galaxyproject/galaxy v23.1.1 on GitHub

What's Changed

Version 23.1.dev by @dannon in #15353
Towards decoupling datatypes and model by @jdavcs in #15186
Fix bad auto-merge of dev. by @jmchilton in #15386
vueify formUpload with composition API by @assuntad23 in #15409
Bump ua-parser-js from 0.7.31 to 0.7.33 in /client by @dependabot in #15425
Outline Deployment Tests by @jmchilton in #15420
Drop defineEmits import from FormUpload by @dannon in #15450
Prettier targeting refinements by @dannon in #15449
Move database access code out of tool_util by @jdavcs in #15467
Follow up to #15186 by @jdavcs in #15388
Make serving address more visible in console by @davelopez in #15468
Merge 23.0 into dev by @mvdbeek in #15492
Stricter typescript config by @ElectronicBlueberry in #15311
Create ToolSuccess route and refactor component by @ahmedhamidawan in #15484
Merge 23.0 into dev by @mvdbeek in #15498
Use connection instead of session for ItemGrabber by @jdavcs in #15496
Implement initial tool/wf test assertions module for JSON data. by @jmchilton in #15494
Update Python dependencies by @galaxybot in #15435
Merge 23.0 into dev by @mvdbeek in #15511
Various Tool Shed Cleanup by @jmchilton in #15247
xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in #15534
Add basic selenium test for shared histories by @davelopez in #15538
Phylocanvas rebuild by @dannon in #15521
Move TS to Alembic by @jdavcs in #15509
Add new release tags to manage_toolshed_db.sh script by @jdavcs in #15542
Merge 23.0 into dev by @mvdbeek in #15546
Use sentry-fastapi integration, expose sampling rate by @mvdbeek in #15550
Merge release_23.0 into dev by @mvdbeek in #15566
Updating build-related dependencies, static cleanup. by @dannon in #15527
Have prettier use a cache. by @dannon in #15575
QUnit elimination by @dannon in #15452
Update browserslist and exclusions, linting. by @dannon in #15524
Drop workflow exports to myexperiment.org by @dannon in #15576
Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance by @hujambo-dunia in #15517
Merge 23.0 into dev by @mvdbeek in #15581
add missing f for f-string by @bernt-matthias in #15584
Fix jest tests run on CI by @davelopez in #15588
Handle "email_from" config option consistently, as per schema description by @jdavcs in #15557
Merge 23.0 into dev by @mvdbeek in #15594
Bump undici from 5.14.0 to 5.19.1 in /client by @dependabot in #15609
Alternatively allow double quotation marks in search filters by @guerler in #15606
Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
Unify url handling with filesources by @nuwang in #15497
Explore tool remote test data by @davelopez in #15510
Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in #15633
Fix call to docker_cached_container_description by @bernt-matthias in #15598
Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643
Changes to match latest playbook by @nuwang in #15647
Merge 23.0 into dev by @mvdbeek in #15652
Install singularity in the integration GitHub workflow by @nsoranzo in #14922
Unpin Beaker requirement by @nsoranzo in #15665
Fix for new style conda packages by @bernt-matthias in #15446
Add transactional state to JobHandlerStopQueue by @jdavcs in #15671
Add transactional state to workflow scheduling manager by @jdavcs in #15683
Drop model mapping unit tests by @jdavcs in #15669
Minor hid display tweak by @dannon in #15662
Remove DELETED_NEW job state from code base by @jdavcs in #15690
Empower Users to Select Storage Destination by @jmchilton in #14073
update the admin activation docs by @martenson in #15670
Follow up on object store selection PR. by @jmchilton in #15654
Use chevrons instead of eye for showing expandable/collapsible sections by @dannon in #15688
Update selenium hid text assertion by @dannon in #15691
Verify that activation and reset emails are properly generated by @guerler in #15681
Cleanup API schema for dropping deleted_new by @jmchilton in #15708
Merge release_23.0 into dev by @mvdbeek in #15711
Tweaks to new object store and quota APIs by @jmchilton in #15709
