v24.0.1

What's Changed

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

New Contributors

• @SaimMomin12 made their first contribution in #17875
• @natwhitaker made their first contribution in #17971

Full Changelog: v24.0.0...v24.0.1

v24.0.0

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

What's Changed

• Version 23.3.dev by @dannon in #17096
• Python 3.8 as minimum by @mr-c in #16954
• SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932
• Add history items display state for collections/lists with failed or new populated_state by @ahmedhamidawan in #16996
• Dataset Display : force reload on subsequent clicks. by @dannon in #16982
• Remove web framework dependency from tools by @davelopez in #17058
• Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /client by @dependabot in #17115
• Vueify Admin User Grid by @guerler in #17030
• Update Python dependencies by @galaxybot in #17123
• SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by @jdavcs in #17122
• Vueify Admin Roles Grid by @guerler in #17118
• Migrate job destination parameters store to Pinia by @davelopez in #17119
• Vueify Admin Groups Grid by @guerler in #17126
• Migrate dataset extra files store to Pinia by @davelopez in #17145
• Vueify Admin Forms and Quota grids by @guerler in #17141
• Don't require admin user to list /api/tool_data by @jozh2008 in #17161
• Update Python dependencies by @galaxybot in #17157
• Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132
• Add keyedCache composable by @davelopez in #17148
• Replace discouraged Mambaforge with Miniforge3 by @nsoranzo in #17177
• Qiskit in galaxy by @thepineapplepirate in #17170
• Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter by @jdavcs in #17184
• Add future=True flag to SA engine by @jdavcs in #17174
• Add future=True flag to SA session by @jdavcs in #17179
• Convert dataset path destination store to composable by @davelopez in #17175
• Clarify the meaning of lexical sorting of discovered datasets by @bernt-matthias in #17190
• Update DatasetError.vue to fix broken link by @jennaj in #17193
• Fix for converter tests by @bernt-matthias in #17188
• xsd: reorder choices for permissive boolean by @bernt-matthias in #17187
• Accept any number of arguments to the secret decoder ring by @natefoo in #17191
• correct dbkey for minerva display app by @hexylena in #17196
• Update Python dependencies by @galaxybot in #17201
• Bump default milestone to 24.0 by @mvdbeek in #17211
• Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in #17153
• Reload built-in converters on toolbox reload by @bernt-matthias in #17209
• Improve links to Hub, Matrix and WGs in CONTRIBUTING.md by @nsoranzo in #17221
• Add a3m datatype by @astrovsky01 in #17217
• Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216
• Vendorize fastapi-utls.cbv by @jdavcs in #17205
• Migrate workflow invocation store to Pinia by @davelopez in #17203
• Update Python dependencies by @galaxybot in #17230
• Expose more tool information / navigability in UI. by @jmchilton in #17105
