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Data intensive science for everyone.

v24.0.2

3 weeks ago

What's Changed

[24.0] Adds logging of messageExceptions in the fastapi exception handler. by @dannon in https://github.com/galaxyproject/galaxy/pull/18041
[24.0] Improve error message for Extract dataset tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18078
[23.2] Fix history export with missing dataset hids by @davelopez in https://github.com/galaxyproject/galaxy/pull/18083
[24.0] CitationsList - fix prop spec and config access. by @dannon in https://github.com/galaxyproject/galaxy/pull/18061
[24.0] Tool linters: allow to skip by old linter names (by allowing to skip linter modules) by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18091
[24.0] History Multiview panel shows pinned histories on top by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18092
[24.0] tool linters: output filters should only consider child filter nodes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18096

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.0.1...v24.0.2

v24.0.1

4 weeks ago

What's Changed

[24.0] Fix hasOwner function for histories in client by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17886
[23.2] Added 4dn_pairs and 4dn_pairsam datatypes by @SaimMomin12 in https://github.com/galaxyproject/galaxy/pull/17875
[24.0] Always serialize element_count and populated when listing contents by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17890
[24.0] Fix release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17894
[24.0] Make wait_for_history_jobs look at jobs, not datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17892
[24.0] Fix deadlock that can occur when changing job state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17896
[24.0] Fix search and version menu in docs by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17898
[24.0] Fix conditional Image imports by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17899
[24.0] Fix workflow run form failing on certain histories by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17869
[23.2] Fix saving workflows with freehand_comments only by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17901
[24.0] do not show copy button when editing by @martenson in https://github.com/galaxyproject/galaxy/pull/17895
[24.0] Do not save workflow on Run without user confirmation by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17907
[24.0] Rebuild config samples by @davelopez in https://github.com/galaxyproject/galaxy/pull/17911
[24.0] Fix lost reports when switching workflow versions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17904
[24.0] Make sure step removal also resets mapOver state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17915
[23.2] Adjust update_cwl_conformance_tests.sh for removed branch by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17916
[24.0] Adjust release notes to use the same language as interface by @martenson in https://github.com/galaxyproject/galaxy/pull/17919
[24.0] Fix saving user preferences crashes tab by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17917
[24.0] Always discard session after __handle_waiting_jobs is done by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17913
[24.0] Fix workflow run form for workflows with null rename PJA by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17929
[24.0] Fix tool form building if select filters from unavailable dataset metadata by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17930
[24.0] Fix InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands. by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17932
[24.0] Never fail dataset serialization if display_peek fails by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17937
[24.0] Drop left-over debug statement by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17939
[23.0] Fix output datatype when uncompressing a dataset with incorrect datatype by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17944
[24.0] Fix tool version switch in editor by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17858
[23.2] Fix missing implicit conversion for mapped over jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17952
[23.0] Fix KeyError in XForwardedHostMiddleware by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17955
[24.0] Revert unnecessary error change by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17948
[24.0] Fix notification display time by @davelopez in https://github.com/galaxyproject/galaxy/pull/17965
[23.2] Fix message input type for notifications in admin panel by @davelopez in https://github.com/galaxyproject/galaxy/pull/17966
[23.2] Set from_tool_form: true when saving new workflow by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17972
[24.0] Update _thanks.rst in the User Release Notes to include new socials and remove inactive ones by @natwhitaker in https://github.com/galaxyproject/galaxy/pull/17971
[24.0] Show dataset image in workflow_outputs display listing. by @dannon in https://github.com/galaxyproject/galaxy/pull/17964
[24.0] Fix filtering workflow outputs by type in markdown directives by @davelopez in https://github.com/galaxyproject/galaxy/pull/17977
[24.0] Fix get_content_as_text for compressed text datatypes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17976
[24.0] History import - show user feedback on completion. by @dannon in https://github.com/galaxyproject/galaxy/pull/17980
[24.0] Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17981
[24.0] Fix LengthValidator if no value passed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17983
[24.0] Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17985
[24.0] Use or copy StoredWorkflow when copying step by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17988
[23.2] Don't attempt to commit in dry_run mode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17987
[23.2] Invenio plugin fixes by @davelopez in https://github.com/galaxyproject/galaxy/pull/17997
[24.0] Update prebuilt client by @dannon in https://github.com/galaxyproject/galaxy/pull/18000
[24.0] Preserve surrounding whitespace when localizing complex nodes by @dannon in https://github.com/galaxyproject/galaxy/pull/18005
[24.0] Use the new column-select component in FormData for multiple select by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17990
[24.0] Don't fail if reporting invalid parameter values by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18002
[24.0] Raise MessageException when report references invalid workflow output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18009
[24.0] Include exception info when something goes wrong while refreshing tokens by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18008
[24.0] Reduce notifications polling frequency by @davelopez in https://github.com/galaxyproject/galaxy/pull/18010
[24.0] Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18011
[24.0] Don't commit without having set a hid by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18014
[24.0] Add a link to histories list in history import message for situations… by @dannon in https://github.com/galaxyproject/galaxy/pull/18021
[24.0] Fix test_get_tags_histories_content test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18026
[24.0] Fix tag regex pattern by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18025
[24.0] Backport colabfold tar file datatype by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18029
[24.0] Fix remote files sources error handling by @davelopez in https://github.com/galaxyproject/galaxy/pull/18027
[24.0] Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18023
[24.0] Change wrong quota_source value from KeyError to ValueError by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18040
[24.0] Fix History Dataset Association creation so that hid is always set by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18036
[24.0] Ensure that offset and limit are never negative by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18044
[24.0] clarify the object store relocate functionality by @martenson in https://github.com/galaxyproject/galaxy/pull/18033
[24.0] Add middleware for logging start and end of request by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18046
[23.2] Updated the datatypes name for FASTK tool by @SaimMomin12 in https://github.com/galaxyproject/galaxy/pull/18053
[24.0] Fix comments lost on import by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18060
[24.0] Fix history export with missing dataset hids by @davelopez in https://github.com/galaxyproject/galaxy/pull/18052
[24.0] Check database connection to issue a rollback if no connection by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18070
[24.0] Fix history update time after bulk operation by @davelopez in https://github.com/galaxyproject/galaxy/pull/18068

New Contributors

@SaimMomin12 made their first contribution in https://github.com/galaxyproject/galaxy/pull/17875
@natwhitaker made their first contribution in https://github.com/galaxyproject/galaxy/pull/17971

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.0.0...v24.0.1

v24.0.0

1 month ago

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

New Contributors

@jozh2008 made their first contribution in https://github.com/galaxyproject/galaxy/pull/17161
@PlushZ made their first contribution in https://github.com/galaxyproject/galaxy/pull/17327
@guillaume-gricourt made their first contribution in https://github.com/galaxyproject/galaxy/pull/17482

