galaxy - v25.0.2

What's Changed

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

New Contributors

• @jianzuoyi made their first contribution in https://github.com/galaxyproject/galaxy/pull/20639
• @Smeds made their first contribution in https://github.com/galaxyproject/galaxy/pull/20634
• @qchiujunhao made their first contribution in https://github.com/galaxyproject/galaxy/pull/20676

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v25.0.1...v25.0.2

- Python
Published by bernt-matthias 10 months ago

galaxy - v25.0.1

What's Changed

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

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v25.0.0...v25.0.1

- Python
Published by natefoo 12 months ago

galaxy - v25.0.0

What's Changed

• Stabilize HistoryView.test.js by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19165
• Fix Pesky warning with PersistentTaskProgressMonitorAlert.test.ts by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19180
• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19181
• Cleanup Jest Test Output (part 2) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19178
• Dynamic options: add data table filter by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/12941
• Cleanup Jest Test Output (part 3) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19185
• Don't calculate dataset hash for datasets in non-OK state by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19191
• Fix UP031 errors - Part 1 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19194
• Cleanup Jest Test Output (part 4) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19186
• Extend image metadata by @kostrykin in https://github.com/galaxyproject/galaxy/pull/18951
• Move phylocanvas to script entry point by @guerler in https://github.com/galaxyproject/galaxy/pull/19193
• Move heatmap visualization to new script endpoint by @guerler in https://github.com/galaxyproject/galaxy/pull/19176
• Fix UP031 errors - Part 2 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19204
• Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot in https://github.com/galaxyproject/galaxy/pull/19189
• Workflow Editor Activity Bar by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18729
• Add plotly.js by @guerler in https://github.com/galaxyproject/galaxy/pull/19206
• Switch h5web to script endpoint by @guerler in https://github.com/galaxyproject/galaxy/pull/19211
• Update visualizations to latest charts package by @guerler in https://github.com/galaxyproject/galaxy/pull/19213
• Fix UP031 errors - Part 3 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19218
• Cleanup test output console for tool panel tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19210
• Update Vizarr package version to 0.1.6 by @davelopez in https://github.com/galaxyproject/galaxy/pull/19228
• Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot in https://github.com/galaxyproject/galaxy/pull/19233
• Fix UP031 errors - Part 4 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19235
• Explicitly add cwl-utils to dependencies by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19257
• Merge 24.2 into dev by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19240
• Refactor for better reuse of workflow parameter type constants by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19260
• [PROCEDURES] Drop thumbs up reaction as pull request approval method by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19202
• Fix UP031 errors - Part 5 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19282
• Merge 24.2 into dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19273
• Merge latest 24.2 into dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19290
• Minor drag style adjustment for activities by @guerler in https://github.com/galaxyproject/galaxy/pull/19299
• Fix UP031 errors - Part 6 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19314
• Update pydantic to 2.10.3 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19326
• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19331
• Extract and typescript-ify datatype selection in wfeditor. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19304
• Refactor and add tests for Popovers by @guerler in https://github.com/galaxyproject/galaxy/pull/19337
• Misc fixes 202412 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19341
• Use popper wrapper for help text popover by @guerler in https://github.com/galaxyproject/galaxy/pull/19340
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19190
• Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19358
• Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot in https://github.com/galaxyproject/galaxy/pull/19369
• Type annotation fixes for mypy 1.14.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19372
• Node 22 unreachable fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19378
• Make conditional discriminators literals instead of generic string/bool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19374
• Remove apptainer-version pin by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19380
• SQLAlchemy 2.0 follow-up by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19388
• Use id entity attribute when setting exampleOfWork property by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19396
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19366
• Display email activation help only if user activation is enabled by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19402
• Prevent negative offset by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19409
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19418
• Set safe default extraction filter for tar archives by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19406
• Let file sources choose a path for uploaded files by @kysrpex in https://github.com/galaxyproject/galaxy/pull/19154
• Enable cloning subworkflows by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19420
• Merge Release 24.2 into dev by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19443
• Add Vitessce Viewer by @guerler in https://github.com/galaxyproject/galaxy/pull/19227
• Type annotations improvements by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19442
• Alternative format_source fix by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19395
• Update main citation to 2024 community paper by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19453
• Reset invocation export wizard after completion by @davelopez in https://github.com/galaxyproject/galaxy/pull/19449
• Remove transaction helper by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19407
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19464
• Document $__user_name__ by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19433
• Improve asynchronous tasks error handling and reporting by @davelopez in https://github.com/galaxyproject/galaxy/pull/19448
• Workflow Editor Auto Zoom by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19451
• Better handling of public pages and workflows authored by deleted users by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19394
• Avoid using custos refresh tokens which are expired by @martenson in https://github.com/galaxyproject/galaxy/pull/19411
• Handles S3 listing errors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19446
• Add test that verifies workflow source_metadata is preserved on landing claim by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19454
• eLabFTW integration via Galaxy file source by @kysrpex in https://github.com/galaxyproject/galaxy/pull/19319
• Add Dataverse RDM repository integration by @KaiOnGitHub in https://github.com/galaxyproject/galaxy/pull/19367
• Type annotation improvements by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19485
• Fix wrong id in testcombinedmappingandsubcollection_mapping by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19481
• Fix preferred object store id reactivity by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19491
• Add author and tools details in RO-Crate by @Marie59 in https://github.com/galaxyproject/galaxy/pull/18820
• Add workflow selection and bulk actions by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19336
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19510
• Prevent users from reusing a banned email after account is purged by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19413
• Fix wrong URI written to ExportObjectResultMetadata when exporting histories to eLabFTW by @kysrpex in https://github.com/galaxyproject/galaxy/pull/19541
• Fix package versions by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19566
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19567
• Add IGB display support for CRAM files by @paige-kulzer in https://github.com/galaxyproject/galaxy/pull/19428
• Change galaxy system user uid for K8s image by @afgane in https://github.com/galaxyproject/galaxy/pull/19403
• Merge 24.2 into dev by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19590
• Hide outdated visualizations from visualizations activity panel by @guerler in https://github.com/galaxyproject/galaxy/pull/19353
• Add vue-tsc baseline comparison to client-lint workflow by @dannon in https://github.com/galaxyproject/galaxy/pull/19593
• Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/19594
• Add eLabFTW file source from file source templates by @kysrpex in https://github.com/galaxyproject/galaxy/pull/19493
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19623
• Fix test_mulled_build.py::test_mulled_build_files_cli with use_mamba=True by @kysrpex in https://github.com/galaxyproject/galaxy/pull/19545
• Use correct plugin_kind in user file sources by @davelopez in https://github.com/galaxyproject/galaxy/pull/19622
• Use discriminated unions in object stores and file source template configs by @davelopez in https://github.com/galaxyproject/galaxy/pull/19621
• Format code with black 25.1.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19625
• Update eLabFTW file source template docs by @kysrpex in https://github.com/galaxyproject/galaxy/pull/19632
• Add InvenioRDM file source template by @davelopez in https://github.com/galaxyproject/galaxy/pull/19619
• Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19620
• Mention default values for truevalue and falsevalue by @pvanheus in https://github.com/galaxyproject/galaxy/pull/19657
• Enhance ListHeader Component for Reusability by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19655
• Relax job status check in testdeleteusercancelall_jobs by @davelopez in https://github.com/galaxyproject/galaxy/pull/19661
• Fix more vue tsc indicated type issues by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19650
• Fix a vue-tsc issue - Login.vue. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19647
• Update testcreatedatasetinsubfolder to check for the dataset presence by @davelopez in https://github.com/galaxyproject/galaxy/pull/19660
• Add Breadcrumb Heading Component by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19656
• Remove unused(?) data_dialog form element type. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19669
• More Vue Typescript Fixes by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19663
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19682
• Workflow landing request - collapse activity bar by default. by @dannon in https://github.com/galaxyproject/galaxy/pull/19652
• Add webdavclient3 to conditional-requirements.txt by @bgruening in https://github.com/galaxyproject/galaxy/pull/19671
• Add forgotten linter test by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19690
• Type annotation improvements by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19642
• Add Zenodo file source template by @davelopez in https://github.com/galaxyproject/galaxy/pull/19638
• Drop support for Python 3.8 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19685
• Fix MarkdownDialog types by @davelopez in https://github.com/galaxyproject/galaxy/pull/19703
• Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19706
• Yet More Vue Typing Error Fixes by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19680
• Improved simplicity and isolation in transiently failing test. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19709
• Move RequiredAppT back into galaxy packages. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19704
• Update TypeScript version to 5.7.3 by @davelopez in https://github.com/galaxyproject/galaxy/pull/19713
• Remote File Sources and Storage Locations redesign by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19521
• Speedup mulled build test by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19712
• Expand workflow metadata for readme. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19591
• Move Markdown components to subdirectory for modularity by @guerler in https://github.com/galaxyproject/galaxy/pull/19719
• Move history watcher and minor fixes by @guerler in https://github.com/galaxyproject/galaxy/pull/19732
• Move vega wrapper to shared common directory and add error handler by @guerler in https://github.com/galaxyproject/galaxy/pull/19718
• Generate correct types for Dataset source transformations on backend. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19666
• Augments popper wrapper, add click and escape handler by @guerler in https://github.com/galaxyproject/galaxy/pull/19717
• Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19726
• ToolShed 2.1 - Various bugfixes and enhancements. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19722
• ToolShed2 - Add more context when navigating between tools an repositories. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19738
• Add linter argument to linter report function calls by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19708
• Refactor tool panel handling, resolve transiently failing jest test by @guerler in https://github.com/galaxyproject/galaxy/pull/19733
• Fix incorrect type in tool_util.deps and fix package structure. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19702
• Enhance breadcrumb navigation UX in small screen sizes by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19737
• Refactor dependencies for tool output actions. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19662
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19727
• Fix Tours and add tooltips to history items by @guerler in https://github.com/galaxyproject/galaxy/pull/19734
• Use fissix also when python3-lib2to3 is not installed by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19749
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19772
• Jest Cleanup (Part 5) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19743
• Preserve workflow labels in final invocation reports by @guerler in https://github.com/galaxyproject/galaxy/pull/19721
• Workflow Run Form Enhancements by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19294
• Update webdav user file source template help text by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/19784
• Revise consistently failing edam tool panel view test. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19762
• Fix wording of API doc string by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19776
• Add better WorkflowSummary type by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19779
• Rebuild API schema for latest dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19789
• Remove unused (define* - compiler macro) imports from TextEditor.vue by @dannon in https://github.com/galaxyproject/galaxy/pull/19793
• Bump @babel/runtime-corejs3 from 7.23.2 to 7.26.10 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/19788
• Bump axios from 1.7.4 to 1.8.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/19773
• Click to edit history name in HistoryPanel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19665
• Fix workflow run graph non input steps not appearing bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19781
• Rework some form components for reuse. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19347
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19816
• Fix Selenium workflow tests not updating param type properly. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19810
• Add cell-based markdown editor for pages by @guerler in https://github.com/galaxyproject/galaxy/pull/19769
• HelpText improvements (content, sizing) and WorkflowInvocationHeader tweaks. by @dannon in https://github.com/galaxyproject/galaxy/pull/19792
• Workflow Run Form Enhancements follow up by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19825
• Update RStudio IT by @afgane in https://github.com/galaxyproject/galaxy/pull/19711
• Syntactic sugar to ease TPV configuration. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19834
• Enable lazy loading for ace-builds by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19847
• Improve markdown editor modularity and structure by @guerler in https://github.com/galaxyproject/galaxy/pull/19835
• More user feedback in FormRulesEdit (for Apply Rules tool) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19827
• Webpack build performance improvements by @dannon in https://github.com/galaxyproject/galaxy/pull/19851
• Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19852
• Migrate from Prism to Monaco for ToolSource display. by @dannon in https://github.com/galaxyproject/galaxy/pull/19861
• Create rucio.cfg from inside Rucio objectstore by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/19863
• Fix most new vue typescript errors discovered in #19851 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19862
• Client circular dependency check by @dannon in https://github.com/galaxyproject/galaxy/pull/19858
• Add bigbed to bed converter and tests by @d-callan in https://github.com/galaxyproject/galaxy/pull/19787
• Fix broken optimisation introduced in #19852 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19871
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19874
• Fix workflow license component typing by @guerler in https://github.com/galaxyproject/galaxy/pull/19878
• Move some store types out into own file to reduce circular dependencies. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19860
• Cleanup circular dependencies around utils.ts. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19857
• Add visualization framework interface to cell-based markdown editor by @guerler in https://github.com/galaxyproject/galaxy/pull/19775
• Merge 24.2 into dev by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19890
• Fix various mypy issues around mapped attributes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19883
• Make job cache generally available by @dannon in https://github.com/galaxyproject/galaxy/pull/19798
• Use direct icon references in FormSelectMany.vue. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19829
• Various styling improvements to Workflow Run and Invocation views by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19905
• Populate image metadata without allocating memory for the entire image content by @kostrykin in https://github.com/galaxyproject/galaxy/pull/19830
• Use FA Component (w/svg) instead of span+font in RunWorkflow header by @dannon in https://github.com/galaxyproject/galaxy/pull/19901
• Fix Galaxy ignoring job objectstoreid for quota check by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19854
• Clarify is_active method usage for Python Social Auth in Galaxy by @dannon in https://github.com/galaxyproject/galaxy/pull/19899
• FITS Graph Viewer - script name tweak. by @dannon in https://github.com/galaxyproject/galaxy/pull/19902
• Allow embedding vitessce visualizations by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19909
• Allow to send notifications when Admins cancel jobs by @davelopez in https://github.com/galaxyproject/galaxy/pull/19547
• Show workflow help (and readme?) in run form by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19736
• Replace backend-based page creation controller endpoint by @guerler in https://github.com/galaxyproject/galaxy/pull/19914
• Enhance OpenAI Chat Integration by @uwwint in https://github.com/galaxyproject/galaxy/pull/19612
• Remove unnecessary code duplications by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19921
• Change wording in the google drive user file source template by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/19927
• Migrate Page editing controller endpoint to API by @guerler in https://github.com/galaxyproject/galaxy/pull/19923
• Fix import and update_page type signature by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19932
• Merge 24.2 into dev by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19933
• Add basic support for icons in tools by @davelopez in https://github.com/galaxyproject/galaxy/pull/19850
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19929
• Fix test_in_directory on osx by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19943
• Fix local import in __resolvers_dict by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19944
• Decrease sentry_sdk.errors log level to INFO by @natefoo in https://github.com/galaxyproject/galaxy/pull/19951
• Fix adding tags popup closing logic on focus out by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19950
• Allow PathLike parameters in make_fast_zipfile() by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19955
• Add link to view history on dataset info page by @natefoo in https://github.com/galaxyproject/galaxy/pull/19956
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19964
• Add type hints around collection copying and job things by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19961
• Remove circular dependency around user store. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19859
• First steps of bootstrap replacement by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19946
• Move FormBoolean back to FormElement field in workflow run form by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19938
• Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. by @jaidevjoshi83 in https://github.com/galaxyproject/galaxy/pull/19689
• Overhaul workflow runtime settings display. by @dannon in https://github.com/galaxyproject/galaxy/pull/19906
• Adds a trimInputs prop to FormGeneric to trim string values on submit. by @dannon in https://github.com/galaxyproject/galaxy/pull/19971
• Remove hgvsift from toolconf.xml.sample by @natefoo in https://github.com/galaxyproject/galaxy/pull/19972
• RStudio IT updates to work on .org by @afgane in https://github.com/galaxyproject/galaxy/pull/19924
• Add share button for invocations by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19959
• Fix ownership check in history contents update route by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19969
• Introduce reusable GCard component for unified card layout by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19785
• Improve type annotation of tool parameter wrapping by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19991
• Unwind more client dependencies at top of stack. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19983
• Job cache allow different names when possible by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19962
• Button replacement batch 1 by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19963
• Allow resizing Visualizations in Markdown editor by @guerler in https://github.com/galaxyproject/galaxy/pull/19958
• Adds validation and alerts for Markdown elements by @guerler in https://github.com/galaxyproject/galaxy/pull/19952
• Removes outdated Markdown visualization insertion wizard by @guerler in https://github.com/galaxyproject/galaxy/pull/19898
• Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20008
• Define simple models for job messages. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19688
• Add missing tool test file by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19763
• Update vitessce version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20016
• Merge Inputs/Parameters and Outputs/Collections Tabs by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20019
• Fix keyedCache never allowing multiple fetches by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20020
• Use lower case extension for setting datatype in data discovery by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19954