• Implement Galaxy Markdown directive history_dataset_as_table. by @jmchilton in #16681
• port invocation API to fastapi by @martenson in #16707
• Update Python dependencies by @galaxybot in #17235
• Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977
• Reuse test instance during non-integration tests by @mvdbeek in #17234
• Workflow node connector improvements by @ElectronicBlueberry in #17240
• Build and cache galaxy client for selenium and startup tests by @mvdbeek in #17239
• tus wants a json response from v2.0.0 by @mira-miracoli in #17246
• Update Python dependencies by @galaxybot in #17247
• Add missing re-usable commit-id output by @mvdbeek in #17248
• Update CONTRIBUTORS.md with new email address for Jeremy Goecks by @jgoecks in #17255
• Make flex panel drag handle more obvious by @ElectronicBlueberry in #17113
• Bump follow-redirects from 1.15.1 to 1.15.4 in /client by @dependabot in #17260
• Migrate models to pydantic 2 by @mvdbeek in #17262
• Optional Reply-to SMTP header in tool error reports by @neoformit in #17243
• Fixes for output discovery by @bernt-matthias in #17266
• Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222
• Fix invocation serialization if no state was set by @mvdbeek in #17278
• Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979
• Render Useful Markdown Components for Mapped Over Steps by @jmchilton in #17198
• Workflow node connector improvements followup by @ElectronicBlueberry in #17244
• Vueifiy History Grids by @guerler in #17219
• Add OIDC backend configuration schema and validation by @uwwint in #17274
• Fix Workflow Comment Model for Pydantic 2 by @ElectronicBlueberry in #17296
• Improve ModelManager type hints by @mvdbeek in #17299
• Fix any type for tool_data_file_path by @mvdbeek in #17293
• Package tests fixes by @nsoranzo in #17301
• Follow-up on #17274 and #17262 by @nsoranzo in #17302
• Scoped Store Refactor and Store Composition Refactor by @ElectronicBlueberry in #17304
• Refactor two of the missing invocation routes to FastAPI by @heisner-tillman in #17237
• Allow job files to consume TUS uploads by @jmchilton in #17242
• Rollback invalidated transaction: catch them earlier by @jdavcs in #17312
• Make Workflow Editor Toolbar Toggleable by @ElectronicBlueberry in #17297
• Enable job resubmissions in k8s runner by @nuwang in #17324
• Adjust Flex Panel Drag Handle and Collapse Button by @ElectronicBlueberry in #17298
• Add accepted extensions to form data input by @ElectronicBlueberry in #17238
• Overhaul Galaxy Markdown Help by @jmchilton in #17228
• Document SQLAlchemy session lifespan by @mvdbeek in #17322
• add documentation for data source tool by @PlushZ in #17327
• [23.2] fix s3fs templating by @bgruening in #17311
• Add support for Python 3.12 by @tuncK in #16796
• Fix quotas ID encoding by @davelopez in #17335
• Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340
• Port HistoryPanel component to composition API and typescript by @Renni771 in #17318
• Merge 23.2 into dev by @jdavcs in ...

