v25.1.1

What's Changed

🔧 Enhancements

• [25.0] Add Sourmash sig new datatype by @SaimMomin12 in #21469
• [25.0] add new datatype for kmindex index data by @Smeds in #21429
• [25.1] Add sample sheet support to many database operation tools by @mvdbeek in #21465
• [25.1] Adds object_expires_after_days example usage to sample config by @davelopez in #21547
• [25.1] Add new jupyter version by @bgruening in #21531
• [25.1] Add tool credentials system documentation and schema updates by @arash77 in #21561
• [25.1] Add new datatype pg and hg for pangenomics by @SaimMomin12 in #21620
• [25.1] Add database operation tool to convert sample sheets to list collections by @mvdbeek in #21625
• [25.1] Add new datatypes required for VG tool by @SaimMomin12 in #21644
• [25.1] Add a few datatypes from the digital humanities domain by @bgruening in #21596
• [25.1] Document security considerations for using secrets by @bernt-matthias in #21654

🐛 Bug Fixes

• [25.1] Update 25.1 release notes with config changes by @ahmedhamidawan in #21444
• [25.1] Fix 25.1 release month on user facing notes by @ahmedhamidawan in #21450
• [25.1] Sample sheet column fix by @mvdbeek in #21446
• [25.1] Fix sample_sheet column display by @mvdbeek in #21457
• [25.1] Maintain column definitions on map over by @mvdbeek in #21468
• [25.1] Record input parameter invocation inputs by @mvdbeek in #21452
• [25.1] Remove ref and polish release-drafter workflow by @ahmedhamidawan in #21467
• [25.0] Add missing test file for sig datatype by @SaimMomin12 in #21473
• [25.1] Remove release-drafter workflow and add a release config file to improve generated notes by @ahmedhamidawan in #21478
• [25.0] Add missing ending newline to test.sig test data file by @nsoranzo in #21485
• [25.1] change locuszoom package version to 0.0.7 by @elmedjadjirayane in #21494
• [25.1] Fix subworkflow runs for disconnected required inputs with defaults by @mvdbeek in #21488
• [25.0] Pin release prebuilt client package exactly by @dannon in #21498
• [25.1] Fix exception message to enable debugging of missing dataset issue. by @jmchilton in #21504
• [25.1] Usability fixes for sample sheet selection. by @jmchilton in #21503
• [25.1] Do not update a user's update_time when an admin archives (and purges) a history by @natefoo in #21484
• [25.0] Fix type annotation for invocation report errors field by @mvdbeek in #21508
• [25.1] Add missing dependencies to galaxy-files package by @nsoranzo in #21518
• [25.1] Filter out failed_metadata HDAs from job cache by @mvdbeek in #21544
• [25.1] Fix job cache collection copy by @mvdbeek in #21558
• [25.1] Show "Expires today" instead of "Expires soon" in Expiration Warning by @mvdbeek in #21560
• [25.1] Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557
• [25.1] Supports Dataverse file access via both persistent and database IDs by @davelopez in #21569
• [25.1] Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by @jmchilton in #21584
• [25.1] Fix passing user id to preferences by @guerler in #21576
• [25.1] Use quotes for Galaxy citation bibtex by @bernt-matthias in #21563
• [25.1] Add belated deprecation of Python 3.9 support by @nsoranzo in #21598
• [25.0] Fix race condition in workflow collection populated state check by @mvdbeek in #21613
• [25.1] Harden Dataverse integration by @davelopez in #21624
• [25.1] Fix loading of credentials when associated tools are missing by @arash77 in #21599
• [25.1] Fix Pulsar with default_file_action: none by @mvdbeek in #21578
• [25.1] Fix condor typo by @gsaudade99 in #21651
• [25.1] Add split paired or unpaired tool to sample tool conf by @bernt-matthias in #21647
• [25.1] Fix secret credential editing and add clear button by @itisAliRH in #21650
• [25.1] Fix HTCondor runner unwatching jobs when stopping containers by @kysrpex in #21656
• [25.1] Fixes storage management check for anonymous users by @davelopez in #21680
• [25.1] Resets selection filter when loading dialog by @davelopez in #21681
• [25.1] Fixes duplicated entries in "share with individual users" component by @davelopez in #21683
• [25.0] Fix data manager .loc file selection logic by @jdavcs in #21664
• [25.1] Remove Discover Tools button in the workflow tool panel by @ahmedhamidawan in #21697
• [25.1] Simplify docker build, use node as specified in requirements by @mvdbeek in #21695
• [25.0] Fix option propagation for workflow inputs connected to multiple subworkflows by @mvdbeek in #21712
• [25.1] Fix collection job state not preserved during history export/import by @mvdbeek in #21716
• [25.1] Strip inline comments in conditional requirements by @mvdbeek in #21720
• [25.1] Exclude node_modules at all depths in Docker builds by @mvdbeek in #21721
• [25.0] Add missing filter_failed_collection_1.1.0.xml tool by @mvdbeek in #21719

