v25.0.0

What's Changed

• Stabilize HistoryView.test.js by @jmchilton in #19165
• Fix Pesky warning with PersistentTaskProgressMonitorAlert.test.ts by @ElectronicBlueberry in #19180
• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181
• Cleanup Jest Test Output (part 2) by @jmchilton in #19178
• Dynamic options: add data table filter by @bernt-matthias in #12941
• Cleanup Jest Test Output (part 3) by @jmchilton in #19185
• Don't calculate dataset hash for datasets in non-OK state by @nsoranzo in #19191
• Fix UP031 errors - Part 1 by @nsoranzo in #19194
• Cleanup Jest Test Output (part 4) by @jmchilton in #19186
• Extend image metadata by @kostrykin in #18951
• Move phylocanvas to script entry point by @guerler in #19193
• Move heatmap visualization to new script endpoint by @guerler in #19176
• Fix UP031 errors - Part 2 by @nsoranzo in #19204
• Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot in #19189
• Workflow Editor Activity Bar by @ElectronicBlueberry in #18729
• Add plotly.js by @guerler in #19206
• Switch h5web to script endpoint by @guerler in #19211
• Update visualizations to latest charts package by @guerler in #19213
• Fix UP031 errors - Part 3 by @nsoranzo in #19218
• Cleanup test output console for tool panel tests. by @jmchilton in #19210
• Update Vizarr package version to 0.1.6 by @davelopez in #19228
• Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot in #19233
• Fix UP031 errors - Part 4 by @nsoranzo in #19235
• Explicitly add cwl-utils to dependencies by @nsoranzo in #19257
• Merge 24.2 into dev by @jmchilton in #19240
• Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260
• [PROCEDURES] Drop thumbs up reaction as pull request approval method by @nsoranzo in #19202
• Fix UP031 errors - Part 5 by @nsoranzo in #19282
• Merge 24.2 into dev. by @jmchilton in #19273
• Merge latest 24.2 into dev. by @jmchilton in #19290
• Minor drag style adjustment for activities by @guerler in #19299
• Fix UP031 errors - Part 6 by @nsoranzo in #19314
• Update pydantic to 2.10.3 by @nsoranzo in #19326
• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331
• Extract and typescript-ify datatype selection in wfeditor. by @jmchilton in #19304
• Refactor and add tests for Popovers by @guerler in #19337
• Misc fixes 202412 by @nsoranzo in #19341
• Use popper wrapper for help text popover by @guerler in #19340
• Update Python dependencies by @galaxybot in #19190
• Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in #19358
• Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot in #19369
• Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372
• Node 22 unreachable fixes by @mvdbeek in #19378
• Make conditional discriminators literals instead of generic string/bool by @mvdbeek in #19374
• Remove apptainer-version pin by @nsoranzo in #19380
• SQLAlchemy 2.0 follow-up by @jdavcs in #19388
• Use id entity attribute when setting exampleOfWork property by @nsoranzo in #19396
• Update Python dependencies by @galaxybot in #19366
• Display email activation help only if user activation is enabled by @jdavcs in #19402
• Prevent negative offset by @jdavcs in #19409
• Update Python dependencies by @galaxybot in #19418
• Set safe default extraction filter for tar archives by @nsoranzo in #19406
• Let file sources choose a path for uploaded files by @kysrpex in #19154
• Enable cloning subworkflows by @ElectronicBlueberry in #19420
• Merge Release 24.2 into dev by @ahmedhamidawan in #19443
• Add Vitessce Viewer by @guerler in #19227
• Type annotations improvements by @nsoranzo in #19442
• Alternative format_source fix by @mvdbeek in #19395
• Update main citation to 2024 community paper by @nsoranzo in #19453
• Reset invocation export wizard after completion by @davelopez in #19449
• Remove transaction helper by @jdavcs in #19407
• Update Python dependencies by @galaxybot in #19464
• Document $__user_name__ by @bernt-matthias in #19433
• Improve asynchronous tasks error handling and reporting by @davelopez in #19448
• Workflow Editor Auto Zoom by @ElectronicBlueberry in #19451
• Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394
• Avoid using custos refresh tokens which are expired by @martenson in #19411
• Handles S3 listing errors by @itisAliRH in #19446
• Add test that verifies workflow source_metadata is preserved on landing claim by @mvdbeek in #19454
• eLabFTW integration via Galaxy file source by @kysrpex in #19319
• Add Dataverse RDM repository integration by @KaiOnGitHub in #19367
• Type annotation improvements by @nsoranzo in #19485
• Fix wrong id in test_combined_mapping_and_subcollection_mapping by @mvdbeek in #19481
• Fix preferred object store id reactivity by @ElectronicBlueberry in #19491
• Add author and tools details in RO-Crate by @Marie59 in #18820
• Add workflow selection and bulk actions by @itisAliRH in #19336
• Update Python dependencies by @galaxybot in #19510
• Prevent users from reusing a banned email after account is purged by @jdavcs in #19413
• Fix wrong URI written to ExportObjectResultMetadata when exporting histories to eLabFTW by @kysrpex in #19541
• Fix package versions by @jdavcs in #19566
• Update Python dependencies by @galaxybot in #19567
• Add IGB display support for CRAM files by @paige-kulzer in #19428
• Change galaxy system user uid for K8s image by @afgane in #19403
• Merge 24.2 into dev by @jdavcs in #19590
• Hide outdated visualizations from visualizations activity panel by @guerler in #19353
• Add vue-tsc baseline comparison to client-lint workflow by @dannon in #19593
• Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594
• Add eLabFTW file source from file source templates by @kysrpex in #19493
• Update Python dependencies by @galaxybot in #19623
• Fix test_mulled_build.py::test_mulled_build_files_cli with use_mamba=True by @kysrpex in #19545
• Use correct plugin_kind in user file sources by @davelopez in #19622
• Use discriminated unions in object stores and file source template configs by @davelopez in #19621
• Format code with black 25.1.0 by @nsoranzo in #19625
• Update eLabFTW file source template docs by @kysrpex in #19632
• Add InvenioRDM file source template by @davelopez in #19619
• Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by @jdavcs in #19620
• Mention default values for truevalue and falsevalue by @pvanheus in #19657
• Enhance ListHeader Component for Reusability by @itisAliRH in #19655
• Relax job status check in test_delete_user_cancel_all_jobs by @davelopez in #19661
• Fix more vue tsc indicated type issues by @jmchilton in #19650
• Fix a vue-tsc issue - Login.vue. by @jmchilton in #19647
• Update test_create_dataset_in_subfolder to check for the dataset presence by @davelopez in #19660
• Add Breadcrumb Heading Component by @itisAliRH in #19656
• Remove unused(?) data_dialog form element type. by @jmchilton in #19669
• More Vue Typescript Fixes by @jmchilton in #19663
• Update Python dependencies by @galaxybot in #19682
• Workflow landing request - collapse activity bar by default. by @dannon in #19652
• Add webdavclient3 to conditional-requirements.txt by @bgruening in #19671
• Add forgotten linter test by @bernt-matthias in #19690
• Type annotation improvements by @nsoranzo in #19642
• Add Zenodo file source template by @davelopez in #19638
• Drop support for Python 3.8 by @nsoranzo in #19685
• Fix MarkdownDialog types by @davelopez in #19703
• Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in #19706
• Yet More Vue Typing Error Fixes by @jmchilton in #19680
• Improved simplicity and isolation in transiently failing test. by @jmchilton in #19709
• Move RequiredAppT back into galaxy packages. by @jmchilton in #19704
• Update TypeScript version to 5.7.3 by @davelopez in #19713
• Remote File Sources and Storage Locations redesign by @itisAliRH in #19521
• Speedup mulled build test by @bernt-matthias in #19712
• Expand workflow metadata for readme. by @jmchilton in #19591
• Move Markdown components to subdirectory for modularity by @guerler in #19719
• Move history watcher and minor fixes by @guerler in #19732