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.2.1...v24.0.0

v23.2.1

3 months ago

What's Changed

[23.2] Drop empty section by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17386
[23.2] Fix notification badge delay by @davelopez in https://github.com/galaxyproject/galaxy/pull/17349
[23.2] Fix upload modal loses its content when closed by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17338
[23.2] Respect upstream_gzip setting when streaming dataset collection archive by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17400
[23.2] Ignore empty lines in packages_by_dep_dag file when building packages by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17395
[23.0] Fix uploading of docs for release_NN.N branches by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17404
[23.1] Set webdav file source to use temp files by default by @davelopez in https://github.com/galaxyproject/galaxy/pull/17388
[23.2] Cleanup versions, formatting in setup.cfg, HISTORY.rst in all packages by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17414
[23.2] Fix target history when uploading files by @davelopez in https://github.com/galaxyproject/galaxy/pull/17431
[23.0] Update python-multipart to 0.0.7 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17429
[23.2] Fix workflow report markdown editor toolbox becoming non-responsive. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17427
[23.1] Encode tool link consistently by @davelopez in https://github.com/galaxyproject/galaxy/pull/17426
[23.2] add a test for multi input element when hda and dces are mixed together by @martenson in https://github.com/galaxyproject/galaxy/pull/17419
[23.1] Fix history bulk operations menu conditions by @davelopez in https://github.com/galaxyproject/galaxy/pull/17433
[23.0] Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17384
[23.2] Backport model store fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17439
[23.0] Fix bug: true >> True by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17446
More defensive access of extra props in filesources by @nuwang in https://github.com/galaxyproject/galaxy/pull/17445
[23.0] Fix datasetStore.saveDatasets bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17448
[23.1] Fix history bulk operations menu (part 2) by @davelopez in https://github.com/galaxyproject/galaxy/pull/17456
[23.1] Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17459
[23.2] Build param dict before creating entrypoint by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17440
[23.2] Fix creating new erronous workflow can produce multiple empty workflows by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17406
Merge release_23.1 into release_23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17471
[23.2] Fix auto-select of file name in upload (Backport of #17466) by @davelopez in https://github.com/galaxyproject/galaxy/pull/17477
[23.2] Set metadata states on dataset association, not dataset by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17474
[23.2] Remove two print statements by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17480
[23.2] Fix succces typo by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17481
[23.2] Fix merge by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17491
[23.2] Add magres datatype by @martenson in https://github.com/galaxyproject/galaxy/pull/17499
[23.2] Provide working routes.url_for every ASGI request by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17497

