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_memorytest 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_25.0intodevby @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
entriesfrom 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
ScrollListcomponent 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
selectedItemscomposable 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
fsspecbase 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
WorkflowRunSuccessby @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
InteractiveToolManagerby @nsoranzo in #20871 - Fix test in
configfile_user_defined.ymlby @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