v26.1.2

What's Changed

🚀 New Features

• [26.1] Add interactivetool tensorboard by @IvoLeist in #23577

🔧 Enhancements

• [26.1] Name DRS-fetched datasets from DRS metadata instead of the URI basename by @dannon in #23275
• [26.1] add title for job metric cgroups v1 memory.oom_control.oom_kill by @cat-bro in #23383
• [26.1] Expand user-defined tool runtime and authoring docs by @mvdbeek in #23392
• [26.1] Backport RMSX datatype registration and viewer 0.0.4 to Galaxy 26.1 by @Finn2400 in #23531
• [26.1] Default missing workflow comment colors by @jmchilton in #23482
• [26.1] Add embedded authoring reference for user-defined tools by @mvdbeek in #23365
• [26.1] Add regression test for history export with extra files but no primary file by @davelopez in #23872
• [26.1] Add Montreal Forced Aligner datatypes by @IvoLeist in #23893
• [26.1] Update TensorBoard tool XML to use biocontainers and improve help texts by @IvoLeist in #23929
• [26.1] Add datatypes sniffer: alto/page/abbyy XML and hOCR (HTML) by @IvoLeist in #23916
• [26.1] Share dir_mtime cache directory listings per process by @mvdbeek in #24017
• [25.1] Pull Docker Hub images through mirror.gcr.io in integration tests by @mvdbeek in #24039
• [26.1] Test first startup from installed Galaxy packages by @mvdbeek in #23259
• [26.1] Share one watchdog observer across all file watchers by @mvdbeek in #24110
• [26.1] add embl.gz as auto compress embl by @bernt-matthias in #24403