🧪 Testing

• [25.1] Improve tempdir cleanup in integration tests by @mvdbeek in #21520

New Contributors

• @gsaudade99 made their first contribution in #21651

Full Changelog: v25.1.0...v25.1.1

v25.1.0

What's Changed

🎉 Major Changes

• Workflow Graph Search by @ElectronicBlueberry in #20390
• Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288
• Add recent downloads page for STS requests by @davelopez in #20585
• Implement Sample Sheets by @jmchilton in #19305
• User preferences redesign by @itisAliRH in #19658
• New History List Using GCard by @itisAliRH in #20744
• Add Hugging Face 🤗 file source and user-defined template by @davelopez in #20805
• Add short term storage expiration indicator to history items by @davelopez in #20332
• Improve Invocation View step display by @ahmedhamidawan in #20912
• Change Advanced Tool Search to a Tool Discovery View by @ahmedhamidawan in #20747
• Split Login and Register, enable OIDC Registration. by @uwwint in #20287
• Adds IGV.js Visualization by @guerler in #20943
• [25.1] Support credentials(secrets/variables) in tool requirements by @arash77 in #19084

🚀 New Features

• Add LocusZoom Visualization by @elmedjadjirayane in #20354
• Add rerun.io web viewer by @guerler in #20202
• 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 Multiple Sequence Alignment Viewer 2.0 by @guerler in #20907
• Allow creation of visualizations without dataset by @guerler in #20914
• Add tags to output datasets from tool form by @PlushZ in #19225
• Wire up and test resource requirement via tpv by @mvdbeek in #20936
• Add tool to add nesting level to collection by @bernt-matthias in #20926
• [25.1] Add Keyboard Navigation to History Lists by @itisAliRH in #21035
• [25.1] [igv] Allow selection of genomes from history fasta/2bit by @guerler in #21269

🔧 Enhancements

• Update Javascript package licenses to MIT by @mr-c in #20264
• Update GitHub workflows to use PostgreSQL 17 image by @nsoranzo in #20292
• Install Visualization plugins as self-contained packages by @guerler in #20348
• 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
• Allow larger viz in pages by @guerler in #20427
• Selenium tests for various 24.2 features. by @jmchilton in #20215
• Implement dataset source requested transformations. by @jmchilton in #20435
• Base Implementation of GFormInput by @ElectronicBlueberry in #20418
• Test case for using URL-based workflow inputs with implicit conversions. by @jmchilton in #20509
• Fixes for invocation import. by @jmchilton in #20528
• Add Dataverse template by @davelopez in #20551
• Add username_key setting to configure python-social-auth OIDC by @marius-mather in #20497
• Display the Galaxy Citation within the Export Tool References List by @mschatz in #20584
• Improve BreadcrumbHeading and add unit tests by @itisAliRH in #20618
• Refactor Object Store Selection Modals UI by @itisAliRH in #19697
• Update location of latest tpv shared db by @nuwang in #20651
• Add markdown hint to schema by @bgruening in #20654
• Update tiffviewer visualization to version 0.0.3 by @davelopez in #20658
• Improve GCard visibility handling and type definitions by @itisAliRH in #20663
• Removes entries from purged filter label in history grid by @guerler in #20664
• Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547
• Sort collection dialog by HID descending. by @jmchilton in #20674
• Unify History export UX using wizard by @davelopez in #20666
• Fix resource watcher composable race condition by @davelopez in #20690
• 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
• Make invocations panel reactive using the invocation store by @ahmedhamidawan in #20738
• Add more info to inheritance chain by @arash77 in #20701
• Make workflow invocation tabs routable by @ahmedhamidawan in #20719
• Hierarchical display collection dataset states by @mvdbeek in #20731
• Attempt to reuse previously materialized datasets by @mvdbeek in #20718
• Fail Jest tests on warn/error console logging. by @jmchilton in #20770
• A production data types checklist to aid creating/reviewing new data types by @jmchilton in #20768
• Stabilize client build after client-dev-server by @davelopez in #20777
• Add selectedItems composable by @ahmedhamidawan in #19973
• Implement Data Landing Requests by @jmchilton in #20592
• 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
• Enable data label column selection in basic Plotly plots and add heatmap by @guerler in #20813
• Fix fsspec fs path handling by @davelopez in #20799
• 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
• Migrate icon defs in CollectionOperations.vue to best practices. by @jmchilton in #20829
• 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
• Support remote file source hashes by @davelopez in #20853
• Drop Python helper script from sort1 tool by @nsoranzo in #20876
• Update JupyterLite version to 0.6.4 by @guerler in #20877
• 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
• Set default option to make datasets accessible only to individual users when sharing histories with particular users by @davelopez in #20886
• Various Container Execution Enhancements (including GCP Batch support) by @jmchilton in #20862
• Allow adding extra steps to the default pipeline of the OIDC authentication by @marius-mather in https://github.com/galaxyproject/gal...