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.2...v23.2.1

v23.1

3 months ago

Release notes

Galaxy 23.1.0 was released on 25th of September 2023

user highlight release notes full release notes

What's Changed

list of all merged PRs

Version 23.1.dev by @dannon in https://github.com/galaxyproject/galaxy/pull/15353
Towards decoupling datatypes and model by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15186
Fix bad auto-merge of dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15386
vueify formUpload with composition API by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15409
Bump ua-parser-js from 0.7.31 to 0.7.33 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/15425
Outline Deployment Tests by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15420
Drop defineEmits import from FormUpload by @dannon in https://github.com/galaxyproject/galaxy/pull/15450
Prettier targeting refinements by @dannon in https://github.com/galaxyproject/galaxy/pull/15449
Move database access code out of tool_util by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15467
Follow up to #15186 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15388
Make serving address more visible in console by @davelopez in https://github.com/galaxyproject/galaxy/pull/15468
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15492
Stricter typescript config by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15311
Create ToolSuccess route and refactor component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15484
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15498
Use connection instead of session for ItemGrabber by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15496
Implement initial tool/wf test assertions module for JSON data. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15494
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15435
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15511
Various Tool Shed Cleanup by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15247
xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15534
Add basic selenium test for shared histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/15538
Phylocanvas rebuild by @dannon in https://github.com/galaxyproject/galaxy/pull/15521
Move TS to Alembic by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15509
Add new release tags to manage_toolshed_db.sh script by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15542
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15546
Use sentry-fastapi integration, expose sampling rate by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15550
Merge release_23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15566
Updating build-related dependencies, static cleanup. by @dannon in https://github.com/galaxyproject/galaxy/pull/15527
Have prettier use a cache. by @dannon in https://github.com/galaxyproject/galaxy/pull/15575
QUnit elimination by @dannon in https://github.com/galaxyproject/galaxy/pull/15452
Update browserslist and exclusions, linting. by @dannon in https://github.com/galaxyproject/galaxy/pull/15524
Drop workflow exports to myexperiment.org by @dannon in https://github.com/galaxyproject/galaxy/pull/15576
Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/15517
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15581
add missing f for f-string by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15584
Fix jest tests run on CI by @davelopez in https://github.com/galaxyproject/galaxy/pull/15588
Handle "email_from" config option consistently, as per schema description by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15557
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15594
Bump undici from 5.14.0 to 5.19.1 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/15609
Alternatively allow double quotation marks in search filters by @guerler in https://github.com/galaxyproject/galaxy/pull/15606
Update database_heartbeat for SA 2.0 compatibility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15611
Unify url handling with filesources by @nuwang in https://github.com/galaxyproject/galaxy/pull/15497
Explore tool remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/15510
Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15633
Fix call to docker_cached_container_description by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15598
Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15643
Changes to match latest playbook by @nuwang in https://github.com/galaxyproject/galaxy/pull/15647
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15652
Install singularity in the integration GitHub workflow by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/14922
Unpin Beaker requirement by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15665
Fix for new style conda packages by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15446
Add transactional state to JobHandlerStopQueue by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15671
Add transactional state to workflow scheduling manager by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15683
Drop model mapping unit tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15669
Minor hid display tweak by @dannon in https://github.com/galaxyproject/galaxy/pull/15662
Remove DELETED_NEW job state from code base by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15690
Empower Users to Select Storage Destination by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14073
update the admin activation docs by @martenson in https://github.com/galaxyproject/galaxy/pull/15670
Follow up on object store selection PR. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15654
Use chevrons instead of eye for showing expandable/collapsible sections by @dannon in https://github.com/galaxyproject/galaxy/pull/15688
Update selenium hid text assertion by @dannon in https://github.com/galaxyproject/galaxy/pull/15691
Verify that activation and reset emails are properly generated by @guerler in https://github.com/galaxyproject/galaxy/pull/15681
Cleanup API schema for dropping deleted_new by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15708
Merge release_23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15711
Tweaks to new object store and quota APIs by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15709
Use Animation Frame in Workflow Editor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15725
Fix Enums in API docs by @davelopez in https://github.com/galaxyproject/galaxy/pull/15740
Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15713
More object store documentation. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15707
Fix occasional package problems related to dependencies. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15734
Merge conflicting db migration branches into one by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15771
fix premature return in user API by @martenson in https://github.com/galaxyproject/galaxy/pull/15781
Implement some initial object store selection end-to-end tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15785
Add API test and refactor code for related:hid history filter by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15786
Quota source labelling bug fixes and improvements by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15795
Enable strict_equality mypy option by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15808
Add selenium test for history Related filter by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15720
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15809
Convert more of the object store selection client to TypeScript. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15783
Add Storage Management API by @davelopez in https://github.com/galaxyproject/galaxy/pull/15295
Fix/Enhance recalculate disk usage API endpoint by @davelopez in https://github.com/galaxyproject/galaxy/pull/15739
Add ensureDefined assertion utility by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15834
Convert utilities to typescript by @dannon in https://github.com/galaxyproject/galaxy/pull/15718
[PROCEDURES] Add Laila as a committer by @dannon in https://github.com/galaxyproject/galaxy/pull/15789
Fix log message by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15838
merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/15830
Enable no-throw-literal eslint rule by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15849
Migrate to MyST-Parser for Markdown docs by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15844
Utils refactor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15837
[PROCEDURES] Remove jxtx from committers list. by @dannon in https://github.com/galaxyproject/galaxy/pull/15790
Drop use_legacy_history from config by @dannon in https://github.com/galaxyproject/galaxy/pull/15861
Fix masthead element padding and improve brand text contrast by @guerler in https://github.com/galaxyproject/galaxy/pull/15689
Adding onFocus and onBlur functionality to editing the history name by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15853
merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/15854
Move @types/d3 to dev dependencies by @davelopez in https://github.com/galaxyproject/galaxy/pull/15864
Fix anonymous user uploads when vault is configured by @tchaussepiedifb in https://github.com/galaxyproject/galaxy/pull/15858
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15564
Fix WorkflowDisplay error message handling by @dannon in https://github.com/galaxyproject/galaxy/pull/15865
Fix information popovers when displaying object stores for selection. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15867
Fix filesource file url support by @nuwang in https://github.com/galaxyproject/galaxy/pull/15794
Initial end-to-end tests for separate quota sources per object store by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15800
Allow typescript unit testing with navigation YAML. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15784
Enable per-destination container_resolver_config_file by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15884
Add StatesInfo component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15745
Allow pending inputs in some collection operation tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15892
Exclude tests from TypeScript compilation by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15900
Merge 23.0 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15902
Advanced tool search result tweaks by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15908
ci: show test classes with non standard names by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15886
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15920
Fix Multi-History infinite loading loop. by @dannon in https://github.com/galaxyproject/galaxy/pull/15931
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15890
Update release notes footer by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15941
Introducing the Activity Bar, initial concept and layout by @guerler in https://github.com/galaxyproject/galaxy/pull/14802
Summarize long Workflow annotations in WorkflowList by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15925
Migrate user and user flags stores to Pinia by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15938
Make container builders use mamba by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15953
Update locale.js by @undergone2345 in https://github.com/galaxyproject/galaxy/pull/15963
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15958
Build container with nodejs by @ksuderman in https://github.com/galaxyproject/galaxy/pull/15979
Migrate history store to pinia by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15108
Add text-break to wrap long published titles by @guerler in https://github.com/galaxyproject/galaxy/pull/15980
Fix Activity Bar toggle reactivity by @davelopez in https://github.com/galaxyproject/galaxy/pull/15988
Convert legacy side panels to flex-compatible panels by @guerler in https://github.com/galaxyproject/galaxy/pull/15935
Emit filterText to HistoryPanel from historyStore by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15926
Drop database views by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15876
Add suggested Training material to Tool Form by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15628
Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15811
Improve display chunk generation for BAMs by @wm75 in https://github.com/galaxyproject/galaxy/pull/15972
Fetcher Mock utility by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15992
Add alter_column migration utility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16009
Mock fetcher followup by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16011
Export tool citations configurable message by @minh-biocommons in https://github.com/galaxyproject/galaxy/pull/15998
Fix for link pop-up window/toaster after Data Library to History import by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16008
Fix nullable deleted column in API Keys table by @davelopez in https://github.com/galaxyproject/galaxy/pull/15956
reorganize user menu for consistency by @martenson in https://github.com/galaxyproject/galaxy/pull/15994
remove inherited title from masthead dropdown items by @martenson in https://github.com/galaxyproject/galaxy/pull/15995
minor tooltip and UI client changes by @martenson in https://github.com/galaxyproject/galaxy/pull/16017
Fix pasting file fails if text starts with file by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16023