• Move vega wrapper to shared common directory and add error handler by @guerler in #19718
• Generate correct types for Dataset source transformations on backend. by @jmchilton in #19666
• Augments popper wrapper, add click and escape handler by @guerler in #19717
• Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in #19726
• ToolShed 2.1 - Various bugfixes and enhancements. by @jmchilton in #19722
• ToolShed2 - Add more context when navigating between tools an repositories. by @jmchilton in #19738
• Add linter argument to linter report function calls by @bernt-matthias in #19708
• Refactor tool panel handling, resolve transiently failing jest test by @guerler in #19733
• Fix incorrect type in tool_util.deps and fix package structure. by @jmchilton in #19702
• Enhance breadcrumb navigation UX in small screen sizes by @itisAliRH in #19737
• Refactor dependencies for tool output actions. by @jmchilton in #19662
• Update Python dependencies by @galaxybot in #19727
• Fix Tours and add tooltips to history items by @guerler in #19734
• Use fissix also when python3-lib2to3 is not installed by @nsoranzo in #19749
• Update Python dependencies by @galaxybot in #19772
• Jest Cleanup (Part 5) by @jmchilton in #19743
• Preserve workflow labels in final invocation reports by @guerler in #19721
• Workflow Run Form Enhancements by @ahmedhamidawan in #19294
• Update webdav user file source template help text by @sanjaysrikakulam in #19784
• Revise consistently failing edam tool panel view test. by @jmchilton in #19762
• Fix wording of API doc string by @bernt-matthias in #19776
• Add better WorkflowSummary type by @ahmedhamidawan in #19779
• Rebuild API schema for latest dev. by @jmchilton in #19789
• Remove unused (define* - compiler macro) imports from TextEditor.vue by @dannon in #19793
• Bump @babel/runtime-corejs3 from 7.23.2 to 7.26.10 in /client by @dependabot in #19788
• Bump axios from 1.7.4 to 1.8.2 in /client by @dependabot in #19773
• Click to edit history name in HistoryPanel by @ahmedhamidawan in #19665
• Fix workflow run graph non input steps not appearing bug by @ahmedhamidawan in #19781
• Rework some form components for reuse. by @jmchilton in #19347
• Update Python dependencies by @galaxybot in #19816
• Fix Selenium workflow tests not updating param type properly. by @jmchilton in #19810
• Add cell-based markdown editor for pages by @guerler in #19769
• HelpText improvements (content, sizing) and WorkflowInvocationHeader tweaks. by @dannon in #19792
• Workflow Run Form Enhancements follow up by @ahmedhamidawan in #19825
• Update RStudio IT by @afgane in #19711
• Syntactic sugar to ease TPV configuration. by @jmchilton in #19834
• Enable lazy loading for ace-builds by @ElectronicBlueberry in #19847
• Improve markdown editor modularity and structure by @guerler in #19835
• More user feedback in FormRulesEdit (for Apply Rules tool) by @jmchilton in #19827
• Webpack build performance improvements by @dannon in #19851
• Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852
• Migrate from Prism to Monaco for ToolSource display. by @dannon in #19861
• Create rucio.cfg from inside Rucio objectstore by @SergeyYakubov in #19863
• Fix most new vue typescript errors discovered in #19851 by @jmchilton in #19862
• Client circular dependency check by @dannon in #19858
• Add bigbed to bed converter and tests by @d-callan in #19787
• Fix broken optimisation introduced in #19852 by @nsoranzo in #19871
• Update Python dependencies by @galaxybot in #19874
• Fix workflow license component typing by @guerler in #19878
• Move some store types out into own file to reduce circular dependencies. by @jmchilton in #19860
• Cleanup circular dependencies around utils.ts. by @jmchilton in #19857
• Add visualization framework interface to cell-based markdown editor by @guerler in #19775
• Merge 24.2 into dev by @ahmedhamidawan in #19890
• Fix various mypy issues around mapped attributes by @mvdbeek in #19883
• Make job cache generally available by @dannon in #19798