🐛 Bug Fixes

• [26.1] Move jsonschema to tool-util test requirements by @nsoranzo in #23256
• [26.1] Allow prebuilt clients for .dev versions by @mvdbeek in #23263
• [26.1] Carry the landing-request destination through OIDC login by @dannon in #23274
• [26.1] Fix bulk storage move for user-defined storage by @davelopez in #23288
• [26.1] Fix doubled proxy prefix on forced object route push by @guerler in #23282
• [26.1] Do not render the rerun workflow button for unowned history by @ahmedhamidawan in #23290
• [26.1] Make PairedOrUnpairedListCollectionCreator reactive to history items changing by @ahmedhamidawan in #23269
• [26.1] Fix WorkflowGraph exposed methods being called without defined ref by @ahmedhamidawan in #23291
• [26.1] Fix workflow SVG image generation crashing on inactive conditional inputs by @ahmedhamidawan in #23293
• [26.1] Fix WorkflowAnnotation flex distribution by @ahmedhamidawan in #23311
• [26.1] Restore tool submission error alert by @jmchilton in #23319
• [25.1] Create /etc/cni/net.d before minikube's none driver chmods it [25.1] by @mvdbeek in #23355
• [26.1] Fix report/page editor loses changes when previewing by @ahmedhamidawan in #23286
• [26.1] Set metadata externally in GCP Batch runner finish_job by @ksuderman in #23361
• [26.1] Fix visualization plugin URLs when Galaxy is served under a URL prefix by @ksuderman in #23357
• [26.1] Bound expression.json read failures in the workflow scheduler by @mvdbeek in #23354
• [26.1] Fixes for package installed Galaxy. by @jmchilton in #23360
• [26.1] Qualify GCP Batch network and subnet names with the project ID by @ksuderman in #23356
• [26.1] Fix workflow run-form option pagination by @mvdbeek in #23384
• [26.1] Preserve tool lint errors after parser failures by @mvdbeek in #23386
• [26.1] Gate user tool build endpoints by @mvdbeek in #23390
• [26.1] Fix null data manager config watcher by @mvdbeek in #23394
• [26.1] Add zlib1g-dev to k8s image build deps by @afgane in #23381
• [26.1] Fix failing Selenium tests on release_26.1 by @mvdbeek in #23406
• [26.1] Fix failing API tests on release_26.1 by @mvdbeek in #23405
• [26.1] Fix display bugs/usability of reports/pages by @ahmedhamidawan in #23310
• [26.1] Bump gravity pin to v1.2.4 to apply a gravity bug fix by @jdavcs in #23377
• [26.1] Fix workflow run-form dropdowns hiding and offering wrong datasets by @mvdbeek in #23407
• [26.1] Harden tool-provided dynamic output collection by @mvdbeek in #23404
• [26.1] Fix TestPublishedHistories Selenium failures by @mvdbeek in #23419
• [26.1] Validate BCO exports against vendored IEEE-2791 schemas by @mvdbeek in #23430
• [26.1] Fix flaky datatype selection in workflow editor selenium tests by @mvdbeek in #23435
• [26.1] Wait for upload rows to be submitted before closing the upload dialog by @mvdbeek in #23443
• [26.1] Skip OIDC token refresh for providers that are no longer configured by @mvdbeek in #23432
• [26.1] fix: filter webhooks by type and activation in Webhook.vue by @itisAliRH in #23452
• [26.1] Retry GETs answered with foreign HTML while bypassing the browser cache by @mvdbeek in #23434
• [25.1] Two Continuous Integration workflow fixes by @nsoranzo in #23461
• [26.0] Fix invalid LN:0 field in @SQ header lines in 1.bam test file by @nsoranzo in #23474
• [26.1] Don't set job state to OK before finish_job runs in the GCP Batch runner by @afgane in #23467
• [26.1] Document unique server names for multi-instance Gunicorn deployments by @mvdbeek in #23488
• [25.1] Fix base_image_for_targets() for newer conda search output by @nsoranzo in #23496
• [26.1] Prevent ScrollList from doing infinite fetches on error by @ahmedhamidawan in #23494
• [26.1] Fix truncated and empty S3 cache downloads by @mvdbeek in #23509
• [25.1] Add zlib1g-dev to k8s image build deps by @ksuderman in #23503
• [26.1] Make Workflow Preview and Tool Source modal content fill the modal height by @itisAliRH in #23518
• [26.1] Keep the center GalaxyAI view mounted across its own route changes by @mvdbeek in #23526
• [25.1] Use pydantic-aware serializer for celery control replies by @mvdbeek in #23525