Add option to create list for all datasets in a history to dropdown by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15947
Refactor badge parsing/serialization/typing for reuse. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15987
Allow importing a workflow from a shared URL by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15903
Code cleanups from ruff and pyupgrade by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16035
Change confusing pulsar logs message by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16038
Object store badges spelling fixes. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16028
Refactor integration tests to create utility for setting up a database vault. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16027
12875/form drilldown vue conversion by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15813
Another round of easy tool shed cleanup. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15540
implement admin jobs filtering by @martenson in https://github.com/galaxyproject/galaxy/pull/16020
Add support for visualizing HDF5 datasets. by @jarrah42 in https://github.com/galaxyproject/galaxy/pull/15394
Add missing fields to HistorySummary schema model by @davelopez in https://github.com/galaxyproject/galaxy/pull/16041
Gitignore update by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16046
Fixes the parcel2 build for hdf5 viz when using node18. by @dannon in https://github.com/galaxyproject/galaxy/pull/16047
New history selector with quick actions by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16040
Vendorise packaging.versions.LegacyVersion by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16058
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15942
Show backend search errors in hist panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15874
Change release note icon by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16049
Rename object stores in config. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16029
Migrate job metrics store and component to use pinia and composition api by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16056
Deprecate tools/evolution by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15656
Use jsdom-worker instead of mock by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16064
Use Filtering class to get and set filter texts by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15996
Drop UserHistories provider by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15993
External Login Flow: Redirect users if account already exists by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15019
Ensure that unselected checkbox inputs emit null instead of an empty array by @guerler in https://github.com/galaxyproject/galaxy/pull/16059
Fix font-awesome library types by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16068
unify workflows grid components by @martenson in https://github.com/galaxyproject/galaxy/pull/16045
Remove legacy form fields from parameter factory by @guerler in https://github.com/galaxyproject/galaxy/pull/15983
Updated doc and tests for attribute value filter by @tuncK in https://github.com/galaxyproject/galaxy/pull/15929
Add create_foreign_key migration utility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16077
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16086
Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16080
Vueify Select field by @guerler in https://github.com/galaxyproject/galaxy/pull/16010
Merge release_23.0 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16088
Fix and test startup with Python 3.11 on macOS by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16082
Refactor a few client object store components by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16051
Use automated naming convention to generate indexes and constraints in database by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16089
Fix minor Switch to History bug in HistoryView by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16095
Use _.+ for unused variables by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16098
Attempt to fix mypy check by @davelopez in https://github.com/galaxyproject/galaxy/pull/16103
De-duplicate code around object store caches. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16108
Improve robustness of collection edit E2E test. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16092
Workflow Editor Infinite Grid with Landmark-Lines by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16097
Workflow Connections Dynamic Radius by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16102
Fix resetting metadata on many repositories at once via the shed API by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14906
Allow HEAD request for requesting metadata files by @martenson in https://github.com/galaxyproject/galaxy/pull/16113
Add hdf4 datatype by @TheoMathurin in https://github.com/galaxyproject/galaxy/pull/16105
Merge branch 'release_23.0' into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16118
Place admin panel section data into computed prop by @guerler in https://github.com/galaxyproject/galaxy/pull/16115
De-duplication and improvements to the in-process object store cache monitor by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16111
Dataset chunking tests (and small fixes) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16069
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16123
Add Storage Dashboard visualizations for histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/14820
add required_files to the tag list for linting by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16129
Upgraded to new multiselect Tags component for Workflows, DatasetList, Attributes by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/15225
Fix : Ignore error messages for admin created accounts by @jvanbraekel in https://github.com/galaxyproject/galaxy/pull/16132
Add count support for listing filters by @davelopez in https://github.com/galaxyproject/galaxy/pull/16075
Selenium test for displaying workflows with problems in pages. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16085
[webhook/gtn] Expand query selector list to encompass 'a' by @hexylena in https://github.com/galaxyproject/galaxy/pull/16100
Disable invalid link for anonymous users. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16147
Improve histories and datasets immutability checks by @davelopez in https://github.com/galaxyproject/galaxy/pull/16143
When writing test error debug directories, create a 'latest' symlink. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16148
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16149
Refactor caching object stores ahead of adding task-based store. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16144
Integrate accessibility testing into Selenium testing by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16122
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16153
Add option to see invocations related to a history by @martenson in https://github.com/galaxyproject/galaxy/pull/16136
Documents use of k8s_extra_job_envs in job_conf sample advanced by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15110
Migrate display applications API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16156
Improve robustness of collection upload tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16093
Move axe-selenium-python to dev dependencies by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16162
FITS data format by @volodymyrss in https://github.com/galaxyproject/galaxy/pull/15905
Scope pinned histories by user ID by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16142
Fix linting of FITS datatype code by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16169
Fix eslint / ts overrides by @dannon in https://github.com/galaxyproject/galaxy/pull/16166
Updates MGnify interactive tool to v1.1.0 by @SandyRogers in https://github.com/galaxyproject/galaxy/pull/16179
Accessibility fixes for workflows, login, and registration. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16146
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16182
Record input datasets and collections at full parameter path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15978
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16186
Merge Target class with CondaTarget by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16181
Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16197
Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16198
Add WorkflowBox to Activity bar Side Panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15944
Hide Activity Bar for anonymous users by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16200
Remove various fallback behaviors by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16199
Add Processing for Custom Icons by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16157
Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16208
Drop TS unit mapping tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16206
adjust grid sharing indicators by @martenson in https://github.com/galaxyproject/galaxy/pull/16163
Update carbon emissions calculations explanation page styling by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16192
FITS file visualization plugin by @francoismg in https://github.com/galaxyproject/galaxy/pull/16187
Ensure session is request-scoped for legacy endpoints by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16207
Add Repository owner field to ToolSearch by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16061
End-to-end tests for new user welcome. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16158
Improved Cache Monitoring for Object Stores by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16110
Merge 23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16228
Fixes initial state of select all checkbox by @guerler in https://github.com/galaxyproject/galaxy/pull/16217
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16227
Allow user customization of the activity bar by @guerler in https://github.com/galaxyproject/galaxy/pull/16184
Handle appending to a results file that does not exists. by @ksuderman in https://github.com/galaxyproject/galaxy/pull/16233
Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15421
Initial e2e test for history storage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16221
tool_util: switch to mambaforge on non-32bit; add arm64 support by @mr-c in https://github.com/galaxyproject/galaxy/pull/16223
Protection against problematic boolean parameters. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15493
Add slack error reporting plugin by @hexylena in https://github.com/galaxyproject/galaxy/pull/15025
Adding fuzzy search functionality to front end search by @tcollins2011 in https://github.com/galaxyproject/galaxy/pull/15855
allow anon access for api/datasets/get_content_as_text by @martenson in https://github.com/galaxyproject/galaxy/pull/16226
Allow users to create new activity bar items by @guerler in https://github.com/galaxyproject/galaxy/pull/16196
Replace bootstrap_history.py with galaxy-release-util by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16231
Fix some drs handling issues by @nuwang in https://github.com/galaxyproject/galaxy/pull/15777
Don't error on missing parameters or unused parameters in UI controllers by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16246
Selenium type fixes and annotations. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16242
Add Galaxy Notification System by @davelopez in https://github.com/galaxyproject/galaxy/pull/15663
Show search in HistoryView by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16225
Selenium test for page history links. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16222
Refine activity bar dragging behavior by @guerler in https://github.com/galaxyproject/galaxy/pull/16245
Paginate History Store by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16084
e2e test for workflow license selector by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16243
Marginally more storage management selenium coverage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16263
Adjust notifications activity item by @guerler in https://github.com/galaxyproject/galaxy/pull/16265
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16267
Add History Archival feature by @davelopez in https://github.com/galaxyproject/galaxy/pull/16003
Add interactive tools activity by @guerler in https://github.com/galaxyproject/galaxy/pull/16266
Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/16255
Small test decorator improvements. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16220
read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15596
Container resolvers: add docs, typing and tests by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15614
bring grids for (published) pages on par with workflows by @martenson in https://github.com/galaxyproject/galaxy/pull/16209
Add zipped mongodb and genenotebook datatypes by @abretaud in https://github.com/galaxyproject/galaxy/pull/16173
Reset autocommit to True (temporarily) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16283
OIDC tokens by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/15300
Display Tags in Workflow Editor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16282
Fix and Improve Workflow Editor Panning by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16178
E2E Tests for Edit Dataset Attributes Page by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16224