• Use direct icon references in FormSelectMany.vue. by @jmchilton in #19829
• Various styling improvements to Workflow Run and Invocation views by @ahmedhamidawan in #19905
• Populate image metadata without allocating memory for the entire image content by @kostrykin in #19830
• Use FA Component (w/svg) instead of span+font in RunWorkflow header by @dannon in #19901
• Fix Galaxy ignoring job object_store_id for quota check by @bernt-matthias in #19854
• Clarify is_active method usage for Python Social Auth in Galaxy by @dannon in #19899
• FITS Graph Viewer - script name tweak. by @dannon in #19902
• Allow embedding vitessce visualizations by @mvdbeek in #19909
• Allow to send notifications when Admins cancel jobs by @davelopez in #19547
• Show workflow help (and readme?) in run form by @ahmedhamidawan in #19736
• Replace backend-based page creation controller endpoint by @guerler in #19914
• Enhance OpenAI Chat Integration by @uwwint in #19612
• Remove unnecessary code duplications by @nsoranzo in #19921
• Change wording in the google drive user file source template by @sanjaysrikakulam in #19927
• Migrate Page editing controller endpoint to API by @guerler in #19923
• Fix import and update_page type signature by @mvdbeek in #19932
• Merge 24.2 into dev by @ahmedhamidawan in #19933
• Add basic support for icons in tools by @davelopez in #19850
• Update Python dependencies by @galaxybot in #19929
• Fix test_in_directory on osx by @mvdbeek in #19943
• Fix local import in __resolvers_dict by @mvdbeek in #19944
• Decrease sentry_sdk.errors log level to INFO by @natefoo in #19951
• Fix adding tags popup closing logic on focus out by @itisAliRH in #19950
• Allow PathLike parameters in make_fast_zipfile() by @nsoranzo in #19955
• Add link to view history on dataset info page by @natefoo in #19956
• Update Python dependencies by @galaxybot in #19964
• Add type hints around collection copying and job things by @mvdbeek in #19961
• Remove circular dependency around user store. by @jmchilton in #19859
• First steps of bootstrap replacement by @ElectronicBlueberry in #19946
• Move FormBoolean back to FormElement field in workflow run form by @ahmedhamidawan in #19938
• Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. by @jaidevjoshi83 in #19689
• Overhaul workflow runtime settings display. by @dannon in #19906
• Adds a trimInputs prop to FormGeneric to trim string values on submit. by @dannon in #19971
• Remove hgv_sift from tool_conf.xml.sample by @natefoo in #19972
• RStudio IT updates to work on .org by @afgane in #19924
• Add share button for invocations by @ahmedhamidawan in #19959
• Fix ownership check in history contents update route by @mvdbeek in #19969
• Introduce reusable GCard component for unified card layout by @itisAliRH in #19785
• Improve type annotation of tool parameter wrapping by @nsoranzo in #19991
• Unwind more client dependencies at top of stack. by @jmchilton in #19983
• Job cache allow different names when possible by @mvdbeek in #19962
• Button replacement batch 1 by @ElectronicBlueberry in #19963
• Allow resizing Visualizations in Markdown editor by @guerler in #19958
• Adds validation and alerts for Markdown elements by @guerler in #19952
• Removes outdated Markdown visualization insertion wizard by @guerler in #19898
• Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008
• Define simple models for job messages. by @jmchilton in #19688
• Add missing tool test file by @jmchilton in #19763
• Update vitessce version by @mvdbeek in #20016
• Merge Inputs/Parameters and Outputs/Collections Tabs by @ahmedhamidawan in #20019
• Fix keyedCache never allowing multiple fetches by @ahmedhamidawan in #20020
• Use lower case extension for setting datatype in data discovery by @bernt-matthias in #19954
• Remove tags used by @ElectronicBlueberry in #19576
• Improvements to package decomposition. by @jmchilton in #19759
• Selenium test cases for running workflow from form upload. by @jmchilton in #19997
• Add env var to skip CircularDependencyPlugin in development mode by @dannon in #20038