• [26.1] Report datasets left shared when making a history private by @mvdbeek in #23527
• [25.1] Don't let extended metadata import set the live job's terminal state by @mvdbeek in #23529
• [26.1] Fix toolbox reload wait shadowed by application interface stub by @mvdbeek in #23535
• [26.1] Handle unknown upload methods gracefully by @davelopez in #23453
• [26.1] Restore root path support for FTP file sources by @davelopez in #23497
• [26.1] Deliver SSE control tasks to webapp processes only by @mvdbeek in #23539
• [26.1] Fix zero defaults for YAML numeric tool parameters by @mvdbeek in #23533
• [25.1] Backport mulled cache seeding to fix flaky integration tests by @mvdbeek in #23541
• [26.1] Harden user-defined tool output declarations by @mvdbeek in #23388
• [26.1] JobHandlerQueue in htcondor logged "Job dispatched" unconditionally by @bgruening in #23538
• [26.1] Reject generating parameter models for upload_dataset inputs by @guerler in #23283
• [26.1] Fix flaky test_workflow_output_handling by @mvdbeek in #23552
• [26.0] Raise InvalidFileFormatError on short rows in UCSC display by @guerler in #22524
• [26.0] Throws error if workflow step dict has no id by @guerler in #22593
• [24.0] Fix attr-defined mypy error in test_expression_basics.py by @nsoranzo in #23569
• [26.1] Expose stock tool versions through the Tool Shed TRS API by @jmchilton in #23565
• [26.1] Fix MCP endpoint routing and lifespan under a URL prefix by @mvdbeek in #23561
• [26.1] Fix Tool Shed searches repeating the last page by @mvdbeek in #23564
• [26.1] Fix collection output assertions in workflow tests by @jmchilton in #23554
• [26.0] Complete subworkflows before their parent invocation by @mvdbeek in #23581
• [26.1] Report unresolvable job markdown labels instead of 500ing by @jmchilton in #23608
• [26.0] Fade in the workflow run settings panel instead of scaling it by @mvdbeek in #23612
• [26.1] Fix dangling discriminator mapping in standalone tool state JSON schemas by @mvdbeek in #23614
• [25.1] Fix doubled URL prefix on the workflow preview Run button by @ksuderman in #23617
• [26.0] Fix 500 on the dataset tool-markdown report endpoint by @jmchilton in #23599
• [26.1] Return 404 when there is no most recently used history by @mvdbeek in #23632
• [26.1] Preserve numeric encoded history IDs in form submissions by @mvdbeek in #23641
• [26.0] Fix link to DRS API by @jdavcs in #23643
• [26.1] Report unparseable tool expression templates as author errors by @jmchilton in #23630
• [26.0] Allow children in any order in the tool XSD by @jmchilton in #23629
• [25.1] Serialize runtime values of unresolved conditionals in populate_state by @mvdbeek in #23649
• [26.1] Return 400 for non-integer dataset ids in /root/display_as by @mvdbeek in #23650
• [26.1] Wrap tooltips instead of overflowing out of width by @ahmedhamidawan in #23342
• [26.1] Return serializable data validation errors by @jmchilton in #23628
• [26.1] Fix flaky test_history_update_reaches_viewer_after_subscription by @mvdbeek in #23656
• [26.1] Do not render several history dropdown options for unowned history by @ahmedhamidawan in #23679
• [26.1] Fix unusable admin quota forms on large instances by @mvdbeek in #23673
• [26.0] Record export result before marking short term download ready by @mvdbeek in #23660
• [26.1] Fix workflow scheduler missing history updates committed mid-attempt by @mvdbeek in #23664
• [26.0] Fix wait_on callback in test_delete_job_with_message by @mvdbeek in #23687
• [25.1] Fix job deletion racing handler enqueue by @mvdbeek in #23686
• [26.1] Don't apply newline conversion to binary deferred datasets by @mvdbeek in #23693
• [25.1] Record export result before marking short term download ready by @mvdbeek in #23658
• [26.1] Don't duplicate MetadataFile rows when re-importing edited metadata by @mvdbeek in #23714
• [26.1] Fix user-defined tool references in workflow steps by @mvdbeek in #23694
• [26.1] Cache concrete user object stores between method calls by @mvdbeek in #23722
• [26.1] Fix disk-usage integration test race after purge by @mvdbeek in #23719
