galaxyproject/galaxy v23.2 on GitHub

Release notes

Galaxy 23.2 was released on 30th of January 2024

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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 #16622
Notifications admin panel by @itisAliRH in #16278
Fix notifications icon not showing in Masthead by @davelopez in #16679
Fix flaky test timing issue in DiskUsageSummary component by @davelopez in #16685
Include regex when linting validators by @davelopez in #16684
Minor: Fix import warning by @davelopez in #16692
Skip node installation for check_indexes tests by @nsoranzo in #16694
Merge release_23.1 into dev by @mvdbeek in #16691
Vueify Tool Form Data Selector by @guerler in #16578
Enhance task monitor composable by @davelopez in #16695
Misc. edits/refactorings to session handling by @jdavcs in #16712
Migrate dataset store to Pinia by @davelopez in #16709
Enhance Short Term Storage Composable by @davelopez in #16711
Update Python dependencies by @galaxybot in #16577
force wrap long parameter names in the workflow form by @martenson in #16731
Update Python dependencies by @galaxybot in #16735
Update build_a_job_runner.rst by @maikenp in #16673
SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in #16434
Reset autocommit to False by @jdavcs in #16745
Account for shared usage between TS and galaxy apps by @jdavcs in #16746
Selective bold text by @hujambo-dunia in #16748
Migrate collection elements store to Pinia by @davelopez in #16725
Don't copy collection elements in test_dataset_collection_hide_originals by @nsoranzo in #16747
Change Sentry error reporting plug-in by @kysrpex in #16686
Drop legacy server-side search by @jdavcs in #16755
Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762
Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690
provide specific example for API docs - tags by @martenson in #16769
Update Python dependencies by @galaxybot in #16770
Fix large gap between labels and form elements by @ElectronicBlueberry in #16753
Tool Shed 2.0 by @jmchilton in #15639
Fix selenium selector for collections by @davelopez in #16754
Initial bug fixes for tool shed 2. by @jmchilton in #16787
SA2.0 fixes for TS2.0 by @jdavcs in #16791
Merge release_23.1 into dev by @mvdbeek in #16768
Fix duplicate key eslint error by @mvdbeek in #16810
Use AlignedSegment.to_string by @mvdbeek in #16803
Fix shed unit test by @mvdbeek in #16811
Add ClientSearchMiss Sentry Capture by @dannon in #16789
Fix package version handling for initial minor releases by @dannon in #16743
move the email and username redacting from the role loop by @martenson in #16805
Update Python dependencies by @galaxybot in #16807
Optimize iteration in DatasetInstance model + SA2.0 fix by @jdavcs in #16776
Another batch of SA2.0 edits in TS 2.0 by @jdavcs in #16799
Fix collection drilling by @davelopez in #16819
Add Time Format to Generated with Galaxy {{ version }} on {{ time }} UTC statement by @assuntad23 in #16757
Migrate collection attributes store to Pinia by @davelopez in #16752
Adjust tz inclusion in workflow reports by @dannon in #16835
Create db head merge revision. by @dannon in #16838
Refactor dataset services by @davelopez in #16839
Merge 23.1 into dev by @mvdbeek in #16848
Create reusable FilterMenu with advanced options by @ahmedhamidawan in #16522
chore: fix typos by @afuetterer in #16851
Improve collection items scrolling by @davelopez in #16738
Update Python dependencies by @galaxybot in #16853
Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by @ahmedhamidawan in #16739
SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in #16724
Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in #16833
Remove remaining legacy backbone form input elements by @guerler in #16834
Fix bug in SQLAlchemy statement by @jdavcs in #16881
Bump @babel/traverse from 7.18.11 to 7.23.2 in /client by @dependabot in #16874
Drop unused HistoryContentManager code and related tests by @jdavcs in #16882
Ruff and flake8 fixes by @nsoranzo in #16884
Fix bug in SA statement: desc() applied to column, not statement by @jdavcs in #16887
Use vue modal instead of global backbone modal in user preferences by @guerler in #16830
Update help in relabel_from_file.xml by @lldelisle in #16891
Tool Shed 2.0 fixes by @nsoranzo in #16825
Restore ToolsApi and create new api route for new panel structure by @ahmedhamidawan in #16872
Update cellxgene interactive tool to 1.1.1 by @pcm32 in #15313
MINERVA display application: enable cors, add for tabular by @hexylena in #16737
Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in #16758
Toolshed client build separation by @dannon in #15000
Update Python dependencies by @galaxybot in #16896
Refactor/OIDC custos by @uwwint in #16497
Add parameter name to validation errors by @bernt-matthias in #15440
Update client dependencies. by @dannon in #16867
Bump undici from 5.19.1 to 5.26.5 in /client by @dependabot in #16897
Fix selenium selector for Workflow Run warnings by @davelopez in #16908