Use Animation Frame in Workflow Editor by @ElectronicBlueberry in #15725
Fix Enums in API docs by @davelopez in #15740
Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in #15713
More object store documentation. by @jmchilton in #15707
Fix occasional package problems related to dependencies. by @jmchilton in #15734
Merge conflicting db migration branches into one by @jdavcs in #15771
fix premature return in user API by @martenson in #15781
Implement some initial object store selection end-to-end tests. by @jmchilton in #15785
Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786
Quota source labelling bug fixes and improvements by @jmchilton in #15795
Enable strict_equality mypy option by @nsoranzo in #15808
Add selenium test for history Related filter by @ahmedhamidawan in #15720
Merge 23.0 into dev by @mvdbeek in #15809
Convert more of the object store selection client to TypeScript. by @jmchilton in #15783
Add Storage Management API by @davelopez in #15295
Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
Add ensureDefined assertion utility by @ElectronicBlueberry in #15834
Convert utilities to typescript by @dannon in #15718
[PROCEDURES] Add Laila as a committer by @dannon in #15789
Fix log message by @bernt-matthias in #15838
merge release_23.0 into dev by @martenson in #15830
Enable no-throw-literal eslint rule by @ElectronicBlueberry in #15849
Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844
Utils refactor by @ElectronicBlueberry in #15837
[PROCEDURES] Remove jxtx from committers list. by @dannon in #15790
Drop use_legacy_history from config by @dannon in #15861
Fix masthead element padding and improve brand text contrast by @guerler in #15689
Adding onFocus and onBlur functionality to editing the history name by @assuntad23 in #15853
merge release_23.0 into dev by @martenson in #15854
Move @types/d3 to dev dependencies by @davelopez in #15864
Fix anonymous user uploads when vault is configured by @tchaussepiedifb in #15858
Update Python dependencies by @galaxybot in #15564
Fix WorkflowDisplay error message handling by @dannon in #15865
Fix information popovers when displaying object stores for selection. by @jmchilton in #15867
Fix filesource file url support by @nuwang in #15794
Initial end-to-end tests for separate quota sources per object store by @jmchilton in #15800
Allow typescript unit testing with navigation YAML. by @jmchilton in #15784
Enable per-destination container_resolver_config_file by @bernt-matthias in #15884
Add StatesInfo component by @ahmedhamidawan in #15745
Allow pending inputs in some collection operation tools by @mvdbeek in #15892
Exclude tests from TypeScript compilation by @ElectronicBlueberry in #15900
Merge 23.0 into dev by @nsoranzo in #15902
Advanced tool search result tweaks by @ElectronicBlueberry in #15908
ci: show test classes with non standard names by @bernt-matthias in #15886
Merge 23.0 into dev by @mvdbeek in #15920
Fix Multi-History infinite loading loop. by @dannon in #15931
Update Python dependencies by @galaxybot in #15890
Update release notes footer by @nsoranzo in #15941
Introducing the Activity Bar, initial concept and layout by @guerler in #14802
Summarize long Workflow annotations in WorkflowList by @ahmedhamidawan in #15925
Migrate user and user flags stores to Pinia by @itisAliRH in #15938
Make container builders use mamba by @bernt-matthias in #15953
Update locale.js by @undergone2345 in #15963
Merge 23.0 into dev by @mvdbeek in #15958
Build container with nodejs by @ksuderman in #15979
Migrate history store to pinia by @itisAliRH in #15108
Add text-break to wrap long published titles by @guerler in #15980
Fix Activity Bar toggle reactivity by @davelopez in #15988
Convert legacy side panels to flex-compatible panels by @guerler in #15935
Emit filterText to HistoryPanel from historyStore by @ahmedhamidawan in #15926
Drop database views by @jdavcs in #15876
Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628
Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811