• Remove tags used by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19576
• Improvements to package decomposition. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19759
• Selenium test cases for running workflow from form upload. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19997
• Add env var to skip CircularDependencyPlugin in development mode by @dannon in https://github.com/galaxyproject/galaxy/pull/20038
• Allow different AI providers (as long as they are openai compatible) by @uwwint in https://github.com/galaxyproject/galaxy/pull/19989
• Add help text popovers for workflow runtime settings by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20031
• Add vitesscejson datatype by @guerler in https://github.com/galaxyproject/galaxy/pull/20027
• Add kepler.gl visualization by @guerler in https://github.com/galaxyproject/galaxy/pull/20005
• Add VTK Visualization Toolkit Plugin by @guerler in https://github.com/galaxyproject/galaxy/pull/20028
• Add Niivue viewer by @guerler in https://github.com/galaxyproject/galaxy/pull/19995
• Add new line to vtpascii test file by @guerler in https://github.com/galaxyproject/galaxy/pull/20051
• Pass host url to visualizations by @guerler in https://github.com/galaxyproject/galaxy/pull/20022
• Fix copying job output from discovered outputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19999
• Update breadcrumb item 'to' type for better routing support by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/20065
• GCard Full Description by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/20064
• Add support for Markdown help text in visualizations by @guerler in https://github.com/galaxyproject/galaxy/pull/20043
• Also chown R lib in RStudio BioC tool by @natefoo in https://github.com/galaxyproject/galaxy/pull/20025
• Migrate WF Collection Input Form Definition to Client Side by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19313
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19998
• Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/20086
• Bump h11 from 0.14.0 to 0.16.0 in /lib/galaxy/dependencies by @dependabot in https://github.com/galaxyproject/galaxy/pull/20088
• Fix test_workflow_run export selenium by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20089
• Enhance Storage Dashboard Selected Item UI by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/20070
• Add sample datasets for visualizations by @guerler in https://github.com/galaxyproject/galaxy/pull/20046
• Upgrade bundled/requested node version to 22.15.0 by @dannon in https://github.com/galaxyproject/galaxy/pull/18710
• Set node version to 22.13.0 by @davelopez in https://github.com/galaxyproject/galaxy/pull/20095
• Gulp build improvements, update. by @dannon in https://github.com/galaxyproject/galaxy/pull/19405
• Use visualization dropdown solely for examples by @guerler in https://github.com/galaxyproject/galaxy/pull/20094
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/20096
• Add flac audio format by @bgruening in https://github.com/galaxyproject/galaxy/pull/20057
• Add markdown datatype by @bgruening in https://github.com/galaxyproject/galaxy/pull/20056
• Remove collapse invocations panel on mouseleave feature by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20074
• Add DOI to workflow metadata by @jdavcs in https://github.com/galaxyproject/galaxy/pull/20033
• Flexible mapping from collection parameter types to collection builder components. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20082
• Add activity panel width to local storage by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20072
• Improve type annotation of galaxy.util submodules by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20104
• Route to creating a new file source in remote file browser modal by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20084
• Drop old galaxy_session records by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19872
• Adds Example Datasets and Help Text for Visualizations by @guerler in https://github.com/galaxyproject/galaxy/pull/20097
• Button replacement batch 2 by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19990
• Add Molstar by @guerler in https://github.com/galaxyproject/galaxy/pull/20101
• Always render Outputs tab in invocation view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20073
• Move README to center panel in workflow editor by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20029
• Show workflow README in split view next to the form inputs by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20026
• Add hid to selection field in visualization creation form by @guerler in https://github.com/galaxyproject/galaxy/pull/20108
• Run integration tests on latest Ubuntu by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20118
• Add alignment.js for multiple sequence alignment rendering by @guerler in https://github.com/galaxyproject/galaxy/pull/20110
• Add role creation form by @guerler in https://github.com/galaxyproject/galaxy/pull/20119
• Wait for Gbutton to become enabled by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20131
• Drop now unused controller method by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20129
• Add logo, description and help for aequatus by @guerler in https://github.com/galaxyproject/galaxy/pull/20128
• Sort visualization datasets by hid by @guerler in https://github.com/galaxyproject/galaxy/pull/20123
• Migrate Transition Systems Visualization by @guerler in https://github.com/galaxyproject/galaxy/pull/20125
• Fix and migrate Drawrna by @guerler in https://github.com/galaxyproject/galaxy/pull/20102
• Add updated PCA plot by @guerler in https://github.com/galaxyproject/galaxy/pull/20140
• Browse multiple trees in phylocanvas by @guerler in https://github.com/galaxyproject/galaxy/pull/20141
• Allow deferred and ok state datasets for vis by @guerler in https://github.com/galaxyproject/galaxy/pull/20143
• Add specific datatypes for Cytoscape and Kepler.gl by @guerler in https://github.com/galaxyproject/galaxy/pull/20117
• Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20150
• Client refactorings ahead of #19377. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20059
• Implement dataset collection support in workflow landing requests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20004
• Create working dir output outside of tool evaluator by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20153
• Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20152
• Yaml parser fixes part2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20162
• Show job ids on job success by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20145
• Yaml parser fixes and improvements (part 1) by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20158
• Remove only the Docker images specific for the test by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20109
• Fixes for GButtons with disabled state by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20121
• Revise transiently failing data source test. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20157
• Hide non-functional and replaced visualizations (e.g. Nora, MSA) by @guerler in https://github.com/galaxyproject/galaxy/pull/20077
• Add rd datatype by @richard-burhans in https://github.com/galaxyproject/galaxy/pull/20060
• Restore Visualization insertion options in Reports Editor by @guerler in https://github.com/galaxyproject/galaxy/pull/20000
• Log controller exceptions by @natefoo in https://github.com/galaxyproject/galaxy/pull/19974
• Improve docs for output filters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19904
• Add Tapis auth support by @dannon in https://github.com/galaxyproject/galaxy/pull/19887
• Rename tool "Citations" to "References" by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19770
• Fix setting env and tags on resubmission by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19753
• Implement tool markdown reports. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19054
• Strip galaxy filename annotation on upload by @GomeChas in https://github.com/galaxyproject/galaxy/pull/18561
• Improved rule builder display for non-nested lists (most of them). by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20156
• Support setting and displaying timezone with the core metrics plugin by @natefoo in https://github.com/galaxyproject/galaxy/pull/19527
• Fix remaining vue-tsc errors by @dannon in https://github.com/galaxyproject/galaxy/pull/20163
• GLink implementation by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/20063
• Add mandatory RO-Crate metadata when exporting by @elichad in https://github.com/galaxyproject/galaxy/pull/19846
• Use backports.zoneinfo in job_metrics package under Python <3.9 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20178
• Add client package by @natefoo in https://github.com/galaxyproject/galaxy/pull/20171
• Rucio templates by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/19720
• Avoid persisting credentials on checkout step of the Github actions by @arash77 in https://github.com/galaxyproject/galaxy/pull/19089
• Fix formatting in webapp and client/install.py by @dannon in https://github.com/galaxyproject/galaxy/pull/20185
• Allow overriding datatypes for planemo lint by @selten in https://github.com/galaxyproject/galaxy/pull/19780
• Fix tapis module typing errors by @jdavcs in https://github.com/galaxyproject/galaxy/pull/20175
• Run the tool working dir backup/restore on Pulsar by @natefoo in https://github.com/galaxyproject/galaxy/pull/16696
• Clarify that extra_scopes is sometimes non-optional by @martenson in https://github.com/galaxyproject/galaxy/pull/19385
• Add config options for tool dependency installs by @afgane in https://github.com/galaxyproject/galaxy/pull/19565
• Documentation around highlighting PRs for release notes. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19390
• Irods objectstore templates by @pauldg in https://github.com/galaxyproject/galaxy/pull/19415
• Add rerun option for workflows by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20032
• Show pre-populated landing data values in workflow run form by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19935
• Add docx datatype by @bgruening in https://github.com/galaxyproject/galaxy/pull/20055
• Allow controlling strict channel priority in mulled-build by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19425
• xsd: use CollectionType for collections in tests by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19802
• Isolate singularity containers more thoroughly for better reproducibility. by @rhpvorderman in https://github.com/galaxyproject/galaxy/pull/18628
• Add a script to reorganize tool data based on the new layout for genomic Data Managers by @natefoo in https://github.com/galaxyproject/galaxy/pull/19728
• Add more metadata, esp infer_from to datatypes configuration by @bgruening in https://github.com/galaxyproject/galaxy/pull/20142
• Update tabular_csv.py to use less memory in tsv->csv conversion by @cat-bro in https://github.com/galaxyproject/galaxy/pull/20187
• Add ZIP explorer to import individual files from local or remote ZIP archives by @davelopez in https://github.com/galaxyproject/galaxy/pull/20054
• Implement file source to integrate Galaxy with RSpace by @kysrpex in https://github.com/galaxyproject/galaxy/pull/20167
• Bump vega from 5.30.0 to 5.32.0 in /client by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20188
• Standalone Galaxy API Client Package by @dannon in https://github.com/galaxyproject/galaxy/pull/20181
• Drop old job metrics by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19936
• G modal implementation by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/20168
• Add JupyterLite by @guerler in https://github.com/galaxyproject/galaxy/pull/20174
• Add visualization test data by @nilchia in https://github.com/galaxyproject/galaxy/pull/20183
• Corrects header levels in Visualization Help Markdown by @guerler in https://github.com/galaxyproject/galaxy/pull/20199
• Bump default milestone to 25.1 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20189
• Add plotly 6.0.1 to JupyterLite by @guerler in https://github.com/galaxyproject/galaxy/pull/20201
• Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19377
• Add User-Defined Tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19434
• Fix unit test import by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20203
• Move UnprivilegedToolResponse into api by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20207
• Package fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20208
• Fix linting with markdown in tool help by @bgruening in https://github.com/galaxyproject/galaxy/pull/20058
• Enable visualizations for anonymous user by @guerler in https://github.com/galaxyproject/galaxy/pull/20210
• Add three AAI providers by @martenson in https://github.com/galaxyproject/galaxy/pull/20165
• IT Activity Panel by @dannon in https://github.com/galaxyproject/galaxy/pull/19996
• Add Katex Equation rendering plugin to Markdown Editor by @guerler in https://github.com/galaxyproject/galaxy/pull/19988
• Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20194
• Make preferences drop down available in single user deployments by @ksuderman in https://github.com/galaxyproject/galaxy/pull/19888
• Add replacement_dataset option to collection filter tools by @simonbray in https://github.com/galaxyproject/galaxy/pull/20166
• Migrate ChiraViz by @guerler in https://github.com/galaxyproject/galaxy/pull/20214
• Fix next milestone by @martenson in https://github.com/galaxyproject/galaxy/pull/20219
• Fix NFDI auth by @bgruening in https://github.com/galaxyproject/galaxy/pull/20217
• Bump axios from 1.7.4 to 1.8.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/20205
• Have make dist in the web_client package build the client by @natefoo in https://github.com/galaxyproject/galaxy/pull/20195
• Add history sharing and accessibility management view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19786
• Enhance external login interface styling by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20100
• Display invocation inputs and outputs in workflow report by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20222
• Bug fixes around wizard usage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20224
• Visualization-First Display functionality by @dannon in https://github.com/galaxyproject/galaxy/pull/20190
• Dataset View Component by @dannon in https://github.com/galaxyproject/galaxy/pull/20154
• Use TUS streaming and remove redundant IndexDB temp store in Zip Explorer by @davelopez in https://github.com/galaxyproject/galaxy/pull/20226
• Support setting masthead height in a theme by @ksuderman in https://github.com/galaxyproject/galaxy/pull/19581
• Bug fix - allow file drops into PasteData widget. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20232
• Fix vue-tsc issue in ParameterStep by @dannon in https://github.com/galaxyproject/galaxy/pull/20245
• Only show custom tool editor in activity bar settings when user has access by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20247
• [25.0] Group Tool Versions in IT Panel by @dannon in https://github.com/galaxyproject/galaxy/pull/20244
• Fix job rerun for dynamic tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20259
• Fix tool-provided metadata for CONVERTERtarto_directory by @mr-c in https://github.com/galaxyproject/galaxy/pull/20260
• Add 25.0 migration tags by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20265
• [25.0] Update version to 25.0.rc1 by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20267
• [25.0] Fix inconsistent header sizes by @guerler in https://github.com/galaxyproject/galaxy/pull/20277
• [25.0] Improve handling of very large files in Tabulator by @guerler in https://github.com/galaxyproject/galaxy/pull/20271
• [25.0] Add more descriptions to custom tool source schema by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20266
• [25.0] Fix theme selector by @guerler in https://github.com/galaxyproject/galaxy/pull/20275
• [25.0] Add non-dev httpx dependency by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20281
• [25.0] Remove duplicated job id in job success view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20289
• [25.0] Skip multiple pasted URLs when checking for remote Zip by @davelopez in https://github.com/galaxyproject/galaxy/pull/20300
• [25.0] Fix masthead logo height by @guerler in https://github.com/galaxyproject/galaxy/pull/20302
• [25.0] Touch up Dataset View by @guerler in https://github.com/galaxyproject/galaxy/pull/20290
• [25.0] Fix display urls by @dannon in https://github.com/galaxyproject/galaxy/pull/20318
• [25.0] Remove type import side-effects by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/20321
• [25.0] Increase proxy API robustness by validating URL before use by @davelopez in https://github.com/galaxyproject/galaxy/pull/20311
• [25.0] Fix workflow bookmark filtering by @davelopez in https://github.com/galaxyproject/galaxy/pull/20325
• [25.0] Rerun workflows for the correct version/instance by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20313
• [25.0] Fix broken admin navigation option and add missing menu items by @dannon in https://github.com/galaxyproject/galaxy/pull/20333
• [25.0] Enable retrieving contents from extra file paths when request contains leading / by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20336
• [25.0] Error on duplicate labels by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/20335
• [25.0] Add test for workflow instance download fix by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20326
• [25.0] Bug fix - auto-pairing step not connected to collection builder in wizard. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20345
• [25.0] Small UI fixes for ag-grid based rule grid. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20358
• [25.0] Add basic validation to workflow creator attribute by @jdavcs in https://github.com/galaxyproject/galaxy/pull/20328
• [25.0] Log invalid vault paths by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20363
• [25.0] Remove redundant badge when creating collection from upload by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20367
• [25.0] Generate a tenant-unique UID for tapis. by @dannon in https://github.com/galaxyproject/galaxy/pull/20370
• [25.0] Fix radio button options in CopyModal by @davelopez in https://github.com/galaxyproject/galaxy/pull/20378
• [25.0] Use router to route to creating a new file source by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20374
• [25.0] Fix conda_link to use platform.machine() for architecture detection by @chrisagrams in https://github.com/galaxyproject/galaxy/pull/20381
• [25.0] Fix selection issue when adding tags to workflows in bulk by @davelopez in https://github.com/galaxyproject/galaxy/pull/20362
• [25.0] Fix create file source button, show only at root by @davelopez in https://github.com/galaxyproject/galaxy/pull/20385
• [25.0] Make invocation errors more compact by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20369
• [25.0] Fix interactive activity highlighting by @guerler in https://github.com/galaxyproject/galaxy/pull/20276
• [25.0] Force Monaco into a separate bundle by @dannon in https://github.com/galaxyproject/galaxy/pull/20396
• [25.0] Avoid displaying dataset tab view in window manager by @guerler in https://github.com/galaxyproject/galaxy/pull/20317
• [25.0] Fix toolshed-installed tool icons by @dannon in https://github.com/galaxyproject/galaxy/pull/20399
• [25.0] Fix form select input sorting by @davelopez in https://github.com/galaxyproject/galaxy/pull/20401
• [25.0] Bug fix: allow any collection type in FormCollectionType. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20403
• [25.0] Add job config variable for singularity --contain by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/20400
• [25.0] Fixes for the admin jobs interface by @martenson in https://github.com/galaxyproject/galaxy/pull/20405
• [25.0] Prevent waiting for history item state to be ok in uploader by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20397
• [25.0] Fix job rerun with tool version change by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20417
• [25.0] Fix $app attribute access in cheetah templates by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20414
• [25.0] Update pulsar-galaxy-lib to 0.15.8 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20419
• [25.0] Fix css alignment styling of login page by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20429
• [25.0] DatasetView and Card Polish by @dannon in https://github.com/galaxyproject/galaxy/pull/20342
• [25.0] Fix workflow logo URL not being persisted. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20428
• [25.0] Fix minor IT panel/display issues by @dannon in https://github.com/galaxyproject/galaxy/pull/20404
• [25.0] Upgrade tensorflow conditional dependency version to 2.15.1 by @cat-bro in https://github.com/galaxyproject/galaxy/pull/20434
• [25.0] Deprecate enable_tool_document_cache by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/20433
• [25.0] Update triggers by @jdavcs in https://github.com/galaxyproject/galaxy/pull/20425
• [25.0] Add user-facing explanation for legacy workflow run form usage by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20431
• [25.0] Improve performance of job cache query by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20319
• [25.0] Fix add button is enabled when empty tag list by @davelopez in https://github.com/galaxyproject/galaxy/pull/20443
• [25.0] Wrap Tool and Workflow run headers properly by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20440
• [25.0] Dataset Display and Preferred Viz fixes by @dannon in https://github.com/galaxyproject/galaxy/pull/20439
• [25.0] Set GALAXY_CONFIG_FILE env var if starting handler with -c by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20449
• [25.0] Fix pagination state in FilesDialog by @davelopez in https://github.com/galaxyproject/galaxy/pull/20452
• [25.0] Data Libraries - persist number of entries displayed in folders by @dannon in https://github.com/galaxyproject/galaxy/pull/20455
• [25.0] Fix copying of job metrics for cached jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20436
• [25.0] Fix multiple remote file upload to collection creator by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20456
• [25.0] Update tiffviewer to latest version supporting more formats by @davelopez in https://github.com/galaxyproject/galaxy/pull/20457
• [25.0] Fix inconsistent styling in List Collection Builder selector by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20442
• [25.0] Bug fix: pairedorunpaired also endswith paired. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20458
• [25.0] Fix bug with handling compressed file names while auto-pairing. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/20459
• [25.0] Add molstar as default viewer for some molecule formats by @bgruening in https://github.com/galaxyproject/galaxy/pull/20467
• [25.0] Add Aladin as standard FITS viewer by @bgruening in https://github.com/galaxyproject/galaxy/pull/20465
• [25.0] Fix dataset error button not using router by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20472
• [25.0] Add /api/datasets/{dataset_id}/extra_files/raw/{filename:path} by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20468
• [25.0] More fixes to FormData drag and drop and typing by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19900
• [25.0] Replace Bootstrap Popover with Popper wrapper by @guerler in https://github.com/galaxyproject/galaxy/pull/20246
• [25.0] Don't fit workflow if it doesn't have steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20480
• [25.0] Use DatasetAsImage component for DatasetView image display by @dannon in https://github.com/galaxyproject/galaxy/pull/20488
• [25.0] Recreate triggers by @jdavcs in https://github.com/galaxyproject/galaxy/pull/20491
• [25.0] Rename vitesscejson fileext to vitessce.json by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20473
• [25.0] Remove rename modal from List Collection Creator by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20487
• [25.0] Release notes by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/20386
• [25.0] Allow workflow description to show full text by @davelopez in https://github.com/galaxyproject/galaxy/pull/20500

