galaxyproject/galaxy v25.1.0 on GitHub

What's Changed

Version 25.1.dev by @ahmedhamidawan in #20268
Update Javascript package licenses to MIT by @mr-c in #20264
Fix a transiently failing API test. by @jmchilton in #20278
Remove backbone-based charts modules by @guerler in #19892
Add missing galaxy slots and memory tool by @mvdbeek in #20262
Fix test timeout in k8s test_slots_and_memory test by @mvdbeek in #20284
Update GitHub workflows to use PostgreSQL 17 image by @nsoranzo in #20292
Fix memory and slots test by @mvdbeek in #20291
Update Python dependencies by @galaxybot in #20139
Update Python dependencies by @galaxybot in #20347
Install Visualization plugins as self-contained packages by @guerler in #20348
Add built visualizations path to .gitignore by @guerler in #20355
Remove legacy visualizations by @guerler in #20173
Merge 25.0 into dev by @ahmedhamidawan in #20380
Prepare ToolBox.dynamic_tool_to_tool() for CWL formats by @nsoranzo in #20364
Use full page width in reports and pages by @guerler in #20384
History CitationsList export improvements by @dannon in #20402
Enhance citations page by @davelopez in #20408
Switch Default Visualization Endpoint to script, migrate to YAML by @guerler in #20303
Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by @dependabot[bot] in #20422
Workflow Graph Search by @ElectronicBlueberry in #20390
Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424
Allow larger viz in pages by @guerler in #20427
Update create_time field to be required in history content items by @davelopez in #20357
Refactor CollectionDescription component props to use HDCASummary by @davelopez in #20356
Small tweaks and cleanup from sample sheets branch by @jmchilton in #20229
Selenium tests for various 24.2 features. by @jmchilton in #20215
Fix client build, set create_time by @mvdbeek in #20445
Update mulled_containers.rst by @ccoulombe in #20446
Implement dataset source requested transformations. by @jmchilton in #20435
Change wording of the client side storage handling by @bgruening in #19815
Restore Nora by @guerler in #20387
Base Implementation of GFormInput by @ElectronicBlueberry in #20418
Update Python dependencies by @galaxybot in #20383
Collection API related spelling fix. by @jmchilton in #20470
Merge release_25.0 into dev by @davelopez in #20484
Merge release_25.0 into dev by @davelopez in #20490
Install visualizations directly to static path, avoid duplication by @guerler in #20372
Fix alembic down_revision for trigger replacement migration by @mvdbeek in #20501
Add a merge migration, revert previous edit by @jdavcs in #20507
Test case for using URL-based workflow inputs with implicit conversions. by @jmchilton in #20509
Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288
Fixes for invocation import. by @jmchilton in #20528
Add LocusZoom Visualization by @elmedjadjirayane in #20354
Add Dataverse template by @davelopez in #20551
Update Python dependencies by @galaxybot in #20537
Add username_key setting to configure python-social-auth OIDC by @marius-mather in #20497
Update Python dependencies by @galaxybot in #20577
Display the Galaxy Citation within the Export Tool References List by @mschatz in #20584
Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20591
Add rerun.io web viewer by @guerler in #20202
Update Python dependencies by @galaxybot in #20601
Add missing cleanup table by @jdavcs in #20594
Fix transient selenium error when adding collection input. by @jmchilton in #20460
Improve BreadcrumbHeading and add unit tests by @itisAliRH in #20618
Require user for visualizations create endpoint by @guerler in #20615
Add recent downloads page for STS requests by @davelopez in #20585
Remove vue-tsc diff comparison from CI by @dannon in #20620
Refactor Object Store Selection Modals UI by @itisAliRH in #19697
Use store to cache step jobs summary by @ahmedhamidawan in #20638
Update location of latest tpv shared db by @nuwang in #20651
Fix typo in lib/galaxy/config/sample/job_conf.sample.yml: enviroment --> environment by @blankenberg in #20652
Add markdown hint to schema by @bgruening in #20654
Update tiffviewer visualization to version 0.0.3 by @davelopez in #20658