• Allow different AI providers (as long as they are openai compatible) by @uwwint in #19989
• Add help text popovers for workflow runtime settings by @ahmedhamidawan in #20031
• Add vitesscejson datatype by @guerler in #20027
• Add kepler.gl visualization by @guerler in #20005
• Add VTK Visualization Toolkit Plugin by @guerler in #20028
• Add Niivue viewer by @guerler in #19995
• Add new line to vtpascii test file by @guerler in #20051
• Pass host url to visualizations by @guerler in #20022
• Fix copying job output from discovered outputs by @mvdbeek in #19999
• Update breadcrumb item 'to' type for better routing support by @itisAliRH in #20065
• GCard Full Description by @itisAliRH in #20064
• Add support for Markdown help text in visualizations by @guerler in #20043
• Also chown R lib in RStudio BioC tool by @natefoo in #20025
• Migrate WF Collection Input Form Definition to Client Side by @jmchilton in #19313
• Update Python dependencies by @galaxybot in #19998
• Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /client by @dependabot in #20086
• Bump h11 from 0.14.0 to 0.16.0 in /lib/galaxy/dependencies by @dependabot in #20088
• Fix test_workflow_run export selenium by @ahmedhamidawan in #20089
• Enhance Storage Dashboard Selected Item UI by @itisAliRH in #20070
• Add sample datasets for visualizations by @guerler in #20046
• Upgrade bundled/requested node version to 22.15.0 by @dannon in #18710
• Set node version to 22.13.0 by @davelopez in #20095
• Gulp build improvements, update. by @dannon in #19405
• Use visualization dropdown solely for examples by @guerler in #20094
• Update Python dependencies by @galaxybot in #20096
• Add flac audio format by @bgruening in #20057
• Add markdown datatype by @bgruening in #20056
• Remove collapse invocations panel on mouseleave feature by @ahmedhamidawan in #20074
• Add DOI to workflow metadata by @jdavcs in #20033
• Flexible mapping from collection parameter types to collection builder components. by @jmchilton in #20082
• Add activity panel width to local storage by @ahmedhamidawan in #20072
• Improve type annotation of galaxy.util submodules by @nsoranzo in #20104
• Route to creating a new file source in remote file browser modal by @ahmedhamidawan in #20084
• Drop old galaxy_session records by @jdavcs in #19872
• Adds Example Datasets and Help Text for Visualizations by @guerler in #20097
• Button replacement batch 2 by @ElectronicBlueberry in #19990
• Add Molstar by @guerler in #20101
• Always render Outputs tab in invocation view by @ahmedhamidawan in #20073
• Move README to center panel in workflow editor by @ahmedhamidawan in #20029
• Show workflow README in split view next to the form inputs by @ahmedhamidawan in #20026
• Add hid to selection field in visualization creation form by @guerler in #20108
• Run integration tests on latest Ubuntu by @nsoranzo in #20118
• Add alignment.js for multiple sequence alignment rendering by @guerler in #20110
• Add role creation form by @guerler in #20119
• Wait for Gbutton to become enabled by @mvdbeek in #20131
• Drop now unused controller method by @mvdbeek in #20129
• Add logo, description and help for aequatus by @guerler in #20128
• Sort visualization datasets by hid by @guerler in #20123
• Migrate Transition Systems Visualization by @guerler in #20125
• Fix and migrate Drawrna by @guerler in #20102
• Add updated PCA plot by @guerler in #20140
• Browse multiple trees in phylocanvas by @guerler in #20141
• Allow deferred and ok state datasets for vis by @guerler in #20143
• Add specific datatypes for Cytoscape and Kepler.gl by @guerler in #20117
• Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in #20150
• Client refactorings ahead of #19377. by @jmchilton in #20059
• Implement dataset collection support in workflow landing requests by @mvdbeek in #20004
• Create working dir output outside of tool evaluator by @mvdbeek in #20153
• Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in #20152
• Yaml parser fixes part2 by @mvdbeek in #20162