Improve display chunk generation for BAMs by @wm75 in #15972
Fetcher Mock utility by @ElectronicBlueberry in #15992
Add alter_column migration utility by @jdavcs in #16009
Mock fetcher followup by @ElectronicBlueberry in #16011
Export tool citations configurable message by @minh-biocommons in #15998
Fix for link pop-up window/toaster after Data Library to History import by @hujambo-dunia in #16008
Fix nullable deleted column in API Keys table by @davelopez in #15956
reorganize user menu for consistency by @martenson in #15994
remove inherited title from masthead dropdown items by @martenson in #15995
minor tooltip and UI client changes by @martenson in #16017
Fix pasting file fails if text starts with file by @ElectronicBlueberry in #16023
Add option to create list for all datasets in a history to dropdown by @assuntad23 in #15947
Refactor badge parsing/serialization/typing for reuse. by @jmchilton in #15987
Allow importing a workflow from a shared URL by @ElectronicBlueberry in #15903
Code cleanups from ruff and pyupgrade by @nsoranzo in #16035
Change confusing pulsar logs message by @kysrpex in #16038
Object store badges spelling fixes. by @jmchilton in #16028
Refactor integration tests to create utility for setting up a database vault. by @jmchilton in #16027
12875/form drilldown vue conversion by @assuntad23 in #15813
Another round of easy tool shed cleanup. by @jmchilton in #15540
implement admin jobs filtering by @martenson in #16020
Add support for visualizing HDF5 datasets. by @jarrah42 in #15394
Add missing fields to HistorySummary schema model by @davelopez in #16041
Gitignore update by @ElectronicBlueberry in #16046
Fixes the parcel2 build for hdf5 viz when using node18. by @dannon in #16047
New history selector with quick actions by @ElectronicBlueberry in #16040
Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058
Update Python dependencies by @galaxybot in #15942
Show backend search errors in hist panel by @ahmedhamidawan in #15874
Change release note icon by @itisAliRH in #16049
Rename object stores in config. by @jmchilton in #16029
Migrate job metrics store and component to use pinia and composition api by @Renni771 in #16056
Deprecate tools/evolution by @bernt-matthias in #15656
Use jsdom-worker instead of mock by @ElectronicBlueberry in #16064
Use Filtering class to get and set filter texts by @ahmedhamidawan in #15996
Drop UserHistories provider by @itisAliRH in #15993
External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019
Ensure that unselected checkbox inputs emit null instead of an empty array by @guerler in #16059
Fix font-awesome library types by @ElectronicBlueberry in #16068
unify workflows grid components by @martenson in #16045
Remove legacy form fields from parameter factory by @guerler in #15983
Updated doc and tests for attribute value filter by @tuncK in #15929
Add create_foreign_key migration utility by @jdavcs in #16077
Update Python dependencies by @galaxybot in #16086
Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in #16080
Vueify Select field by @guerler in #16010
Merge release_23.0 into dev by @nsoranzo in #16088
Fix and test startup with Python 3.11 on macOS by @nsoranzo in #16082
Refactor a few client object store components by @jmchilton in #16051
Use automated naming convention to generate indexes and constraints in database by @jdavcs in #16089
Fix minor Switch to History bug in HistoryView by @ahmedhamidawan in #16095
Use _.+ for unused variables by @ElectronicBlueberry in #16098
Attempt to fix mypy check by @davelopez in #16103
De-duplicate code around object store caches. by @jmchilton in #16108
Improve robustness of collection edit E2E test. by @jmchilton in #16092
Workflow Editor Infinite Grid with Landmark-Lines by @ElectronicBlueberry in #16097
Workflow Connections Dynamic Radius by @ElectronicBlueberry in #16102
Fix resetting metadata on many repositories at once via the shed API by @jmchilton in #14906
Allow HEAD request for requesting metadata files by @martenson in #16113