New Contributors

• @KaiOnGitHub made their first contribution in https://github.com/galaxyproject/galaxy/pull/19367
• @Marie59 made their first contribution in https://github.com/galaxyproject/galaxy/pull/18820
• @paige-kulzer made their first contribution in https://github.com/galaxyproject/galaxy/pull/19428
• @d-callan made their first contribution in https://github.com/galaxyproject/galaxy/pull/19787
• @GomeChas made their first contribution in https://github.com/galaxyproject/galaxy/pull/18561
• @chrisagrams made their first contribution in https://github.com/galaxyproject/galaxy/pull/20381

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.2.4...v25.0.0

- Python
Published by ahmedhamidawan 12 months ago

galaxy - v24.2.4

What's Changed

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

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.2.3...v24.2.4

- Python
Published by natefoo 12 months ago

galaxy - v24.2.3

What's Changed

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

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.2.2...v24.2.3

- Python
Published by mvdbeek about 1 year ago

galaxy - v24.2.2

What's Changed

• [24.2] Backport #19620 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19725
• [24.2] Allow tool state changes in refactor actions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19730
• [24.2] Update fs.dropboxfs conditional dependency version to 1.0.3 by @davelopez in https://github.com/galaxyproject/galaxy/pull/19741
• [24.2] Fix conditional dependency path resolution by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19723
• [24.2] Skip slow tests for managedb, dbdev scripts by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19744
• [24.2] Fix dataypes linter: allow auto for output tags by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19757
• [24.2] Fix RDM token access for user-defined file sources by @davelopez in https://github.com/galaxyproject/galaxy/pull/19768
• [24.2] Move Workflow Editor save button by @davelopez in https://github.com/galaxyproject/galaxy/pull/19761
• [24.2] Follow-up to #19651: Do not reassign: method modifies object in-place by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19746
• [24.2] Assertion linter fixes by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19715
• [24.2] add missing linter name argument to linter report function calls by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19707
• [24.2] Fix recording transform action name. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19672
• [24.2] Make k8s user and group ids overriddable per job by @nuwang in https://github.com/galaxyproject/galaxy/pull/19568
• [24.2] Add bwamem2index directory datatype, framework enhancements for testing directories by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19694

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.2.1...v24.2.2

- Python
Published by mvdbeek about 1 year ago

galaxy - v24.2.1

What's Changed

• [24.2] Updated registration warning message by @dannon in https://github.com/galaxyproject/galaxy/pull/19598
• [24.2] Fix missing name in user-defined object store list by @davelopez in https://github.com/galaxyproject/galaxy/pull/19599
• [24.2] Add upgrade_codes.json to tool-util package by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19605
• [24.2] Remove redundant Create Collection ok button from collection creator by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19613
• [24.0] Fix user preferences secret (without vault) lost on save by @davelopez in https://github.com/galaxyproject/galaxy/pull/19610
• [24.2] Set content-type to text/plain if dataset not safe by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19563
• [24.2] Fix dangling workflow store references by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19618
• [24.2] Remove unused and broken methods by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19614
• [24.0] Fix mulled tests by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19626
• [24.2] Raise RequestParameterInvalidException on invalid input_format parameter by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19631
• [24.2] Disable chatgxy wizard for anon users by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19628
• [24.2] Fail request explicitly when sqlite provider used on non-sqlite file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19630
• [24.2] Add fastkktabtar datatype required for fastk tool by @SaimMomin12 in https://github.com/galaxyproject/galaxy/pull/19615
• [24.2] Raise MessageException when using data provider on incompatible data by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19639
• [24.2] Make tool ids readable in invocation metrics by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19634
• [24.2] Raise serializable exception on invalid workflow connection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19636
• [24.2] Remove unused/deprecated Cloud Authorization preference by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19643
• [24.1] Initialize dictionary used to set connection execution options by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19653
• [24.0] Apply exec options to connection by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19651
• [24.2] xsd: fix format by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19683
• [24.2] Fix various bugs around tool data table bundles by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19659
• [24.1] Pin mercurial to >=6.8.1 for Python 3.12 support by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19693
• [24.2] Backport of workflow landing sidebar toggle fix. by @dannon in https://github.com/galaxyproject/galaxy/pull/19698
• [24.2] Fix validation of required floats specified as empty strings in tool XML. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19701
• [24.0] Fix container building by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19714