v25.0.4

What's Changed

• [25.0] Fix select field cut off in dataset view by @ahmedhamidawan in #20947
• [25.0] Deactivate user file source on unknown error by @mvdbeek in #20962
• [25.0] Check for expiration in refresh token dictionary by @jdavcs in #20954
• [24.2] Fix test_multiple_decorators unit test for FastAPI 0.118.0 by @nsoranzo in #20982
• [25.0] Don't create workflow outputs to recover input parameter outputs by @mvdbeek in #20980
• [25.0] Skip sam metadata if we have too many references by @mvdbeek in #20820
• [25.0] Add Auspice JSON datatype by @pvanheus in #20466
• [25.0] Backport of #20984 by @davelopez in #20994
• [25.0] Improves zip file type detection for uploads under windows by @caroott in #20999
• [25.0] Add safetensors datatype by @nilchia in #20754
• [25.0] Add LAS and LAZ file format by @bgruening in #21049
• [25.0] Fix PUT /api/workflows for user defined tools by @mvdbeek in #20987
• [25.0] Fix InvalidRequestError when saving workflow step with dynamic tool by @mvdbeek in #21056
• [25.0] New datatype addition: beast.trees datatype by @SaimMomin12 in #21055
• [25.0] Add display_in_upload to LAZ and LAS by @bgruening in #21060
• [25.0] Fix has_size assertion by @bernt-matthias in #21081
• [25.0] Fix workflow run form input restrictions by @mvdbeek in #21095
• [25.0] Run landing request state through validator by @mvdbeek in #21087
• [25.0] New datatype addition: gam for vg toolkit by @SaimMomin12 in #21096
• [25.0] Prefix download link by @martenson in #21112
• [25.0] Use job cache also for implicit conversions by @mvdbeek in #21021
• [25.0] Create new datasets when creating skipped database operation tool outputs by @mvdbeek in #21142
• [25.0] Fix workflow landing rendering if public query param not provided by @mvdbeek in #21165
• [25.0] Backport Fix proxy endpoint encoding by @davelopez in #21184
• [25.0] Harden proxy redirect validation by @davelopez in #21185
• [25.0] Backport fix anndata datatype update by @nilchia in #21111
• [25.0] Fix MIME type for LAZ datatype by @kysrpex in #21202
• [25.0] Fix optional param unset in RO-Crate export by @davelopez in #21192
• [25.0] Require OK datasets for filtering empty datasets by @bernt-matthias in #21023
• [25.0] Fix refresh token expiration retrieval logic by @nuwang in #21213
• [25.0] Fix direct tool execution not using the latest version by @jmchilton in #21240
• [25.0] Add SpatialData datatype by @nilchia in #21000
• [25.0] support ZARR v3 for Spatialdata dt by @nilchia in #21265
• [25.0] Swap to NPM trusted publishing for prebuilt client by @dannon in #21290
• [25.0] Fix proxy url validation for non-printable characters by @davelopez in #21280
• [25.0] Store pulsar job prep error messages by @mvdbeek in #21013