v.23.2.1

What's Changed

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

Full Changelog: v23.2...v23.2.1

v23.2.0

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 #16293
• Update Python dependencies by @galaxybot in #16305
• Add Python string formatting best practices by @nsoranzo in #16312
• Drop (admin only) userskeys controller by @dannon in #16318
• Client import sorting by @dannon in #16345
• Merge 23.1->dev by @dannon in #16361
• Update Python dependencies by @galaxybot in #16360
• Add carbon emissions admin configuration options by @Renni771 in #16307
• Replace Persistedstate Pinia Plugin with User-Scoped Composable by @ElectronicBlueberry in #16371
• Exclude auto-generated schema file from labeler by @ElectronicBlueberry in #16378
• Display beginning of non-text files as text instead of triggering a download by @SergeyYakubov in #15447
• Bump semver from 5.7.1 to 5.7.2 in /client by @dependabot in #16388
• Merge release_23.1 into dev by @nsoranzo in #16393
• Update Python dependencies by @galaxybot in #16389
• Standardize, lint vue component name casing. by @dannon in #16398
• Update carbon emissions methodology page to match current feature spe… by @Renni771 in #16392
• Limit number of celery task executions per second per user by @claudiofr in #16232
• Disable verbose parso logging in db_shell.py by @mvdbeek in #16410
• Refactor FilesDialog services to use Fetcher by @davelopez in #16414
• Bump word-wrap from 1.2.3 to 1.2.4 in /client by @dependabot in #16417
• Update Python dependencies by @galaxybot in #16409
• Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264
• Fix SA2.0 syntax in scripts/helper.py, fix ancient bug by @jdavcs in #16425
• Merge release_23.1 into dev by @mvdbeek in #16430
• Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431
• Update Python dependencies by @galaxybot in #16436
• Prepare Uploader Vueification by removing jQuery by @guerler in #16408
• Fix labeler for UI UX labels by @ElectronicBlueberry in #16456
• Never consider _galaxy_ conda env as unused by @bernt-matthias in #16460
• Force makefile client targets to use .venv-shipped node if it exists by @dannon in #16462
• pin fs.dropboxfs to >=1 by @bernt-matthias in #16451
• Migrate some Remote Files Export components to composition API + TS by @davelopez in #16391
• Bump tough-cookie from 4.1.2 to 4.1.3 in /client by @dependabot in #16385
• Add new datatype: STL by @TanguyGen in #16478
• Update Python dependencies by @galaxybot in #16485
• Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825
• Migrate cloud API to Fast API by @heisner-tillman in #16296
• Re-add missing type guard by @mvdbeek in #16486
• Rename MetadataEqualsValidator by @bernt-matthias in #16489
• Test that object store cache file gets updated by @mvdbeek in #16493
• Migrate a part of the users API to Fast API by @heisner-tillman in #16341
• Make it obvious that WorkflowInvocationStep is clickable/expandable by @ahmedhamidawan in #16507
• Add framework test for profile behavior of format="input" by @bernt-matthias in #15482
• Update interactivetool_mgnify_notebook to v1.2.2 by @SandyRogers in #16517
• Migrate configuration store to Pinia by @davelopez in #16514
• Scope Workflow Stores to Workflow ID by @ElectronicBlueberry in #16523
• Fix and update visualization plugins by @mahendrapaipuri in #16119
• Merge 23.1 into dev by @mvdbeek in #16534
• Move database access code out of galaxy.util by @jdavcs in #16526
• Document that required text parameters need a validator by @bernt-matthias in #16538
• Published Workflow Sharing Page Overhaul by @ElectronicBlueberry in #16510
• Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420
• Update Python dependencies by @galaxybot in #16521
• Vueify Data Uploader by @guerler in #16472
• Make form repeat blocks reordarable by @ElectronicBlueberry in #14892
• Remove unnecessary check: item cannot be None by @jdavcs in #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 #16503
• Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in #16553
• Add uploader test cases, consolidate payload processing by @guerler in #16554
• Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561
• Drop syncConfigToGalaxy by @davelopez in #16562
• Add support for CILogon deployments in different regions than the US by @uwwint in #16490
• Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536
• Support new genome browser chain file format by @claudiofr in #16576
• Run eslint autofix as a part of client format when using Makefile by @dannon in #16586
• Implement datatype upload warnings by @jmchilton in #16564
• Remove xml remnant in sample yml job conf by @bernt-matthias in #16609
• Add Invenio RDM repository integration by @davelopez in #16381
• Make tool id searchable in side panel search by @ahmedhamidawan in #16543
• Explicitly document default of multiple by @bernt-matthias in #16625
• Run poetry under Python 3.8 by @nsoranzo in #16638
• Fix dependency update GitHub workflow by @nsoranzo in #16639
• Switch out conditional requirement parser by @mvdbeek in #16636
• Vueify _fieldDialog by @assuntad23 in #16236
• Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar by @nsoranzo in #16649
• Ensure Job belongs to current SA session by @jdavcs in #16647
• cwl testing: use the proposed 1.2.1 CWL conformance tests. by @mr-c in #16658
• Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642
• Bump samtools converters by @bernt-matthias in #16668
• Clarify documentation on how to build a job runner by @jdavcs in #16665
• Enhance disk quota usage summary by @davelopez in #16670
• History MultiView drag-drop on history picker creates new history by @ahmedhamidawan in #16644
• Create GDateTime component by @itisAliRH in https://github.com/g...

v23.1.4

What's Changed

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

Full Changelog: v23.1.3...v23.1.4

v23.1.3

What's Changed

• [23.1] Allow re-click of display with force reloading if already on the route. by @dannon in #17111
• [23.1] Add missing optional description field, fixes ephemeris data library example by @mvdbeek in #17116