• Show job ids on job success by @ahmedhamidawan in #20145
• Yaml parser fixes and improvements (part 1) by @mvdbeek in #20158
• Remove only the Docker images specific for the test by @nsoranzo in #20109
• Fixes for GButtons with disabled state by @ahmedhamidawan in #20121
• Revise transiently failing data source test. by @jmchilton in #20157
• Hide non-functional and replaced visualizations (e.g. Nora, MSA) by @guerler in #20077
• Add rd datatype by @richard-burhans in #20060
• Restore Visualization insertion options in Reports Editor by @guerler in #20000
• Log controller exceptions by @natefoo in #19974
• Improve docs for output filters by @bernt-matthias in #19904
• Add Tapis auth support by @dannon in #19887
• Rename tool "Citations" to "References" by @nsoranzo in #19770
• Fix setting env and tags on resubmission by @bernt-matthias in #19753
• Implement tool markdown reports. by @jmchilton in #19054
• Strip galaxy filename annotation on upload by @GomeChas in #18561
• Improved rule builder display for non-nested lists (most of them). by @jmchilton in #20156
• Support setting and displaying timezone with the core metrics plugin by @natefoo in #19527
• Fix remaining vue-tsc errors by @dannon in #20163
• GLink implementation by @ElectronicBlueberry in #20063
• Add mandatory RO-Crate metadata when exporting by @elichad in #19846
• Use backports.zoneinfo in job_metrics package under Python <3.9 by @nsoranzo in #20178
• Add client package by @natefoo in #20171
• Rucio templates by @SergeyYakubov in #19720
• Avoid persisting credentials on checkout step of the Github actions by @arash77 in #19089
• Fix formatting in webapp and client/install.py by @dannon in #20185
• Allow overriding datatypes for planemo lint by @selten in #19780
• Fix tapis module typing errors by @jdavcs in #20175
• Run the tool working dir backup/restore on Pulsar by @natefoo in #16696
• Clarify that extra_scopes is sometimes non-optional by @martenson in #19385
• Add config options for tool dependency installs by @afgane in #19565
• Documentation around highlighting PRs for release notes. by @jmchilton in #19390
• Irods objectstore templates by @pauldg in #19415
• Add rerun option for workflows by @ahmedhamidawan in #20032
• Show pre-populated landing data values in workflow run form by @ahmedhamidawan in #19935
• Add docx datatype by @bgruening in #20055
• Allow controlling strict channel priority in mulled-build by @bernt-matthias in #19425
• xsd: use CollectionType for collections in tests by @bernt-matthias in #19802
• Isolate singularity containers more thoroughly for better reproducibility. by @rhpvorderman in #18628
• Add a script to reorganize tool data based on the new layout for genomic Data Managers by @natefoo in #19728
• Add more metadata, esp infer_from to datatypes configuration by @bgruening in #20142
• Update tabular_csv.py to use less memory in tsv->csv conversion by @cat-bro in #20187
• Add ZIP explorer to import individual files from local or remote ZIP archives by @davelopez in #20054
• Implement file source to integrate Galaxy with RSpace by @kysrpex in #20167
• Bump vega from 5.30.0 to 5.32.0 in /client by @mvdbeek in #20188
• Standalone Galaxy API Client Package by @dannon in #20181
• Drop old job metrics by @jdavcs in #19936
• G modal implementation by @ElectronicBlueberry in #20168
• Add JupyterLite by @guerler in #20174
• Add visualization test data by @nilchia in #20183
• Corrects header levels in Visualization Help Markdown by @guerler in #20199
• Bump default milestone to 25.1 by @mvdbeek in #20189
• Add plotly 6.0.1 to JupyterLite by @guerler in #20201
• Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377
• Add User-Defined Tools by @mvdbeek in #19434
• Fix unit test import by @mvdbeek in #20203
• Move UnprivilegedToolResponse into api by @mvdbeek in #20207
• Package fixes by @nsoranzo in #20208
• Fix linting with markdown in tool help by @bgruening in #20058
• Enable visualizations for anonymous user by @guerler in #20210
• Add three AAI providers by @martenson in #20165
