v24.0.0

For a list of curated highlights see the release announcement at https://docs.galaxyproject.org/en/latest/releases/24.0_announce_user.html

What's Changed

• Version 23.3.dev by @dannon in #17096
• Python 3.8 as minimum by @mr-c in #16954
• SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932
• Add history items display state for collections/lists with failed or new populated_state by @ahmedhamidawan in #16996
• Dataset Display : force reload on subsequent clicks. by @dannon in #16982
• Remove web framework dependency from tools by @davelopez in #17058
• Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /client by @dependabot in #17115
• Vueify Admin User Grid by @guerler in #17030
• Update Python dependencies by @galaxybot in #17123
• SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by @jdavcs in #17122
• Vueify Admin Roles Grid by @guerler in #17118
• Migrate job destination parameters store to Pinia by @davelopez in #17119
• Vueify Admin Groups Grid by @guerler in #17126
• Migrate dataset extra files store to Pinia by @davelopez in #17145
• Vueify Admin Forms and Quota grids by @guerler in #17141
• Don't require admin user to list /api/tool_data by @jozh2008 in #17161
• Update Python dependencies by @galaxybot in #17157
• Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132
• Add keyedCache composable by @davelopez in #17148
• Replace discouraged Mambaforge with Miniforge3 by @nsoranzo in #17177
• Qiskit in galaxy by @thepineapplepirate in #17170
• Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter by @jdavcs in #17184
• Add future=True flag to SA engine by @jdavcs in #17174
• Add future=True flag to SA session by @jdavcs in #17179
• Convert dataset path destination store to composable by @davelopez in #17175
• Clarify the meaning of lexical sorting of discovered datasets by @bernt-matthias in #17190
• Update DatasetError.vue to fix broken link by @jennaj in #17193
• Fix for converter tests by @bernt-matthias in #17188
• xsd: reorder choices for permissive boolean by @bernt-matthias in #17187
• Accept any number of arguments to the secret decoder ring by @natefoo in #17191
• correct dbkey for minerva display app by @hexylena in #17196
• Update Python dependencies by @galaxybot in #17201
• Bump default milestone to 24.0 by @mvdbeek in #17211
• Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in #17153
• Reload built-in converters on toolbox reload by @bernt-matthias in #17209
• Improve links to Hub, Matrix and WGs in CONTRIBUTING.md by @nsoranzo in #17221
• Add a3m datatype by @astrovsky01 in #17217
• Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216
• Vendorize fastapi-utls.cbv by @jdavcs in #17205
• Migrate workflow invocation store to Pinia by @davelopez in #17203
• Update Python dependencies by @galaxybot in #17230
• Expose more tool information / navigability in UI. by @jmchilton in #17105
• Implement Galaxy Markdown directive history_dataset_as_table. by @jmchilton in #16681
• port invocation API to fastapi by @martenson in #16707
• Update Python dependencies by @galaxybot in #17235
• Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977
• Reuse test instance during non-integration tests by @mvdbeek in #17234
• Workflow node connector improvements by @ElectronicBlueberry in #17240
• Build and cache galaxy client for selenium and startup tests by @mvdbeek in #17239
• tus wants a json response from v2.0.0 by @mira-miracoli in #17246
• Update Python dependencies by @galaxybot in #17247
• Add missing re-usable commit-id output by @mvdbeek in #17248
• Update CONTRIBUTORS.md with new email address for Jeremy Goecks by @jgoecks in #17255
• Make flex panel drag handle more obvious by @ElectronicBlueberry in #17113
• Bump follow-redirects from 1.15.1 to 1.15.4 in /client by @dependabot in #17260
• Migrate models to pydantic 2 by @mvdbeek in #17262
• Optional Reply-to SMTP header in tool error reports by @neoformit in #17243
• Fixes for output discovery by @bernt-matthias in #17266
• Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222
• Fix invocation serialization if no state was set by @mvdbeek in #17278
• Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979
• Render Useful Markdown Components for Mapped Over Steps by @jmchilton in #17198
• Workflow node connector improvements followup by @ElectronicBlueberry in #17244
• Vueifiy History Grids by @guerler in #17219
• Add OIDC backend configuration schema and validation by @uwwint in #17274
• Fix Workflow Comment Model for Pydantic 2 by @ElectronicBlueberry in #17296
