject/galaxy/pull/16321 +.. _Pull Request 16322: https://github.com/galaxyproject/galaxy/pull/16322 +.. _Pull Request 16328: https://github.com/galaxyproject/galaxy/pull/16328 +.. _Pull Request 16338: https://github.com/galaxyproject/galaxy/pull/16338 +.. _Pull Request 16355: https://github.com/galaxyproject/galaxy/pull/16355 +.. _Pull Request 16356: https://github.com/galaxyproject/galaxy/pull/16356 +.. _Pull Request 16365: https://github.com/galaxyproject/galaxy/pull/16365 +.. _Pull Request 16367: https://github.com/galaxyproject/galaxy/pull/16367 +.. _Pull Request 16369: https://github.com/galaxyproject/galaxy/pull/16369 +.. _Pull Request 16372: https://github.com/galaxyproject/galaxy/pull/16372 +.. _Pull Request 16380: https://github.com/galaxyproject/galaxy/pull/16380 +.. _Pull Request 16384: https://github.com/galaxyproject/galaxy/pull/16384 +.. _Pull Request 16400: https://github.com/galaxyproject/galaxy/pull/16400 +.. _Pull Request 16401: https://github.com/galaxyproject/galaxy/pull/16401 +.. _Pull Request 16419: https://github.com/galaxyproject/galaxy/pull/16419 +.. _Pull Request 16432: https://github.com/galaxyproject/galaxy/pull/16432 +.. _Pull Request 16465: https://github.com/galaxyproject/galaxy/pull/16465 +.. _Pull Request 16466: https://github.com/galaxyproject/galaxy/pull/16466 +.. _Pull Request 16475: https://github.com/galaxyproject/galaxy/pull/16475 +.. _Pull Request 16481: https://github.com/galaxyproject/galaxy/pull/16481 +.. _Pull Request 16483: https://github.com/galaxyproject/galaxy/pull/16483 +.. _Pull Request 16484: https://github.com/galaxyproject/galaxy/pull/16484 +.. _Pull Request 16500: https://github.com/galaxyproject/galaxy/pull/16500 +.. _Pull Request 16509: https://github.com/galaxyproject/galaxy/pull/16509 +.. _Pull Request 16515: https://github.com/galaxyproject/galaxy/pull/16515 +.. _Pull Request 16520: https://github.com/galaxyproject/galaxy/pull/16520 +.. _Pull Request 16529: https://github.com/galaxyproject/galaxy/pull/16529 +.. _Pull Request 16530: https://github.com/galaxyproject/galaxy/pull/16530 +.. _Pull Request 16531: https://github.com/galaxyproject/galaxy/pull/16531 +.. _Pull Request 16533: https://github.com/galaxyproject/galaxy/pull/16533 +.. _Pull Request 16537: https://github.com/galaxyproject/galaxy/pull/16537 +.. _Pull Request 16542: https://github.com/galaxyproject/galaxy/pull/16542 +.. _Pull Request 16573: https://github.com/galaxyproject/galaxy/pull/16573 +.. _Pull Request 16579: https://github.com/galaxyproject/galaxy/pull/16579 +.. _Pull Request 16581: https://github.com/galaxyproject/galaxy/pull/16581 +.. _Pull Request 16591: https://github.com/galaxyproject/galaxy/pull/16591 +.. _Pull Request 16592: https://github.com/galaxyproject/galaxy/pull/16592 +.. _Pull Request 16594: https://github.com/galaxyproject/galaxy/pull/16594 +.. _Pull Request 16597: https://github.com/galaxyproject/galaxy/pull/16597 +.. _Pull Request 16601: https://github.com/galaxyproject/galaxy/pull/16601 +.. _Pull Request 16604: https://github.com/galaxyproject/galaxy/pull/16604 +.. _Pull Request 16605: https://github.com/galaxyproject/galaxy/pull/16605 +.. _Pull Request 16606: https://github.com/galaxyproject/galaxy/pull/16606 +.. _Pull Request 16611: https://github.com/galaxyproject/galaxy/pull/16611 +.. _Pull Request 16616: https://github.com/galaxyproject/galaxy/pull/16616 +.. _Pull Request 16620: https://github.com/galaxyproject/galaxy/pull/16620 +.. _Pull Request 16621: https://github.com/galaxyproject/galaxy/pull/16621 +.. _Pull Request 16641: https://github.com/galaxyproject/galaxy/pull/16641 +.. _Pull Request 16652: https://github.com/galaxyproject/galaxy/pull/16652 +.. _Pull Request 16655: https://github.com/galaxyproject/galaxy/pull/16655 +.. _Pull Request 16656: https://github.com/galaxyproject/galaxy/pull/16656 +.. _Pull Request 16661: https://github.com/galaxyproject/galaxy/pull/16661 +.. _Pull Request 16663: https://github.com/galaxyproject/galaxy/pull/16663 +.. _Pull Request 16667: https://github.com/galaxyproject/galaxy/pull/16667 +.. _Pull Request 16674: https://github.com/galaxyproject/galaxy/pull/16674 +.. _Pull Request 16678: https://github.com/galaxyproject/galaxy/pull/16678 +.. _Pull Request 16680: https://github.com/galaxyproject/galaxy/pull/16680 +.. _Pull Request 16683: https://github.com/galaxyproject/galaxy/pull/16683 +.. _Pull Request 16687: https://github.com/galaxyproject/galaxy/pull/16687 +.. _Pull Request 16703: https://github.com/galaxyproject/galaxy/pull/16703 +.. _Pull Request 16704: https://github.com/galaxyproject/galaxy/pull/16704 +.. _Pull Request 16705: https://github.com/galaxyproject/galaxy/pull/16705 +.. _Pull Request 16710: https://github.com/galaxyproject/galaxy/pull/16710 +.. _Pull Request 16718: https://github.com/galaxyproject/galaxy/pull/16718 +.. _Pull Request 16714: https://github.com/galaxyproject/galaxy/pull/16714 +.. _Pull Request 14073: https://github.com/galaxyproject/galaxy/pull/14073 +.. _Pull Request 14572: https://github.com/galaxyproject/galaxy/pull/14572 +.. _Pull Request 14802: https://github.com/galaxyproject/galaxy/pull/14802 +.. _Pull Request 14820: https://github.com/galaxyproject/galaxy/pull/14820 +.. _Pull Request 14906: https://github.com/galaxyproject/galaxy/pull/14906 +.. _Pull Request 14922: https://github.com/galaxyproject/galaxy/pull/14922 +.. _Pull Request 15019: https://github.com/galaxyproject/galaxy/pull/15019 +.. _Pull Request 15025: https://github.com/galaxyproject/galaxy/pull/15025 +.. _Pull Request 15085: https://github.com/galaxyproject/galaxy/pull/15085 +.. _Pull Request 15108: https://github.com/galaxyproject/galaxy/pull/15108 +.. _Pull Request 15110: https://github.com/galaxyproject/galaxy/pull/15110 +.. _Pull Request 15131: https://github.com/galaxyproject/galaxy/pull/15131 +.. _Pull Request 15186: https://github.com/galaxyproject/galaxy/pull/15186 +.. _Pull Request 15225: https://github.com/galaxyproject/galaxy/pull/15225 +.. _Pull Request 15247: https://github.com/galaxyproject/galaxy/pull/15247 +.. _Pull Request 15295: https://github.com/galaxyproject/galaxy/pull/15295 +.. _Pull Request 15300: https://github.com/galaxyproject/galaxy/pull/15300 +.. _Pull Request 15311: https://github.com/galaxyproject/galaxy/pull/15311 +.. _Pull Request 15329: https://github.com/galaxyproject/galaxy/pull/15329 +.. _Pull Request 15349: https://github.com/galaxyproject/galaxy/pull/15349 +.. _Pull Request 15386: https://github.com/galaxyproject/galaxy/pull/15386 +.. _Pull Request 15388: https://github.com/galaxyproject/galaxy/pull/15388 +.. _Pull Request 15394: https://github.com/galaxyproject/galaxy/pull/15394 +.. _Pull Request 15409: https://github.com/galaxyproject/galaxy/pull/15409 +.. _Pull Request 15420: https://github.com/galaxyproject/galaxy/pull/15420 +.. _Pull Request 15421: https://github.com/galaxyproject/galaxy/pull/15421 +.. _Pull Request 15425: https://github.com/galaxyproject/galaxy/pull/15425 +.. _Pull Request 15435: https://github.com/galaxyproject/galaxy/pull/15435 +.. _Pull Request 15446: https://github.com/galaxyproject/galaxy/pull/15446 +.. _Pull Request 15449: https://github.com/galaxyproject/galaxy/pull/15449 +.. _Pull Request 15450: https://github.com/galaxyproject/galaxy/pull/15450 +.. _Pull Request 15452: https://github.com/galaxyproject/galaxy/pull/15452 +.. _Pull Request 15467: https://github.com/galaxyproject/galaxy/pull/15467 +.. _Pull Request 15468: https://github.com/galaxyproject/galaxy/pull/15468 +.. _Pull Request 15483: https://github.com/galaxyproject/galaxy/pull/15483 +.. _Pull Request 15493: https://github.com/galaxyproject/galaxy/pull/15493 +.. _Pull Request 15494: https://github.com/galaxyproject/galaxy/pull/15494 +.. _Pull Request 15496: https://github.com/galaxyproject/galaxy/pull/15496 +.. _Pull Request 15497: https://github.com/galaxyproject/galaxy/pull/15497 +.. _Pull Request 15509: https://github.com/galaxyproject/galaxy/pull/15509 +.. _Pull Request 15510: https://github.com/galaxyproject/galaxy/pull/15510 +.. _Pull Request 15517: https://github.com/galaxyproject/galaxy/pull/15517 +.. _Pull Request 15521: https://github.com/galaxyproject/galaxy/pull/15521 +.. _Pull Request 15524: https://github.com/galaxyproject/galaxy/pull/15524 +.. _Pull Request 15527: https://github.com/galaxyproject/galaxy/pull/15527 +.. _Pull Request 15534: https://github.com/galaxyproject/galaxy/pull/15534 +.. _Pull Request 15538: https://github.com/galaxyproject/galaxy/pull/15538 +.. _Pull Request 15540: https://github.com/galaxyproject/galaxy/pull/15540 +.. _Pull Request 15542: https://github.com/galaxyproject/galaxy/pull/15542 +.. _Pull Request 15550: https://github.com/galaxyproject/galaxy/pull/15550 +.. _Pull Request 15557: https://github.com/galaxyproject/galaxy/pull/15557 +.. _Pull Request 15564: https://github.com/galaxyproject/galaxy/pull/15564 +.. _Pull Request 15566: https://github.com/galaxyproject/galaxy/pull/15566 +.. _Pull Request 15575: https://github.com/galaxyproject/galaxy/pull/15575 +.. _Pull Request 15576: https://github.com/galaxyproject/galaxy/pull/15576 +.. _Pull Request 15584: https://github.com/galaxyproject/galaxy/pull/15584 +.. _Pull Request 15588: https://github.com/galaxyproject/galaxy/pull/15588 +.. _Pull Request 15594: https://github.com/galaxyproject/galaxy/pull/15594 +.. _Pull Request 15596: https://github.com/galaxyproject/galaxy/pull/15596 +.. _Pull Request 15598: https://github.com/galaxyproject/galaxy/pull/15598 +.. _Pull Request 15609: https://github.com/galaxyproject/galaxy/pull/15609 +.. _Pull Request 15611: https://github.com/galaxyproject/galaxy/pull/15611 +.. _Pull Request 15614: https://github.com/galaxyproject/galaxy/pull/15614 +.. _Pull Request 15628: https://github.com/galaxyproject/galaxy/pull/15628 +.. _Pull Request 15633: https://github.com/galaxyproject/galaxy/pull/15633 +.. _Pull Request 15643: https://github.com/galaxyproject/galaxy/pull/15643 +.. _Pull Request 15647: https://github.com/galaxyproject/galaxy/pull/15647 +.. _Pull Request 15654: https://github.com/galaxyproject/galaxy/pull/15654 +.. _Pull Request 15656: https://github.com/galaxyproject/galaxy/pull/15656 +.. _Pull Request 15662: https://github.com/galaxyproject/galaxy/pull/15662 +.. _Pull Request 15663: https://github.com/galaxyproject/galaxy/pull/15663 +.. _Pull Request 15665: https://github.com/galaxyproject/galaxy/pull/15665 +.. _Pull Request 15669: https://github.com/galaxyproject/galaxy/pull/15669 +.. _Pull Request 15670: https://github.com/galaxyproject/galaxy/pull/15670 +.. _Pull Request 15671: https://github.com/galaxyproject/galaxy/pull/15671 +.. _Pull Request 15681: https://github.com/galaxyproject/galaxy/pull/15681 +.. _Pull Request 15683: https://github.com/galaxyproject/galaxy/pull/15683 +.. _Pull Request 15688: https://github.com/galaxyproject/galaxy/pull/15688 +.. _Pull Request 15689: https://github.com/galaxyproject/galaxy/pull/15689 +.. _Pull Request 15690: https://github.com/galaxyproject/galaxy/pull/15690 +.. _Pull Request 15691: https://github.com/galaxyproject/galaxy/pull/15691 +.. _Pull Request 15707: https://github.com/galaxyproject/galaxy/pull/15707 +.. _Pull Request 15708: https://github.com/galaxyproject/galaxy/pull/15708 +.. _Pull Request 15709: https://github.com/galaxyproject/galaxy/pull/15709 +.. _Pull Request 15713: https://github.com/galaxyproject/galaxy/pull/15713 +.. _Pull Request 15718: https://github.com/galaxyproject/galaxy/pull/15718 +.. _Pull Request 15720: https://github.com/galaxyproject/galaxy/pull/15720 +.. _Pull Request 15725: https://github.com/galaxyproject/galaxy/pull/15725 +.. _Pull Request 15734: https://github.com/galaxyproject/galaxy/pull/15734 +.. _Pull Request 15739: https://github.com/galaxyproject/galaxy/pull/15739 +.. _Pull Request 15740: https://github.com/galaxyproject/galaxy/pull/15740 +.. _Pull Request 15745: https://github.com/galaxyproject/galaxy/pull/15745 +.. _Pull Request 15771: https://github.com/galaxyproject/galaxy/pull/15771 +.. _Pull Request 15777: https://github.com/galaxyproject/galaxy/pull/15777 +.. _Pull Request 15783: 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