Update Python dependencies by @galaxybot in #20653
Improve GCard visibility handling and type definitions by @itisAliRH in #20663
Remove select and deselect labels from visualization select field by @guerler in #20665
Removes entries from purged filter label in history grid by @guerler in #20664
Update core.history tour by @pavanvidem in #20576
Fix UI Bug - don't allow checking deferred for local files. by @jmchilton in #20609
Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547
Sort collection dialog by HID descending. by @jmchilton in #20674
Update Python dependencies by @galaxybot in #20680
Unify History export UX using wizard by @davelopez in #20666
Fix resource watcher composable race condition by @davelopez in #20690
Fix assertion on python version by @ccoulombe in #20696
Update Python dependencies by @galaxybot in #20699
Refactor and use ScrollList component in more places by @mvdbeek in #19318
History Components Navigation/Heading Improvements by @itisAliRH in #20702
Remove deprecated tool document cache by @nsoranzo in #20510
Implement Sample Sheets by @jmchilton in #19305
Clean up code from pyupgrade by @nsoranzo in #20642
Remove decoded ids from job/dataset error report email by @ahmedhamidawan in #20714
Drop ucsc test server from sample build sites by @mvdbeek in #20723
Update Python dependencies by @galaxybot in #20732
Fix Client Linting Run Error by @itisAliRH in #20734
User preferences redesign by @itisAliRH in #19658
Make invocations panel reactive using the invocation store by @ahmedhamidawan in #20738
Update Python dependencies by @galaxybot in #20753
Various client unit test fixes and cleanup. by @jmchilton in #20752
More client unit test clean up. by @jmchilton in #20755
Add a "Debug" (email report) tab to Workflow Invocations by @ahmedhamidawan in #20624
Add embed-compatible view for galaxy pages by @dannon in #20737
Add more info to inheritance chain by @arash77 in #20701
Consolidate visualization mako, avoid user agent styles by @guerler in #20760
Fix WorkflowComment tests warnings by @davelopez in #20762
Make workflow invocation tabs routable by @ahmedhamidawan in #20719
Fix various collection descriptions in history panel. by @jmchilton in #20736
Hierarchical display collection dataset states by @mvdbeek in #20731
Attempt to reuse previously materialized datasets by @mvdbeek in #20718
Increase wait time (retry) in UCSC data source test by @davelopez in #20772
More cleanup for Jest output. by @jmchilton in #20769
Fail Jest tests on warn/error console logging. by @jmchilton in #20770
Apply eslint fixes by @mvdbeek in #20775
Drop old load_workflow controller method, use API by @mvdbeek in #20774
A production data types checklist to aid creating/reviewing new data types by @jmchilton in #20768
Update Python dependencies by @galaxybot in #20779
Stabilize client build after client-dev-server by @davelopez in #20777
Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749
Add selectedItems composable by @ahmedhamidawan in #19973
Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728
Implement Data Landing Requests by @jmchilton in #20592
Fix visualization installs by @dannon in #20788
Allow fine-grained selection of included files in Invocation Export Wizard by @davelopez in #20776
Add fsspec base implementation for File Source plugins by @davelopez in #20698
Fix Switch to history link click actions and add extensive jests by @ahmedhamidawan in #20783
Add tool_id and tool_version column to tool_landing_request table by @mvdbeek in #20795
Remove Backbone from UI bootstrap initialization by @guerler in #20786
New History List Using GCard by @itisAliRH in #20744
Refactor MESSAGES constant in FileSourceTypeSpan.vue by @davelopez in #20806
Update Python dependencies by @galaxybot in #20812
Fix new linting errors in unit test mounts by @davelopez in #20807
Enable data label column selection in basic Plotly plots and add heatmap by @guerler in #20813
Only show breadcrumb when on history permissions route (not in sharing view) by @ahmedhamidawan in #20800
Fix fsspec fs path handling by @davelopez in #20799
Adapt S3 file source to fsspec by @davelopez in #20794