• Improve ModelManager type hints by @mvdbeek in #17299
• Fix any type for tool_data_file_path by @mvdbeek in #17293
• Package tests fixes by @nsoranzo in #17301
• Follow-up on #17274 and #17262 by @nsoranzo in #17302
• Scoped Store Refactor and Store Composition Refactor by @ElectronicBlueberry in #17304
• Refactor two of the missing invocation routes to FastAPI by @heisner-tillman in #17237
• Allow job files to consume TUS uploads by @jmchilton in #17242
• Rollback invalidated transaction: catch them earlier by @jdavcs in #17312
• Make Workflow Editor Toolbar Toggleable by @ElectronicBlueberry in #17297
• Enable job resubmissions in k8s runner by @nuwang in #17324
• Adjust Flex Panel Drag Handle and Collapse Button by @ElectronicBlueberry in #17298
• Add accepted extensions to form data input by @ElectronicBlueberry in #17238
• Overhaul Galaxy Markdown Help by @jmchilton in #17228
• Document SQLAlchemy session lifespan by @mvdbeek in #17322
• add documentation for data source tool by @PlushZ in #17327
• [23.2] fix s3fs templating by @bgruening in #17311
• Add support for Python 3.12 by @tuncK in #16796
• Fix quotas ID encoding by @davelopez in #17335
• Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340
• Port HistoryPanel component to composition API and typescript by @Renni771 in #17318
• Merge 23.2 into dev by @jdavcs in #17345
• Escape pipe character in tool XSD docs by @neoformit in #17359
• Remove unused statements in job search function by @mvdbeek in #17361
• Convert entryPointStore to composition API + TS by @davelopez in #17356
• XSD schema doc building: quote pipe characters in attribute tables by @bernt-matthias in #17364
• Add explicit cache_ok attribute to JSONType subclass by @mvdbeek in #17376
• Fix type annotation of code using XML etree by @nsoranzo in #17367
• Merge 23.2 into dev (minor release notes edit) by @jdavcs in #17387
• Remove remaining Vuex stores and dependencies by @davelopez in #17348
• Fix minor oidc_backends_config comment bug by @ahmedhamidawan in #17385
• Unify continuous polling with composable by @davelopez in #17355
• Update Python dependencies by @galaxybot in #17333
• Adds delete, purge and undelete batch operations to History Grid by @guerler in #17282
• More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381
• Fix activity-settings hidden behind left side panel bug by @ahmedhamidawan in #17392
• Update to black 2024 stable style by @nsoranzo in #17391
• New Activity bar - Notifications by @itisAliRH in #17300
• Update current version to 24.0.dev0 by @jdavcs in #17402
• Merge 23.2 into dev by @jdavcs in #17407
• Fix z-index in BroadcastContainer.vue by @davelopez in #17401
• Fix IUC best practices links, mention data_source_async in XSD by @wm75 in #17409
• Enable comments in package dag file by @jdavcs in #17408
• Cancel all active jobs when the user is deleted by @davelopez in #17390
• Purge groups and roles from DB (for real) by @davelopez in #17411
• Add signpost to training material by @nuwang in #17421
• Refactor MarkdownDialog.vue to ts+composition. by @jmchilton in #17399
• Remove legacy tool versions list from admin panel by @guerler in #17155
• Some additional typing for test interactor stuff. by @jmchilton in #17398
• Fix model store exports that include implicit conversions. by @jmchilton in #17346
• Combines legacy qv-pattern and advanced filter pattern in history index endpoint by @guerler in #17368
• API endpoint that allows "changing" the objectstore for "safe" scenarios. by @jmchilton in #17329
• Much simpler default dataset permissions for typical users. by @jmchilton in #17166
• Fix text to match options in HistoryStorageOverview by @jmchilton in #17450
• Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster by @guerler in #17415
• Removes outdated Grid controller and backbone modules by @guerler in #17434
• Refactor Common components by @itisAliRH in #17441
• Enable warn_unreachable mypy option by @mvdbeek in #17365
• Custom Multiselect by @ElectronicBlueberry in #17331
• Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @ahmedhamidawan in #17444
• Allow removing last value from multi select field by @guerler in #17403
• Add tool XML schema documention for outputs - collection - data by @bernt-matthias in #17465
• Update release process documentation by @mvdbeek in #17461
• Move Activity Bar Settings to Activity by @ElectronicBlueberry in #17457
• Use short link for TPV shared database by @nuwang in #17467
• Add select parameter with options from remote resources by @mvdbeek in #17087