New Contributors

• @caroott made their first contribution in #20999

Full Changelog: v25.0.3...v25.0.4

v25.0.3

What's Changed

• [25.0] Cascade newly created windows in window manager by @guerler in #20780
• [25.0] Remove packages/meta/requirements.txt by @nsoranzo in #20782
• [25.0] Ensure that workflow invocations are persisted with state by @mvdbeek in #20784
• [25.0] Fix password reset functionality for lowercase emails by @jdavcs in #20801
• [25.0] Render Tool Descriptions in Markdown in TRS imports by @itisAliRH in #20814
• [24.2] Include galaxy user agent in data source tools by @mvdbeek in #20836
• [24.2] Fix token refresh bug (cilogon) by @jdavcs in #20821
• [25.0] Undo accidental push by @bernt-matthias in #20854
• [24.2] Update Celery section in admin docs by @jdavcs in #20856
• [25.0] Drop eager argument from invocation related methods by @mvdbeek in #20863
• [25.0] Use populated_optimized when serializing collection by @mvdbeek in #20872
• [25.0] Disable Run Tool button when there are errors by @ahmedhamidawan in #20839
• [25.0] Improve dataset collection fetch performance in the invocation view by @ahmedhamidawan in #20870
• [24.2] Fix role.description bug by @jdavcs in #20883
• [25.0] Add HiC datatype by @abretaud in #20874
• [25.0] Bump up integration test k8s version by @mvdbeek in #20889
• [25.0] Speed up ImplicitCollectionJobs.job_list by @mvdbeek in #20887
• [25.0] Make check for existing user in custos_authnz.py case insensitive by @cat-bro in #20893
• [25.0] Add LDDA purged property by @mvdbeek in #20895
• [25.0] Fix DOCX detection and add PPTX support by @arash77 in #20827
• [25.0] Avoid potential race condition in replacement_for_connection by @mvdbeek in #20909
• [25.0] Fix sessionless tag creation by @mvdbeek in #20925
• [25.0] Fix collection element sorting in extended_metadata by @mvdbeek in #20928