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.2.0...v24.2.1

- Python
Published by bernt-matthias over 1 year ago

galaxy - v24.2.0

What's Changed

• Update version to 24.2.dev by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18185
• Change default milestone to target 24.2 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18186
• Update versions of GitHub actions by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18197
• Play nice with password managers by @martenson in https://github.com/galaxyproject/galaxy/pull/18206
• Drop "Send to cloud" tool and associated cloudauthz code by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18196
• Merge 24.0, 24.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18288
• new edits and now using a docker image with qiskit1.0 by @thepineapplepirate in https://github.com/galaxyproject/galaxy/pull/18225
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18226
• Fix loading error for built in tool sift by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18357
• Merge latest 24.1 into dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18360
• More data access tests, some refactoring and cleanup by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18312
• Update GPU JupyterLab tool by @anuprulez in https://github.com/galaxyproject/galaxy/pull/18220
• Merge 24.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18386
• [24.1] Fix Object store empty list alert by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18413
• Bump ws from 8.11.0 to 8.17.1 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18417
• Prepare for NumPy 2.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18422
• Add pod5 datatype by @TomHarrop in https://github.com/galaxyproject/galaxy/pull/18419
• [PROCEDURES] Minor adjustments to SECURITY.md to reflect that we call yearly releases LTS by @dannon in https://github.com/galaxyproject/galaxy/pull/18171
• Minor additions to release process by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18450
• Masthead Revision by @guerler in https://github.com/galaxyproject/galaxy/pull/17927
• Updates the About Page by @guerler in https://github.com/galaxyproject/galaxy/pull/18461
• Update plausible script name in mako templates by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/18458
• Move workflow preview to primary link for workflows card list -- easi… by @dannon in https://github.com/galaxyproject/galaxy/pull/18463
• Fix some deprecations by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18433
• Fixed Podman 5 issue in sample job config file by @sveinugu in https://github.com/galaxyproject/galaxy/pull/18439
• Fix Workflow Preview Selenium Test Error by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18483
• Workflow Card Buttons Refactors [GCC2024_COFEST] by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18465
• Stray small changes from structuredtoolstate branch. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18453
• Move Workflow List Files to New Location [GCC2024_COFEST] by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18466
• Update package dev versions by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18489
• Moves Libraries from Masthead to Activity Bar by @guerler in https://github.com/galaxyproject/galaxy/pull/18468
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18406
• Raise Message Exception when displaying binary data by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18503
• [PROCEDURES] remove davebx from committers list by @martenson in https://github.com/galaxyproject/galaxy/pull/18452
• Add missing version in the file sources and object store templates by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/18497
• Improve invocation export UI by @davelopez in https://github.com/galaxyproject/galaxy/pull/18512
• Fix "worklfow" typo here and there by @abretaud in https://github.com/galaxyproject/galaxy/pull/18523
• Update openapi-typescript dependency to version 6.7.6 by @davelopez in https://github.com/galaxyproject/galaxy/pull/18519
• Minor config documentation enhancements by @bgruening in https://github.com/galaxyproject/galaxy/pull/18499
• Mixed enhancements from CWL branch by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18539
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18505
• Adds an option to restore activity bar defaults by @guerler in https://github.com/galaxyproject/galaxy/pull/18469
• Fix some Toolshed 2.0 development paper-cuts by @davelopez in https://github.com/galaxyproject/galaxy/pull/18538
• Add errors fast api by @arash77 in https://github.com/galaxyproject/galaxy/pull/18093
• Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18524
• Fix MessageException handling in get_edit by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18529
• Fix bugs in tool shed tool API. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18558
• Improvements to Tool Test Parsing by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18560
• Improve datasets permissions API schema typing by @davelopez in https://github.com/galaxyproject/galaxy/pull/18563
• Add task expiration to persistent task monitor by @davelopez in https://github.com/galaxyproject/galaxy/pull/18551
• Drop unused datasets controller methods by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18568
• Group tool templating exceptions in sentry by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18570
• Add a new version of the production s3fs file source template with the writable configuration variable added by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/18575
• Consistent type imports, fixes and linting. by @dannon in https://github.com/galaxyproject/galaxy/pull/18589
• Tighten user notification API response types by @davelopez in https://github.com/galaxyproject/galaxy/pull/18599
• Move history multiview item actions to top by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18265
• Improve update user API payload schema by @davelopez in https://github.com/galaxyproject/galaxy/pull/18602
• More tool test typing. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18590
• Record container id and type in core job metrics by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18579
• Bump requirejs from 2.3.6 to 2.3.7 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18610
• Implement Declarative Testing for Workflow Behaviors by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18542
• [24.1] Fix collection type drag and drop validation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18623
• Improve update history payload schema by @davelopez in https://github.com/galaxyproject/galaxy/pull/18618
• Rev pinned gxformat2. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18624
• Fixes for errors reported by mypy 1.11.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18608
• Improve typing for archived histories API schema by @davelopez in https://github.com/galaxyproject/galaxy/pull/18586
• Remove unused functions in dataset managers by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18631
• Reduce unnecessary requests when browsing tool repositories in Admin Panel by @davelopez in https://github.com/galaxyproject/galaxy/pull/18632
• Refactor FolderTopBar to TypeScript by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18488
• Bug fix for invalid duplicate id in function test tools. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18644
• Handle output parsing when tool is not available for tool-centric API. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18643
• Enable verbatimModuleSyntax, fix jest usage by @dannon in https://github.com/galaxyproject/galaxy/pull/18595
• Improve types around User in schema and client by @davelopez in https://github.com/galaxyproject/galaxy/pull/18645
• Rip repository_registry out of tool shed 2.0 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18647
• Another shot at tool shed API fixes by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18646
• Better Typing for Tool Execution Plumbing by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18626
• Undo stack UI by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18548
• Restore interactive tools watcher by @guerler in https://github.com/galaxyproject/galaxy/pull/18581
• Parameter Model Improvements by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18641
• [PROCEDURES] Add Alireza to committers group by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18613
• Improve accept header API schema by @davelopez in https://github.com/galaxyproject/galaxy/pull/18668
• Another round of parameter model improvements. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18673
• De-couple XML from tool interface for test collections. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18676
• Allow connecting text param into data column parameter by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18674
• Update mercurial by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18686
• Restore repository update in the tool shed 2.0. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18655
• Update ExportToRemoteModal.vue to use TypeScript by @davelopez in https://github.com/galaxyproject/galaxy/pull/18706
• Upgrade openapi-typescript to 7.0.2 + swap to openapi-fetch by @davelopez in https://github.com/galaxyproject/galaxy/pull/18532
• Fix "Latest Updates" order in tool shed 2.0 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16894
• Replace types-pkg-resources with types-setuptools by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18708
• Fix tag processing in library upload by @davelopez in https://github.com/galaxyproject/galaxy/pull/18714
• Update ruff to 0.6.1 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18716
• Bump axios from 1.6.2 to 1.7.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18717
• Allow access to invocation via shared or published history by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18707
• Another round of parameter model enhancements and tool tests by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18678
• Dynamic Models for Tool Test Validation by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18679
• add data source doc to the list in index by @PlushZ in https://github.com/galaxyproject/galaxy/pull/18742
• Allow specifying multi-select workflow parameters by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18715
• Implement tool upgrade assistant. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18728
• Remove Build Dataset Pair option from history actions by @guerler in https://github.com/galaxyproject/galaxy/pull/18740
• Fix workflow invocation accessibility check by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18746
• Fix new flake8-bugbear B039 and mypy type-var errors by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18755
• Improvements to help terms & tool help. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18722
• Bump webpack from 5.89.0 to 5.94.0 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18768
• Remove defaults channel for conda usage by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18757
• Add onedata templates by @bwalkowi in https://github.com/galaxyproject/galaxy/pull/18457
• Support high-availability setups for the interactive tools proxy by @kysrpex in https://github.com/galaxyproject/galaxy/pull/18481
• Fix MSA viz, new dependency specification options. by @dannon in https://github.com/galaxyproject/galaxy/pull/18760
• Add BlobToolkit to the list of interactive tools by @Delphine-L in https://github.com/galaxyproject/galaxy/pull/18630
• Handle compressed content in dataset preview for all sequence classes by @PlushZ in https://github.com/galaxyproject/galaxy/pull/18776
• Refactor LibraryDatasetsManager and fix type annotation issue by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18773
• More typing, docs, and decomposition around tool execution by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18758
• Cache pip directory as part of setup-python action by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18789
• Migrate Visualizations API to FastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/18721
• Fix Masthead error when user not loaded yet by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18794
• Improvements for K8S deployment (especially ITs) by @almahmoud in https://github.com/galaxyproject/galaxy/pull/18514
• Update Visualization FastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/18792
• [24.1] Fix response if dataset requested by display application is deleted by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18803
• Parse stored config details to script-based visualizations by @guerler in https://github.com/galaxyproject/galaxy/pull/18651
• Update Mypy to 1.11.2 and fix new signature override errors by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18811
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18578
• Replace History Dataset Picker in Library Folder by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18518
• Modelling for Test Assertions by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18787
• Bump express from 4.19.2 to 4.21.0 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18808
• Fix transiently failing selenium tooltip issues by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18847
• Add wizard-like export view for workflow invocations by @davelopez in https://github.com/galaxyproject/galaxy/pull/18796
• Add docs on indexing for filter column by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18844
• Improvements to parameter models for test case inputs by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18743
• Fix merge conflict in advanced step workflow by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18852
• Format dev to fix linting. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18860
• Fix link to public-server mailing list by @bgruening in https://github.com/galaxyproject/galaxy/pull/18866
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18864
• Fix flaky test/integration_selenium/test_toolbox_filters.py::TestToolboxFiltersSeleniumIntegration::test_toolbox_filters by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18854
• Bump dompurify from 3.0.6 to 3.1.3 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18821
• Add unique constraints to the email and username fields in the galaxy_user table by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18493
• Backend handling of setting user-role, user-group, and group-role associations by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18777
• Fix migration data fixes tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18885
• Implement Pydantic model for workflow test format. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18884
• datacolumn params: offer same columns with and without useheader_names by @wm75 in https://github.com/galaxyproject/galaxy/pull/18879
• Refactor migration testing setup code by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18886
• Raise exception if CompressedFile used on incompatible file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18888
• Enable ignore-without-code mypy error code by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18898
• Improvements to Planemo test format based on feedback/discussions. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18889
• Update a localized word with a more appropriate one by @mpalmada in https://github.com/galaxyproject/galaxy/pull/18910
• Type annotations and fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18911
• Fixes and tests for data fetch models. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18834
• Workflow Landing Requests by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18807
• Allow using tracks and groups in visualization xml by @guerler in https://github.com/galaxyproject/galaxy/pull/18779
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18904
• Rename framework workflow test script for easier test collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18923
• Remove some unused dynamic drill down options. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18892
• Fix commas that shouldn't be in biotools_mappings.tsv by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18919
• Add filter null collection operation tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18928
• Remove outdated fimo wrapper and galaxy-sequence-utils dependency by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18937
• Add support for arbitrarily ordered image axes in image content assertions by @kostrykin in https://github.com/galaxyproject/galaxy/pull/18891
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18943
• Allow setting a few global defaults for file source plugin types. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18909
• Migrate Library Contents API to FastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/18838
• Libraries Modernisation: Directory Dataset Picker by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18638
• Allow users with 'canmodifyfolder' permission to delete items in libraries by @npinter in https://github.com/galaxyproject/galaxy/pull/18924
• Fix backend role sharing bug by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18942
• Install npm-package viz to the package prefix explicitly. by @dannon in https://github.com/galaxyproject/galaxy/pull/18950
• Fix WorkflowInvocationHeader import type and current user errors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18956
• Explicitly display dataset preview in pages and workflow reports by @guerler in https://github.com/galaxyproject/galaxy/pull/18968
• Allow CORS requests to /api/workflow_landings by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18963
• Fix extra files path type hint by @davelopez in https://github.com/galaxyproject/galaxy/pull/18958
• Add BioBlend tests by @arash77 in https://github.com/galaxyproject/galaxy/pull/18975
• Optimize tohistorydatasetassociation in createdatasetsfromlibrary_folder by @arash77 in https://github.com/galaxyproject/galaxy/pull/18970
• Ignore preflight options in API schema by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18983
• Add workflow to update PR title based on target branch version by @arash77 in https://github.com/galaxyproject/galaxy/pull/18835
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18982
• Bring your own file sources: Add the WebDAV template and configuration by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/18598
• Define environment variables in env: section by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18987
• Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18272
• Make vite tool shed client proxy configurable by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18988
• Fix the bioblend test failures by @arash77 in https://github.com/galaxyproject/galaxy/pull/18991
• Fix job directory not being cleaned up by @davelopez in https://github.com/galaxyproject/galaxy/pull/18997
• More concise, readable tool execution testing. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18977
• Enable extra user preferences for remotely authorized users by @maartenschermer in https://github.com/galaxyproject/galaxy/pull/18887
• Fixes random job failures in kubernetes by @mapk-amazon in https://github.com/galaxyproject/galaxy/pull/19001
• Disallow /tool_runner? in robots.txt by @dannon in https://github.com/galaxyproject/galaxy/pull/19020
• Migrate NGL viewer to npm package by @guerler in https://github.com/galaxyproject/galaxy/pull/18946
• Fix test_stock.py unit test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19037
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19031
• Workflow landing improvements by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18979
• UI Improvements for Tool Shed 2.0 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19041
• Fix auto-detect metadata from Edit Dataset Attributes panel by @davelopez in https://github.com/galaxyproject/galaxy/pull/19025
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19062
• Annotate DatasetAssociationManager as generic type by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19063
• Better logging around tool loading by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19029
• Allow recovering a normalized version of workflow request state from API by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18985
• Run installed Galaxy with no config and a simplified entry point by @natefoo in https://github.com/galaxyproject/galaxy/pull/19050
• A variety of improvements around tool parameter modeling (second try) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19027
• Add galaxy-upload link to UploadModal by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19055
• Bump http-proxy-middleware from 2.0.6 to 2.0.7 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/19060
• Do not skip CI tests on missing tools. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19002
• Add a filter for labels (tags) in Tool Search by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19076
• Move TRS import into WorkflowContentManager by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19070
• Improve usability of Directory datatype by @wm75 in https://github.com/galaxyproject/galaxy/pull/17614
• Replace poetry with uv by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19075
• Add Python 3.13 support by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18449
• Avoid possible negative offset in LibraryFolder by @martenson in https://github.com/galaxyproject/galaxy/pull/19090
• Add hint to the tool schema about runtime conditional changes by @martenson in https://github.com/galaxyproject/galaxy/pull/18996
• Fix numerous issues with tool input format "21.01" by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19030
• Allow deferred datasets to behave as URIs by @davelopez in https://github.com/galaxyproject/galaxy/pull/19077
• Support deferred datasets in visualizations by @davelopez in https://github.com/galaxyproject/galaxy/pull/19097
• uv: Do not recalculate dependencies when exporting by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19099
• Prevent purged users from logging in by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19094
• Fix issue with generating slug for sharing by @arash77 in https://github.com/galaxyproject/galaxy/pull/18986
• Test hash validation also for upload by path by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19109
• Integrate Tool Parameter Modeling into Linting (for Planemo) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19073
• Access public history in job cache / job search by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19108
• Better search stuff in Tool Shed 2.0. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19047
• Add job metrics per invocation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19048
• Run uv lock under Python 3.9 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19111
• Enable specifying dataset hash in test jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19113
• Always validate hashes when provided by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19110
• Add linter to check validity of output filters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19114
• Also use miniforge docker for container building by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19128
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19123
• Add type annotations to JobRunnerMapper and related code by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19115
• Silence the quota manager for updates by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19046
• Allow modes z and Z for docker volumes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18998
• Add some Zarr-based datatypes by @davelopez in https://github.com/galaxyproject/galaxy/pull/19040
• Enhance relabelfromfile to work with any column pair in mapping file by @wm75 in https://github.com/galaxyproject/galaxy/pull/19022
• Irods ssl connection by @pauldg in https://github.com/galaxyproject/galaxy/pull/19014
• Bump dompurify from 2.3.10 to 3.1.6 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/18880
• Allow to overwrite real_system_username per destination by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18945
• Jupyter Interactive Tool 1.0.1/24.07 by @natefoo in https://github.com/galaxyproject/galaxy/pull/18861
• Workflow Invocation view improvements by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18615
• Dynamics options add library dataset by @gagayuan in https://github.com/galaxyproject/galaxy/pull/18198
• Fix handling of v2 hashes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18522
• Update Japanese locale.js by @manabuishii in https://github.com/galaxyproject/galaxy/pull/19101
• Openlayer update to npm package by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/19134
• Remove OpenLayers legacy files and add SVG logo by @guerler in https://github.com/galaxyproject/galaxy/pull/19135
• Fix phylocanvas visualization build by @davelopez in https://github.com/galaxyproject/galaxy/pull/19138
• Add Vizarr visualization by @davelopez in https://github.com/galaxyproject/galaxy/pull/19061
• Update vizarr version to 0.1.5 by @guerler in https://github.com/galaxyproject/galaxy/pull/19142
• Replace static Cytoscape plugin with npm package by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19127
• Fix destentation typo by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19140
• Allow a posix file source to prefer linking. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19132
• Fix word wrapping in invocation panel list items by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19141
• Restore access to saved visualizations by @guerler in https://github.com/galaxyproject/galaxy/pull/19136
• 2 small uv config fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19146
• Add Workflow Title and Annotation sections by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/18762
• Implement workflow parameter validators. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19092
• Assert that data_column parameters have a valid data_ref by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18949
• Add Interactive Tool Ilastik by @lldelisle in https://github.com/galaxyproject/galaxy/pull/16837
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/19149
• Switch update annotate image to new script entry_point by @guerler in https://github.com/galaxyproject/galaxy/pull/19150
• Update tiff viewer to use script entry_point by @guerler in https://github.com/galaxyproject/galaxy/pull/19151
• Add XML based vtk datatype by @tStehling in https://github.com/galaxyproject/galaxy/pull/19104
• Migrate Venn Diagram to Script-Tag by @guerler in https://github.com/galaxyproject/galaxy/pull/19153
• Workflow license and creator edit keyboard access by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18936
• Feature - stdout live reporting by @gecage952 in https://github.com/galaxyproject/galaxy/pull/16975
• Add clean up job working directory as celery task by @sanjaysrikakulam in https://github.com/galaxyproject/galaxy/pull/15816
• Allow directory_uri workflow parameters. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19093
• Normalize usernames to lowercase in OIDC authentication by @arash77 in https://github.com/galaxyproject/galaxy/pull/19131
• FITS file table graph visualization plugin by @francoismg in https://github.com/galaxyproject/galaxy/pull/19003
• Bump cross-spawn from 7.0.3 to 7.0.5 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/19152
• Experimental galactic wizard by @dannon in https://github.com/galaxyproject/galaxy/pull/15860
• clarify that higher python versions are also supported by @martenson in https://github.com/galaxyproject/galaxy/pull/19156
• Decouple user email from role name by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18966
• Add a retry when deleting a k8s job by @afgane in https://github.com/galaxyproject/galaxy/pull/18744
• Add merge migration to merge 2 heads by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19163
• Consolidate tag validation by @dannon in https://github.com/galaxyproject/galaxy/pull/19166
• Add 24.2 migration tags by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19169
• [24.2] Update version to 24.2.rc1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19170
• Version 24.3.dev by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19171
• Fix version: 24.3 >> 25.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19173
• Enhance UTF-8 support for filename handling in downloads by @arash77 in https://github.com/galaxyproject/galaxy/pull/19161
• [24.2] Add requirement/resource to schema docs by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19172
• [24.2] Add gtf to autocompressedtypes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19175
• [24.2] Better cleanup of sharing roles on user purge by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19096
• [24.2] Add linters for datatypes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17600
• [24.2] Move invocation view running actions and improve styling of annotation section by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19168
• [24.2] Fix mulled_hash by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19199
• [24.2] release testing - UI tests for new workflow parameters by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19182
• [24.2] Fix default value handling for parameters connected to required parameters by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19219
• [24.2] Guide users to collection builders by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18857
• [24.2] Avoid a class of unhelpful accepted format drop downs. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19241
• [24.2] Improve the empty history message for guiding users to collections. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19242
• [24.2] Backport of Workflow Editor Activity Bar by @dannon in https://github.com/galaxyproject/galaxy/pull/19212
• [24.2] Fix PSA Redirect by @dannon in https://github.com/galaxyproject/galaxy/pull/19247
• [24.2] Fix version number by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19254
• [24.2] Login redirect followup by @dannon in https://github.com/galaxyproject/galaxy/pull/19251
• [24.2] Build collection only if populated in collection builder by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19250
• [24.2] Only allow moving activity bar icons when editing the bar. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19258
• [24.2] Fix CollectionCreatorModal being reopened on history by @davelopez in https://github.com/galaxyproject/galaxy/pull/19276
• [24.2] Fix some collection builder help and language choices. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19244
• [24.2] Fix usability of workflow best practice attribute checking. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19230
• [24.2] Workflow Inputs Activity by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19252
• [24.2] Fix invocation metrics usability by providing job context. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19279
• [24.2] Fix problem with multiple layers in workflow metrics. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19283
• [24.2] Various list of pairs builder usability fixes. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19248
• [24.2] Fix workflow change stack broken with #19230 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19288
• [24.2] Fix workflow metrics chart style by @davelopez in https://github.com/galaxyproject/galaxy/pull/19291
• [24.2] Fix cancellation of workflow scheduling by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19238
• [24.2] Release testing - selenium tests for workflow invocation export. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19262
• [24.2] Fix inconsistent tab handling in invocation view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19298
• [24.2] Prefer our package index server by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19284
• [24.2] Don't show published workflows in workflow activity of workflow editor by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19312
• [24.2] Fix import of previously-deleted TRS workflow by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19311
• [24.1] Fix multi select clipping in some places by @davelopez in https://github.com/galaxyproject/galaxy/pull/19309
• [24.2] Fix activity-bar-id handling wrt activityStore by @dannon in https://github.com/galaxyproject/galaxy/pull/19316
• [24.2] Activity bar add new workflow button by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19281
• [24.0] Replace mambaforge Docker image with miniforge3 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19327
• [24.1] Use correct label to display in ObjectStoreActions by @davelopez in https://github.com/galaxyproject/galaxy/pull/19333
• [24.1] Backport #19001 kubernetes api client fix by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19338
• [24.2] Partial backport of #19331 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19342
• [24.1] Fix importing shared workflows with deeply nested subworkflows by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19335
• [24.0] Fix selection break warning reappearing after page refresh by @davelopez in https://github.com/galaxyproject/galaxy/pull/19348
• [24.0] Backport fix for test_singularity_container_test test by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19349
• [24.1] quota: do not complain on no-change of default by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19045
• [24.1] Use selectfromurl test data from github, not usegalaxy.org by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19352
• [24.2] Fix handling of step id offsets when duplicating selections by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19351
• [24.1] Add bcsp datatype by @SantaMcCloud in https://github.com/galaxyproject/galaxy/pull/19365
• [24.2] Fix workflows with optional non-default parameter input by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19332
• [24.2] Fix simple activity panel item style by @guerler in https://github.com/galaxyproject/galaxy/pull/19350
• [24.0] Remove unnecessary quoting in conda package specification by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19382
• [24.2] Fix timeout handling for planemo / galaxy-tool-util by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19384
• [24.2] Fix for empty string in regex validator message. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19387
• [24.2] Fixes for console logging. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19381
• [24.2] Fix to not display upload when creating collections from existing datasets. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19373
• [24.2] Fix to only show ChatGXY when available. by @dannon in https://github.com/galaxyproject/galaxy/pull/19389
• [24.1] Record implicitly converted dataset as input dataset by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19301
• [24.2] Update visualizations package versions by @guerler in https://github.com/galaxyproject/galaxy/pull/19232
• [24.2] Backport fix from #19396 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19399
• [24.2] Outputs filter linter fixes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19208
• [24.1] Fix config template validation for file sources and object store templates by @davelopez in https://github.com/galaxyproject/galaxy/pull/19414
• [24.2] Display upload help highlight only once and include Rule-based upload info by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19393
• [24.2] Fix Activity Bar state lost on page reload by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19426
• [24.1] Catch errors in toolStore and ToolPanel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19423
• [24.2] Fixes window manager scrolling and resizing by @guerler in https://github.com/galaxyproject/galaxy/pull/19308
• [24.1] Fix quota usage with user object stores by @davelopez in https://github.com/galaxyproject/galaxy/pull/19323
• [24.2] mulled-build-tool fix for packages wo version by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19450
• [24.2] Fix parsing of validators with inf limits by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19459
• [24.2] List private file sources first in Remote Files Dialog by @davelopez in https://github.com/galaxyproject/galaxy/pull/19455
• [24.1] Fix failing selenium in test/integration_selenium/test_edam_tool_panel_views.py by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19462
• [24.2] Also check trs_tool_id for imported workflow indicator by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19460
• [24.2] Fix help text overflow breaking tool inspector by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19465
• [24.1] add MuData as subclass of H5 by @pavanvidem in https://github.com/galaxyproject/galaxy/pull/19416
• [24.2] Show message for mixed extensions in collection creator by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19404
• [24.2] Fix object not found handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19468
• [24.2] Fix job parameter summary for inputs without label by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19427
• [24.2] Show Keycloak provider label in UI by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19447
• [24.2] Remove print statement by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19469
• [24.1] Fix display tags in FormSelect when available by @davelopez in https://github.com/galaxyproject/galaxy/pull/18918
• [24.1] Expression tool format source backport by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19466
• [24.2] backport of defensive refresh tokens by @martenson in https://github.com/galaxyproject/galaxy/pull/19471
• [24.1] Add missing ActivityBar to PageEditor by @davelopez in https://github.com/galaxyproject/galaxy/pull/19474
• [24.2] Bump typescript target to es2020 by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19473
• [24.1] Paginate tabular datasets in tables to load invocation reports quicker by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19470
• [24.1] Fix version flicker on job rerun by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19478
• [24.1] Improve relabel from file error if file doesn't contain enough lines by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19480
• [24.2] Serialize message exceptions on execution error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19483
• [24.2] Fix invocation query in JobInformation.vue component by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19496
• [24.2] Fail with error message when submitting invalid request by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19489
• [24.2] Fix minor typo in event name in collection creator by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19499
• [24.1] Fix userOwnsPage computed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19502
• [24.2] Fix library dataset current user potentially null by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/19505
• [24.0] Fix deleting lddas in batch by @davelopez in https://github.com/galaxyproject/galaxy/pull/19506
• [24.2] Fix workflowID assignment in Markdown.vue by @davelopez in https://github.com/galaxyproject/galaxy/pull/19507
• [24.2] Skip token refresh without refresh token in psa by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19514
• [24.0] Fix test_storage_show API test by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19522
• [24.2] Downgrade 'InteractiveTools are not enabled' to warning by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19518
• [24.2] Set a hard limit of 100 invocations per request in api/invocations by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19497
• [24.2] Fix tool search constantly loading bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19528
• [24.0] Fix admin cancel job message not being displayed to the user by @davelopez in https://github.com/galaxyproject/galaxy/pull/19537
• [24.2] Use visualizations api in trackster by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19495
• [24.1] Fix extracting workflows from purged and deleted histories by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19525
• [24.2] Fix WSGI response status handling in controller methods by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19520
• [24.0] Prevent cycling through failing conversion jobs in trackster by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19494
• [24.1] Fix remap for parameter called id by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19532
• [24.2] Fix error message when subworkflow input connection missing by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19526
• [24.2] Add tool_id index on job table by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19543
• [24.2] Use instance wide default real_system_username if not defined on destination by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19544
• [24.2] Update 24.2 db revision tags by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19550
• [24.2] Provide guidance in case of deadlock during db migration by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19551
• [24.2] Release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19223
• [24.0] Fix libraries folder include deleted by @davelopez in https://github.com/galaxyproject/galaxy/pull/19553
• [24.2] Fix saved visualization (non-trackster ones) not displaying by @davelopez in https://github.com/galaxyproject/galaxy/pull/19561
• [24.2] Fix "export datasets" tool displaying dialog right away by @davelopez in https://github.com/galaxyproject/galaxy/pull/19555
• [24.2] Add Python 3.13 classifier to packages by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19569
• [24.0] Fix type annotations for pysam 0.23.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19571
• [24.2] Allow unused query params in workflows/export_to_file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19574
• [24.1] Fix collection load error handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19585
• [24.2] Handle isatools dependency by @jdavcs in https://github.com/galaxyproject/galaxy/pull/19582
• [24.1] Fix job paused on user defined object store by @davelopez in https://github.com/galaxyproject/galaxy/pull/19578