Full Changelog: v23.1.2...v23.1.3

v23.1.2

What's Changed

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

New Contributors

• @kostrykin made their first contribution in #16952

Full Changelog: v23.1.1...v23.1.2

v23.1.1

What's Changed

• Version 23.1.dev by @dannon in #15353
• Towards decoupling datatypes and model by @jdavcs in #15186
• Fix bad auto-merge of dev. by @jmchilton in #15386
• vueify formUpload with composition API by @assuntad23 in #15409
• Bump ua-parser-js from 0.7.31 to 0.7.33 in /client by @dependabot in #15425
• Outline Deployment Tests by @jmchilton in #15420
• Drop defineEmits import from FormUpload by @dannon in #15450
• Prettier targeting refinements by @dannon in #15449
• Move database access code out of tool_util by @jdavcs in #15467
• Follow up to #15186 by @jdavcs in #15388
• Make serving address more visible in console by @davelopez in #15468
• Merge 23.0 into dev by @mvdbeek in #15492
• Stricter typescript config by @ElectronicBlueberry in #15311
• Create ToolSuccess route and refactor component by @ahmedhamidawan in #15484
• Merge 23.0 into dev by @mvdbeek in #15498
• Use connection instead of session for ItemGrabber by @jdavcs in #15496
• Implement initial tool/wf test assertions module for JSON data. by @jmchilton in #15494
• Update Python dependencies by @galaxybot in #15435
• Merge 23.0 into dev by @mvdbeek in #15511
• Various Tool Shed Cleanup by @jmchilton in #15247
• xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in #15534
• Add basic selenium test for shared histories by @davelopez in #15538
• Phylocanvas rebuild by @dannon in #15521
• Move TS to Alembic by @jdavcs in #15509
• Add new release tags to manage_toolshed_db.sh script by @jdavcs in #15542
• Merge 23.0 into dev by @mvdbeek in #15546
• Use sentry-fastapi integration, expose sampling rate by @mvdbeek in #15550
• Merge release_23.0 into dev by @mvdbeek in #15566
• Updating build-related dependencies, static cleanup. by @dannon in #15527
• Have prettier use a cache. by @dannon in #15575
• QUnit elimination by @dannon in #15452
• Update browserslist and exclusions, linting. by @dannon in #15524
• Drop workflow exports to myexperiment.org by @dannon in #15576
• Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance by @hujambo-dunia in #15517
• Merge 23.0 into dev by @mvdbeek in #15581
• add missing f for f-string by @bernt-matthias in #15584
• Fix jest tests run on CI by @davelopez in #15588
• Handle "email_from" config option consistently, as per schema description by @jdavcs in #15557
• Merge 23.0 into dev by @mvdbeek in #15594
• Bump undici from 5.14.0 to 5.19.1 in /client by @dependabot in #15609
• Alternatively allow double quotation marks in search filters by @guerler in #15606
• Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
• Unify url handling with filesources by @nuwang in #15497
• Explore tool remote test data by @davelopez in #15510
• Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in #15633
• Fix call to docker_cached_container_description by @bernt-matthias in #15598
• Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643
• Changes to match latest playbook by @nuwang in #15647
• Merge 23.0 into dev by @mvdbeek in #15652
• Install singularity in the integration GitHub workflow by @nsoranzo in #14922
• Unpin Beaker requirement by @nsoranzo in #15665
• Fix for new style conda packages by @bernt-matthias in #15446
• Add transactional state to JobHandlerStopQueue by @jdavcs in #15671
• Add transactional state to workflow scheduling manager by @jdavcs in #15683
• Drop model mapping unit tests by @jdavcs in #15669
• Minor hid display tweak by @dannon in #15662
• Remove DELETED_NEW job state from code base by @jdavcs in #15690
• Empower Users to Select Storage Destination by @jmchilton in #14073
• update the admin activation docs by @martenson in #15670
• Follow up on object store selection PR. by @jmchilton in #15654
• Use chevrons instead of eye for showing expandable/collapsible sections by @dannon in #15688
• Update selenium hid text assertion by @dannon in #15691
• Verify that activation and reset emails are properly generated by @guerler in #15681
• Cleanup API schema for dropping deleted_new by @jmchilton in #15708
• Merge release_23.0 into dev by @mvdbeek in #15711
• Tweaks to new object store and quota APIs by @jmchilton in #15709
• Use Animation Frame in Workflow Editor by @ElectronicBlueberry in #15725
• Fix Enums in API docs by @davelopez in #15740
• Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in #15713
• More object store documentation. by @jmchilton in #15707
• Fix occasional package problems related to dependencies. by @jmchilton in #15734
• Merge conflicting db migration branches into one by @jdavcs in #15771
• fix premature return in user API by @martenson in #15781
• Implement some initial object store selection end-to-end tests. by @jmchilton in #15785
• Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786
• Quota source labelling bug fixes and improvements by @jmchilton in #15795
• Enable strict_equality mypy option by @nsoranzo in #15808
• Add selenium test for history Related filter by @ahmedhamidawan in #15720
• Merge 23.0 into dev by @mvdbeek in #15809
• Convert more of the object store selection client to TypeScript. by @jmchilton in #15783
• Add Storage Management API by @davelopez in #15295
• Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
• Add ensureDefined assertion utility by @ElectronicBlueberry in #15834
• Convert utilities to typescript by @dannon in #15718
• [PROCEDURES] Add Laila as a committer by @dannon in #15789
• Fix log message by @bernt-matthias in #15838
• merge release_23.0 into dev by @martenson in #15830
• Enable no-throw-literal eslint rule by @ElectronicBlueberry in #15849
• Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844
• Utils refactor by @ElectronicBlueberry in #15837
• [PROCEDURES] Remove jxtx from com...