Decompress history data for testing assertions by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15085
Bump msal version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16285
Fixes for two framework test tools by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15483
Expose additional beaker caching backends by @claudiofr in https://github.com/galaxyproject/galaxy/pull/15349
Bump default milestone to 23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16287
Merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16289
Set Initial Filter for Paired List Collection Creator Based on Initial Elements by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16279
Improve container resolver documentation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16280
Update version to 23.1.rc1 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16292
[23.1] Update 23.1 release tags for migration scripts by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16294
[23.1] Open latest version of tool from tool panel link by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16290
[23.1] Fix recalculate_quota throug kombu message by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16299
[23.1] handle prefix in dataset contents properly by @martenson in https://github.com/galaxyproject/galaxy/pull/16301
[23.1] Fix form builder value handling by @guerler in https://github.com/galaxyproject/galaxy/pull/16304
[23.1] Fix ordering of data libraries from API by @martenson in https://github.com/galaxyproject/galaxy/pull/16300
[23.1] qualify querying for an api-key by @martenson in https://github.com/galaxyproject/galaxy/pull/16320
[23.1] Remove pin on packaging in packages by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16322
[23.1] Fix tool remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/16311
[23.1] Fix 'news' webhook to account for the RC one more time. by @dannon in https://github.com/galaxyproject/galaxy/pull/16328
[23.1] Filter deleted keys from api_keys relationship by @dannon in https://github.com/galaxyproject/galaxy/pull/16321
[23.1] Makefile-based setting of NODE_OPTIONS for client build by @dannon in https://github.com/galaxyproject/galaxy/pull/16324
[23.1] Refactor workflow store to be more reliable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16334
[23.1] Include workflow invocations in default activity by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16338
[23.1] Sanitize substring in matchingTerm by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16351
[23.1] Make tags in public histories read-only by @davelopez in https://github.com/galaxyproject/galaxy/pull/16348
[23.1] Improve help text for conditional workflow step by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16355
[23.1] Hide conditionally skipped output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16356
[23.1] Fix invocation progress bar for skipped and deleted jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16365
[23.1] Fix workflow invocation detail reactivity by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16369
[23.1] Add missing singularity_no_mount prop parsing by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16367
[23.1] Disable console instead of dropping by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16372
[23.1] Fix Nested Tool Panel Labels by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16376
[23.1] Fix disk usage recalculation for distributed object stores by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16380
[23.1] Add message showing console disable/enable, along with instructions o… by @dannon in https://github.com/galaxyproject/galaxy/pull/16401
[23.1] Fix histories count by @davelopez in https://github.com/galaxyproject/galaxy/pull/16400
[23.1] Job cache fixes for DCEs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16384
[23.1] Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16421
[23.1] Fix toolform creator by @dannon in https://github.com/galaxyproject/galaxy/pull/16419
[23.1] For display (only) allow control+click for new window opening by @dannon in https://github.com/galaxyproject/galaxy/pull/16432
[23.1] Fix webhook release note seen pin by @dannon in https://github.com/galaxyproject/galaxy/pull/16446
[23.1] Fix multi-broadcast overlap by @davelopez in https://github.com/galaxyproject/galaxy/pull/16444
[23.1] Fix error_reports linting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16465
[23.1] Swap datatype&convert tab to a static 'datatypes' tab. by @dannon in https://github.com/galaxyproject/galaxy/pull/16466
[23.1] Fix history items repeated search bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16452
[23.1] Fix Storage Dashboard missing archived histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16473
[23.1] Restore resolution of Conda environments generated from non-lowercase package names by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16474
[23.1] Add missing archived filter in saved histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16475
[23.1] use router instead of hard links for certain page urls by @martenson in https://github.com/galaxyproject/galaxy/pull/16297
[23.1] Fix tagging component for anonymous users by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16481
[23.1] Bump bx-python to 0.10.0 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16484
[23.1] Remove blinking animation from icons by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16471
[23.1] Fix up unit tests for local use by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16483
[23.1] Fix tags ownership by @davelopez in https://github.com/galaxyproject/galaxy/pull/16339
[23.1] Make ToolBox v-b-tooltip.hover directives noninteractive by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16506
[23.1] Fix ToolBoxWorkflow search delay bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16505
[23.1] Fix history item states help display to apply same styling attributes by @dannon in https://github.com/galaxyproject/galaxy/pull/16500
[23.1] H5web updates by @dannon in https://github.com/galaxyproject/galaxy/pull/16509
[23.1] Fix for Accessibility, on Workflows List page Tooltip by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16520
[23.1] fix font-weight disparity between browsers by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16515
[23.0] Fix upload paramfile handling (for real user setups) by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16504
[23.1] Fix double-encoding notification content by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16530
[23.1] Exclude selenium version with broken type hints by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16531
[23.1] Restore tmp mounting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16533
[23.1] Run through tmp_dir_creation_statement only once by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16529
[23.1] Limit tool document cache to tool configs with explicit cache path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16537
[22.01] Fix up tox.ini by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16567
[23.0] Add missing unit-coverage environment by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16570
[23.0] Fix dataset collection url in workflow reports by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16571
[23.0] Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16569
[23.0] Fix incorrect ASGI request host by @davelopez in https://github.com/galaxyproject/galaxy/pull/16574
[22.01] Fix incorrect ASGI request host by @davelopez in https://github.com/galaxyproject/galaxy/pull/16575
[23.1] Fix shared item notification link by @davelopez in https://github.com/galaxyproject/galaxy/pull/16581
[23.0] Fix conditional step evaluation with datasets in repeats by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16584
[23.1] Don't use docker run --user flag on OSX by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16573
[23.1] Ignore errors with user-set job resources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16579
[23.0] Don't read request body into memory by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16585
[23.0] Fix extra files path handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16541
[23.1] Bump minimum tpv version to 2.3.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16597
[23.1] make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16594
[23.1] Fix replacement parameters for subworkflows. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16592
[23.0] Fixes for extra files handling and cached object stores by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16595
[23.1] Drop expunge_all() call in WebTransactionRequest by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16606
[23.1] Drop RecursiveMiddleware by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16605
[23.1] Fix multiple remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/16542
[23.1] Optimize getting current user session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16604
[23.1] Backport tool mem fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16601
[23.1] Only reindex tool search once after forking by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16611
[23.1] Fix Published Pages and Pages view showing same content by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16614
[23.1] Remove render.py script from iSEE by @neoformit in https://github.com/galaxyproject/galaxy/pull/16616
[23.1] Reload toolbox after forking when using --preload by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16620
[22.01] Passing Identifier for div to Write the Chart Panel to by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16598
[23.1] Account for expires/expires_in when refreshing token by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16621
[23.0] Allow the legacy DELETE dataset endpoint to accept any string for the history_id by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16593
[23.1] Make datatype edit default value a string instead of list of strings by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16591
[23.0] Don't fail invocation message without dependent_workflow_step_id by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16628
[23.1] Fixes for conditional subworkflow steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16632
[23.0] Lazy load tool data tables in celery worker by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16640
[23.1] Fix nested conditional workflow steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16641
[23.1] Make sort_collection tool require terminal datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16661
[23.1] xsd: allow name attribute of test collections by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16663
[23.1] Fix expression evaluation for nested state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16656
[23.0] Force __DUPLICATE_FILE_TO_COLLECTION__ 'size' param to integer by @simonbray in https://github.com/galaxyproject/galaxy/pull/16659
[22.05] Switch to upstream setup-chromedriver action by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16669
[23.1] Push to object store even if set_meta fails by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16667
[23.1] Ensure Job belongs to current SA session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16655
[23.1] Login/Register fixes by @dannon in https://github.com/galaxyproject/galaxy/pull/16652
[23.1] Fix regex validation for global inline flags by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16683
[23.1] Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16678
[23.1] Only show 'edit' on published pages when viewer is the owner. by @dannon in https://github.com/galaxyproject/galaxy/pull/16680
[23.1] Update galaxyproject/charts utilizing visualizations by @dannon in https://github.com/galaxyproject/galaxy/pull/16674
[23.1] Fix closed transaction error on galaxy startup/check jobs by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16687
[23.1] FileInput no longer accept 'U' in the file mode by @bgruening in https://github.com/galaxyproject/galaxy/pull/16704
[23.1] List extra files only for terminal datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16705
[23.0] Update pulsar client library to 0.15.5 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16701
[23.1] Fix legend not scrollable in storage overview charts by @davelopez in https://github.com/galaxyproject/galaxy/pull/16703
[23.1] Add missing join condition in job search by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16710
[23.1] Fix job search query by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16714
[23.1] Fix collection id encoding by @davelopez in https://github.com/galaxyproject/galaxy/pull/16718
[23.1] Fix unittest mocks to support us checking geturl() by @dannon in https://github.com/galaxyproject/galaxy/pull/16726
[23.1] Fix allowlist deserialization in file sources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16729
[23.1] Workaround for XML nodes of job resource parameters losing their children by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16728
[23.1] force wrap long parameter names in the workflow form by @martenson in https://github.com/galaxyproject/galaxy/pull/16732
[23.1] prevent toolbox scrollbar by @martenson in https://github.com/galaxyproject/galaxy/pull/16734
[23.1] Copy the collection contents by default when copying a collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16717
[23.1] 23.1 Release Notes by @dannon in https://github.com/galaxyproject/galaxy/pull/16329