New Contributors

• @sanjaysrikakulam made their first contribution in https://github.com/galaxyproject/galaxy/pull/18458
• @mpalmada made their first contribution in https://github.com/galaxyproject/galaxy/pull/18910
• @maartenschermer made their first contribution in https://github.com/galaxyproject/galaxy/pull/18887
• @mapk-amazon made their first contribution in https://github.com/galaxyproject/galaxy/pull/19001
• @gagayuan made their first contribution in https://github.com/galaxyproject/galaxy/pull/18198
• @tStehling made their first contribution in https://github.com/galaxyproject/galaxy/pull/19104
• @SantaMcCloud made their first contribution in https://github.com/galaxyproject/galaxy/pull/19365

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.1.4...v24.2.0

- Python
Published by jdavcs over 1 year ago

galaxy - v24.1.4

What's Changed

• [24.1] Unpin social-auth-core in galaxy-data package by @natefoo in https://github.com/galaxyproject/galaxy/pull/19052
• [24.1] Fix very slow workflow editor loading by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19068
• [24.0] Fetch invocation id only once on the job info page by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19079
• [24.0] Optimize/fix sqlite hid update statement by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19106
• [24.1] Persist uploaded data between Regular and Collection upload tabs by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/19083
• [24.1] Don't call jobrunner.stopjob on jobs in new state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18495
• [24.1] Add buffer as a devDependency in phylocanvas package.json by @dannon in https://github.com/galaxyproject/galaxy/pull/19160
• [24.1] Prefer auto-decompressed datatype when picking conversion target by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19162
• [24.1] Remove the default Incoming suffix in GenericModel class by @davelopez in https://github.com/galaxyproject/galaxy/pull/19174
• [24.1] Fix productionawsprivate_bucket.yml by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19155
• [24.0] Update title of edited PRs only if base ref changed by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19183
• [24.1] Make runtime value in optional parameter open legacy workflow run form by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19159
• [24.0] Update PR title handling for changing base ref by @arash77 in https://github.com/galaxyproject/galaxy/pull/19195
• [24.0] Fix various invocation export issues by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19215
• [24.0] Create harmonized collections from correct tool outputs by @wm75 in https://github.com/galaxyproject/galaxy/pull/19222
• [24.1] flip default value for use_mamba to false by @bgruening in https://github.com/galaxyproject/galaxy/pull/19295
• [24.1] Fix bad merge conflict resolution by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/19297
• [24.0] Linter: allow dynamic option definition by from_url by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/19300

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.1.3...v24.1.4

- Python
Published by bernt-matthias over 1 year ago

galaxy - v24.1.3

What's Changed

• [24.1] Limit max number of items in dataproviders by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18881
• [24.1] Allow cors in biom and q2view display applications by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18890
• [23.1] Fix toolshed sessionless access to a few APIs broken with.. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18680
• [24.1] Access tool data table filters in workflow building mode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18900
• [24.0] fix FormSelectMany doesn't deselect bulk selected items by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18908
• [24.1] Disable storage dashboard button for anon users by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18922
• [24.1] Fix extension not showing in DataDialog for collection elements by @davelopez in https://github.com/galaxyproject/galaxy/pull/18925
• [24.1] Fix username used in invocation report by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18932
• [24.1] Replace Edit button with Import button on WorkflowInvocationHeader by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18930
• [23.2] Fix bug in sharing ui by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18939
• [24.1] Don't use async def where not appropriate by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18944
• [24.1] Ctrl/Cmd-click on SwitchHistoryLink opens in new tab by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18940
• [24.0] Pin black version to 24.8.0 in workflow action by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18955
• [23.2] Don't check availability of shellescape by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18954
• [23.2] Pin Ubuntu to 22.04 for Python 3.7 workflow by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18959
• [24.1] Allow passing anything into format="data" inputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18961
• [24.1] Pin ubuntu 22.04 for minikube setup action by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18965
• [24.0] Backport 2 CI fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18973
• [24.1] Disable locking when opening h5 files, add missing with by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18976
• [24.1] fix CILogon redirect by @laperlej in https://github.com/galaxyproject/galaxy/pull/18974
• [24.1] Fix Workflow card controllers and indicators bleeding by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/19008
• [24.0] Fix job search statement building by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19010
• [24.1] Put cached jobs back into queue on handler restart by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/19012
• [24.1] Fix extra call to testdatapath that requires an admin key by @jmchilton in https://github.com/galaxyproject/galaxy/pull/19011
• [24.1] Fix collectionElementsStore's hasLoadingCollectionElementsError computed. by @dannon in https://github.com/galaxyproject/galaxy/pull/19015
• [24.0] Backporting PR title update workflow by @arash77 in https://github.com/galaxyproject/galaxy/pull/19019
• [24.1] Remove defaults channel for conda usage by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18859

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.1.2...v24.1.3

- Python
Published by bernt-matthias over 1 year ago

galaxy - v24.1.2

What's Changed

• [24.1] fix no-op workflow "relabel" shouldn't result in a notification by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18473
• [24.1] Make default_panel_view a _by_host option by @natefoo in https://github.com/galaxyproject/galaxy/pull/18471
• [24.1] Stabilize testpurgewhilejobrunning test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18498
• [24.1] Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18494
• [24.0] Return generic message for password reset email by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18479
• [24.1] Backport pod5 datatype by @TomHarrop in https://github.com/galaxyproject/galaxy/pull/18507
• [23.2] Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18510
• [24.0] Follow-up on #18212 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18516
• [24.0] Fix view parameter type in Job index API by @davelopez in https://github.com/galaxyproject/galaxy/pull/18521
• [24.1] Prevent job submission if input collection element is deleted by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18517
• [24.1] Use name instead of ID for displaying object stores + revise user-facing language in UI by @davelopez in https://github.com/galaxyproject/galaxy/pull/18525
• [24.1] Check if dataset has any data before running provider checks by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18526
• [24.1] Strip unicode null from tool stdio by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18527
• [24.1] Simplify and fix useDatatypesMapper by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18550
• [24.1] Also check dataset.deleted when determining if data can be displayed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18547
• [24.1] Fix map over calculation for runtime inputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18535
• [24.1] Fix shared caches with extended metadata collection. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18520
• [24.1] Fix undo removing all freehand comments by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18557
• [24.1] Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18559
• [24.1] Apply statsd arg sanitization to all pages by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18509
• [24.1] Raise appropriate exception if ldda not found by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18569
• [24.1] Fix history changes switch to simple form by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18574
• [24.0] Fix Archive header encoding by @arash77 in https://github.com/galaxyproject/galaxy/pull/18583
• [24.0] Fix for not-null in 'column_list' object by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/18553
• [23.0] Fix API key reveals on mouse hover by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18593
• [24.0] Fix sqlalchemy statement in tooltagmanager reset output by @dannon in https://github.com/galaxyproject/galaxy/pull/18591
• [24.0] Set minimum weasyprint version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18606
• [24.1] Adjust sentry default config -- drop replay by @dannon in https://github.com/galaxyproject/galaxy/pull/18622
• [24.1] More datatype deprecation warnings by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18612
• [23.0] Fix for Numeric form field to allow Null min/max values in validation methods by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/18585
• [24.1] xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18605
• [24.1] Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18634
• [24.1] Include workflow invocation id in exception logs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18594
• [24.1] Fix invocation view steps scroll bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18614
• [24.1] Fix resumepausedjobs if no session provided by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18640
• [24.0] Close install model session when request ends by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18629
• [24.1] Update h5web by @dannon in https://github.com/galaxyproject/galaxy/pull/18552
• [24.0] Don't set file size to zero by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18653
• [23.2] Strip whitespace when listifying admin users by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18656
• [24.1] Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18661
• [24.1] Optimize useInvocationGraph for Invocation view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18663
• [24.0] Improve workflow creating/saving UX by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18657
• [24.1] Fix export_remote include/exclude metadata flag by @davelopez in https://github.com/galaxyproject/galaxy/pull/18659
• [24.0] Remove unnecessary assert for file_size by @davelopez in https://github.com/galaxyproject/galaxy/pull/18669
• [24.1] Fix h5ad metadata by @nilchia in https://github.com/galaxyproject/galaxy/pull/18635
• [24.1] Return error when following a link to a non-ready display application by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18672
• [24.1] Only load authnz routes when oidc enabled by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18683
• [24.1] File source and object store instance api fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18685
• [24.0] Fix import all datasets from library folder by @davelopez in https://github.com/galaxyproject/galaxy/pull/18687
• [24.0] Make sure we set file size also for purged outputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18681
• [24.1] Fix sorting users in admin by last login by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18694
• [24.1] Fix change datatype PJA on expression tool data outputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18691
• [24.1] Fix upload when current history changes by @davelopez in https://github.com/galaxyproject/galaxy/pull/18703
• [24.1] Fix output hover for workflow parameter outputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18720
• [24.1] Fill in missing help for cross product tools. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18698
• [24.1] Add error handling in WorkflowInvocationState by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18726
• [24.1] Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18731
• [24.1] Fix invocation grid selenium that fails intermittently by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18735
• [24.1] Fix resume paused jobs response handling by @dannon in https://github.com/galaxyproject/galaxy/pull/18733
• [24.1] Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18734
• [24.1] Fix datatype validation of newly built collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18738
• [24.1] Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18730
• [24.1] Show items with same hid but different id in history by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18689
• [24.0] Fix rules runtime editable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18741
• [24.1] Fix directory get or create logic by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18752
• [24.1] Fix scratch storage modal title by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18753
• [24.1] Fix job summary for optional unset job data inputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18754
• [24.1] Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18751
• [24.1] Fix infinite rapid polling in useKeyedCache by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18756
• [24.0] Fix TypeError from Pydantic 2.9.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18788
• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in https://github.com/galaxyproject/galaxy/pull/18670
• [24.1] Fixing RegisterForm.vue not appending prefix when set. by @mcuaya1 in https://github.com/galaxyproject/galaxy/pull/18786
• [24.0] Update ENA url in ebi_sra tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18771
• [24.1] Fix wrong extension on pick data output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18798
• [24.1] Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by @cat-bro in https://github.com/galaxyproject/galaxy/pull/18784
• [24.1] Fix copying workflow with subworkflow step for step that you own by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18802
• [24.1] Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18805
• [24.1] Collect job metrics also when job failed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18809
• [24.1] Fix optional text handling in LibraryEditField by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18814
• [24.1] Make pylibmagic import optional by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18813
• [24.1] Add error handling for SwitchToHistoryLink by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18765
• [24.1] Allow drag and drop for collection elements by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18699
• [24.1] Prevent optional output to required input connection in editor by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18810
• [24.1] Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in https://github.com/galaxyproject/galaxy/pull/18818
• [24.1] Start job handler only after building InteractiveToolManager by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18824
• [24.1] Fix named cursor is not valid anymore by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18825
• [24.1] Fix wrong celery_app config on job and workflow handlers by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18819
• [24.1] Maybe fix flaky navigation v2 ts tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18833
• [24.1] Make all fields optional for HelpForumPost by @davelopez in https://github.com/galaxyproject/galaxy/pull/18839
• [24.1] prevent "missing refreshtoken" errors by supporting <extrascopes> also with Keycloak backend by @ljocha in https://github.com/galaxyproject/galaxy/pull/18826
• [24.1] Fix alert handling in workflow label handler by @guerler in https://github.com/galaxyproject/galaxy/pull/18836
• [24.1] Extend on disk checks to running, queued and error states by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18846
• [24.1] Skip metric collection if job working directory doesn't exist by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18845
• [24.1] Tighten TRS url check by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18841
• [24.0] Ignore converted datasets in invalid input states by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18850
• [24.1] Allow to change only the description of a quota by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18775
• [24.1] Fix Workflow index bookmark filter by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18842
• [24.0] Fix discovered outputs with directory metadata and distributed object by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18855
• [24.1] Fix check dataset check by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18856
• [24.1] Retry container monitor POST if it fails (don't assume it succeeded) by @natefoo in https://github.com/galaxyproject/galaxy/pull/18863
• [24.0] Fix wrong final state when init_from is used by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18871
• [24.1] Raise MessageException instead of assertions on rerun problems by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18858
• [24.1] Fix history import when parent_hda not serialized by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18873
• [24.1] Fix loading very old workflows with data inputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18876
• [24.1] Fix data_column ref to nested collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18875