Add hdf4 datatype by @TheoMathurin in #16105
Merge branch 'release_23.0' into dev by @mvdbeek in #16118
Place admin panel section data into computed prop by @guerler in #16115
De-duplication and improvements to the in-process object store cache monitor by @jmchilton in #16111
Dataset chunking tests (and small fixes) by @jmchilton in #16069
Update Python dependencies by @galaxybot in #16123
Add Storage Dashboard visualizations for histories by @davelopez in #14820
add required_files to the tag list for linting by @bernt-matthias in #16129
Upgraded to new multiselect Tags component for Workflows, DatasetList, Attributes by @hujambo-dunia in #15225
Fix : Ignore error messages for admin created accounts by @jvanbraekel in #16132
Add count support for listing filters by @davelopez in #16075
Selenium test for displaying workflows with problems in pages. by @jmchilton in #16085
[webhook/gtn] Expand query selector list to encompass 'a' by @hexylena in #16100
Disable invalid link for anonymous users. by @jmchilton in #16147
Improve histories and datasets immutability checks by @davelopez in #16143
When writing test error debug directories, create a 'latest' symlink. by @jmchilton in #16148
Merge 23.0 into dev by @mvdbeek in #16149
Refactor caching object stores ahead of adding task-based store. by @jmchilton in #16144
Integrate accessibility testing into Selenium testing by @jmchilton in #16122
Update Python dependencies by @galaxybot in #16153
Add option to see invocations related to a history by @martenson in #16136
Documents use of k8s_extra_job_envs in job_conf sample advanced by @pcm32 in #15110
Migrate display applications API to Fast API by @heisner-tillman in #16156
Improve robustness of collection upload tests. by @jmchilton in #16093
Move axe-selenium-python to dev dependencies by @nsoranzo in #16162
FITS data format by @volodymyrss in #15905
Scope pinned histories by user ID by @ElectronicBlueberry in #16142
Fix linting of FITS datatype code by @mvdbeek in #16169
Fix eslint / ts overrides by @dannon in #16166
Updates MGnify interactive tool to v1.1.0 by @SandyRogers in #16179
Accessibility fixes for workflows, login, and registration. by @jmchilton in #16146
Update Python dependencies by @galaxybot in #16182
Record input datasets and collections at full parameter path by @mvdbeek in #15978
Merge 23.0 into dev by @mvdbeek in #16186
Merge Target class with CondaTarget by @nsoranzo in #16181
Merge 23.0 into dev by @mvdbeek in #16197
Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198
Add WorkflowBox to Activity bar Side Panel by @ahmedhamidawan in #15944
Hide Activity Bar for anonymous users by @ahmedhamidawan in #16200
Remove various fallback behaviors by @mvdbeek in #16199
Add Processing for Custom Icons by @ElectronicBlueberry in #16157
Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by @jdavcs in #16208
Drop TS unit mapping tests by @jdavcs in #16206
adjust grid sharing indicators by @martenson in #16163
Update carbon emissions calculations explanation page styling by @Renni771 in #16192
FITS file visualization plugin by @francoismg in #16187
Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207
Add Repository owner field to ToolSearch by @ahmedhamidawan in #16061
End-to-end tests for new user welcome. by @jmchilton in #16158
Improved Cache Monitoring for Object Stores by @jmchilton in #16110
Merge 23.0 into dev by @martenson in #16228
Fixes initial state of select all checkbox by @guerler in #16217
Update Python dependencies by @galaxybot in #16227
Allow user customization of the activity bar by @guerler in #16184
Handle appending to a results file that does not exists. by @ksuderman in #16233
Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421
Initial e2e test for history storage. by @jmchilton in #16221
tool_util: switch to mambaforge on non-32bit; add arm64 support by @mr-c in #16223
Protection against problematic boolean parameters. by @jmchilton in #15493
Add slack error reporting plugin by @hexylena in #15025