Full Changelog: v25.0.2...v25.0.3

v25.0.2

What's Changed

• [25.0] Use venv instead of virtualenv in package make setup-venv by @natefoo in #20536
• [24.2] Move definition of DatasetCollectionDescriptionT before its use by @nsoranzo in #20539
• [24.2] Fix docs versioning by @nsoranzo in #20542
• [25.0] Prevent DCE collections from being renamed by @ahmedhamidawan in #20534
• [25.0] Remove num_unique_values tiff metadata element by @mvdbeek in #20464
• [25.0] Fix restricting user defined tool input datasets extensions by @mvdbeek in #20545
• [25.0] Fix PDF preview functionality in dataset view by @dannon in #20552
• [25.0] Fix activity bar reordering persistence by @dannon in #20550
• [25.0] Fix workflow invocation report pdf generate by @itisAliRH in #20558
• [25.0] Fix description and metadata of some packages by @nsoranzo in #20546
• [25.0] Fix Storage Dashboard Link to Dataset Details by @itisAliRH in #20565
• [24.2] Upgrade requests-unixsocket for requests compatibility by @natefoo in #20566
• [25.0] Don't assume cwd = job directory when running prepare dirs by @natefoo in #20571
• [25.0] Add redis conditional dependency by @davelopez in #20502
• [24.2] Fix apply rules ownership check by @mvdbeek in #20582
• [25.0] Don't fail volume mount construction for tools without tool directory by @mvdbeek in #20593
• [25.0] Prevent importing workflows with invalid step UUID by @davelopez in #20596
• [24.1] Do not set attribute on a namedtuple by @jdavcs in #20599
• [25.0] Fix workflow loading error handling by @davelopez in #20597
• [25.0] Constraint conditional redis version to allow only minor updates by @davelopez in #20603
• [25.0] Bump up python for for pulsar package tests by @mvdbeek in #20521
• [25.0] Clarify how to separate job and workflow scheduling by @mvdbeek in #20625
• [25.0] fix Admin job limit query by @martenson in #20626
• [24.2] Require user for visualizations create endpoint by @mvdbeek in #20629
• [25.0] Add mzMLb and MBI datatypes by @chambm in #20632
• [25.0] Fix HistoryDatasetAsTable by @mvdbeek in #20636
• [25.0] Fix bug: tool output file may be overwritten by Runner's multi work t… by @jianzuoyi in #20639
• [25.0] Fix IntersectionObserver updates when replacing items by @davelopez in #20646
• [24.2] Correct visualization response schema by @guerler in #20627
• [25.0] Avoid postgres truncation of aliases and labels by @mvdbeek in #20649
• [25.0] Fix optional unspecified input to conditional step by @mvdbeek in #20647
• [24.2] Fix empty default Optionals for tool_shed_repositories API. by @jmchilton in #20656
• [25.0] Ignore webob http exceptions for logging purposes by @mvdbeek in #20630
• [25.0] Pairtool updated format and sniffers by @Smeds in #20634
• [25.0] Add num_unique_values tiff metadata element, fixed by @kostrykin in #20669
• [25.0] Bump up pulsar dependency to 0.15.9 by @mvdbeek in #20672
• [24.2] Fix invocation header by @qchiujunhao in #20676
• Merge 24.2 into 25.0 by @ahmedhamidawan in #20681
• [25.0] Add support for M4A audio files by @arash77 in #20667
• [25.0] add fasta.bz2 as auto_compressed type by @bernt-matthias in #20496
• [25.0] Fix Invenio file downloads for published records with draft by @davelopez in #20685
• [25.0] Input linter: add missing attribute to sort_by by @bernt-matthias in #20693
• [24.2] Update Gravity to 1.0.8 by @natefoo in #20523
• [25.0] Fix dataset serializers and response models by @arash77 in #20694
• [25.0] Add datatype for LexicMap index by @Smeds in #20586
• [25.0] Propagate cached job output replacement to copies of outputs by @mvdbeek in #20553
• [25.0] Add username filter to published pages grid by @ahmedhamidawan in #20703
• [25.0] Fix scratchbook display by @dannon in #20684
• [25.0] Prevent negative offset in historyStore handleTotalCountChange by @davelopez in #20708
• [24.2] Fix planemo serve, need user list by @mvdbeek in #20575
• [25.0] Fix click to edit link by @mvdbeek in #20710
• [24.2] Fix test_base_image_for_targets mulled test to use mzmine by @nsoranzo in #20713
• [25.0] Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650
• [25.0] Improve workflow monitor loop times by @mvdbeek in #20522
• [25.0] Fix parameter models for optional color params. by @jmchilton in #20705
• [25.0] Remove content from packages/meta/requirements.txt by @nsoranzo in #20662
• [25.0] DatasetView Header - fixes text wrapping issues on small screens by @dannon in #20721
• [25.0] Fix maximum workflow invocation duration test by @mvdbeek in #20729
• [25.0] Update galaxy-release-util by @mvdbeek in #20727
• [25.0] Remove base_dir from zip in make_fast_zipfile by @davelopez in #20739
• [25.0] fix config for nginx in docs by @martenson in #20757

New Contributors

• @jianzuoyi made their first contribution in #20639
• @Smeds made their first contribution in #20634
• @qchiujunhao made their first contribution in #20676

Full Changelog: v25.0.1...v25.0.2

v25.0.1

What's Changed

• [24.0] Fix single data element identifier to be a regular string by @mvdbeek in #20438
• [25.0] Fix link in user release notes by @bgruening in #20518
• [24.2] Relax validation of XML test assertion parsing by @mvdbeek in #20511
• [25.0] Fixes for static handling and the web_client package by @natefoo in #20516
• [24.2] Add id-token: write for npm publishing by @mvdbeek in #20519
• [25.0] Bump gravity dependency to 1.1.0 by @mvdbeek in #20520
• [25.0] Fix import of galaxy.tool_util.cwl module by @nsoranzo in #20529
• [25.0] Update the dev package build and install script by @natefoo in #20526
• [25.0] Pin isa-rwval 0.10.11, drop conditional import handling by @natefoo in #20527
• [25.0] Fix galaxy-config script, move install to galaxy-dependencies in app package by @natefoo in #20531
• [24.2] Do not expose user info to non authenticated users by @bernt-matthias in #20524
• [25.0] names of package extras cannot contain underscores by @mr-c in #20525
• [25.0] Bump Gravity to 1.1.1 by @natefoo in #20533