Fix link to mercurial tip in tool shed 2.0. by @jmchilton in #16895
Fix navigation error in tool shed tests. by @jmchilton in #16902
Fix type annotation of lib/tool_shed/test/functional/ by @nsoranzo in #16901
Refactor client API packages by @davelopez in #16847
Fix subtle bug in listify function + simplify list munging by @jdavcs in #16904
Convert historyItemsStore to ts+composition by @ahmedhamidawan in #16873
Update datatypes_conf.xml.sample with docx type by @yvanlebras in #16713
Fix import in historyItemsStore.ts by @davelopez in #16916
Allow partial matches in workflow name tag search and search all tags for unquoted query by @ahmedhamidawan in #16860
Enable some flake8-logging-format rules in ruff by @nsoranzo in #16915
Fix GQL infinite scrolling in tool shed. by @jmchilton in #16914
merge release_23.1 into dev by @martenson in #16933
Merge 23.1 into dev by @mvdbeek in #16940
Update Python dependencies by @galaxybot in #16939
Fix select parameter doesn't show parameter name in UI by @ElectronicBlueberry in #16942
Change api/tool_panel to api/tool_panels/... by @ahmedhamidawan in #16928
Remove record access handling for Invenio RDM plugin by @davelopez in #16900
Workflow Comments 💬 by @ElectronicBlueberry in #16612
Allow switching histories from Storage Dashboard Visualizations by @davelopez in #16945
Standardize to W3C naming for color. by @dannon in #16949
Publish tool shed frontend to npm. by @jmchilton in #16924
Allow to permanently delete non-deleted items in Storage Dashboard Visualizations by @davelopez in #16944
Add helper to get dataset or collection via src and id by @mr-c in #16953
Move and re-use persist_extra_files by @mvdbeek in #16955
Enhance Invenio RDM integration by @davelopez in #16964
Remove sentry.py from mypy exclusions. by @jmchilton in #16959
Augment pgcleanup to allow periodically deleting old datasets. by @jmchilton in #16340
Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in #16672
Allow non-optional integer/float params without value attribute by @nsoranzo in #16966
prep for updated h5py and typos by @mr-c in #16963
Update Python dependencies by @galaxybot in #16978
Implement default locations for data and collection parameters. by @jmchilton in #14955
Expose Workflow Checkpoint in Workflow Reports by @assuntad23 in #16760
Fix maf_thread_for_species.py by @lldelisle in #16971
Fix rendering of an empty page by @dannon in #16985
Implement instance URLs in Galaxy markdown. by @jmchilton in #16675
Minor clarification/typo fix in datatypes.data by @dannon in #16993
Workflow Embed by @ElectronicBlueberry in #16657
Remove "Create Workflow" form and allow workflow creation in editor by @ahmedhamidawan in #16938
Replace file_name property with get_file_name function by @SergeyYakubov in #16783
Fixes for job metrics Galaxy markdown component. by @jmchilton in #16994
Merge 23.1 into dev by @mvdbeek in #17000
SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in #16852
Update Python dependencies by @galaxybot in #17011
Update API tool_panels route conditions by @dannon in #16991
Upgrade job manager's index_query method to SA2.0 by @jdavcs in #17020
Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in #16252
Show current tool panel view name on top of tool panel by @ahmedhamidawan in #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 #16795
Remove eventHub custom module, swap to appropriate alternatives. by @dannon in #17037
Restyle Vue Multiselect and Adapt Option Order by @ElectronicBlueberry in #17015
Change Broadcast Notifications Style by @ElectronicBlueberry in #17032
Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in #17038
Open HistoryStorageOverview in center panel from HistoryPanel by @ahmedhamidawan in #17043
Update Python dependencies by @galaxybot in #17050
Vueify Visualizations Grid by @guerler in #16892
optimize object store cache operations by @SergeyYakubov in #17025
Upgrade axios to 1.6.2 by @dannon in #17053
Quote singularity env parameters by @bernt-matthias in #17055
Merge release_23.1 into dev by @mvdbeek in #17056
Use debounce instead of timeout utility by @guerler in #17057
Disable conda_auto_init in embedded pulsar test cases by @mvdbeek in #17061
Fix testing of the galaxy-tool-shed package by @nsoranzo in #17062
Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778
Fix typescript warning for grid list operation by @guerler in #17065
Migrate groups API to fastAPI by @arash77 in #17051
Merge release_23.1 into dev by @mvdbeek in #17069
New select component for selecting a large amount of options by @ElectronicBlueberry in #17059
Update Python dependencies by @galaxybot in #17084
Merge release_23.1 into dev by @mvdbeek in #17086
Add docs for tool panel and panel view administration by @bernt-matthias in #17078
Migrate ItemTags API to FastAPI by @arash77 in #17064
[PROCEDURES] Add Ahmed as a committer by @dannon in #17017
Use eventbus to emit route request in grid list by @guerler in #17070
Fix for fits_image_viewer visualization plugin by @francoismg in #17002