Adding fuzzy search functionality to front end search by @tcollins2011 in #15855
allow anon access for api/datasets/get_content_as_text by @martenson in #16226
Allow users to create new activity bar items by @guerler in #16196
Replace bootstrap_history.py with galaxy-release-util by @mvdbeek in #16231
Fix some drs handling issues by @nuwang in #15777
Don't error on missing parameters or unused parameters in UI controllers by @mvdbeek in #16246
Selenium type fixes and annotations. by @jmchilton in #16242
Add Galaxy Notification System by @davelopez in #15663
Show search in HistoryView by @ahmedhamidawan in #16225
Selenium test for page history links. by @jmchilton in #16222
Refine activity bar dragging behavior by @guerler in #16245
Paginate History Store by @ahmedhamidawan in #16084
e2e test for workflow license selector by @jmchilton in #16243
Marginally more storage management selenium coverage. by @jmchilton in #16263
Adjust notifications activity item by @guerler in #16265
Update Python dependencies by @galaxybot in #16267
Add History Archival feature by @davelopez in #16003
Add interactive tools activity by @guerler in #16266
Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in #16255
Small test decorator improvements. by @jmchilton in #16220
read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in #15596
Container resolvers: add docs, typing and tests by @bernt-matthias in #15614
bring grids for (published) pages on par with workflows by @martenson in #16209
Add zipped mongodb and genenotebook datatypes by @abretaud in #16173
Reset autocommit to True (temporarily) by @jdavcs in #16283
OIDC tokens by @SergeyYakubov in #15300
Display Tags in Workflow Editor by @ElectronicBlueberry in #16282
Fix and Improve Workflow Editor Panning by @ElectronicBlueberry in #16178
E2E Tests for Edit Dataset Attributes Page by @jmchilton in #16224
Decompress history data for testing assertions by @bernt-matthias in #15085
Bump msal version by @mvdbeek in #16285
Fixes for two framework test tools by @bernt-matthias in #15483
Expose additional beaker caching backends by @claudiofr in #15349
Bump default milestone to 23.2 by @mvdbeek in #16287
Merge release_23.0 into dev by @martenson in #16289
Set Initial Filter for Paired List Collection Creator Based on Initial Elements by @assuntad23 in #16279
Improve container resolver documentation by @mvdbeek in #16280
Update version to 23.1.rc1 by @mvdbeek in #16292
[23.1] Update 23.1 release tags for migration scripts by @jdavcs in #16294
[23.1] Open latest version of tool from tool panel link by @mvdbeek in #16290
[23.1] Fix recalculate_quota throug kombu message by @mvdbeek in #16299
[23.1] handle prefix in dataset contents properly by @martenson in #16301
[23.1] Fix form builder value handling by @guerler in #16304
[23.1] Fix ordering of data libraries from API by @martenson in #16300
[23.1] qualify querying for an api-key by @martenson in #16320
[23.1] Remove pin on packaging in packages by @nsoranzo in #16322
[23.1] Fix tool remote test data by @davelopez in #16311
[23.1] Fix 'news' webhook to account for the RC one more time. by @dannon in #16328
[23.1] Filter deleted keys from api_keys relationship by @dannon in #16321
[23.1] Makefile-based setting of NODE_OPTIONS for client build by @dannon in #16324
[23.1] Refactor workflow store to be more reliable by @ElectronicBlueberry in #16334
[23.1] Include workflow invocations in default activity by @mvdbeek in #16338
[23.1] Sanitize substring in matchingTerm by @ElectronicBlueberry in #16351
[23.1] Make tags in public histories read-only by @davelopez in #16348
[23.1] Improve help text for conditional workflow step by @mvdbeek in #16355
[23.1] Hide conditionally skipped output by @mvdbeek in #16356
[23.1] Fix invocation progress bar for skipped and deleted jobs by @mvdbeek in #16365
[23.1] Fix workflow invocation detail reactivity by @mvdbeek in #16369
[23.1] Add missing singularity_no_mount prop parsing by @mvdbeek in #16367
[23.1] Disable console instead of dropping by @ElectronicBlueberry in #16372