New Contributors

• @nilchia made their first contribution in https://github.com/galaxyproject/galaxy/pull/18635
• @mcuaya1 made their first contribution in https://github.com/galaxyproject/galaxy/pull/18786
• @ljocha made their first contribution in https://github.com/galaxyproject/galaxy/pull/18826

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.1.1...v24.1.2

- Python
Published by mvdbeek over 1 year ago

galaxy - v24.1.1

What's Changed

• [24.1] Support usage of vue mounting helpers in a context without existing pinia/vue. by @dannon in https://github.com/galaxyproject/galaxy/pull/18429
• [24.1] Add note on fastapi to admin release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18431
• [24.0] Install node from setup-node action by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18435
• [24.0] Fix mounting utility usage of pinia (fixes charts form components) by @dannon in https://github.com/galaxyproject/galaxy/pull/18430
• [24.1] Update mercurial to non-yanked 6.7.4 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18434
• [24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18428
• [24.1] Improve workflow-related exception reporting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18447
• [24.0] Disable password reset for deleted users [GCC2024_COFEST] by @laperlej in https://github.com/galaxyproject/galaxy/pull/18459
• [24.0] Fix subwofklow tags serialization type by @arash77 in https://github.com/galaxyproject/galaxy/pull/18456
• [24.0] Add input extra files to get_input_fnames by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18462
• [22.05] pin bleach to 5.0.1 by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18472
• [24.0] Fix dropped when_expression on step upgrade by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18446
• [24.0] Backport 18458 by @martenson in https://github.com/galaxyproject/galaxy/pull/18474

New Contributors

• @laperlej made their first contribution in https://github.com/galaxyproject/galaxy/pull/18459

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.1...v24.1.1

- Python
Published by jdavcs almost 2 years ago

galaxy - v24.0.3

What's Changed

• [24.0] Backport OIDC schema fix by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18111
• [23.2] Allow purge query param, deprecate purge body param by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18105
• [24.0] Fix switching between nested collection elements by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18115
• [24.0] Fix deprecated deprecated argument by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18119
• [24.0] Ignore AdminRequired and RegisteredUserRequired Sentry events by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18118
• [24.0] Include traceback when logging email PJA exception by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18122
• [24.0] Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18123
• [24.0] Don't log exception if cancelled slurm job doesn't have stderr file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18121
• [24.0] Raise exception if collection elements missing during download by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18094
• [24.0] Fix and unify axios error handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18112
• [24.0] Fix activity bar touch events on iOS devices by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18109
• [24.0] Fix vanishing connections on workflow upgrade by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18107
• [24.0] Fix listing possibly untitled records in Invenio Plugin by @davelopez in https://github.com/galaxyproject/galaxy/pull/18130
• [24.0] Don't commit in DeleteIntermediatesAction by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18131
• [24.0] Fix data default values not getting added to history by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18132
• [24.0] Fix undefined reading 'produces_entry_points' TypeError by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18141
• [24.0] Fix config access in StorageManager by @dannon in https://github.com/galaxyproject/galaxy/pull/18143
• [24.0] Fix Legacy HTML page view by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18145
• [24.0] Delay tool form rendering until config is loaded by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18151
• [24.0] Raise RequestParameterInvalidException when url is invalid by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18155
• [24.0] Drop redundant error message by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18156
• [24.0] Fix error message when accessing restricted Zenodo records by @davelopez in https://github.com/galaxyproject/galaxy/pull/18169
• [24.0] Downgrade count lines error to warning by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18175
• [24.0] Emit warning when user-cancelled job already complete by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18178
• [24.0] Fix typos in create release documentation page by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18181
• [24.0] Fix on success redirect by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18187
• [24.0] Fix Edit Dataset UI when there is an error retrieving the dataset by @davelopez in https://github.com/galaxyproject/galaxy/pull/18188
• [24.0] Avoid object store path lookup when constructing JobState object by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18190
• [24.0] Fix make all histories private with immutable histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18200
• [24.0] Remove legacy code, reference to sqlalchemy migrate by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18202
• [24.0] Fix submitted value in workflow run form if data is constrained by tag filter by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18193
• [24.0] Add string cast for dbkey / genome_build by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18207
• [24.0] Include stack when reporting delete error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18208
• [24.0] Replace Multiselect selectLabel with icons in FormSelect by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18194
• [24.0] Fix pca 3d rendering of tabular files and visualization error handling in general by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18211
• [24.0] Don't fail metadata if we only have an extra output files dir by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18179
• [24.0] Add GenericItem error handling by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18203
• [24.0] Backport #18197 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18212
• [24.0] Use config_section to distinguish between galaxy and ts or other apps by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18215
• [24.0] Prevent anonymous and inactive users from running workflows by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18192
• [24.0] Restrict job_files access to jobs that are not terminal by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18217
• [24.0] Check dataset state when attempting to acces dataset contents by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18214
• [24.0] do not expand datasets that are known to be inaccessible by @martenson in https://github.com/galaxyproject/galaxy/pull/17818
• [24.0] Raise RequestParameterInvalidException if url can't be verified by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18230
• [24.0] Don't set dataset peek for errored jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18231
• [24.0] Decrease log level for expected visualization errors by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18229
• [24.0] Raise appropriate exception if accessing deleted input file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18223
• [24.0] Reset content-length for unhandled exceptions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18233
• [24.0] Fix element serialization for collections that aren't populated yet by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18235
• [24.0] Fix userOwnsHistory conditions by @davelopez in https://github.com/galaxyproject/galaxy/pull/18243
• [23.1] Minor fix to enable external hgweb process by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18256
• [24.0] Skip tests if toolshed, dx.doi not responding by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18250
• [23.1] Add missing TS migration by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18267
• [23.2] Add hgweb_repo_prefix attribute to TestToolShedConfig by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18268
• [24.0] Format with black by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18273
• [24.0] Transparently open compressed files in DatasetDataProvider by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18248
• [24.0] Raise exception when extracting dataset from collection without datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18249
• [24.0] Fix Invenio credentials handling by @davelopez in https://github.com/galaxyproject/galaxy/pull/18255
• [23.1] Add revision tags for TS migration in 23.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18271
• [24.0] Only log error if deleting directory really failed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18236
• [24.0] Don't attempt to download purged datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18278
• [24.0] Set page importable to false when serializing by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18263
• [24.0] Fix firstdatasetelement type hint by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18284
• [23.2] Add toolshed database revision tags for 23.2 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18293
• [24.0] Add TS db revision tags for 24.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18294
• [24.0] Use correct link for log in or register in Copy Modal by @davelopez in https://github.com/galaxyproject/galaxy/pull/18289
• [24.0] Redirect anonymous users to home when importing public histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18286
• [24.0] Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in https://github.com/galaxyproject/galaxy/pull/18283
• [24.0] Move tool shed specific driver function to tool_shed.test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18296
• [24.0] Don't serialize display application links for deleted datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18307
• [23.1] More fixes for running the TS with external hgweb by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18279
• Merge 23.1 into 23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18320
• [23.2] Fix integration tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18326
• [23.2] Fix tool_shed package unit tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18327
• [23.2] Fix one more tool shed unit test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18328
• [23.1] Make toolshed repo permissions world-readable by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18332
• [24.0] Downgrade doi fetch error to debug by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18330
• [24.0] Fix users API serialization when listing users by @davelopez in https://github.com/galaxyproject/galaxy/pull/18329
• [23.2] Skip new history creation if user is anonymous and login is required by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18319
• [24.0] Fix seek in slurm memory check by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18338
• [24.0] Fix authentication error for anonymous users querying jobs by @davelopez in https://github.com/galaxyproject/galaxy/pull/18333
• [23.2] Allow DCE as outer input to to_cwl by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18349
• [24.0] Fix anonymous user job retrieval logic by @davelopez in https://github.com/galaxyproject/galaxy/pull/18358
• [24.0] Do not copy purged outputs to object store by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18342
• [24.0] Sanitize FormElement error messages by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18377
• [24.0] Drop unnecessary escaping for workflow name and annotation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18376
• [24.0] Fix user's private role can be missing by @davelopez in https://github.com/galaxyproject/galaxy/pull/18381
• [24.0] Make sure that all Linter subclasses are imported for listing them by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18339
• [24.0] Kill pulsar job if job stopped on galaxy side by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18348
• [24.0] Fix null inputs in database operation tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18385
• [24.0] Fix workflow editor tool form scroll memory by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18390
• [24.0] Fix update group API payload model by @davelopez in https://github.com/galaxyproject/galaxy/pull/18374
• [24.0] Allow in_range validator for selects by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18403
• [24.0] Fix invocation stepjobsummary for new collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18402
• [24.0] Fix get_accessible_job if called without session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18400
• [24.0] Fix collection map over status for dragged collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18416
• [24.0] Serialize purged flag for datasets in collections by @davelopez in https://github.com/galaxyproject/galaxy/pull/18420
• [24.0] Really allow in-range validator for txt by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18411
• [24.0] Assign default data extension on discovered collection output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18389
• [24.0] Minor linting cleanup by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18421
• [24.0] Install node from setup-node action by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18435
• [24.0] Fix mounting utility usage of pinia (fixes charts form components) by @dannon in https://github.com/galaxyproject/galaxy/pull/18430
• [24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18428