• Exclude password reset link from login form where users don't have the ability to manage accounts by @dannon in #17473
• Modernize bits and pieces of storage display by @jmchilton in #17436
• Fix for a regression change - auto-select/highlight file name text by @hujambo-dunia in #17466
• Fix data_source and data_source_async bugs by @wm75 in #17422
• Move Visualizations Activity to Side Panel by @ElectronicBlueberry in #17458
• History refactors by @itisAliRH in #17353
• Update Python dependencies by @galaxybot in #17420
• Tag Autocomplete Rework by @ElectronicBlueberry in #17469
• Adds published histories to grid list by @guerler in #17449
• LDAP3 fix for attributes returned as strings by @bernt-matthias in #17305
• Type annotation and refactoring of tests by @nsoranzo in #17484
• UI for "relocating" a dataset to a new object store (when safe) by @jmchilton in #17437
• New Workflow List and Card View by @itisAliRH in #16607
• Split linters in separate classes by @bernt-matthias in #17081
• Citation refactors by @itisAliRH in #17483
• Bump undici from 5.26.5 to 5.28.3 in /client by @dependabot in #17485
• Display workflow invocation counts. by @jmchilton in #17488
• Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435
• build_mulled: also use namespace for building singularity images by @bernt-matthias in #15657
• Update k8s docker python to 3.12 by @nuwang in #17494
• Faster FASTA and FASTQ metadata setting by @bernt-matthias in #17462
• Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460
• Removes legacy history xml makos by @guerler in #17505
• Add documentation on how to use vault keys in file sources by @bernt-matthias in #17498
• Add gxadmin to docker and update branch by @nuwang in #17521
• Stringify cgroups metrics formatted value return by @dannon in #17520
• [23.2] Fix bug: create new PSAAssociation if not in database by @jdavcs in #17516
• Update Python dependencies by @galaxybot in #17486
• Add History Multiview activity+panel, add "Show Recent" mode to multiview by @ahmedhamidawan in #17251
• Update RStudio GxIT to use the reworked 23.1 image by @natefoo in #17533
• add encode ID API endpoint by @mira-miracoli in #17510
• Consolidate resource grids into tab views by @guerler in #17487
• Consider Null inputs by @bernt-matthias in #17271
• data_column parameter: use column_names metadata if present by @bernt-matthias in #17478
• [23.2] Fix social_core methods by @jdavcs in #17530
• Workflow list small tweaks by @ElectronicBlueberry in #17538
• freeze (make sticky) header row in tabular files by @hujambo-dunia in #17455
• Update Python dependencies by @galaxybot in #17541
• [23.2] Fix emission estimates typo by @nsoranzo in #17543
• Workflow anonymous user buttons by @itisAliRH in #17537
• add npy datatype by @astrovsky01 in #17517
• Fixing data_source tools and incrementing tool profile by @wm75 in #17515
• has_size assertion: implement size (as synonym for value) by @bernt-matthias in #17490
• Hide wig_to_bigWig tool by @bernt-matthias in #17328
• Allow for upper case container tags by @bernt-matthias in #17254
• Change default milestone to target 24.1 by @jdavcs in #17549
• Add harmonize collections tool (or whatever other name) by @lldelisle in #16662
• Fix test_index_advanced_filter API test re-running by @nsoranzo in #17547
• Refactor Workflow API routes - Part 1 by @heisner-tillman in #17463
• Enable workflow buttons right click by @itisAliRH in #17529
• Enhance Avivator display app to support regular Tiffs by @davelopez in #17554
• Add basic TIFF Image visualization by @davelopez in #17553
• Add name_eq and genome_build_eq filters to HistoryFilters by @ahmedhamidawan in #17389
• Remove virtual scroller from History by @ElectronicBlueberry in #17546
• Update .gitignore by @davelopez in #17559
• [23.2] Associate default history with session when creating a new session by @mvdbeek in #17557
• tests: check ftype and decompress interaction by @bernt-matthias in #17545
• Filter out subworkflow invocations by @mvdbeek in #17558
• Drop plugin-based new user welcome. by @dannon in #17568
• add shm_size based on ShmSize by @richard-burhans in #17565
• Refactor Workflow Import components by @itisAliRH in #17495
• Add help text to workflow invocation states by @jmchilton in #17569
• Add multiple drag/drop and keyboard accessible selection to HistoryPanel items by @ahmedhamidawan in #17502
• Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357
• Add support for (fast5.tar).xz binary compressed files by @tuncK in #17106
• Update tour testing selector usage. by @jmchilton in #14005
• Feature SBOL datatypes by @guillaume-gricourt in #17482