Enhance Global Drag-and-Drop feature for Upload component by @hujambo-dunia in #16995
Make job state param optional again by @mvdbeek in #17077
Prevent excessive api/tool_panels calls by keeping views in store by @ahmedhamidawan in #17039
Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in #17018
[EGD 2023 Cofest] Galaxy help forum integration by @ElectronicBlueberry in #16798
Allow relative URLs in broadcasts action links by @davelopez in #17042
Fix invocation report to target correct workflow version. by @jmchilton in #17008
Visually indicate currently viewed/edited dataset by @ahmedhamidawan in #16859
Make notification message input multi-line by @davelopez in #17091
Enhance Notification Broadcasts Admin Panel by @davelopez in #17090
Add EGI Check-in as OIDC authentication option by @enolfc in #16782
[23.2] Update version to 23.2.rc1 by @dannon in #17095
[23.2] Fix .file_name access in merge forward by @mvdbeek in #17097
[23.2] Disable admin notifications management if notifications are disabled in config by @davelopez in #17114
[23.2] Tool panel views overflow bug by @ahmedhamidawan in #17112
[23.2] Fix hid/elementindex for collection displays by @dannon in #17110
[23.2] Fix CSS issue affecting all dropdown menus by @davelopez in #17124
[23.2] Expose file_name property in DatasetFilenameWrapper by @jdavcs in #17107
[23.2] Fix job search when command_version is None by @nsoranzo in #17129
[23.2] Enhance xsd schema and allow simpler assertion lists by @mvdbeek in #17134
[23.2] Make payload optional again for create tag API by @nsoranzo in #17144
[23.2] Fix select option appears for single select by @ElectronicBlueberry in #17146
[23.2] Support configuring job metrics inline, update documentation by @natefoo in #17178
[23.2] Add rerun and show details buttons in expanded collection by @mvdbeek in #17182
[23.2] Fix job destination extra params by @dannon in #17186
[23.2] Add support for Cgroupsv2 by @natefoo in #17169
[23.2] Fix tools missing in panel bug by @ahmedhamidawan in #17192
[23.2] Disable Workflow Report and Generate PDF buttons unless workflow is successful by @assuntad23 in #17149
[23.2] Fix Multiselect in BModal overflows out of view bug by @ahmedhamidawan in #17197
[23.2] Fix ToolSearch bug for StaticToolPanelViews by @ahmedhamidawan in #17213
[23.2] Fix categories in ToolShed repo create API by @nsoranzo in #17218
[23.2] Fix cardinality violation error: subquery returns multiple results by @jdavcs in #17224
[23.2] Remove SingleItemSelector deselect label, fix history filters hidden on smaller screen by @ahmedhamidawan in #17199
[23.2] Fix job parameter display by @mvdbeek in #17226
[23.2] Fix Display Application link generation by @mvdbeek in #17227
[23.2] Display application fixes and tests by @mvdbeek in #17233
[23.1] Add back 1.1.0 version of Filtering1 tool by @mvdbeek in #16883
[23.2] Tagging component performance improvements by @ElectronicBlueberry in #17253
[23.1] Add binary datatypes for intermediate output of fastk tools by @astrovsky01 in #17265
[23.1] Remove duplicates when copying sections for tool panel view by @bernt-matthias in #17117
[23.1] Fix to_cwl for nested collections by @mvdbeek in #17276
[23.2] Rollback invalidated transaction by @jdavcs in #17280
[23.1] Always copy datasets in collection builder modals by @mvdbeek in #17268
[23.2] Install newer celery on python 3.8+ by @mvdbeek in #17309
[23.2] Discard sqlalchemy session after task completion by @mvdbeek in #17317
[23.2] Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in #17315
[23.2] Scope session for job runner monitor loop by @mvdbeek in #17319
[23.1] Enable job resubmissions in k8s runner by @pcm32 in #15238
Revert "[23.1] Enable job resubmissions in k8s runner" by @nuwang in #17323
[23.2] Improve Embed Performance by @ElectronicBlueberry in #17326
[23.2] Fix Subworkflow Edit Button by @ElectronicBlueberry in #17330
[23.1] Disable tag editing on non-owned Pages by @davelopez in #17337
[23.2] Initial release notes for 23.2 by @dannon in #17259
[23.2] Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342
Merge 23.1 into 23.2 by @davelopez in #17343
[23.2] Ensure release notes include all PRs added during the freeze by re-running the release note bootstrapping by @jdavcs in #17344
[23.2] make release titles consistent by @martenson in #17341
[23.2] Write to a temp filename in posix file source plugin by @natefoo in #17350
[23.2] Always store multi select data input values in fixed order by @guerler in #17352
[23.2] Add latest PRs to release by @jdavcs in #17383
[23.2] Fix the purge historyless HDAs pgcleanup action by @natefoo in #17382

New Contributors

@TanguyGen made their first contribution in #16478
@khaled196 made their first contribution in #16503
@sebastian-schaaf made their first contribution in #16762
@lopiola made their first contribution in #16690
@afuetterer made their first contribution in #16851
@arash77 made their first contribution in #17051
@enolfc made their first contribution in #16782

Full Changelog: v23.1.4...v23.2