New Contributors

@tchaussepiedifb made their first contribution in https://github.com/galaxyproject/galaxy/pull/15858
@undergone2345 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15963
@minh-biocommons made their first contribution in https://github.com/galaxyproject/galaxy/pull/15998
@jarrah42 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15394
@TheoMathurin made their first contribution in https://github.com/galaxyproject/galaxy/pull/16105
@volodymyrss made their first contribution in https://github.com/galaxyproject/galaxy/pull/15905
@tcollins2011 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15855

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.5...v23.1

v23.2

3 months ago

Release notes

Galaxy 23.2.0 was released on 30th of January 2024

user highlight release notes full release notes

What's Changed

list of all merged PRs

Version 23.2.dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16293
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16305
Add Python string formatting best practices by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16312
Drop (admin only) userskeys controller by @dannon in https://github.com/galaxyproject/galaxy/pull/16318
Client import sorting by @dannon in https://github.com/galaxyproject/galaxy/pull/16345
Merge 23.1->dev by @dannon in https://github.com/galaxyproject/galaxy/pull/16361
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16360
Add carbon emissions admin configuration options by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16307
Replace Persistedstate Pinia Plugin with User-Scoped Composable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16371
Exclude auto-generated schema file from labeler by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16378
Display beginning of non-text files as text instead of triggering a download by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/15447
Bump semver from 5.7.1 to 5.7.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16388
Merge release_23.1 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16393
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16389
Standardize, lint vue component name casing. by @dannon in https://github.com/galaxyproject/galaxy/pull/16398
Update carbon emissions methodology page to match current feature spe… by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16392
Limit number of celery task executions per second per user by @claudiofr in https://github.com/galaxyproject/galaxy/pull/16232
Disable verbose parso logging in db_shell.py by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16410
Refactor FilesDialog services to use Fetcher by @davelopez in https://github.com/galaxyproject/galaxy/pull/16414
Bump word-wrap from 1.2.3 to 1.2.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16417
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16409
Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16264
Fix SA2.0 syntax in scripts/helper.py, fix ancient bug by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16425
Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16430
Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16431
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16436
Prepare Uploader Vueification by removing jQuery by @guerler in https://github.com/galaxyproject/galaxy/pull/16408
Fix labeler for UI UX labels by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16456
Never consider _galaxy_ conda env as unused by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16460
Force makefile client targets to use .venv-shipped node if it exists by @dannon in https://github.com/galaxyproject/galaxy/pull/16462
pin fs.dropboxfs to >=1 by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16451
Migrate some Remote Files Export components to composition API + TS by @davelopez in https://github.com/galaxyproject/galaxy/pull/16391
Bump tough-cookie from 4.1.2 to 4.1.3 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16385
Add new datatype: STL by @TanguyGen in https://github.com/galaxyproject/galaxy/pull/16478
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16485
Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15825
Migrate cloud API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16296
Re-add missing type guard by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16486
Rename MetadataEqualsValidator by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16489
Test that object store cache file gets updated by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16493
Migrate a part of the users API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16341
Make it obvious that WorkflowInvocationStep is clickable/expandable by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16507
Add framework test for profile behavior of format="input" by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15482
Update interactivetool_mgnify_notebook to v1.2.2 by @SandyRogers in https://github.com/galaxyproject/galaxy/pull/16517
Migrate configuration store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16514
Scope Workflow Stores to Workflow ID by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16523
Fix and update visualization plugins by @mahendrapaipuri in https://github.com/galaxyproject/galaxy/pull/16119
Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16534
Move database access code out of galaxy.util by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16526
Document that required text parameters need a validator by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16538
Published Workflow Sharing Page Overhaul by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16510
Refactor FilesDialog + Remote Files API schema improvements by @davelopez in https://github.com/galaxyproject/galaxy/pull/16420
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16521
Vueify Data Uploader by @guerler in https://github.com/galaxyproject/galaxy/pull/16472
Make form repeat blocks reordarable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/14892
Remove unnecessary check: item cannot be None by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16550
add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools by @khaled196 in https://github.com/galaxyproject/galaxy/pull/16503
Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16553
Add uploader test cases, consolidate payload processing by @guerler in https://github.com/galaxyproject/galaxy/pull/16554
Fix: serialize tool_shed_urls directly from the API by @davelopez in https://github.com/galaxyproject/galaxy/pull/16561
Drop syncConfigToGalaxy by @davelopez in https://github.com/galaxyproject/galaxy/pull/16562
Add support for CILogon deployments in different regions than the US by @uwwint in https://github.com/galaxyproject/galaxy/pull/16490
Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16536
Support new genome browser chain file format by @claudiofr in https://github.com/galaxyproject/galaxy/pull/16576
Run eslint autofix as a part of client format when using Makefile by @dannon in https://github.com/galaxyproject/galaxy/pull/16586
Implement datatype upload warnings by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16564
Remove xml remnant in sample yml job conf by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16609
Add Invenio RDM repository integration by @davelopez in https://github.com/galaxyproject/galaxy/pull/16381
Make tool id searchable in side panel search by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16543
Explicitly document default of multiple by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16625
Run poetry under Python 3.8 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16638
Fix dependency update GitHub workflow by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16639
Switch out conditional requirement parser by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16636
Vueify _fieldDialog by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16236
Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16649
Ensure Job belongs to current SA session by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16647
cwl testing: use the proposed 1.2.1 CWL conformance tests. by @mr-c in https://github.com/galaxyproject/galaxy/pull/16658
Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16642
Bump samtools converters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16668
Clarify documentation on how to build a job runner by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16665
Enhance disk quota usage summary by @davelopez in https://github.com/galaxyproject/galaxy/pull/16670
History MultiView drag-drop on history picker creates new history by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16644
Create GDateTime component by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16622
Notifications admin panel by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16278
Fix notifications icon not showing in Masthead by @davelopez in https://github.com/galaxyproject/galaxy/pull/16679
Fix flaky test timing issue in DiskUsageSummary component by @davelopez in https://github.com/galaxyproject/galaxy/pull/16685
Include regex when linting validators by @davelopez in https://github.com/galaxyproject/galaxy/pull/16684
Minor: Fix import warning by @davelopez in https://github.com/galaxyproject/galaxy/pull/16692
Skip node installation for check_indexes tests by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16694
Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16691
Vueify Tool Form Data Selector by @guerler in https://github.com/galaxyproject/galaxy/pull/16578
Enhance task monitor composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/16695
Misc. edits/refactorings to session handling by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16712
Migrate dataset store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16709
Enhance Short Term Storage Composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/16711
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16577
force wrap long parameter names in the workflow form by @martenson in https://github.com/galaxyproject/galaxy/pull/16731
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16735
Update build_a_job_runner.rst by @maikenp in https://github.com/galaxyproject/galaxy/pull/16673
SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16434
Reset autocommit to False by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16745
Account for shared usage between TS and galaxy apps by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16746
Selective bold text by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16748
Migrate collection elements store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16725
Don't copy collection elements in test_dataset_collection_hide_originals by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16747
Change Sentry error reporting plug-in by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16686
Drop legacy server-side search by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16755
Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in https://github.com/galaxyproject/galaxy/pull/16762
Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in https://github.com/galaxyproject/galaxy/pull/16690
provide specific example for API docs - tags by @martenson in https://github.com/galaxyproject/galaxy/pull/16769
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16770
Fix large gap between labels and form elements by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16753
Tool Shed 2.0 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15639
Fix selenium selector for collections by @davelopez in https://github.com/galaxyproject/galaxy/pull/16754
Initial bug fixes for tool shed 2. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16787
SA2.0 fixes for TS2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16791
Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16768
Fix duplicate key eslint error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16810
Use AlignedSegment.to_string by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16803
Fix shed unit test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16811
Add ClientSearchMiss Sentry Capture by @dannon in https://github.com/galaxyproject/galaxy/pull/16789
Fix package version handling for initial minor releases by @dannon in https://github.com/galaxyproject/galaxy/pull/16743
move the email and username redacting from the role loop by @martenson in https://github.com/galaxyproject/galaxy/pull/16805
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16807
Optimize iteration in DatasetInstance model + SA2.0 fix by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16776
Another batch of SA2.0 edits in TS 2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16799
Fix collection drilling by @davelopez in https://github.com/galaxyproject/galaxy/pull/16819
Add Time Format to Generated with Galaxy {{ version }} on {{ time }} UTC statement by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16757
Migrate collection attributes store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16752
Adjust tz inclusion in workflow reports by @dannon in https://github.com/galaxyproject/galaxy/pull/16835
Create db head merge revision. by @dannon in https://github.com/galaxyproject/galaxy/pull/16838
Refactor dataset services by @davelopez in https://github.com/galaxyproject/galaxy/pull/16839
Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16848
Create reusable FilterMenu with advanced options by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16522
chore: fix typos by @afuetterer in https://github.com/galaxyproject/galaxy/pull/16851
Improve collection items scrolling by @davelopez in https://github.com/galaxyproject/galaxy/pull/16738
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16853
Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16739
SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16724
Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16833
Remove remaining legacy backbone form input elements by @guerler in https://github.com/galaxyproject/galaxy/pull/16834
Fix bug in SQLAlchemy statement by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16881
Bump @babel/traverse from 7.18.11 to 7.23.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16874
Drop unused HistoryContentManager code and related tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16882
Ruff and flake8 fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16884
Fix bug in SA statement: desc() applied to column, not statement by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16887
Use vue modal instead of global backbone modal in user preferences by @guerler in https://github.com/galaxyproject/galaxy/pull/16830
Update help in relabel_from_file.xml by @lldelisle in https://github.com/galaxyproject/galaxy/pull/16891
Tool Shed 2.0 fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16825
Restore ToolsApi and create new api route for new panel structure by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16872