Full Changelog: v25.0.0...v25.0.1

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 https://github.com/galaxyproject/galaxy/...

v24.2.4

What's Changed

• [24.1] Backport parts of #19659 by @bernt-matthias in #19805
• [24.2] Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819
• [24.2] Backport #19810: Fix workflow param tests not updating param type. by @mvdbeek in #19820
• [24.2] Bump up max_peek_size to 50MB by @mvdbeek in #19823
• [24.2] Remove unused client route for standalone wizard interface by @dannon in #19836
• [24.2] Try to recover from recurring activation link error by @jdavcs in #19844
• [24.2] Add spacing between workflow author and invocation count by @ahmedhamidawan in #19849
• [24.2] Point install_requires at requirements.txt file by @mvdbeek in #19864
• [24.2] Handle directories with percents directories with export_remote.xml. by @jmchilton in #19865
• [24.2] Don't collect unnamed outputs twice in extended metadata mode by @mvdbeek in #19868
• [24.0] Check if index exists before creating by @jdavcs in #19873
• [24.2] Publish pre-built client with (point-)release by @mvdbeek in #19879
• [24.2] Lazy-load invocation step jobs as needed by @mvdbeek in #19877
• [24.2] Fix drag and drop for dataset collection elements by @ahmedhamidawan in #19866
• [24.2] Fix various job concurrency limit issues by @mvdbeek in #19824
• [24.2] Fix tabular metadata setting on pulsar with remote metadata by @mvdbeek in #19891
• [24.2] Decode/encode FormDirectory paths to allow spaces (and other characters) by @ahmedhamidawan in #19841
• [24.2] Fix collection builder input states by @mvdbeek in #19797
• [24.0] Drop unused alembic-utils from galaxy-data package requirements by @nsoranzo in #19896
• [24.2] Fix default ordering of items sorted by name by @jdavcs in #19853
• [24.2] Do not reorder options in FormSelect component when multiselect disabled by @jdavcs in #19837
• [24.2] Fix duplicate extensions for data inputs by @ahmedhamidawan in #19903
• [24.2] Skip implicit HDA conversions in DataToolParameter options by @davelopez in #19911
• [24.2] Skip data_meta filter in run form by @mvdbeek in #19895
• [24.2] Let pysam use extra threads available in job by @mvdbeek in #19917
• [24.2] Fix duplicate entries when using drag and drop in multiple mode by @davelopez in #19913
• [24.2] Report TestCaseValidation as linter error for 24.2 and above by @bernt-matthias in #19928
• [24.1] Handle special charater in raw SQL by @jdavcs in #19925
• [24.1] Fix Invenio file source downloads not working with some Invenio instances by @davelopez in #19930
• [24.2] Better interactive tool entry point query by @mvdbeek in #19942
• [24.2] Drop unnecessary job cache job subquery by @mvdbeek in #19945
• [24.2] Use make_fast_zipfile directly by @mvdbeek in #19947
• [24.2] Fix attempt restriction on multiple connections by @mvdbeek in #19948
• [24.2] Sort intersected options by @mvdbeek in #19953
• [23.1] Do not print OIDC access tokens to the logs by @kysrpex in #19966
• [24.2] Renew OIDC access tokens using valid refresh tokens by @kysrpex in #19967
• [24.2] Fix bug in psa-authnz redirect handling by @dannon in #19968
• [24.2] Add missing job state history entry for queued state by @mvdbeek in #19977
• [24.2] Restrict job cache to terminal jobs (and other fixes) by @mvdbeek in #19978
• [24.2] Fix dynamic filter option access when building command line by @mvdbeek in #19982
• [24.2] Do not display default labels obscuring selectable options in a vue-multiselect component by @jdavcs in #19981
• [24.2] ChatGXY Error Handling by @dannon in #19987
• [24.2] Always set copy_elements to true by @mvdbeek in #19985
• [24.2] Update selectable object stores after adding or editing them by @davelopez in #19992
• [24.2] Fix various parameter validation issues. by @jmchilton in #19949
• [24.2] Ensure job states are fetched in invocation view by @ahmedhamidawan in #20010
• [24.2] Fix edit permission for datasets delete button in storage dashboard overview by location by @itisAliRH in #20066
• [24.2] Job cache backports by @mvdbeek in #20078
• [24.2] Skip param_value filter if ref value is runtime value by @mvdbeek in #20144
• [24.2] Fix edam selenium test by @mvdbeek in #20134
• [24.2] Fix DataCollectionParameterModel factory by @mvdbeek in #20164
• [24.2] Update dev package version in meta package by @natefoo in #20159
• [23.1] Renew access tokens from PSA using valid refresh tokens by @kysrpex in #20040
• [24.0] Fix invocation failure dataset reference by @mvdbeek in #20200
• [24.2] Fix #19515 - invalid citation handling changed with 24.2. by @jmchilton in #19716
• [24.2] Conditionally import from galaxy.config in galaxy.model.mapping if TYPE_CHECKING by @natefoo in #20209
• [24.0] Fall back to name in job summary if no input label given by @mvdbeek in #20258
• [24.1] Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by @natefoo in #20239
• [24.2] Fix WF Run RO-Crate logo width in Firefox by @davelopez in #20305
• [24.2] Fix searching roles in admin UI by @jdavcs in #20394
• [24.2] Fix unit tests returning values by @nsoranzo in #20413
• [24.2] Fix mull_targets() with mamba 2.x by @nsoranzo in #20416
• [24.2] Skip validation of expression.json input in workflow parameter validator by @mvdbeek in #20412
• [24.2] Fix mulled-search --destination quay, add index reuse by @natefoo in #20107
• [24.2] Prevent running datatype autodetect on purged datasets by @mvdbeek in #20479
• [24.2] Fix legacy get_metadata_file controller route by @mvdbeek in #20477
• [24.2] Make response header values strings by @mvdbeek in #20475
• [24.2] Link workflow invocation outputs upon importing invocation by @mvdbeek in #20485
• [24.2] Make optional edam-ontology in datatypes registry optional by @natefoo in #20492