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.0.2...v24.0.3

- Python
Published by bernt-matthias almost 2 years ago

galaxy - v24.1

What's Changed

• Update version to 24.1.dev by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17592
• Add colabfold tar file datatype by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/17567
• Bump es5-ext from 0.10.62 to 0.10.63 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17555
• Enables activity bar by default by @guerler in https://github.com/galaxyproject/galaxy/pull/17531
• Adding object store plugin for Rucio by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/17156
• Better display of estimated line numbers and add number of columns for tabular by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17492
• Bump yaml from 2.1.1 to 2.3.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17125
• Add test and doc showing how dynamic selects are used by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16885
• Unpin social-auth-core dependency by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17607
• Type annotation improvements by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17601
• Type annotation and CWL-related improvements by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17630
• Code cleanups from ruff and pyupgrade by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17654
• Modernization and cleanup of job state related client code. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17593
• Npz sniffing: do not read the whole file by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17672
• Login components refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17564
• Fix syntax for SA2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17663
• Tool linter: check for valid bio.tools entries by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17655
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17653
• Collections common refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17571
• Add content assertion XML tags for test output verification using images by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17581
• Add browser and operating system info to issue template by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17696
• Issue #17631: Make it possible to use custom invfile.lua if needed by @martin-g in https://github.com/galaxyproject/galaxy/pull/17693
• remove reference to a non-existent component by @martenson in https://github.com/galaxyproject/galaxy/pull/17686
• Activity bar preference handling fixes. by @dannon in https://github.com/galaxyproject/galaxy/pull/17701
• Fix bug in image_util.py by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17749
• Fix bug in galaxy.xsd by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17752
• Fix bug in assert_has_image_n_labels by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17754
• Add carbon_intensity.csv to package by @nuwang in https://github.com/galaxyproject/galaxy/pull/17748
• Bump follow-redirects from 1.15.4 to 1.15.6 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17766
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17764
• Add support for floating point TIFF files in verification of image-based tool outputs by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17797
• Datasets refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17799
• Bump webpack-dev-middleware from 5.3.3 to 5.3.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17820
• Merge release_24.0 -> dev by @dannon in https://github.com/galaxyproject/galaxy/pull/17833
• Fix odd object store exception by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17810
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17819
• Bump express from 4.18.1 to 4.19.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17840
• Fixes for mapping workflow labels to markdown dialogs. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17424
• Add tool linting for valid EDAM terms by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17839
• Enable storage management by object store by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17500
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17870
• Remove duplicate tool panel insertion, rely on activity bar by @guerler in https://github.com/galaxyproject/galaxy/pull/17872
• Update labels in Markdown editor when workflow labels change. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17863
• [24.0] Fix release notes images and videos by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17889
• SQLAlchemy 2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17778
• Add pin_labels attribute for image_diff comparison method by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17866
• Disable published item copy button when editing slug by @martenson in https://github.com/galaxyproject/galaxy/pull/17888
• Enable managing object store usage within a history. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17853
• Rename JupyTool to something more searchable (i.e. JupyterLab which includes the substring Jupyter) by @hexylena in https://github.com/galaxyproject/galaxy/pull/17849
• Collection components refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17647
• Bump undici from 5.28.3 to 5.28.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17905
• Fix client types around history items by @davelopez in https://github.com/galaxyproject/galaxy/pull/17924
• Update config docs about Celery by @davelopez in https://github.com/galaxyproject/galaxy/pull/17918
• Workflow editor undo/redo by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17774
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17923
• Consolidates data dialog components by @guerler in https://github.com/galaxyproject/galaxy/pull/17802
• merge 24.0 to dev by @martenson in https://github.com/galaxyproject/galaxy/pull/17942
• Add admin activity to activity bar by @guerler in https://github.com/galaxyproject/galaxy/pull/17877
• Replace sample Celery result_backend in config by @davelopez in https://github.com/galaxyproject/galaxy/pull/17949
• Use typed API client for reporting job errors. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17969
• Model edits and bug fixes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17922
• Drop unused workflow controller methods by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17974
• Model typing and SA2.0 follow-up by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17958
• Dataset information refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17804
• Error reporting unit tests by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17968
• Outline use of typeannotationmap to fix mypy issues by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17902
• Adds pages to the activity bar by @guerler in https://github.com/galaxyproject/galaxy/pull/17925
• Revises visualizations activity by @guerler in https://github.com/galaxyproject/galaxy/pull/17931
• Enable warn_unused_ignores mypy option by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17991
• Add email notifications channel by @davelopez in https://github.com/galaxyproject/galaxy/pull/17914
• Implement a page object accessibility dialog by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17225
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17982
• Add tags to data dialog display, restores update_time and extension columns by @guerler in https://github.com/galaxyproject/galaxy/pull/17992
• Make celery fixture available in framework tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18020
• Add some admin facing docs on data tables by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17585
• Add section divider to activity bar, fix click handler by @guerler in https://github.com/galaxyproject/galaxy/pull/18007
• Ensures that the activity bar is not shown when use_panels is set to false by @guerler in https://github.com/galaxyproject/galaxy/pull/17926
• Refactor convert HistoryExport component to Typescript by @davelopez in https://github.com/galaxyproject/galaxy/pull/18028
• Add Zenodo integration by @davelopez in https://github.com/galaxyproject/galaxy/pull/18022
• Tweak export records UI by @davelopez in https://github.com/galaxyproject/galaxy/pull/18038
• More typing in galaxy.files. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18037
• Remove deprecated BCO export endpoint by @martenson in https://github.com/galaxyproject/galaxy/pull/16645
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18035
• Refactor galaxy.files plugin loading + config handling. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18049
• Fix (I think) a transiently failing selenium error. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18065
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18063
• Add stronger type annotations in file sources + refactoring by @davelopez in https://github.com/galaxyproject/galaxy/pull/18050
• Enable flake8-implicit-str-concat ruff rules by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18067
• Persistent toggle sections of job info by @dannon in https://github.com/galaxyproject/galaxy/pull/16983
• Visualizing workflow runs with an invocation graph view by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17413
• Consolidate Visualization container, avoid using default iframe by @guerler in https://github.com/galaxyproject/galaxy/pull/18016
• Make urgent notifications mandatory by @davelopez in https://github.com/galaxyproject/galaxy/pull/17975
• Add Attributes section to Edit Collection view as well by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18071
• Fix toolbar header z-index by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18084
• Ensure history update_time is set when exporting by @davelopez in https://github.com/galaxyproject/galaxy/pull/18086
• Chore: remove repetitive words by @tianzedavid in https://github.com/galaxyproject/galaxy/pull/18076
• Add Net datatype by @martenson in https://github.com/galaxyproject/galaxy/pull/18080
• Add a button that filters out a tool section in the tool panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18034
• Dynamic tool fixes by @dcore94 in https://github.com/galaxyproject/galaxy/pull/18085
• Overhaul Azure storage infrastructure. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18087
• Fix AWS object store for us-east-2 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18100
• Tests and bugfixes for cloudbridge object store. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18099
• Hide bookmark toggle on deleted workflows by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18103
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18095
• Automatically bind galaxy_data_manager_data_path in containers by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17596
• Workflow editor item selection by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17615
• Fix for unexpected OIDC XML validation error by @Edmontosaurus in https://github.com/galaxyproject/galaxy/pull/18106
• [24.0] Backport OIDC schema fix by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18111
• [23.2] Allow purge query param, deprecate purge body param by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18105
• Fairly critical fix for #18087 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18110
• [24.0] Fix switching between nested collection elements by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18115
• [24.0] Fix deprecated deprecated argument by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18119
• Add vue sentry integration by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18120
• [24.0] Ignore AdminRequired and RegisteredUserRequired Sentry events by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18118
• [24.0] Include traceback when logging email PJA exception by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18122
• [24.0] Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18123
• [24.0] Don't log exception if cancelled slurm job doesn't have stderr file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18121
• Add datasets/collections filter to history panel filters by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18039
• Drop "?" (Help) from DatasetActions list by @dannon in https://github.com/galaxyproject/galaxy/pull/18124
• [24.0] Raise exception if collection elements missing during download by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18094
• [24.0] Fix and unify axios error handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18112
• [24.0] Fix activity bar touch events on iOS devices by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18109
• [24.0] Fix vanishing connections on workflow upgrade by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18107
• [24.0] Fix listing possibly untitled records in Invenio Plugin by @davelopez in https://github.com/galaxyproject/galaxy/pull/18130
• [24.0] Don't commit in DeleteIntermediatesAction by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18131
• Revises handling of warnings in the workflow run form by @guerler in https://github.com/galaxyproject/galaxy/pull/18126
• [24.0] Fix data default values not getting added to history by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18132
• Workflow preview improvements by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18108
• Enable all-vs-all collection analysis patterns. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17366
• Tool linter: check for leaf nodes with unstripped text content by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17656
• Fix permissions for temporary upload file for API uploads by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17850
• Document syntax for accessing nested parameters in change_format - when tags by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18018
• Mailing list wording tweaks by @dannon in https://github.com/galaxyproject/galaxy/pull/17867
• Update s3fs dependency. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18135
• Script for deleting userless histories from database + testing + drop unused model testing code by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18079
• [24.0] Fix undefined reading 'produces_entry_points' TypeError by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18141
• [24.0] Fix config access in StorageManager by @dannon in https://github.com/galaxyproject/galaxy/pull/18143
• [24.0] Fix Legacy HTML page view by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18145
• Fix import broken with forward merge by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18152
• [24.0] Delay tool form rendering until config is loaded by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18151
• Only include tool stdout/stderr in HDA info by @natefoo in https://github.com/galaxyproject/galaxy/pull/16730
• [24.0] Raise RequestParameterInvalidException when url is invalid by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18155
• More unit testing for object store stuff. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18136
• [24.0] Drop redundant error message by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18156
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/18125
• Display DOIs in Archived Histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18134
• Addition of release process doc by @dannon in https://github.com/galaxyproject/galaxy/pull/17680
• [24.0] Fix error message when accessing restricted Zenodo records by @davelopez in https://github.com/galaxyproject/galaxy/pull/18169
• Small refinements and fixes to new release process doc by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18170
• Add onedata objectstore by @bwalkowi in https://github.com/galaxyproject/galaxy/pull/17540
• Change InvocationsList into a grid using GridList by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18088
• Add support for additional media types by @arash77 in https://github.com/galaxyproject/galaxy/pull/18054
• [24.0] Downgrade count lines error to warning by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18175
• [24.0] Emit warning when user-cancelled job already complete by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18178
• Fix boto3-stubs typecheck dependency by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18173
• Add an Invocations Panel for the Invocations activity by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18137
• Enhance form drilldown by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/18074
• Merge 24.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18177
• Set minimal metadata also for empty bed datasets by @wm75 in https://github.com/galaxyproject/galaxy/pull/17586
• De-duplication of onedata objectstore code. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18174
• Add galaxy to user agent by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18003
• Add message to Invocations panel for no invocations by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18180
• Empower users to bring their own storage and file sources by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18127
• Harden User Object Store and File Source Creation by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18172
• [24.0] Fix typos in create release documentation page by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18181
• Update db revision 24.1 release tags by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18183
• [24.1] Move activity panel go to button to top by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18182
• [24.1] Update version to 24.1.rc1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18184
• [24.0] Fix on success redirect by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18187
• Add pagination support to Files Source plugins by @davelopez in https://github.com/galaxyproject/galaxy/pull/18059
• [24.0] Fix Edit Dataset UI when there is an error retrieving the dataset by @davelopez in https://github.com/galaxyproject/galaxy/pull/18188
• [24.0] Avoid object store path lookup when constructing JobState object by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18190
• [24.0] Fix make all histories private with immutable histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18200
• [24.1] Fix selection highlight in Files Dialog when using items provider by @davelopez in https://github.com/galaxyproject/galaxy/pull/18201
• [24.0] Remove legacy code, reference to sqlalchemy migrate by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18202
• [24.0] Fix submitted value in workflow run form if data is constrained by tag filter by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18193
• [24.0] Add string cast for dbkey / genome_build by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18207
• [24.0] Include stack when reporting delete error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18208
• [24.0] Replace Multiselect selectLabel with icons in FormSelect by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18194
• [24.1] Fix file source search query with empty string value by @davelopez in https://github.com/galaxyproject/galaxy/pull/18191
• [24.0] Fix pca 3d rendering of tabular files and visualization error handling in general by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18211
• [24.0] Don't fail metadata if we only have an extra output files dir by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18179
• [24.0] Add GenericItem error handling by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18203
• [24.0] Backport #18197 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18212
• [24.0] Use config_section to distinguish between galaxy and ts or other apps by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18215
• [24.0] Prevent anonymous and inactive users from running workflows by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18192
• [24.1] Revert some requests import changes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18199
• [24.0] Restrict job_files access to jobs that are not terminal by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18217
• [24.0] Check dataset state when attempting to acces dataset contents by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18214
• [24.0] do not expand datasets that are known to be inaccessible by @martenson in https://github.com/galaxyproject/galaxy/pull/17818
• [24.0] Raise RequestParameterInvalidException if url can't be verified by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18230
• [24.0] Don't set dataset peek for errored jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18231
• [24.0] Decrease log level for expected visualization errors by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18229
• [24.0] Raise appropriate exception if accessing deleted input file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18223
• [24.0] Reset content-length for unhandled exceptions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18233
• [24.0] Fix element serialization for collections that aren't populated yet by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18235
• [24.0] Fix userOwnsHistory conditions by @davelopez in https://github.com/galaxyproject/galaxy/pull/18243
• Merge 24.0 into 24.1 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18239
• [24.1] Tighten axt sniffer by @martenson in https://github.com/galaxyproject/galaxy/pull/18204
• [24.1] Drop restriction to switch to immutable histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18234
• [24.1] Allow bookmarking public workflows by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18247
• [24.1] Change ActivityPanel go to button to primary by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18244
• [23.1] Minor fix to enable external hgweb process by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18256
• [24.0] Skip tests if toolshed, dx.doi not responding by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18250
• [23.1] Add missing TS migration by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18267
• [24.1] Merge 24.0 into 24.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18270
• [23.2] Add hgweb_repo_prefix attribute to TestToolShedConfig by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18268
• [24.0] Format with black by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18273
• [24.1] Fix handler: access to result row items changed in SA2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18274
• [24.0] Transparently open compressed files in DatasetDataProvider by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18248
• [24.0] Raise exception when extracting dataset from collection without datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18249
• [24.0] Fix Invenio credentials handling by @davelopez in https://github.com/galaxyproject/galaxy/pull/18255
• [24.1] Fix history export error handling by @davelopez in https://github.com/galaxyproject/galaxy/pull/18251
• [23.1] Add revision tags for TS migration in 23.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18271
• [24.1] Remove linter for unstripped text content for tool xml leaves by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18252
• [24.0] Only log error if deleting directory really failed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18236
• [24.0] Don't attempt to download purged datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18278
• [24.0] Set page importable to false when serializing by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18263
• [24.0] Fix firstdatasetelement type hint by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18284
• [23.2] Add toolshed database revision tags for 23.2 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18293
• [24.0] Add TS db revision tags for 24.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18294
• [24.0] Use correct link for log in or register in Copy Modal by @davelopez in https://github.com/galaxyproject/galaxy/pull/18289
• [24.0] Redirect anonymous users to home when importing public histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18286
• [24.0] Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in https://github.com/galaxyproject/galaxy/pull/18283
• [24.0] Move tool shed specific driver function to tool_shed.test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18296
• [24.1] Fix "label updated" popup triggers too often by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18303
• [24.1] Fix various packages' issues by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18301
• [24.1] Adds pinia to manually mounted vue components by @guerler in https://github.com/galaxyproject/galaxy/pull/18299
• [24.0] Don't serialize display application links for deleted datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18307
• [24.1] Fix non-history items drag&drop into histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/18308
• [24.1] Small bug fixes for user data plugins by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18246
• [24.1] Backport Qiskit Jupyter Notebook update to 24.1 by @natefoo in https://github.com/galaxyproject/galaxy/pull/18310
• [24.1] Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in https://github.com/galaxyproject/galaxy/pull/18305
• Fix the link to the carbon config by @bgruening in https://github.com/galaxyproject/galaxy/pull/18314
• [24.1] Display error message if not an image in reports by @davelopez in https://github.com/galaxyproject/galaxy/pull/18309
• [24.1] Fix pinia in manually mounted components by @davelopez in https://github.com/galaxyproject/galaxy/pull/18315
• [23.1] More fixes for running the TS with external hgweb by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18279
• Merge 23.1 into 23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18320
• [23.2] Fix integration tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18326
• [23.2] Fix tool_shed package unit tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18327
• [23.2] Fix one more tool shed unit test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18328
• [24.1] Filter data dialog entries by dataset state, only display ok state by @guerler in https://github.com/galaxyproject/galaxy/pull/18313
• [23.1] Make toolshed repo permissions world-readable by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18332
• [24.0] Downgrade doi fetch error to debug by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18330
• [24.0] Fix users API serialization when listing users by @davelopez in https://github.com/galaxyproject/galaxy/pull/18329
• [24.1] Disable state filter for collections in HistoryFilters by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18324
• [23.2] Skip new history creation if user is anonymous and login is required by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18319
• [24.1] Fix word bleeding in modals, sharing page and history rename by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18306
• [24.1] Rebuild Galaxy config by @bgruening in https://github.com/galaxyproject/galaxy/pull/18325
• [24.1] Update parcel-built visualizations to use parcel v2 by @dannon in https://github.com/galaxyproject/galaxy/pull/18311
• [24.0] Fix seek in slurm memory check by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18338
• [24.1] Fix typing issue in reused variable by @davelopez in https://github.com/galaxyproject/galaxy/pull/18344
• [24.1] Fix visualizations compatible dataset filtering by @davelopez in https://github.com/galaxyproject/galaxy/pull/18343
• [24.0] Fix authentication error for anonymous users querying jobs by @davelopez in https://github.com/galaxyproject/galaxy/pull/18333
• Fix #18316 (anonymous file sources) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18352
• [24.1] Merge 24.0 into 24.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18353
• [23.2] Allow DCE as outer input to to_cwl by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18349
• [24.1] More structured indexing for user data objects. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/18291
• [24.0] Fix anonymous user job retrieval logic by @davelopez in https://github.com/galaxyproject/galaxy/pull/18358
• [24.1] Fix check for anonymous by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18364
• [24.1] Merge 24.0 into 24.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18365
• [24.0] Do not copy purged outputs to object store by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18342
• [24.1] Add copy link to published workflow in WorkflowCard by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18370
• [24.0] Sanitize FormElement error messages by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18377
• [24.0] Drop unnecessary escaping for workflow name and annotation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18376
• [24.0] Fix user's private role can be missing by @davelopez in https://github.com/galaxyproject/galaxy/pull/18381
• [24.0] Make sure that all Linter subclasses are imported for listing them by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18339
• [24.1] Allow running and editing workflows for specific versions by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18378
• [24.0] Kill pulsar job if job stopped on galaxy side by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18348
• [24.0] Fix null inputs in database operation tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18385
• [24.1] Fix empty usernames in database + bug in username generation by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18379
• [24.1] Fix duplicated requests when browsing files sources with pagination by @davelopez in https://github.com/galaxyproject/galaxy/pull/18387
• [24.1] Fix dataset details polling re-render by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18388
• [24.0] Fix workflow editor tool form scroll memory by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18390
• [24.1] Onedada object store and files source stability fixes by @bwalkowi in https://github.com/galaxyproject/galaxy/pull/18372
• [24.1] Merge 24.0 into 24.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18393
• [24.1] Reset current page when browsing sub-folders in FilesSources by @davelopez in https://github.com/galaxyproject/galaxy/pull/18395
• [24.0] Fix update group API payload model by @davelopez in https://github.com/galaxyproject/galaxy/pull/18374
• [24.0] Allow in_range validator for selects by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18403
• [24.0] Fix invocation stepjobsummary for new collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18402
• [24.0] Fix get_accessible_job if called without session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18400
• [24.1] Ensure datatypes match on dragging elements into FormData by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18410
• [24.0] Fix collection map over status for dragged collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18416
• [24.0] Serialize purged flag for datasets in collections by @davelopez in https://github.com/galaxyproject/galaxy/pull/18420
• [24.1] Add TypedDict for JobsSummary by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18418
• [24.0] Really allow in-range validator for txt by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18411
• [24.0] Assign default data extension on discovered collection output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18389
• [24.1] Fix workflow tags initialisation in workflow editor by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/18396
• [24.1] Fix input_step_parameters missing values that don't have a label by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18405
• [24.0] Minor linting cleanup by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18421
• [24.1] Pin pydantic to >=2.7.4 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/18423
• [24.1] Release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18218
• [24.1] Add latest PRs to release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18424

New Contributors

• @martin-g made their first contribution in https://github.com/galaxyproject/galaxy/pull/17693
• @tianzedavid made their first contribution in https://github.com/galaxyproject/galaxy/pull/18076
• @dcore94 made their first contribution in https://github.com/galaxyproject/galaxy/pull/18085
• @Edmontosaurus made their first contribution in https://github.com/galaxyproject/galaxy/pull/18106
• @bwalkowi made their first contribution in https://github.com/galaxyproject/galaxy/pull/17540

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.0.2...v24.1

- Python
Published by jdavcs almost 2 years ago

galaxy - v24.0.2

What's Changed

• [24.0] Adds logging of messageExceptions in the fastapi exception handler. by @dannon in https://github.com/galaxyproject/galaxy/pull/18041
• [24.0] Improve error message for Extract dataset tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18078
• [23.2] Fix history export with missing dataset hids by @davelopez in https://github.com/galaxyproject/galaxy/pull/18083
• [24.0] CitationsList - fix prop spec and config access. by @dannon in https://github.com/galaxyproject/galaxy/pull/18061
• [24.0] Tool linters: allow to skip by old linter names (by allowing to skip linter modules) by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18091
• [24.0] History Multiview panel shows pinned histories on top by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/18092
• [24.0] tool linters: output filters should only consider child filter nodes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/18096