Update cellxgene interactive tool to 1.1.1 by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15313
MINERVA display application: enable cors, add for tabular by @hexylena in https://github.com/galaxyproject/galaxy/pull/16737
Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16758
Toolshed client build separation by @dannon in https://github.com/galaxyproject/galaxy/pull/15000
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16896
Refactor/OIDC custos by @uwwint in https://github.com/galaxyproject/galaxy/pull/16497
Add parameter name to validation errors by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15440
Update client dependencies. by @dannon in https://github.com/galaxyproject/galaxy/pull/16867
Bump undici from 5.19.1 to 5.26.5 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16897
Fix selenium selector for Workflow Run warnings by @davelopez in https://github.com/galaxyproject/galaxy/pull/16908
Fix link to mercurial tip in tool shed 2.0. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16895
Fix navigation error in tool shed tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16902
Fix type annotation of lib/tool_shed/test/functional/ by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16901
Refactor client API packages by @davelopez in https://github.com/galaxyproject/galaxy/pull/16847
Fix subtle bug in listify function + simplify list munging by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16904
Convert historyItemsStore to ts+composition by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16873
Update datatypes_conf.xml.sample with docx type by @yvanlebras in https://github.com/galaxyproject/galaxy/pull/16713
Fix import in historyItemsStore.ts by @davelopez in https://github.com/galaxyproject/galaxy/pull/16916
Allow partial matches in workflow name tag search and search all tags for unquoted query by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16860
Enable some flake8-logging-format rules in ruff by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16915
Fix GQL infinite scrolling in tool shed. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16914
merge release_23.1 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16933
Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16940
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16939
Fix select parameter doesn't show parameter name in UI by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16942
Change api/tool_panel to api/tool_panels/... by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16928
Remove record access handling for Invenio RDM plugin by @davelopez in https://github.com/galaxyproject/galaxy/pull/16900
Workflow Comments 💬 by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16612
Allow switching histories from Storage Dashboard Visualizations by @davelopez in https://github.com/galaxyproject/galaxy/pull/16945
Standardize to W3C naming for color. by @dannon in https://github.com/galaxyproject/galaxy/pull/16949
Publish tool shed frontend to npm. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16924
Allow to permanently delete non-deleted items in Storage Dashboard Visualizations by @davelopez in https://github.com/galaxyproject/galaxy/pull/16944
Add helper to get dataset or collection via src and id by @mr-c in https://github.com/galaxyproject/galaxy/pull/16953
Move and re-use persist_extra_files by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16955
Enhance Invenio RDM integration by @davelopez in https://github.com/galaxyproject/galaxy/pull/16964
Remove sentry.py from mypy exclusions. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16959
Augment pgcleanup to allow periodically deleting old datasets. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16340
Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16672
Allow non-optional integer/float params without value attribute by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16966
prep for updated h5py and typos by @mr-c in https://github.com/galaxyproject/galaxy/pull/16963
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16978
Implement default locations for data and collection parameters. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14955
Expose Workflow Checkpoint in Workflow Reports by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16760
Fix maf_thread_for_species.py by @lldelisle in https://github.com/galaxyproject/galaxy/pull/16971
Fix rendering of an empty page by @dannon in https://github.com/galaxyproject/galaxy/pull/16985
Implement instance URLs in Galaxy markdown. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16675
Minor clarification/typo fix in datatypes.data by @dannon in https://github.com/galaxyproject/galaxy/pull/16993
Workflow Embed by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16657
Remove "Create Workflow" form and allow workflow creation in editor by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16938
Replace file_name property with get_file_name function by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/16783
Fixes for job metrics Galaxy markdown component. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16994
Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17000
SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16852
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17011
Update API tool_panels route conditions by @dannon in https://github.com/galaxyproject/galaxy/pull/16991
Upgrade job manager's index_query method to SA2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17020
Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16252
Show current tool panel view name on top of tool panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17021
Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in https://github.com/galaxyproject/galaxy/pull/16795
Remove eventHub custom module, swap to appropriate alternatives. by @dannon in https://github.com/galaxyproject/galaxy/pull/17037
Restyle Vue Multiselect and Adapt Option Order by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17015
Change Broadcast Notifications Style by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17032
Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17038
Open HistoryStorageOverview in center panel from HistoryPanel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17043
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17050
Vueify Visualizations Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/16892
optimize object store cache operations by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/17025
Upgrade axios to 1.6.2 by @dannon in https://github.com/galaxyproject/galaxy/pull/17053
Quote singularity env parameters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17055
Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17056
Use debounce instead of timeout utility by @guerler in https://github.com/galaxyproject/galaxy/pull/17057
Disable conda_auto_init in embedded pulsar test cases by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17061
Fix testing of the galaxy-tool-shed package by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17062
Migrate a part of the jobs API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16778
Fix typescript warning for grid list operation by @guerler in https://github.com/galaxyproject/galaxy/pull/17065
Migrate groups API to fastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/17051
Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17069
New select component for selecting a large amount of options by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17059
Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17084
Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17086
Add docs for tool panel and panel view administration by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17078
Migrate ItemTags API to FastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/17064
[PROCEDURES] Add Ahmed as a committer by @dannon in https://github.com/galaxyproject/galaxy/pull/17017
Use eventbus to emit route request in grid list by @guerler in https://github.com/galaxyproject/galaxy/pull/17070
Fix for fits_image_viewer visualization plugin by @francoismg in https://github.com/galaxyproject/galaxy/pull/17002
Enhance Global Drag-and-Drop feature for Upload component by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16995
Make job state param optional again by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17077
Prevent excessive api/tool_panels calls by keeping views in store by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17039
Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/17018
[EGD 2023 Cofest] Galaxy help forum integration by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16798
Allow relative URLs in broadcasts action links by @davelopez in https://github.com/galaxyproject/galaxy/pull/17042
Fix invocation report to target correct workflow version. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17008
Visually indicate currently viewed/edited dataset by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16859
Make notification message input multi-line by @davelopez in https://github.com/galaxyproject/galaxy/pull/17091
Enhance Notification Broadcasts Admin Panel by @davelopez in https://github.com/galaxyproject/galaxy/pull/17090
Add EGI Check-in as OIDC authentication option by @enolfc in https://github.com/galaxyproject/galaxy/pull/16782
[23.2] Update version to 23.2.rc1 by @dannon in https://github.com/galaxyproject/galaxy/pull/17095
[23.2] Fix .file_name access in merge forward by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17097
[23.2] Disable admin notifications management if notifications are disabled in config by @davelopez in https://github.com/galaxyproject/galaxy/pull/17114
[23.2] Tool panel views overflow bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17112
[23.2] Fix hid/elementindex for collection displays by @dannon in https://github.com/galaxyproject/galaxy/pull/17110
[23.2] Fix CSS issue affecting all dropdown menus by @davelopez in https://github.com/galaxyproject/galaxy/pull/17124
[23.2] Expose file_name property in DatasetFilenameWrapper by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17107
[23.2] Fix job search when command_version is None by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17129
[23.2] Enhance xsd schema and allow simpler assertion lists by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17134
[23.2] Make payload optional again for create tag API by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17144
[23.2] Fix select option appears for single select by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17146
[23.2] Support configuring job metrics inline, update documentation by @natefoo in https://github.com/galaxyproject/galaxy/pull/17178
[23.2] Add rerun and show details buttons in expanded collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17182
[23.2] Fix job destination extra params by @dannon in https://github.com/galaxyproject/galaxy/pull/17186
[23.2] Add support for Cgroupsv2 by @natefoo in https://github.com/galaxyproject/galaxy/pull/17169
[23.2] Fix tools missing in panel bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17192
[23.2] Disable Workflow Report and Generate PDF buttons unless workflow is successful by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/17149
[23.2] Fix Multiselect in BModal overflows out of view bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17197
[23.2] Fix ToolSearch bug for StaticToolPanelViews by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17213
[23.2] Fix categories in ToolShed repo create API by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17218
[23.2] Fix cardinality violation error: subquery returns multiple results by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17224
[23.2] Remove SingleItemSelector deselect label, fix history filters hidden on smaller screen by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17199
[23.2] Fix job parameter display by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17226
[23.2] Fix Display Application link generation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17227
[23.2] Display application fixes and tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17233
[23.1] Add back 1.1.0 version of Filtering1 tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16883
[23.2] Tagging component performance improvements by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17253
[23.1] Add binary datatypes for intermediate output of fastk tools by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/17265
[23.1] Remove duplicates when copying sections for tool panel view by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17117
[23.1] Fix to_cwl for nested collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17276
[23.2] Rollback invalidated transaction by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17280
[23.1] Always copy datasets in collection builder modals by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17268
[23.2] Install newer celery on python 3.8+ by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17309
[23.2] Discard sqlalchemy session after task completion by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17317
[23.2] Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17315
[23.2] Scope session for job runner monitor loop by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17319
[23.1] Enable job resubmissions in k8s runner by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15238
Revert "[23.1] Enable job resubmissions in k8s runner" by @nuwang in https://github.com/galaxyproject/galaxy/pull/17323
[23.2] Improve Embed Performance by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17326
[23.2] Fix Subworkflow Edit Button by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17330
[23.1] Disable tag editing on non-owned Pages by @davelopez in https://github.com/galaxyproject/galaxy/pull/17337
[23.2] Initial release notes for 23.2 by @dannon in https://github.com/galaxyproject/galaxy/pull/17259
[23.2] Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17342
Merge 23.1 into 23.2 by @davelopez in https://github.com/galaxyproject/galaxy/pull/17343
[23.2] Ensure release notes include all PRs added during the freeze by re-running the release note bootstrapping by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17344
[23.2] make release titles consistent by @martenson in https://github.com/galaxyproject/galaxy/pull/17341
[23.2] Write to a temp filename in posix file source plugin by @natefoo in https://github.com/galaxyproject/galaxy/pull/17350
[23.2] Always store multi select data input values in fixed order by @guerler in https://github.com/galaxyproject/galaxy/pull/17352
[23.2] Add latest PRs to release by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17383
[23.2] Fix the purge historyless HDAs pgcleanup action by @natefoo in https://github.com/galaxyproject/galaxy/pull/17382

