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-...

v23.0.5

What's Changed

• [22.05] Slugify username received from oidc by @nuwang in #16251
• [23.0] Don't attempt to call a bool when using mem-self handler assignment. by @natefoo in #16359
• [23.0] Fix dataset create time convert by @itisAliRH in #15329
• [23.0] Minor bug fix for default mail templates by @neoformit in #16362
• [23.0] Fix display of named tags in mako by @davelopez in #16368
• [23.0] Fix active step display in workflow editor side panel by @mvdbeek in #16364
• [23.0] Copy when_expression when copying workflow step by @mvdbeek in #16377
• [23.0] Pin black version to 23.3.0 in workflow action by @nsoranzo in #16390
• [23.0] Don't always install node in the virtualenv by @nsoranzo in #16395
• [23.0] Fix test discovery in vscode by @mvdbeek in #16413
• [23.0] Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by @bernt-matthias in #16403
• [23.0] Allow duplicate labels in linter if outputs contain filters by @bernt-matthias in #15933
• [23.0] Media player fix issue 16415 by @bdwheele in #16443
• [23.0] Fix static file serving for robots.txt and favicon.ico when using per_host settings by @mira-miracoli in #16459
• [22.05] Bump version of chromedriver setup action by @mvdbeek in #16461
• [23.0] Fixes for (gitlab) error reporting by @bernt-matthias in #16424
• [23.0] Fix filtering of disabled user preferences in UI by @davelopez in #16464
• [23.0] Fix parsing tool metadata from bio.tools by @kysrpex in #16449
• [23.0] Adjust test_data_download method in GalaxyInteractorApi so an admin user is not required by @simonbray in #16482
• [23.0] Linter: fix regex for profile version by @bernt-matthias in #16480

New Contributors

• @bdwheele made their first contribution in #16443
• @mira-miracoli made their first contribution in #16459

Full Changelog: v23.0.4...v23.0.5

v23.0.4

What's Changed

• [23.0] Fix tool recommendations shown in a d3 js tree by @anuprulez in #15852
• [23.0] Fix folder access for anonymous user by @mvdbeek in #16330
• [23.0] Fix default when statement evaluation by @mvdbeek in #16332
• [23.0] Redact private role name and description when purging user by @mvdbeek in #16349
• [23.0] Pin pydantic in packages to <2 by @natefoo in #16354

Full Changelog: v23.0.3...v23.0.4

v23.0.3

What's Changed

• [23.0] Bump galaxy-release-util version to 0.1.2 by @mvdbeek in #16241
• [23.0] When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247
• [23.0] Load data tables in Celery worker by @mvdbeek in #16244
• [23.0] xsd: add missing sep attribute for has_n_columns by @bernt-matthias in #16262
• [23.0] Fix converting Enum value to str for Python 3.11 by @nsoranzo in #16284
• [23.0] Forward port of slugify username received from oidc by @nuwang in #16271
• [23.0] Missing init prevents models.py being bundled into tool_util by @nuwang in #16308

Full Changelog: v23.0.2...v23.0.3

23.0.2

What's Changed

• [23.0] Fix Text File Busy errors at the source by @mvdbeek in #16212
• [23.0] Point release deps fixes and docs by @mvdbeek in #16214
• [23.0] Rename galaxy-webapps back to galaxy-web-apps by @mvdbeek in #16216
• [23.0] Port selenium setup to non-deprecated selenium options by @mvdbeek in #16215
• [23.0] Don't fail CWL tool parsing when Cheetah not installed by @mvdbeek in #16219
• [23.0] Allow skipping expect_num_outputs when expect_failure is set in tool test by @bernt-matthias in #16237
• [23.0] Use galaxy-release-util to upload python packages by @mvdbeek in #16240
• [22.05] Fix dropbox import to support newer versions by @nuwang in #16239

Full Changelog: v23.0.1...v23.0.2

23.0.1

A note about this release

This is the first Galaxy point release for which all Python packages are published to the Python Package Index.
Changes listed here and in the package changelog only include changes made since the v23.0 tag was published and do not include changes made in between the v22.5 and v23.0.1 tags. We will include all changes for future releases going forward and we strive for more frequent point releases.