Full Changelog: v24.2.3...v24.2.4

v24.2.3

What's Changed

• [24.2] Fix masthead webhook click/nav. by @dannon in #19764
• [24.2] Fix anndata metadata setting for data with integer indexes by @mvdbeek in #19774
• [24.2] Add rDock prm datatype by @nsoranzo in #19783
• [24.2] Fix private role name performance issue by @jdavcs in #19679
• [24.2] Fix parameter model constructions with leading underscores, fixes converter linting by @mvdbeek in #19790
• [24.2] Fix tool directory pulsar transfer by @mvdbeek in #19799
• [24.2] Use materialized datasets in pulsar job runner by @mvdbeek in #19807

Full Changelog: v24.2.2...v24.2.3

v24.2.2

What's Changed

• [24.2] Backport #19620 by @nsoranzo in #19725
• [24.2] Allow tool state changes in refactor actions by @mvdbeek in #19730
• [24.2] Update fs.dropboxfs conditional dependency version to 1.0.3 by @davelopez in #19741
• [24.2] Fix conditional dependency path resolution by @mvdbeek in #19723
• [24.2] Skip slow tests for manage_db, db_dev scripts by @jdavcs in #19744
• [24.2] Fix dataypes linter: allow auto for output tags by @bernt-matthias in #19757
• [24.2] Fix RDM token access for user-defined file sources by @davelopez in #19768
• [24.2] Move Workflow Editor save button by @davelopez in #19761
• [24.2] Follow-up to #19651: Do not reassign: method modifies object in-place by @jdavcs in #19746
• [24.2] Assertion linter fixes by @jmchilton in #19715
• [24.2] add missing linter name argument to linter report function calls by @bernt-matthias in #19707
• [24.2] Fix recording transform action name. by @jmchilton in #19672
• [24.2] Make k8s user and group ids overriddable per job by @nuwang in #19568
• [24.2] Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

Full Changelog: v24.2.1...v24.2.2