github galaxyproject/galaxy v26.0.2
on GitHub

latest release: v26.1.2
pre-release3 hours ago

What's Changed

🔧 Enhancements

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

🐛 Bug Fixes

  • [26.0] Drop console scripts from packages' setup.cfg files by @nsoranzo in #22832
  • [26.0] Move classifiers and keywords from setup.cfg to pyproject.toml by @jdavcs in #22834
  • [26.0] Fix tag creation self-deadlock under SQLite by @mvdbeek in #22846
  • [26.0] Prevent crash on pgcleanup script when attempting to delete files in user-defined object stores by @davelopez in #22833
  • [26.0] Stop workflow editor leaking UI metadata into Apply Rules tool_state by @jmchilton in #22823
  • [26.0] Pin galaxy-tool-util-models to current minor version in dependents by @jdavcs in #22877
  • [26.0] Use default_panel_view in docs by @jdavcs in #22892
  • [25.1] Allow workflows with optional credentials to run without credentials set by @arash77 in #22858
  • [26.0] Require gravity 1.2.2 by @jdavcs in #23050
  • [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
  • [26.0] Fix ToolPanelElements._section_by_tool being class-level shared state by @mvdbeek in #23062
  • [26.0] Use requests rather than urllib for Invenio authenticated downloads by @martenson in #23096
  • [26.0] Fix typo in irods object store cache size by @davelopez in #23124
  • [26.0] Fix clean jwd task by @davelopez in #23121
  • [26.0] Fix WES workflow completion and add missing WES docs by @jmchilton in #22857
  • [26.0] Handle sample_sheet and paired_or_unpaired collections in output_to_cwl_json by @mvdbeek in #23152
  • [26.0] Fix fasta preview rendering for sequences larger than 100 KB by @mvdbeek in #23163
  • [26.0] Fix AssertionError remapping malformed galaxy markdown blocks by @mvdbeek in #23176
  • [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
  • [26.0] Fix invalid LN:0 field in @SQ header lines in 1.bam test file by @nsoranzo in #23474
  • [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
  • [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
  • [26.0] Complete subworkflows before their parent invocation by @mvdbeek in #23581
  • [26.0] Fade in the workflow run settings panel instead of scaling it by @mvdbeek in #23612
  • [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
  • [26.0] Fix link to DRS API by @jdavcs in #23643
  • [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
  • [26.0] Record export result before marking short term download ready by @mvdbeek in #23660
  • [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
  • [25.1] Record export result before marking short term download ready by @mvdbeek in #23658
  • [26.0] Bug fix - Galaxy would delete composite files it shouldn't during data_fetch.py sometimes. by @jmchilton in #23733
  • [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
  • [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
  • [26.0] Cap social-auth-core below 6 by @jmchilton in #23940
  • [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
  • [26.0] Fix flaky test_history_export_tracking selenium test by @mvdbeek in #24029
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [26.0] 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
  • [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

🧰 Refactoring

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Full Changelog: v26.0.1...v26.0.2

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