• Make columns types an empty list for empty tabular data by @bernt-matthias in #13918
• Remove legacy phyloviz, circster and sweepster artifacts by @guerler in #17573
• Links to individual invocations. by @jmchilton in #17566
• [23.2] Account for newlines in CIF Datatype sniffer by @patrick-austin in #17582
• Update Python dependencies by @galaxybot in #17580
• consistently compare profile versions by @bernt-matthias in #16492
• Apply default theme to theme selector by @ElectronicBlueberry in #17583
• Add image_diff comparison method for test output verification using images by @kostrykin in #17556
• Add migrations revision identifier for 24.0 by @jdavcs in #17589
• [23.2] Fix test_page_encoding and test_collection_explicit_and_implicit integration tests by @nsoranzo in #17584
• [23.1] Fix ancient bug: incorrect usage of func.coalesce in User model by @jdavcs in #17577
• [24.0] Update version to 24.0.rc1 by @jdavcs in #17591
• [24.0] Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294
• [23.2] Fix tool shed webapp by @mvdbeek in #17597
• [24.0] Extend regex groups in stdio regex matches by @bernt-matthias in #17016
• [24.0] Fix test_oidc_login_existing_user test by @nsoranzo in #17612
• [23.2] Don't call get_or_create_default_history() twice for invalidated sessions by @nsoranzo in #17613
• [23.2] Anticipate PendingRollbackError in check_database_connection by @mvdbeek in #17598
• [24.0] Fix bugs relating to history keyboard navigation by @ahmedhamidawan in #17587
• [24.0] Make latest_workflow_uuid optional by @mvdbeek in #17629
• [24.0] Increase ContentItem clickable area by @ahmedhamidawan in #17621
• [23.2] Fix switch to history in invocations list by @davelopez in #17616
• [24.0] default sort all grid histories the same by @martenson in #17635
• [24.0] do not link to invocations for workflow that has never run by @martenson in #17626
• [24.0] More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632
• [24.0] Fix workflow person validation by @dannon in #17636
• [24.0] Make WorkflowInput label, value and uuid optional by @mvdbeek in #17638
• [23.1] Fix DataResult type by @mvdbeek in #17639
• [24.0] Prevent 500 for anon /api/invocations by @mvdbeek in #17640
• Merge 23.2 into 24.0 by @mvdbeek in #17644
• [24.0] Don't fail for anon /api/users request by @mvdbeek in #17645
• [23.2] Fix tool panel workflow and favorites button bugs by @ahmedhamidawan in #17634
• [24.0] Don't index tasks without task_uuid by @mvdbeek in #17646
• [24.0] Add basic model import attribute validation by @mvdbeek in #17628
• [23.2] Yaml nested assertions: fix parsing by @bernt-matthias in #17641
• [24.0] Fix history panel arrow navigate by id bug, add HistoryOperations to HistoryView and prevent item selection in unowned histories by @ahmedhamidawan in #17648
• [24.0] fix shared item details and initial filters by @martenson in #17651
• [23.2] Npz sniffing: do not read the whole file by @bernt-matthias in #17674
• [24.0] Drop release notes webhook by @dannon in #17675
• [24.0] Fix contentitem display routing. by @dannon in #17687
• [23.2] Assert that at least one file in npz zipfile ends with .npy by @mvdbeek in #17679
• [23.2] Separate ConnectedValue from RuntimeValue by @mvdbeek in #17678
• [23.2] Limit new anon histories by @mvdbeek in #17657
• [24.0] Purge history from history panel by @ahmedhamidawan in #17685
• [24.0] Moves archived histories from Masthead to Histories Grid by @guerler in #17649
• [24.0] Fix incorrect history item count in histories lists by @davelopez in #17714
• [24.0] Fix archived histories tab anonymous access by @davelopez in #17719
• [24.0] Improve published histories listing performance in UI by @davelopez in #17717
• [24.0] Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in #17716
• [24.0] Workflow Comment Indexing by @ElectronicBlueberry in #17700
• [24.0] Fix date range popover cutoff in history swtich by @jmchilton in #17724
• [24.0] Always display grid pagination on the right by @guerler in #17722
• [24.0] Fix Workflow Name Display in WorkflowCard to Prevent Bleeding Over Borders by @itisAliRH in #17721
• [24.0] Fix Collection Scrolling not showing all items by @ElectronicBlueberry in #17720
• [24.0] fix overflowing and hiding of storage popovers by @martenson in #17742
• [24.0] Prevent dragover for item from same history in history panel by @ahmedhamidawan in #17761
• [24.0] Fix usage of DISTINCT by @jdavcs in #17759
• [24.0] Fix tag sorting by @ElectronicBlueberry in #17753
• [24.0] Fix histories API index_query serialization by @davelopez in #17726