• IT Activity Panel by @dannon in #19996
• Add Katex Equation rendering plugin to Markdown Editor by @guerler in #19988
• Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in #20194
• Make preferences drop down available in single user deployments by @ksuderman in #19888
• Add replacement_dataset option to collection filter tools by @simonbray in #20166
• Migrate ChiraViz by @guerler in #20214
• Fix next milestone by @martenson in #20219
• Fix NFDI auth by @bgruening in #20217
• Bump axios from 1.7.4 to 1.8.2 in /client by @dependabot in #20205
• Have make dist in the web_client package build the client by @natefoo in #20195
• Add history sharing and accessibility management view by @ahmedhamidawan in #19786
• Enhance external login interface styling by @ahmedhamidawan in #20100
• Display invocation inputs and outputs in workflow report by @mvdbeek in #20222
• Bug fixes around wizard usage. by @jmchilton in #20224
• Visualization-First Display functionality by @dannon in #20190
• Dataset View Component by @dannon in #20154
• Use TUS streaming and remove redundant IndexDB temp store in Zip Explorer by @davelopez in #20226
• Support setting masthead height in a theme by @ksuderman in #19581
• Bug fix - allow file drops into PasteData widget. by @jmchilton in #20232
• Fix vue-tsc issue in ParameterStep by @dannon in #20245
• Only show custom tool editor in activity bar settings when user has access by @mvdbeek in #20247
• [25.0] Group Tool Versions in IT Panel by @dannon in #20244
• Fix job rerun for dynamic tools by @mvdbeek in #20259
• Fix tool-provided metadata for CONVERTER_tar_to_directory by @mr-c in #20260
• Add 25.0 migration tags by @ahmedhamidawan in #20265
• [25.0] Update version to 25.0.rc1 by @ahmedhamidawan in #20267
• [25.0] Fix inconsistent header sizes by @guerler in #20277
• [25.0] Improve handling of very large files in Tabulator by @guerler in #20271
• [25.0] Add more descriptions to custom tool source schema by @mvdbeek in #20266
• [25.0] Fix theme selector by @guerler in #20275
• [25.0] Add non-dev httpx dependency by @mvdbeek in #20281
• [25.0] Remove duplicated job id in job success view by @ahmedhamidawan in #20289
• [25.0] Skip multiple pasted URLs when checking for remote Zip by @davelopez in #20300
• [25.0] Fix masthead logo height by @guerler in #20302
• [25.0] Touch up Dataset View by @guerler in #20290
• [25.0] Fix display urls by @dannon in #20318
• [25.0] Remove type import side-effects by @ElectronicBlueberry in #20321
• [25.0] Increase proxy API robustness by validating URL before use by @davelopez in #20311
• [25.0] Fix workflow bookmark filtering by @davelopez in #20325
• [25.0] Rerun workflows for the correct version/instance by @ahmedhamidawan in #20313
• [25.0] Fix broken admin navigation option and add missing menu items by @dannon in #20333
• [25.0] Enable retrieving contents from extra file paths when request contains leading / by @mvdbeek in #20336
• [25.0] Error on duplicate labels by @ElectronicBlueberry in #20335
• [25.0] Add test for workflow instance download fix by @ahmedhamidawan in #20326
• [25.0] Bug fix - auto-pairing step not connected to collection builder in wizard. by @jmchilton in #20345
• [25.0] Small UI fixes for ag-grid based rule grid. by @jmchilton in #20358
• [25.0] Add basic validation to workflow creator attribute by @jdavcs in #20328
• [25.0] Log invalid vault paths by @mvdbeek in #20363
• [25.0] Remove redundant badge when creating collection from upload by @ahmedhamidawan in #20367
• [25.0] Generate a tenant-unique UID for tapis. by @dannon in #20370
• [25.0] Fix radio button options in CopyModal by @davelopez in #20378
• [25.0] Use router to route to creating a new file source by @ahmedhamidawan in #20374
• [25.0] Fix conda_link to use platform.machine() for architecture detection by @chrisagrams in #20381
• [25.0] Fix selection issue when adding tags to workflows in bulk by @davelopez in #20362
• [25.0] Fix create file source button, show only at root by @davelopez in #20385