New Contributors

@TanguyGen made their first contribution in https://github.com/galaxyproject/galaxy/pull/16478
@khaled196 made their first contribution in https://github.com/galaxyproject/galaxy/pull/16503
@sebastian-schaaf made their first contribution in https://github.com/galaxyproject/galaxy/pull/16762
@lopiola made their first contribution in https://github.com/galaxyproject/galaxy/pull/16690
@afuetterer made their first contribution in https://github.com/galaxyproject/galaxy/pull/16851
@arash77 made their first contribution in https://github.com/galaxyproject/galaxy/pull/17051
@enolfc made their first contribution in https://github.com/galaxyproject/galaxy/pull/16782

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.4...v23.2

v23.1.4

4 months ago

What's Changed

[23.1] Properly clear session on OIDC logout by @guerler in https://github.com/galaxyproject/galaxy/pull/17120
[23.0] Assert that tus uploader instance has URL by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17133
[23.1] Fix workflow index total matches counting by @davelopez in https://github.com/galaxyproject/galaxy/pull/17176
[23.1] Fix url_for in tool error reports by @davelopez in https://github.com/galaxyproject/galaxy/pull/17210
[23.1] Fix User.current_galaxy_session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17232
[23.1] Backport #17188: Fix for converter tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17231
[23.1] Separate collection and non-collection data element by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17236

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.3...v23.1.4

v23.1.3

5 months ago

What's Changed

[23.1] Allow re-click of display with force reloading if already on the route. by @dannon in https://github.com/galaxyproject/galaxy/pull/17111
[23.1] Add missing optional description field, fixes ephemeris data library example by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17116

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.2...v23.1.3

v23.1.2

6 months ago

What's Changed

[23.1] Fix History item deletion/undeletion reactivity with filter and ToolForm input field by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16889
[23.1] Fix unbound runner variable when there is an error in the job config by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16906
[23.1] Provide error message instead of internal server error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16905
[23.1] Fix missing grep input in sort1 tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16910
[23.1] Improve invocation error reporting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16917
[23.1] Fix library import from path linking files by @davelopez in https://github.com/galaxyproject/galaxy/pull/16919
[23.1] Test link data with extended metadata by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16921
[23.1] Skip change_datatype things if we're not actually changing the extension by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16931
[23.1] Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16937
[23.1] Add execute back to published workflows list by @dannon in https://github.com/galaxyproject/galaxy/pull/16934
[23.1] Include owner's annotation when exporting workflow by @dannon in https://github.com/galaxyproject/galaxy/pull/16930
[23.1] Fix discarded dataset ordering in Storage Dashboard by @davelopez in https://github.com/galaxyproject/galaxy/pull/16929
[23.1] Backport Fix select parameter doesn't show parameter name in UI by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16943
[23.1] Adds biii as supported xref reference type by @kostrykin in https://github.com/galaxyproject/galaxy/pull/16952
[23.1] Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16961
[23.1] Workaround issue in Routes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16981
[23.1] Backport Fix maf_thread_for_species.py by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16989
[23.1] Empty page render fix - backport by @dannon in https://github.com/galaxyproject/galaxy/pull/16992
[23.1] Client publication by @dannon in https://github.com/galaxyproject/galaxy/pull/16999
[23.1] Don't store job in JobIO instance attributes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16965
[23.1] Fix copying metadata to copied job outputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17007
[23.1] Update tar_to_directory dependency by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17009
[23.0] Upgrade minimum conda to be compatible with latest conda-build by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17013
[23.1] Change log level for duplicate data table entries to warning by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16988
[23.1] Fix duplicated tools in tool panel view section copying by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17036
[23.1] Fix filtering of active broadcasts for admins by @davelopez in https://github.com/galaxyproject/galaxy/pull/17049
[23.1] Prevent workflow submission with missing input values by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17048
[23.0] Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17067
[23.1] Remove rollback from __check_jobs_at_startup by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17085
[23.1] Assert that DatasetCollectioElement has an associated object by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17071
[23.1] Fix input dates in notifications: consider timezone offset by @davelopez in https://github.com/galaxyproject/galaxy/pull/17088
[23.1] Add HEAD route to job_files endpoint by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17072
[23.1] Add support for larch datatypes by @patrick-austin in https://github.com/galaxyproject/galaxy/pull/17080
[23.1] Allow relative URLs in broadcasts action links by @davelopez in https://github.com/galaxyproject/galaxy/pull/17093
[23.1] Implement missing upload for S3 file sources by @davelopez in https://github.com/galaxyproject/galaxy/pull/17100
[23.1] Fix web_apps dependencies by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17099
[23.1] Ensure that plugin build hash actually has a git hash to compare with… by @dannon in https://github.com/galaxyproject/galaxy/pull/17104
[23.1] Set correct tool_path for packaged galaxy by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17102

New Contributors

@kostrykin made their first contribution in https://github.com/galaxyproject/galaxy/pull/16952

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.1...v23.1.2

v23.1.1

7 months ago

What's Changed

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

New Contributors

@tchaussepiedifb made their first contribution in https://github.com/galaxyproject/galaxy/pull/15858
@undergone2345 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15963
@minh-biocommons made their first contribution in https://github.com/galaxyproject/galaxy/pull/15998
@jarrah42 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15394
@tuncK made their first contribution in https://github.com/galaxyproject/galaxy/pull/15929
@TheoMathurin made their first contribution in https://github.com/galaxyproject/galaxy/pull/16105
@volodymyrss made their first contribution in https://github.com/galaxyproject/galaxy/pull/15905
@francoismg made their first contribution in https://github.com/galaxyproject/galaxy/pull/16187
@tcollins2011 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15855

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.6...v23.1.1