What's Changed

• [23.0] Fix Toast variant color for errors by @davelopez in #15928
• [23.0] Fix defineProps warning in client build. by @dannon in #15930
• [22.05] Fix mixed outputs_to_working_directory pulsar destinations by @mvdbeek in #15927
• [23.0] Prevent anonymous access to Storage Dashboard by @davelopez in #15934
• [23.0] Update Gravity to 1.0.3 by @natefoo in #15939
• [23.0] Add ca_certs option for sentry client by @mvdbeek in #15943
• [23.0] Fix History Import Bugs by @ahmedhamidawan in #15923
• [23.0] Fix folder listing via file browser by @mvdbeek in #15950
• [23.0] Change default watchdog inotify_buffer log level to info by @mvdbeek in #15967
• [23.0] Fix RO-crate invocation export with complex collections by @davelopez in #15971
• [23.0] Fix Webhooks not rendering by @ElectronicBlueberry in #15985
• [23.0] Fix invalid link to "workflows by owner" by @ElectronicBlueberry in #15986
• [23.0] Fix History filters includes related filter bug by @ahmedhamidawan in #15975
• [23.0] Fix history export papercuts by @davelopez in #15991
• [23.0] Fix build collection not resetting selection by @davelopez in #16005
• [23.0] Backport Improve display chunk generation for BAMs by @mvdbeek in #16007
• [23.0] Allow setting auto_decompress property in staging interface by @mvdbeek in #16014
• [23.0] Clarify search behavior in placeholder text in Published Histories by @davelopez in #16006
• [23.0] Make Expression Tools searchable in ToolBoxWorkflow by @ahmedhamidawan in #16022
• [23.0] Reports app fixes by @dannon in #16015
• [23.0] Workflow connections performance with SVG by @ElectronicBlueberry in #16000
• [23.0] Tabular Dataset Display Fixes by @dannon in #15970
• [23.0] Backport #16023: Fix pasting file fails if text starts with file by @mvdbeek in #16024
• [23.0] Ensure history export contains all expected datasets by @davelopez in #16013
• [23.0] Add support for launching workflows via Tutorial Mode by @hexylena in #15684
• [23.0] Fix gcsfs test discovery by @mvdbeek in #16039
• [23.0] Install node from setup-node action in more tests by @mvdbeek in #16043
• [23.0] Replace httpbin service with pytest-httpserver by @mvdbeek in #16042
• [23.0] Fix case sensitive filtering by name in histories by @davelopez in #16036
• [23.0] Various fixes to path prefix handling by @mvdbeek in #16033
• [23.0] Update pulsar to 0.15.2 by @mvdbeek in #16050
• [23.0] Fix minor error in WorkflowList help modal by @ahmedhamidawan in #16057
• [23.0] Backport fix pop-up link by @davelopez in #16060
• [22.05] Fix assertion linting to not fail on byte suffixes by @bernt-matthias in #15873
• [23.0] Anonymous User tool link bug fix by @ahmedhamidawan in #16065
• [23.0] Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744
• [23.0] merge 22.05 by @martenson in #16073
• [23.0] Fix BCO export by updating gxformat2 by @mvdbeek in #16081
• [23.0] Add missing dates for versions that contain changelog entries by @mvdbeek in #16090
• [23.0] Fix job failure handling when condor indicates job failure by @mvdbeek in #16096
• [23.0] Fix mypy error due to alembic 1.11.0 by @nsoranzo in #16104
• [23.0] Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099
• [23.0] Don't build Docker image when pushing to release branches by @ksuderman in #16055
• [23.0] Fix extended metadata file size handling by @mvdbeek in #16109
• [23.0] Ignore invalid query params in display_by_username_and_slug by @mvdbeek in #16117
• [23.0] Extract HDA for code_file validate_input hook by @mvdbeek in #16120
• [23.0] Backport Improve robustness and abstractions used by collection edit tests. by @mvdbeek in #16116
• [23.0] Fix sort error when re-running job with DCE collection input by @mvdbeek in #16126
• [23.0] Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in #16137
• [23.0] Fix backbone-based data selector to materialize consistent attribute set by @guerler in #15981
• [23.0] Fix related-hid in bulk contents API by @mvdbeek in #16128
• [23.0] Fix implicit converters with optional parameters by @mvdbeek in #16133
• [22.05] Fix get_test_from_anaconda() and base_image_for_targets() functions by @nsoranzo in #16125
• [23.0] Make ctx_rev optional in InstalledToolShedRepository response model by @dannon in #16139
• [23.0] Add script for creating (point) releases by @mvdbeek in #16076
• [23.0] Converge release process auth discovery. by @jmchilton in #16160
• [23.0] Show bug error for failed_meta state by @dannon in #16165
• [23.0] Fix test search for mulled container hashes by @mvdbeek in #16170
• [23.0] Tool filtering fix for label handling by @dannon in #16168
• [23.0] Fix optional fields being validated as missing in ts api by @jmchilton in #16141
• [23.0] Tool warnings can either be None or a Dictionary but not a String by @guerler in #16183
• [23.0] Startup fix when tool removed between reboot by @mvdbeek in #16175
• [23.0] Make point release script compatible with docutils 0.16 by @mvdbeek in #16190
• [23.0] Support ro crate 0.8.0 and 0.7.0 by @mvdbeek in #16193
• [23.0] Assert that local branches are up to date in release point script by @mvdbeek in #16195
• [23.0] Pin minimum tpv version by @mvdbeek in #16201
• [23.0] Verify existence of default value attribute for user forms fields by @guerler in #16205

Full Changelog: v23.0...v23.0.1