galaxyproject/galaxy v25.0.0 on GitHub

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