• [26.1] Resolve param_value filters against siblings in inactive conditional cases by @jmchilton in #23734
• [26.0] Bug fix - Galaxy would delete composite files it shouldn't during data_fetch.py sometimes. by @jmchilton in #23733
• [26.1] Handle history item fetch errors before rendering content by @mvdbeek in #23746
• [26.1] Fix TRS import and library permission selenium test races by @mvdbeek in #23753
• [26.1] Keep each user's newest session in galaxy-delete-sessions by @mvdbeek in #23752
• [26.1] Fix history initialization failure handling and retries by @mvdbeek in #23739
• [26.1] Handle failed history item deletions by @mvdbeek in #23738
• [25.1] Fix tool recommendations for anonymous Galaxy sessions by @mvdbeek in #23745
• [26.1] Handle rejected upload submissions started from the upload view by @mvdbeek in #23765
• [26.1] Fix upload modal crash when removing an already uploaded row by @mvdbeek in #23764
• [26.1] Fix remote files ctime crash and eLabFTW listing and sorting by @mvdbeek in #23770
• [26.1] Handle denied history permissions requests by @mvdbeek in #23744
• [26.1] Apply fix from 23744 to the other permissions component. by @jmchilton in #23788
• [26.1] Distinguish ppm, pgm and pbm image types when sniffing by @bernt-matthias in #23759
• [26.1] Throw more specific exceptions in workflow extraction by @jmchilton in #23651
• [26.1] Fix published history list card indicator and title-click by @ahmedhamidawan in #23675
• [26.1] Compare published histories against the grid's own query in selenium tests by @mvdbeek in #23795
• [26.1] Fix deferred materialization fd double close and wait for gx-it-proxy in tests by @mvdbeek in #23793
• [26.1] Pair list:paired builder elements that arrive in separate history updates by @mvdbeek in #23775
• [26.1] Serve deferred materialization test data from the mock HTTP server by @mvdbeek in #23794
• [26.1] Store connected inputs as ConnectedValue on workflow import by @jmchilton in #23785
• [26.1] Synchronize tool cache hash initialization by @mvdbeek in #23740
• [26.1] End SSE streams when a gunicorn worker starts draining by @mvdbeek in #23798
• [26.1] Handle superseded workflow form edits by @mvdbeek in #23741
• [26.1] fix naming of deferred datasets by @bgruening in #23810
• [26.1] Keep config file links inside the job working directory by @mvdbeek in #23826
• [26.1] Add redirect for an old shed URL pattern. by @jmchilton in #19937
• [26.1] Exclude private user-defined tools from the public dynamic tools index by @mvdbeek in #23823
• [26.1] Handle startup request failures and allow user loading to recover by @mvdbeek in #23743
• [26.1] Fix built-in converter registration during toolbox reload by @mvdbeek in #23797
• [26.1] Render client markup through a v-sanitize-html directive by @dannon in #23791
• [26.1] Fix OIDC PKCE login by carrying the code verifier in a cookie by @bgruening in #23836
• [26.1] Skip anaconda and WorkflowHub tests when those sites are unavailable by @mvdbeek in #23842
• [26.1] Stop filling user-defined tool output labels as Cheetah templates by @mvdbeek in #23803
• [26.1] Validate stored user-defined tools before loading them by @mvdbeek in #23841
• [26.1] Restrict from_work_dir paths of user-defined tools and shell-quote the copy command by @mvdbeek in #23840
• [26.1] Save only edited fields from the history details editor by @mvdbeek in #23837
• [26.1] Handle frontend request failures that escaped as unhandled rejections by @mvdbeek in #23844
• [25.1] Return 400 for request bodies that webob cannot parse by @rmz-oz in #23839
• [26.1] Fix export include options switches not updating the wizards by @davelopez in #23849
• [26.1] Match empty collections in the job cache by @mvdbeek in #23863
• [26.1] Fix client crashes reported to Sentry by @mvdbeek in #23867
• [26.1] Disable RST file insertion in tool help and bound the help cache by @mvdbeek in #23825
• [26.1] Rank exact and prefix matches first in datatype selectors by @davelopez in #23871
• [25.1] Fix 500 on reading pages with non-ASCII slugs by @mvdbeek in #23854
• [25.1] Keep numeric changeset hashes as strings when installing shed repositories by @mvdbeek in #23875
