galaxyproject/galaxy v25.1.3 on GitHub

What's Changed

🔧 Enhancements

[25.1] Pull Docker Hub images through mirror.gcr.io in integration tests by @mvdbeek in #24039

🐛 Bug Fixes

[25.1] Fix dataset collection tag duplication when copying a history by @mvdbeek in #21984
[25.1] Fix preferred_object_store_id not respected for discovered outputs with extended metadata by @mvdbeek in #22056
[25.0] Fix legacy_expose_api error callable returning str instead of bytes by @mvdbeek in #22106
[25.1] Fix make all histories private controller None id bug by @ahmedhamidawan in #22174
[25.1] Do not queue paused jobs by @martenson in #22156
[25.1] Use /api/tool_data endpoints in DataTables.vue & DataManagerTable.vue by @mvdbeek in #22229
[25.1] Restore file doesn't match sniffed datatype message by @mvdbeek in #21988
[25.1] Fix refresh time in object store caches by @bgruening in #22279
[25.1] Sequence datatypes: only read first character per line for setting metadata by @bernt-matthias in #22276
[25.1] Fix flaky job search for HDCA inputs on PostgreSQL by @mvdbeek in #22290
[25.1] Discard rest of line in chunks in iter_start_of_line by @mvdbeek in #22332
[25.1] Fix timestamp parsing in job import/export by @mvdbeek in #22372
[25.1] Use correct timezone to compare step scheduling by @mvdbeek in #22446
[25.1] Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by @mvdbeek in #22778
[25.1] Sniff spatialdata archives whose directory does not end in .zarr by @nilchia in #22802
[25.1] Allow workflows with optional credentials to run without credentials set by @arash77 in #22858
[25.0] Fix NameError, move assignation of days prior to get_failed_jobs call by @ccoulombe in #23053
[25.0] Pin Ansible version by @ksuderman in #23057
[25.1] Fix broken calls to InteractiveToolManager methods by @nsoranzo in #23216
[25.1] Create /etc/cni/net.d before minikube's none driver chmods it [25.1] by @mvdbeek in #23355
[25.1] Two Continuous Integration workflow fixes by @nsoranzo in #23461
[25.1] Fix base_image_for_targets() for newer conda search output by @nsoranzo in #23496
[25.1] Add zlib1g-dev to k8s image build deps by @ksuderman in #23503
[25.1] Use pydantic-aware serializer for celery control replies by @mvdbeek in #23525
[25.1] Don't let extended metadata import set the live job's terminal state by @mvdbeek in #23529
[25.1] Backport mulled cache seeding to fix flaky integration tests by @mvdbeek in #23541
[24.0] Fix attr-defined mypy error in test_expression_basics.py by @nsoranzo in #23569
[25.1] Fix doubled URL prefix on the workflow preview Run button by @ksuderman in #23617
[25.1] Serialize runtime values of unresolved conditionals in populate_state by @mvdbeek in #23649
[25.1] Fix job deletion racing handler enqueue by @mvdbeek in #23686
[25.1] Record export result before marking short term download ready by @mvdbeek in #23658
[25.1] Fix tool recommendations for anonymous Galaxy sessions by @mvdbeek in #23745
[25.1] Return 400 for request bodies that webob cannot parse by @rmz-oz in #23839
[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
[25.1] Skip Rucio object store tests when the Rucio container cannot start by @mvdbeek in #23905
[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
[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
[25.1] Cap pulsar-galaxy-lib below 0.16 for galaxy-app package by @mvdbeek in #24056
[25.1] Bind OIDC account confirmation to the authenticated browser flow by @mvdbeek in #24084
[25.1] Fix flaky test_timeout_kills_worker_under_waiting_wrapper by @mvdbeek in #24109
[25.1] Fix tool shed model cache directory creation race by @mvdbeek in #24191
[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
[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
[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
[25.1] Ignore stale user and history object store preferences by @davelopez in #24280
[25.1] Fix ok_to_edit_metadata checking HDA job associations for LDDAs by @mvdbeek in #24306
[25.1] Better API Handling for Custom Builds by @jmchilton in #24310
[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
[25.0] Update certifi for eMudhra intermediate cert compromise by @natefoo in #24343
[25.1] Fix uploading files to Dataverse by @davelopez in #24327
[25.1] Apply default permissions to discovered collection elements by @mvdbeek in #24284
[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
[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
[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

New Contributors

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

Full Changelog: v25.1.2...v25.1.3