[23.1] Fix Nested Tool Panel Labels by @ElectronicBlueberry in #16376
[23.1] Fix disk usage recalculation for distributed object stores by @mvdbeek in #16380
[23.1] Add message showing console disable/enable, along with instructions o… by @dannon in #16401
[23.1] Fix histories count by @davelopez in #16400
[23.1] Job cache fixes for DCEs by @mvdbeek in #16384
[23.1] Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in #16421
[23.1] Fix toolform creator by @dannon in #16419
[23.1] For display (only) allow control+click for new window opening by @dannon in #16432
[23.1] Fix webhook release note seen pin by @dannon in #16446
[23.1] Fix multi-broadcast overlap by @davelopez in #16444
[23.1] Fix error_reports linting by @mvdbeek in #16465
[23.1] Swap datatype&convert tab to a static 'datatypes' tab. by @dannon in #16466
[23.1] Fix history items repeated search bug by @ahmedhamidawan in #16452
[23.1] Fix Storage Dashboard missing archived histories by @davelopez in #16473
[23.1] Restore resolution of Conda environments generated from non-lowercase package names by @nsoranzo in #16474
[23.1] Add missing archived filter in saved histories by @davelopez in #16475
[23.1] use router instead of hard links for certain page urls by @martenson in #16297
[23.1] Fix tagging component for anonymous users by @mvdbeek in #16481
[23.1] Bump bx-python to 0.10.0 by @mvdbeek in #16484
[23.1] Remove blinking animation from icons by @itisAliRH in #16471
[23.1] Fix up unit tests for local use by @mvdbeek in #16483
[23.1] Fix tags ownership by @davelopez in #16339
[23.1] Make ToolBox v-b-tooltip.hover directives noninteractive by @ahmedhamidawan in #16506
[23.1] Fix ToolBoxWorkflow search delay bug by @ahmedhamidawan in #16505
[23.1] Fix history item states help display to apply same styling attributes by @dannon in #16500
[23.1] H5web updates by @dannon in #16509
[23.1] Fix for Accessibility, on Workflows List page Tooltip by @hujambo-dunia in #16520
[23.1] fix font-weight disparity between browsers by @hujambo-dunia in #16515
[23.1] Fix double-encoding notification content by @mvdbeek in #16530
[23.1] Exclude selenium version with broken type hints by @mvdbeek in #16531
[23.1] Restore tmp mounting by @mvdbeek in #16533
[23.1] Run through tmp_dir_creation_statement only once by @mvdbeek in #16529
[23.1] Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537
[23.1] Fix shared item notification link by @davelopez in #16581
[23.1] Don't use docker run --user flag on OSX by @mvdbeek in #16573
[23.1] Ignore errors with user-set job resources by @mvdbeek in #16579
[23.1] Bump minimum tpv version to 2.3.2 by @mvdbeek in #16597
[23.1] make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in #16594
[23.1] Fix replacement parameters for subworkflows. by @jmchilton in #16592
[23.1] Drop expunge_all() call in WebTransactionRequest by @mvdbeek in #16606
[23.1] Drop RecursiveMiddleware by @mvdbeek in #16605
[23.1] Fix multiple remote test data by @davelopez in #16542
[23.1] Optimize getting current user session by @mvdbeek in #16604
[23.1] Backport tool mem fixes by @mvdbeek in #16601
[23.1] Only reindex tool search once after forking by @mvdbeek in #16611
[23.1] Fix Published Pages and Pages view showing same content by @ahmedhamidawan in #16614
[23.1] Remove render.py script from iSEE by @neoformit in #16616
[23.1] Reload toolbox after forking when using --preload by @mvdbeek in #16620
[23.1] Account for expires/expires_in when refreshing token by @mvdbeek in #16621
[23.1] Make datatype edit default value a string instead of list of strings by @mvdbeek in #16591
[23.1] Fixes for conditional subworkflow steps by @mvdbeek in #16632
[23.1] Fix nested conditional workflow steps by @mvdbeek in #16641
[23.1] Make sort_collection tool require terminal datasets by @mvdbeek in #16661
[23.1] xsd: allow name attribute of test collections by @bernt-matthias in #16663
[23.1] Fix expression evaluation for nested state by @mvdbeek in #16656