• [26.1] Apply max_discovered_files to collection operation tools that multiply inputs by @mvdbeek in #23859
• [26.1] Include non-rST help in Tool.to_dict(tool_help=True) by @jmchilton in #23853
• [26.1] Fix collection type_source for inputs in conditionals and _ names by @jmchilton in #23890
• [26.1] Fix MP3 fallback misclassifying UTF-16 uploads by @mvdbeek in #23899
• [26.1] Validate workflow parameter inputs and support scalar batches by @mvdbeek in #23887
• [26.0] Quit selenium driver in test teardown to stop leaking chromedriver processes by @mvdbeek in #23901
• [25.1] Skip Rucio object store tests when the Rucio container cannot start by @mvdbeek in #23905
• [26.1] Show history and workflow card owner actions once the current user loads by @itisAliRH in #23909
• [26.1] Fix Safari workflow connection drags by @mvdbeek in #23928
• [26.0] Cap social-auth-core below 6 by @jmchilton in #23940
• [26.1] Fix Tool Shed repository update swapping short and long descriptions by @jmchilton in #23936
• [26.1] Show most recently updated jobs first in admin jobs list by @zepedroc in #23934
• [26.1] Open external links from the GTN webhook iframe in a new tab by @itisAliRH in #23949
• [26.1] Fix GTN webhook tool links with formatted tool names by @itisAliRH in #23950
• [26.1] Make GTN webhook tool and workflow buttons keyboard accessible by @itisAliRH in #23952
• [26.1] Improve tool shed username validation. by @jmchilton in #23955
• [25.1] Don't resolve DNS in HTTP file source and URI validation unit tests by @mvdbeek in #23982
• [25.1] Fix CI failures and flaky tests by @mvdbeek in #24028
• [26.1] Ignore data table entries for already registered values when merging tables by @mvdbeek in #24003
• [26.1] Load datatypes only for datatype help terms and share in-flight requests by @jmchilton in #23995
• [25.1] Respect allow_uri_if_protocol for single deferred data inputs by @davelopez in #24001
• [25.1] Run the ftp file source tests against a local ftp server by @mvdbeek in #24044
• [26.1] Backport chat proxy fixes from #24032 to release_26.1 by @guerler in #24047
• [26.0] Fix flaky test_history_export_tracking selenium test by @mvdbeek in #24029
• [26.1] Resolve implicitly converted inputs in the YAML tool runtime by @davelopez in #24004
• [26.1] Fix empty "My workflows" list when workflows load before the user by @itisAliRH in #24066
• [25.1] Cap pulsar-galaxy-lib below 0.16 for galaxy-app package by @mvdbeek in #24056
• [26.1] Improved Rendering of Tool Shed READMEs by @jmchilton in #24053
• [26.1] Percent-encode unsafe characters in HTTP file source URLs by @itisAliRH in #24071
• [25.1] Bind OIDC account confirmation to the authenticated browser flow by @mvdbeek in #24084
• [26.1] Collapse duplicate tool versions in tool panel search results by @itisAliRH in #23155
• [26.1] Don't inherit preferred visualizations from sibling datatypes by @mvdbeek in #24097
• [26.1] Show the failure reason first in data fetch URL errors by @itisAliRH in #24070
• [25.1] Fix flaky test_timeout_kills_worker_under_waiting_wrapper by @mvdbeek in #24109
• [26.1] Cancel tool test jobs that exceed the test timeout by @mvdbeek in #24092
• [26.0] Fix export-on-complete wizard ignoring the user-entered file name by @ksuderman in #24128
• [26.0] Derive OIDC username from email when IdP sends no username claim by @jdavcs in #24129
• [26.1] Show the error when selecting a folder fails in FilesDialog by @arash77 in #24149
• [26.1] Fix select all in the admin jobs list by @itisAliRH in #24183
• [26.1] Jittered backoff for client API retries; skip hidden workflow counts by @jmchilton in #24141
• [26.1] Fix 500 when invoking a workflow with a nonexistent dataset input by @jmchilton in #24171
• [26.1] Reject unknown workflow scheduler IDs instead of queueing invocations that never run by @jmchilton in #24169
• [25.1] Fix tool shed model cache directory creation race by @mvdbeek in #24191
• [26.1] Stop all installed Galaxy processes in the installed startup check cleanup by @mvdbeek in #24195
• [26.1] Don't read files or evaluate Python from untrusted tools in the Tool Shed by @mvdbeek in #24239