• [25.0] Make invocation errors more compact by @ahmedhamidawan in #20369
• [25.0] Fix interactive activity highlighting by @guerler in #20276
• [25.0] Force Monaco into a separate bundle by @dannon in #20396
• [25.0] Avoid displaying dataset tab view in window manager by @guerler in #20317
• [25.0] Fix toolshed-installed tool icons by @dannon in #20399
• [25.0] Fix form select input sorting by @davelopez in #20401
• [25.0] Bug fix: allow any collection type in FormCollectionType. by @jmchilton in #20403
• [25.0] Add job config variable for singularity --contain by @bernt-matthias in #20400
• [25.0] Fixes for the admin jobs interface by @martenson in #20405
• [25.0] Prevent waiting for history item state to be ok in uploader by @ahmedhamidawan in #20397
• [25.0] Fix job rerun with tool version change by @mvdbeek in #20417
• [25.0] Fix $app attribute access in cheetah templates by @mvdbeek in #20414
• [25.0] Update pulsar-galaxy-lib to 0.15.8 by @mvdbeek in #20419
• [25.0] Fix css alignment styling of login page by @ahmedhamidawan in #20429
• [25.0] DatasetView and Card Polish by @dannon in #20342
• [25.0] Fix workflow logo URL not being persisted. by @jmchilton in #20428
• [25.0] Fix minor IT panel/display issues by @dannon in #20404
• [25.0] Upgrade tensorflow conditional dependency version to 2.15.1 by @cat-bro in #20434
• [25.0] Deprecate enable_tool_document_cache by @nsoranzo in #20433
• [25.0] Update triggers by @jdavcs in #20425
• [25.0] Add user-facing explanation for legacy workflow run form usage by @ahmedhamidawan in #20431
• [25.0] Improve performance of job cache query by @mvdbeek in #20319
• [25.0] Fix add button is enabled when empty tag list by @davelopez in #20443
• [25.0] Wrap Tool and Workflow run headers properly by @ahmedhamidawan in #20440
• [25.0] Dataset Display and Preferred Viz fixes by @dannon in #20439
• [25.0] Set GALAXY_CONFIG_FILE env var if starting handler with -c by @mvdbeek in #20449
• [25.0] Fix pagination state in FilesDialog by @davelopez in #20452
• [25.0] Data Libraries - persist number of entries displayed in folders by @dannon in #20455
• [25.0] Fix copying of job metrics for cached jobs by @mvdbeek in #20436
• [25.0] Fix multiple remote file upload to collection creator by @ahmedhamidawan in #20456
• [25.0] Update tiffviewer to latest version supporting more formats by @davelopez in #20457
• [25.0] Fix inconsistent styling in List Collection Builder selector by @ahmedhamidawan in #20442
• [25.0] Bug fix: paired_or_unpaired also endswith paired. by @jmchilton in #20458
• [25.0] Fix bug with handling compressed file names while auto-pairing. by @jmchilton in #20459
• [25.0] Add molstar as default viewer for some molecule formats by @bgruening in #20467
• [25.0] Add Aladin as standard FITS viewer by @bgruening in #20465
• [25.0] Fix dataset error button not using router by @ahmedhamidawan in #20472
• [25.0] Add /api/datasets/{dataset_id}/extra_files/raw/{filename:path} by @mvdbeek in #20468
• [25.0] More fixes to FormData drag and drop and typing by @ahmedhamidawan in #19900
• [25.0] Replace Bootstrap Popover with Popper wrapper by @guerler in #20246
• [25.0] Don't fit workflow if it doesn't have steps by @mvdbeek in #20480
• [25.0] Use DatasetAsImage component for DatasetView image display by @dannon in #20488
• [25.0] Recreate triggers by @jdavcs in #20491
• [25.0] Rename vitessce_json file_ext to vitessce.json by @mvdbeek in #20473
• [25.0] Remove rename modal from List Collection Creator by @ahmedhamidawan in #20487
• [25.0] Release notes by @ahmedhamidawan in #20386
• [25.0] Allow workflow description to show full text by @davelopez in #20500

New Contributors

• @KaiOnGitHub made their first contribution in #19367
• @Marie59 made their first contribution in #18820
• @paige-kulzer made their first contribution in #19428
• @d-callan made their first contribution in #19787
• @GomeChas made their first contribution in #18561
• @chrisagrams made their first contribution in #20381

Full Changelog: v24.2.4...v25.0.0