[23.1] Push to object store even if set_meta fails by @mvdbeek in #16667
[23.1] Ensure Job belongs to current SA session by @mvdbeek in #16655
[23.1] Login/Register fixes by @dannon in #16652
[23.1] Fix regex validation for global inline flags by @mvdbeek in #16683
[23.1] Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in #16678
[23.1] Only show 'edit' on published pages when viewer is the owner. by @dannon in #16680
[23.1] Update galaxyproject/charts utilizing visualizations by @dannon in #16674
[23.1] Fix closed transaction error on galaxy startup/check jobs by @jdavcs in #16687
[23.1] FileInput no longer accept 'U' in the file mode by @bgruening in #16704
[23.1] List extra files only for terminal datasets by @mvdbeek in #16705
[23.1] Fix legend not scrollable in storage overview charts by @davelopez in #16703
[23.1] Add missing join condition in job search by @mvdbeek in #16710
[23.1] Fix job search query by @mvdbeek in #16714
[23.1] Fix collection id encoding by @davelopez in #16718
[23.1] Fix unittest mocks to support us checking geturl() by @dannon in #16726
[23.1] Fix allowlist deserialization in file sources by @mvdbeek in #16729
[23.1] Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728
[23.1] force wrap long parameter names in the workflow form by @martenson in #16732
[23.1] prevent toolbox scrollbar by @martenson in #16734
[23.1] Copy the collection contents by default when copying a collection by @mvdbeek in #16717
[23.1] 23.1 Release Notes by @dannon in #16329
[23.1] Fix workflow output display without label by @mvdbeek in #16749
[23.1] Add deprecation notice for api/search by @jdavcs in #16756
[23.1] Add missing requirements to perl tools by @mvdbeek in #16763
[23.1] Don't allow empty selection on required select field by @mvdbeek in #16759
[23.1] Fix public archived histories not importable by @davelopez in #16766
[23.1] Fix ItemOwnerShipException in tag removal by @mvdbeek in #16773
[23.1] Allow importing history with same name as original history by @ahmedhamidawan in #16741
[23.1] Fix short ids in tool panel views. by @jmchilton in #16800
[23.1] Disable button in CopyModal for histories when copying history by @ahmedhamidawan in #16793
[23.1] move history and tool panel tooltips out of the way by @martenson in #16808
[23.1] Fix tool panel views for versionless tool ids by @mvdbeek in #16809
[23.1] Fix parameter display in job info page for tools with sections by @mvdbeek in #16821
[23.1] move the email and username redacting from the role loop by @martenson in #16820
[23.1] backport of pysam tostring by @martenson in #16822
[23.1] Increase CustosAuthnzToken.external_user_id column size by @davelopez in #16818
[23.1] Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in #16829
[23.1] Fix up local tool version handling by @mvdbeek in #16836
[23.1] Exclude on_opened and on_closed from watcher events by @mvdbeek in #16850
[23.1] Specify uid for the k8s image by @afgane in #16844
[23.1] Fix and prevent persisting null file_size by @mvdbeek in #16855
[23.1] Fix safe update version handling in run form by @mvdbeek in #16865
[23.1] Fix workflow import losing tool_version by @mvdbeek in #16869
[23.1] Allow referring to steps by label only in markdown editor by @mvdbeek in #16861
[23.1] Remove more flushes in database operation tools by @mvdbeek in #16875
[23.1] Fix tag ownership check by @mvdbeek in #16877
[23.1] Fix join condition for nested collection query by @mvdbeek in #16880
[23.1] Fix delete collection + elements by @davelopez in #16879

New Contributors

@tchaussepiedifb made their first contribution in #15858
@undergone2345 made their first contribution in #15963
@minh-biocommons made their first contribution in #15998
@jarrah42 made their first contribution in #15394
@tuncK made their first contribution in #15929
@TheoMathurin made their first contribution in #16105
@volodymyrss made their first contribution in #15905
@francoismg made their first contribution in #16187
@tcollins2011 made their first contribution in #15855

Full Changelog: v23.0.6...v23.1.1