• [25.1] Replace the Singularity Hub test container with a native SIF from ghcr.io by @mvdbeek in #24232
• [25.1] Validate preferred object store ids on tool runs and workflow invocations by @mvdbeek in #24214
• [26.1] Bump gxformat2 to 0.28.0 (keep format2 parameter validators) by @mvdbeek in #24215
• [25.1] Fix Tool Shed FastAPI app for fastapi 0.146.0 by @mvdbeek in #24246
• [25.1] Fix dataset permissions set when upload and discovery jobs finish by @mvdbeek in #24233
• [25.1] Drop fiona requirement from shapefile_composite test tool by @mvdbeek in #24253
• [25.1] Poll for workflow handler assignment in db-skip-locked tests by @mvdbeek in #24254
• [26.0] Fix supports_returning() probe always returning False by @mvdbeek in #24252
• [25.1] Don't let resubmitted jobs block each other on concurrency limits by @davelopez in #24257
• [25.1] Restore batch info for collections mapped over a collection input by @jmchilton in #24223
• [26.1] Fix serving and downloading of directory-backed datasets (Zarr, OME-Zarr, Directory subclasses) by @mvdbeek in #23953
• [25.1] Ignore stale user and history object store preferences by @davelopez in #24280
• [26.1] Fix workflow import KeyError on missing __job_resource selector by @ksuderman in #24272
• [26.1] Return users to their destination after login, add allowed_login_redirect_hosts by @mvdbeek in #24111
• [25.1] Fix ok_to_edit_metadata checking HDA job associations for LDDAs by @mvdbeek in #24306
• [26.0] Fix workflow editor map-over onto :paired_or_unpaired inputs the server rejects by @jmchilton in #24227
• [25.1] Better API Handling for Custom Builds by @jmchilton in #24310
• [26.0] Bug fix - missing unit tests needed for dataset details. by @jmchilton in #24297
• [25.1] Don't overwrite inputs when skipping database operations on nested collections by @mvdbeek in #24286
• [25.1] Improve Dataverse file source search by @davelopez in #24324
• [26.1] Order +galaxyN tool versions numerically in toolbox lineages by @mvdbeek in #24320
• [25.0] Update certifi for eMudhra intermediate cert compromise by @natefoo in #24343
• [25.1] Fix uploading files to Dataverse by @davelopez in #24327
• [26.0] Return 400 when a custom build's dataset can't be converted to len by @jmchilton in #24313
• [25.1] Apply default permissions to discovered collection elements by @mvdbeek in #24284
• [26.0] Show workflow integer/float input bounds on the run form by @jmchilton in #24212
• [25.1] Run FTP user file source Selenium test against a local server by @mvdbeek in #24360
• [25.1] Pin CI runners to ubuntu-24.04 by @mvdbeek in #24382
• [26.0] Prevent selecting the root of RDM repositories as a directory by @davelopez in #24358
• [26.0] Fix CI on ubuntu-26.04 runners by @mvdbeek in #24390
• [26.1] Bump markdown-it to 14.3.3 by @mvdbeek in #24392
• [26.1] Run main tool tests outside the tmpfs /tmp by @mvdbeek in #24387
• [26.0] Check an access token's issuer before looking up its signing key by @dannon in #24340
• [25.1] Lock HDCAs with FOR NO KEY UPDATE when touching update_time by @mvdbeek in #24404
• [25.1] Match tool shed GUIDs when looking up job resource parameters by @monsterlag in #24355
• [26.1] Fix 500 on PUT of a workflow that embeds a subworkflow by @richard-burhans in #24413
• [25.1] Skip Quay search tests on runtime API outages by @mvdbeek in #24432
• [25.1] Import unregistered dataset extensions from model stores as data by @mvdbeek in #24433
• [25.1] Fix numeric column stats in tabular raw_data requests by @davelopez in #24359
• [26.1] Keep workflow parameter input validators as declared by @mvdbeek in #24282
• [26.1] Don't fail HTCondor jobs removed while the user is deleting or stopping them by @mvdbeek in #24431

🧰 Refactoring

• [26.1] Stop caching the Galaxy virtualenv in CI by @mvdbeek in #23754
• [26.0] Remove GHCR container build job by @mvdbeek in #24040

New Contributors

• @rmz-oz made their first contribution in #23839
• @zepedroc made their first contribution in #23934
• @monsterlag made their first contribution in #24355

Full Changelog: v26.1.1...v26.1.2