galaxyproject/galaxy v24.0.0 on GitHub

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