v23.0.6

What's Changed

• [23.0] Fix upload paramfile handling (for real user setups) by @bernt-matthias in #16504
• [22.01] Fix up tox.ini by @mvdbeek in #16567
• [23.0] Add missing unit-coverage environment by @mvdbeek in #16570
• [23.0] Fix dataset collection url in workflow reports by @mvdbeek in #16571
• [23.0] Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569
• [23.0] Fix incorrect ASGI request host by @davelopez in #16574
• [22.01] Fix incorrect ASGI request host by @davelopez in #16575
• [23.0] Fix conditional step evaluation with datasets in repeats by @mvdbeek in #16584
• [23.0] Don't read request body into memory by @mvdbeek in #16585
• [23.0] Fix extra files path handling by @mvdbeek in #16541
• [23.0] Fixes for extra files handling and cached object stores by @mvdbeek in #16595
• [22.01] Passing Identifier for div to Write the Chart Panel to by @assuntad23 in #16598
• [23.0] Allow the legacy DELETE dataset endpoint to accept any string for the history_id by @assuntad23 in #16593
• [23.0] Don't fail invocation message without dependent_workflow_step_id by @mvdbeek in #16628
• [23.0] Lazy load tool data tables in celery worker by @mvdbeek in #16640
• [23.0] Force __DUPLICATE_FILE_TO_COLLECTION__ 'size' param to integer by @simonbray in #16659
• [22.05] Switch to upstream setup-chromedriver action by @mvdbeek in #16669
• [23.0] Update pulsar client library to 0.15.5 by @mvdbeek in #16701
• [23.0] Fix RE for new version scheme in doc/source/conf.versioning.py by @mvdbeek in #16765
• [23.0] Show MessageException in invocation UI by @mvdbeek in #16772
• [23.0] Fix create/install commands for conda 23.9.0 by @nsoranzo in #16831