Upgrade Prettier 3 by @dannon in #20815
Fix webpack dev server detection by @mvdbeek in #20822
Modernize and Refactor Tour components by @ahmedhamidawan in #20771
Update 2 docs pages by @nsoranzo in #20824
Add small improvements for running CWL tools by @nsoranzo in #20826
Ignore yaml and json in prettier pre-commit hook by @mvdbeek in #20823
Add Hugging Face 🤗 file source and user-defined template by @davelopez in #20805
Migrate icon defs in CollectionOperations.vue to best practices. by @jmchilton in #20829
Remove Backbone dependency from webhook wrappers by @guerler in #20797
Bump requirement of directory converters by @bernt-matthias in #20834
Fix lint error in WorkflowRunSuccess by @ahmedhamidawan in #20837
Update Python dependencies by @galaxybot in #20841
Add configfiles support and various enhancements for user defined tools by @mvdbeek in #20761
Add support for hierarchical module systems in lmod + module dependency resolvers by @t1mk1k in #20866
Fix Ipynb datatype sniffer and add unit tests. by @ksuderman in #20811
Workaround to numeric sorting in the local portion of tool versions if they are galaxy "build" numbers by @natefoo in #13570
Update Python dependencies by @galaxybot in #20869
Improve type annotation for job runners and InteractiveToolManager by @nsoranzo in #20871
Fix test in configfile_user_defined.yml by @nsoranzo in #20873
Support remote file source hashes by @davelopez in #20853
Fix multiple="true" data collection map over for shell_command tools by @mvdbeek in #20859
Drop Python helper script from sort1 tool by @nsoranzo in #20876
Update JupyterLite version to 0.6.4 by @guerler in #20877
Fix anndata metadata by @nilchia in #20778
Add visualization navigation guard by @dannon in #20881
Add axt and maf to auto_compressed_types by @richard-burhans in #20875
Add main tool CI tests by @nsoranzo in #20884
Refactor sharing logic for unified type handling by @davelopez in #20888
Set default option to make datasets accessible only to individual users when sharing histories with particular users by @davelopez in #20886
Replace deprecated codecs.open() by @nsoranzo in #20891
Update requirements of sort1 tool by @nsoranzo in #20892
Likely fix for transiently failing published histories test. by @jmchilton in #20890
Validate sample sheet column definitions in workflow definitions on backend. by @jmchilton in #20880
Update Python dependencies by @galaxybot in #20905
Various Container Execution Enhancements (including GCP Batch support) by @jmchilton in #20862
Avoid overscroll behavior by @guerler in #20908
Allow adding extra steps to the default pipeline of the OIDC authentication by @marius-mather in #20845
Merge 25.0 into dev by @ahmedhamidawan in #20911
Add Multiple Sequence Alignment Viewer 2.0 by @guerler in #20907
Update Integration tests by @nsoranzo in #20844
Add short term storage expiration indicator to history items by @davelopez in #20332
Allow creation of visualizations without dataset by @guerler in #20914
Enable dependabot version updates for GitHub actions by @nsoranzo in #20915
Bump docker/login-action from 2 to 3 by @dependabot[bot] in #20918
Bump docker/build-push-action from 4 to 6 by @dependabot[bot] in #20919
Bump docker/setup-buildx-action from 2 to 3 by @dependabot[bot] in #20922
Bump codecov/codecov-action from 3 to 5 by @dependabot[bot] in #20920
Bump actions/setup-node from 4 to 5 by @dependabot[bot] in #20921
Include format in internal json model by @mvdbeek in #20917
Update Python dependencies by @galaxybot in #20930
Allow addressing user defined tools in job config by @mvdbeek in #20932
Bump actions/checkout from 4 to 5 by @dependabot[bot] in #20937
Bump peter-evans/create-pull-request from 6 to 7 by @dependabot[bot] in #20938
Bump actions/github-script from 7 to 8 by @dependabot[bot] in #20941
Bump docker/metadata-action from 4 to 5 by @dependabot[bot] in #20939

New Contributors

@ccoulombe made their first contribution in #20446
@elmedjadjirayane made their first contribution in #20354
@marius-mather made their first contribution in #20497
@t1mk1k made their first contribution in #20866

Full Changelog: v25.0.4...v25.1.0