• [24.0] Don't require history to calculate anon disk usage by @mvdbeek in #17765
• [23.1] Handle missing indexer for a dataset by @ahmedhamidawan in #17736
• [24.0] Fix input parameter step type by @mvdbeek in #17767
• [24.0] Fix anon user values again by @mvdbeek in #17772
• [24.0] Revise language around non-private object stores by @martenson in #17744
• [24.0] Fix include_nested_invocations parameter use by @mvdbeek in #17768
• [24.0] change user-facing language from "object store" to "storage location" by @martenson in #17763
• [24.0] Add missing fields in histories listings by @davelopez in #17775
• [24.0] Grid filtering bug fixes by @ahmedhamidawan in #17684
• [24.0] Minor log cleanup. by @dannon in #17789
• [24.0] Clarify language about the activity bar being beta by @dannon in #17790
• [24.0] Swap history dropdown from using the tiny caret to faBars. by @dannon in #17791
• [24.0] Avoid showing a shareable URL with the default slug/username. by @dannon in #17788
• [24.0] Use hg clone --stream to clone repos by @mvdbeek in #17786
• [24.0] Fix visualization activity plugin list images by @dannon in #17792
• [24.0] Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777
• [24.0] Defer job attributes that are usually not needed by @mvdbeek in #17795
• [24.0] Prompt user to change default history permissions... by @jmchilton in #17782
• [24.0] Restore histories API behavior for keys query parameter by @davelopez in #17779
• [24.0] Fix new default history creation when in remote or single user mode by @dannon in #17796
• [24.0] Fix anonymous user create, run and import workflows by @itisAliRH in #17776
• [24.0] Fix history filters taking up space in GridList by @ahmedhamidawan in #17652
• [24.0] Fix source history update_time being updated when importing a public history by @jmchilton in #17728
• [24.0] Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803
• [24.0] Fix datasets API custom keys encoding by @davelopez in #17793
• [24.0] Return published histories first in display_by_username_and_slug by @mvdbeek in #17808
• [24.0] Improve Shift+Click select in history panel and add it for ContentItem selector checkboxes as well by @ahmedhamidawan in #17762
• [24.0] Datasets list anonymous access and history link fixes. by @dannon in #17756
• [24.0] remove link to non existent page from Data menu by @martenson in #17816
• [24.0] Show full Data menu when in single user mode. by @dannon in #17815
• [23.2] Backport of #17796 by @bernt-matthias in #17824
• [24.0] Simplify nested collection joins by @mvdbeek in #17817
• [23.0] Fix excessive memory usage for npz files by @mvdbeek in #17828
• [24.0] Fix very slow user data table query by @mvdbeek in #17830
• [24.0] Update db revision 24.0 release tags by @jdavcs in #17834
• [24.0] Fix optional types in Help Forum API by @davelopez in #17832
• [24.0] Improved error messages for runtime sharing problems. by @jmchilton in #17794
• [24.0] Minor refactor of query building logic for readability by @jdavcs in #17835
• [23.2] Fix error in release notes by @jdavcs in #17837
• [24.0] Allow admin to sharpen language about selected object stores. by @jmchilton in #17806
• [24.0] Fix Help Forum Integration uses Long ID by @ElectronicBlueberry in #17844
• [23.2] Proxy Access-Control-* headers when using x-accel-redirect by @mvdbeek in #17842
• [24.0] Fix incorrect miscinfo 'fix this' display by @dannon in #17851
• [23.2] Fix user login when duplicate UserRoleAssociation exists by @mvdbeek in #17854
• [24.0] Fix Multi-History status bar reactivity by @davelopez in #17812
• [24.0] Embed fix by @ElectronicBlueberry in #17852
• [24.0] Fix activity bar unreachable in some pages by @davelopez in #17860
• [24.0] Fix tool panel loading delay by @ahmedhamidawan in #17847
• [24.0] Embed download fix by @ElectronicBlueberry in #17861
• [24.0] wait for config to load with user prefs options by @martenson in #17865
• [23.1] Normalize extensions when loading tool by @mvdbeek in #17868
• [24.0] Record missing outputs as test errors by @bernt-matthias in #17874
• [24.0] Ignore user data table errors for now by @mvdbeek in #17880
• [24.0] 24.0 release notes by @jdavcs in #17610
• [24.0] Fix archived histories mixing with active in histories list by @davelopez in #17856
• [24.0] Add more last minute PRs to release notes by @jdavcs in #17887

New Contributors

• @jozh2008 made their first contribution in #17161
• @PlushZ made their first contribution in #17327
• @guillaume-gricourt made their first contribution in #17482

Full Changelog: v23.2.1...v24.0.0