Full Changelog: v23.0.5...v23.0.6

v23.1.0

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 #15353
• Towards decoupling datatypes and model by @jdavcs in #15186
• Fix bad auto-merge of dev. by @jmchilton in #15386
• vueify formUpload with composition API by @assuntad23 in #15409
• Bump ua-parser-js from 0.7.31 to 0.7.33 in /client by @dependabot in #15425
• Outline Deployment Tests by @jmchilton in #15420
• Drop defineEmits import from FormUpload by @dannon in #15450
• Prettier targeting refinements by @dannon in #15449
• Move database access code out of tool_util by @jdavcs in #15467
• Follow up to #15186 by @jdavcs in #15388
• Make serving address more visible in console by @davelopez in #15468
• Merge 23.0 into dev by @mvdbeek in #15492
• Stricter typescript config by @ElectronicBlueberry in #15311
• Create ToolSuccess route and refactor component by @ahmedhamidawan in #15484
• Merge 23.0 into dev by @mvdbeek in #15498
• Use connection instead of session for ItemGrabber by @jdavcs in #15496
• Implement initial tool/wf test assertions module for JSON data. by @jmchilton in #15494
• Update Python dependencies by @galaxybot in #15435
• Merge 23.0 into dev by @mvdbeek in #15511
• Various Tool Shed Cleanup by @jmchilton in #15247
• xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in #15534
• Add basic selenium test for shared histories by @davelopez in #15538
• Phylocanvas rebuild by @dannon in #15521
• Move TS to Alembic by @jdavcs in #15509
• Add new release tags to manage_toolshed_db.sh script by @jdavcs in #15542
• Merge 23.0 into dev by @mvdbeek in #15546
• Use sentry-fastapi integration, expose sampling rate by @mvdbeek in #15550
• Merge release_23.0 into dev by @mvdbeek in #15566
• Updating build-related dependencies, static cleanup. by @dannon in #15527
• Have prettier use a cache. by @dannon in #15575
• QUnit elimination by @dannon in #15452
• Update browserslist and exclusions, linting. by @dannon in #15524
• Drop workflow exports to myexperiment.org by @dannon in #15576
• Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance by @hujambo-dunia in #15517
• Merge 23.0 into dev by @mvdbeek in #15581
• add missing f for f-string by @bernt-matthias in #15584
• Fix jest tests run on CI by @davelopez in #15588
• Handle "email_from" config option consistently, as per schema description by @jdavcs in #15557
• Merge 23.0 into dev by @mvdbeek in #15594
• Bump undici from 5.14.0 to 5.19.1 in /client by @dependabot in #15609
• Alternatively allow double quotation marks in search filters by @guerler in #15606
• Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
• Unify url handling with filesources by @nuwang in #15497
• Explore tool remote test data by @davelopez in #15510
• Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in #15633
• Fix call to docker_cached_container_description by @bernt-matthias in #15598
• Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643
• Changes to match latest playbook by @nuwang in #15647
• Merge 23.0 into dev by @mvdbeek in #15652
• Install singularity in the integration GitHub workflow by @nsoranzo in #14922
• Unpin Beaker requirement by @nsoranzo in #15665
• Fix for new style conda packages by @bernt-matthias in #15446
• Add transactional state to JobHandlerStopQueue by @jdavcs in #15671
• Add transactional state to workflow scheduling manager by @jdavcs in #15683
• Drop model mapping unit tests by @jdavcs in #15669
• Minor hid display tweak by @dannon in #15662
• Remove DELETED_NEW job state from code base by @jdavcs in #15690
• Empower Users to Select Storage Destination by @jmchilton in #14073
• update the admin activation docs by @martenson in #15670
• Follow up on object store selection PR. by @jmchilton in #15654
• Use chevrons instead of eye for showing expandable/collapsible sections by @dannon in #15688
• Update selenium hid text assertion by @dannon in #15691
• Verify that activation and reset emails are properly generated by @guerler in #15681
• Cleanup API schema for dropping deleted_new by @jmchilton in #15708
• Merge release_23.0 into dev by @mvdbeek in #15711
• Tweaks to new object store and quota APIs by @jmchilton in #15709
• Use Animation Frame in Workflow Editor by @ElectronicBlueberry in #15725
• Fix Enums in API docs by @davelopez in #15740
• Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in #15713
• More object store documentation. by @jmchilton in #15707
• Fix occasional package problems related to dependencies. by @jmchilton in #15734
• Merge conflicting db migration branches into one by @jdavcs in #15771
• fix premature return in user API by @martenson in #15781
• Implement some initial object store selection end-to-end tests. by @jmchilton in #15785
• Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786
• Quota source labelling bug fixes and improvements by @jmchilton in #15795
• Enable strict_equality mypy option by @nsoranzo in #15808
• Add selenium test for history Related filter by @ahmedhamidawan in #15720
• Merge 23.0 into dev by @mvdbeek in #15809
• Convert more of the object store selection client to TypeScript. by @jmchilton in #15783
• Add Storage Management API by @davelopez in #15295
• Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
• Add ensureDefined assertion utility by @ElectronicBlueberry in #15834
• Convert utilities to typescript by @dannon in #15718
• [PROCEDURES] Add Laila as a committer by @dannon in #15789
• Fix log message by @bernt-matthias in #15838
• merge release_23.0 into dev by @martenson in #15830
• Enable no-...