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.0.1...v24.0.2

- Python
Published by mvdbeek about 2 years ago

galaxy - v24.0.1

What's Changed

• [24.0] Fix hasOwner function for histories in client by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17886
• [23.2] Added 4dnpairs and 4dnpairsam datatypes by @SaimMomin12 in https://github.com/galaxyproject/galaxy/pull/17875
• [24.0] Always serialize element_count and populated when listing contents by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17890
• [24.0] Fix release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17894
• [24.0] Make wait_for_history_jobs look at jobs, not datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17892
• [24.0] Fix deadlock that can occur when changing job state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17896
• [24.0] Fix search and version menu in docs by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17898
• [24.0] Fix conditional Image imports by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17899
• [24.0] Fix workflow run form failing on certain histories by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17869
• [23.2] Fix saving workflows with freehand_comments only by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17901
• [24.0] do not show copy button when editing by @martenson in https://github.com/galaxyproject/galaxy/pull/17895
• [24.0] Do not save workflow on Run without user confirmation by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17907
• [24.0] Rebuild config samples by @davelopez in https://github.com/galaxyproject/galaxy/pull/17911
• [24.0] Fix lost reports when switching workflow versions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17904
• [24.0] Make sure step removal also resets mapOver state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17915
• [23.2] Adjust updatecwlconformance_tests.sh for removed branch by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17916
• [24.0] Adjust release notes to use the same language as interface by @martenson in https://github.com/galaxyproject/galaxy/pull/17919
• [24.0] Fix saving user preferences crashes tab by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17917
• [24.0] Always discard session after _handlewaiting_jobs is done by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17913
• [24.0] Fix workflow run form for workflows with null rename PJA by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17929
• [24.0] Fix tool form building if select filters from unavailable dataset metadata by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17930
• [24.0] Fix InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands. by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17932
• [24.0] Never fail dataset serialization if display_peek fails by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17937
• [24.0] Drop left-over debug statement by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17939
• [23.0] Fix output datatype when uncompressing a dataset with incorrect datatype by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17944
• [24.0] Fix tool version switch in editor by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17858
• [23.2] Fix missing implicit conversion for mapped over jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17952
• [23.0] Fix KeyError in XForwardedHostMiddleware by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17955
• [24.0] Revert unnecessary error change by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17948
• [24.0] Fix notification display time by @davelopez in https://github.com/galaxyproject/galaxy/pull/17965
• [23.2] Fix message input type for notifications in admin panel by @davelopez in https://github.com/galaxyproject/galaxy/pull/17966
• [23.2] Set fromtoolform: true when saving new workflow by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17972
• [24.0] Update _thanks.rst in the User Release Notes to include new socials and remove inactive ones by @natwhitaker in https://github.com/galaxyproject/galaxy/pull/17971
• [24.0] Show dataset image in workflow_outputs display listing. by @dannon in https://github.com/galaxyproject/galaxy/pull/17964
• [24.0] Fix filtering workflow outputs by type in markdown directives by @davelopez in https://github.com/galaxyproject/galaxy/pull/17977
• [24.0] Fix getcontentas_text for compressed text datatypes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17976
• [24.0] History import - show user feedback on completion. by @dannon in https://github.com/galaxyproject/galaxy/pull/17980
• [24.0] Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17981
• [24.0] Fix LengthValidator if no value passed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17983
• [24.0] Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17985
• [24.0] Use or copy StoredWorkflow when copying step by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17988
• [23.2] Don't attempt to commit in dry_run mode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17987
• [23.2] Invenio plugin fixes by @davelopez in https://github.com/galaxyproject/galaxy/pull/17997
• [24.0] Update prebuilt client by @dannon in https://github.com/galaxyproject/galaxy/pull/18000
• [24.0] Preserve surrounding whitespace when localizing complex nodes by @dannon in https://github.com/galaxyproject/galaxy/pull/18005
• [24.0] Use the new column-select component in FormData for multiple select by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17990
• [24.0] Don't fail if reporting invalid parameter values by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18002
• [24.0] Raise MessageException when report references invalid workflow output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18009
• [24.0] Include exception info when something goes wrong while refreshing tokens by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18008
• [24.0] Reduce notifications polling frequency by @davelopez in https://github.com/galaxyproject/galaxy/pull/18010
• [24.0] Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18011
• [24.0] Don't commit without having set a hid by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18014
• [24.0] Add a link to histories list in history import message for situations… by @dannon in https://github.com/galaxyproject/galaxy/pull/18021
• [24.0] Fix test_get_tags_histories_content test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18026
• [24.0] Fix tag regex pattern by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18025
• [24.0] Backport colabfold tar file datatype by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18029
• [24.0] Fix remote files sources error handling by @davelopez in https://github.com/galaxyproject/galaxy/pull/18027
• [24.0] Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18023
• [24.0] Change wrong quota_source value from KeyError to ValueError by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18040
• [24.0] Fix History Dataset Association creation so that hid is always set by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18036
• [24.0] Ensure that offset and limit are never negative by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18044
• [24.0] clarify the object store relocate functionality by @martenson in https://github.com/galaxyproject/galaxy/pull/18033
• [24.0] Add middleware for logging start and end of request by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/18046
• [23.2] Updated the datatypes name for FASTK tool by @SaimMomin12 in https://github.com/galaxyproject/galaxy/pull/18053
• [24.0] Fix comments lost on import by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/18060
• [24.0] Fix history export with missing dataset hids by @davelopez in https://github.com/galaxyproject/galaxy/pull/18052
• [24.0] Check database connection to issue a rollback if no connection by @jdavcs in https://github.com/galaxyproject/galaxy/pull/18070
• [24.0] Fix history update time after bulk operation by @davelopez in https://github.com/galaxyproject/galaxy/pull/18068

New Contributors

• @SaimMomin12 made their first contribution in https://github.com/galaxyproject/galaxy/pull/17875
• @natwhitaker made their first contribution in https://github.com/galaxyproject/galaxy/pull/17971

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v24.0.0...v24.0.1

- Python
Published by mvdbeek about 2 years ago

galaxy - v24.0.0

For a list of curated highlights see the release announcement at https://docs.galaxyproject.org/en/latest/releases/24.0announceuser.html

What's Changed

• Version 23.3.dev by @dannon in https://github.com/galaxyproject/galaxy/pull/17096
• Python 3.8 as minimum by @mr-c in https://github.com/galaxyproject/galaxy/pull/16954
• SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16932
• Add history items display state for collections/lists with failed or new populated_state by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16996
• Dataset Display : force reload on subsequent clicks. by @dannon in https://github.com/galaxyproject/galaxy/pull/16982
• Remove web framework dependency from tools by @davelopez in https://github.com/galaxyproject/galaxy/pull/17058
• Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17115
• Vueify Admin User Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/17030
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17123
• SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17122
• Vueify Admin Roles Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/17118
• Migrate job destination parameters store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/17119
• Vueify Admin Groups Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/17126
• Migrate dataset extra files store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/17145
• Vueify Admin Forms and Quota grids by @guerler in https://github.com/galaxyproject/galaxy/pull/17141
• Don't require admin user to list /api/tool_data by @jozh2008 in https://github.com/galaxyproject/galaxy/pull/17161
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17157
• Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17132
• Add keyedCache composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/17148
• Replace discouraged Mambaforge with Miniforge3 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17177
• Qiskit in galaxy by @thepineapplepirate in https://github.com/galaxyproject/galaxy/pull/17170
• Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17184
• Add future=True flag to SA engine by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17174
• Add future=True flag to SA session by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17179
• Convert dataset path destination store to composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/17175
• Clarify the meaning of lexical sorting of discovered datasets by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17190
• Update DatasetError.vue to fix broken link by @jennaj in https://github.com/galaxyproject/galaxy/pull/17193
• Fix for converter tests by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17188
• xsd: reorder choices for permissive boolean by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17187
• Accept any number of arguments to the secret decoder ring by @natefoo in https://github.com/galaxyproject/galaxy/pull/17191
• correct dbkey for minerva display app by @hexylena in https://github.com/galaxyproject/galaxy/pull/17196
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17201
• Bump default milestone to 24.0 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17211
• Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/17153
• Reload built-in converters on toolbox reload by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17209
• Improve links to Hub, Matrix and WGs in CONTRIBUTING.md by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17221
• Add a3m datatype by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/17217
• Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17216
• Vendorize fastapi-utls.cbv by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17205
• Migrate workflow invocation store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/17203
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17230
• Expose more tool information / navigability in UI. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17105
• Implement Galaxy Markdown directive historydatasetas_table. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16681
• port invocation API to fastapi by @martenson in https://github.com/galaxyproject/galaxy/pull/16707
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17235
• Support for OIDC API Auth and OIDC integration tests by @nuwang in https://github.com/galaxyproject/galaxy/pull/16977
• Reuse test instance during non-integration tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17234
• Workflow node connector improvements by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17240
• Build and cache galaxy client for selenium and startup tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17239
• tus wants a json response from v2.0.0 by @mira-miracoli in https://github.com/galaxyproject/galaxy/pull/17246
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17247
• Add missing re-usable commit-id output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17248
• Update CONTRIBUTORS.md with new email address for Jeremy Goecks by @jgoecks in https://github.com/galaxyproject/galaxy/pull/17255
• Make flex panel drag handle more obvious by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17113
• Bump follow-redirects from 1.15.1 to 1.15.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17260
• Migrate models to pydantic 2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17262
• Optional Reply-to SMTP header in tool error reports by @neoformit in https://github.com/galaxyproject/galaxy/pull/17243
• Fixes for output discovery by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17266
• Convert sample object store configuration to YAML and support configuring inline by @natefoo in https://github.com/galaxyproject/galaxy/pull/17222
• Fix invocation serialization if no state was set by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17278
• Toward declarative help for Galaxy markdown directives. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16979
• Render Useful Markdown Components for Mapped Over Steps by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17198
• Workflow node connector improvements followup by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17244
• Vueifiy History Grids by @guerler in https://github.com/galaxyproject/galaxy/pull/17219
• Add OIDC backend configuration schema and validation by @uwwint in https://github.com/galaxyproject/galaxy/pull/17274
• Fix Workflow Comment Model for Pydantic 2 by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17296
• Improve ModelManager type hints by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17299
• Fix any type for tooldatafile_path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17293
• Package tests fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17301
• Follow-up on #17274 and #17262 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17302
• Scoped Store Refactor and Store Composition Refactor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17304
• Refactor two of the missing invocation routes to FastAPI by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/17237
• Allow job files to consume TUS uploads by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17242
• Rollback invalidated transaction: catch them earlier by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17312
• Make Workflow Editor Toolbar Toggleable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17297
• Enable job resubmissions in k8s runner by @nuwang in https://github.com/galaxyproject/galaxy/pull/17324
• Adjust Flex Panel Drag Handle and Collapse Button by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17298
• Add accepted extensions to form data input by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17238
• Overhaul Galaxy Markdown Help by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17228
• Document SQLAlchemy session lifespan by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17322
• add documentation for data source tool by @PlushZ in https://github.com/galaxyproject/galaxy/pull/17327
• [23.2] fix s3fs templating by @bgruening in https://github.com/galaxyproject/galaxy/pull/17311
• Add support for Python 3.12 by @tuncK in https://github.com/galaxyproject/galaxy/pull/16796
• Fix quotas ID encoding by @davelopez in https://github.com/galaxyproject/galaxy/pull/17335
• Fixes for flake8-bugbear 24.1.17 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17340
• Port HistoryPanel component to composition API and typescript by @Renni771 in https://github.com/galaxyproject/galaxy/pull/17318
• Merge 23.2 into dev by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17345
• Escape pipe character in tool XSD docs by @neoformit in https://github.com/galaxyproject/galaxy/pull/17359
• Remove unused statements in job search function by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17361
• Convert entryPointStore to composition API + TS by @davelopez in https://github.com/galaxyproject/galaxy/pull/17356
• XSD schema doc building: quote pipe characters in attribute tables by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17364
• Add explicit cache_ok attribute to JSONType subclass by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17376
• Fix type annotation of code using XML etree by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17367
• Merge 23.2 into dev (minor release notes edit) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17387
• Remove remaining Vuex stores and dependencies by @davelopez in https://github.com/galaxyproject/galaxy/pull/17348
• Fix minor oidcbackendsconfig comment bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17385
• Unify continuous polling with composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/17355
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17333
• Adds delete, purge and undelete batch operations to History Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/17282
• More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17381
• Fix activity-settings hidden behind left side panel bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17392
• Update to black 2024 stable style by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17391
• New Activity bar - Notifications by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17300
• Update current version to 24.0.dev0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17402
• Merge 23.2 into dev by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17407
• Fix z-index in BroadcastContainer.vue by @davelopez in https://github.com/galaxyproject/galaxy/pull/17401
• Fix IUC best practices links, mention datasourceasync in XSD by @wm75 in https://github.com/galaxyproject/galaxy/pull/17409
• Enable comments in package dag file by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17408
• Cancel all active jobs when the user is deleted by @davelopez in https://github.com/galaxyproject/galaxy/pull/17390
• Purge groups and roles from DB (for real) by @davelopez in https://github.com/galaxyproject/galaxy/pull/17411
• Add signpost to training material by @nuwang in https://github.com/galaxyproject/galaxy/pull/17421
• Refactor MarkdownDialog.vue to ts+composition. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17399
• Remove legacy tool versions list from admin panel by @guerler in https://github.com/galaxyproject/galaxy/pull/17155
• Some additional typing for test interactor stuff. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17398
• Fix model store exports that include implicit conversions. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17346
• Combines legacy qv-pattern and advanced filter pattern in history index endpoint by @guerler in https://github.com/galaxyproject/galaxy/pull/17368
• API endpoint that allows "changing" the objectstore for "safe" scenarios. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17329
• Much simpler default dataset permissions for typical users. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17166
• Fix text to match options in HistoryStorageOverview by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17450
• Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster by @guerler in https://github.com/galaxyproject/galaxy/pull/17415
• Removes outdated Grid controller and backbone modules by @guerler in https://github.com/galaxyproject/galaxy/pull/17434
• Refactor Common components by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17441
• Enable warn_unreachable mypy option by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17365
• Custom Multiselect by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17331
• Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17444
• Allow removing last value from multi select field by @guerler in https://github.com/galaxyproject/galaxy/pull/17403
• Add tool XML schema documention for outputs - collection - data by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17465
• Update release process documentation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17461
• Move Activity Bar Settings to Activity by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17457
• Use short link for TPV shared database by @nuwang in https://github.com/galaxyproject/galaxy/pull/17467
• Add select parameter with options from remote resources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17087
• Exclude password reset link from login form where users don't have the ability to manage accounts by @dannon in https://github.com/galaxyproject/galaxy/pull/17473
• Modernize bits and pieces of storage display by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17436
• Fix for a regression change - auto-select/highlight file name text by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/17466
• Fix datasource and datasource_async bugs by @wm75 in https://github.com/galaxyproject/galaxy/pull/17422
• Move Visualizations Activity to Side Panel by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17458
• History refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17353
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17420
• Tag Autocomplete Rework by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17469
• Adds published histories to grid list by @guerler in https://github.com/galaxyproject/galaxy/pull/17449
• LDAP3 fix for attributes returned as strings by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17305
• Type annotation and refactoring of tests by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17484
• UI for "relocating" a dataset to a new object store (when safe) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17437
• New Workflow List and Card View by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16607
• Split linters in separate classes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17081
• Citation refactors by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17483
• Bump undici from 5.26.5 to 5.28.3 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/17485
• Display workflow invocation counts. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17488
• Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17435
• build_mulled: also use namespace for building singularity images by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15657
• Update k8s docker python to 3.12 by @nuwang in https://github.com/galaxyproject/galaxy/pull/17494
• Faster FASTA and FASTQ metadata setting by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17462
• Allow filtering history datasets by object store ID and quota source. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17460
• Removes legacy history xml makos by @guerler in https://github.com/galaxyproject/galaxy/pull/17505
• Add documentation on how to use vault keys in file sources by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17498
• Add gxadmin to docker and update branch by @nuwang in https://github.com/galaxyproject/galaxy/pull/17521
• Stringify cgroups metrics formatted value return by @dannon in https://github.com/galaxyproject/galaxy/pull/17520
• [23.2] Fix bug: create new PSAAssociation if not in database by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17516
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17486
• Add History Multiview activity+panel, add "Show Recent" mode to multiview by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17251
• Update RStudio GxIT to use the reworked 23.1 image by @natefoo in https://github.com/galaxyproject/galaxy/pull/17533
• add encode ID API endpoint by @mira-miracoli in https://github.com/galaxyproject/galaxy/pull/17510
• Consolidate resource grids into tab views by @guerler in https://github.com/galaxyproject/galaxy/pull/17487
• Consider Null inputs by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17271
• data_column parameter: use column_names metadata if present by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17478
• [23.2] Fix social_core methods by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17530
• Workflow list small tweaks by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17538
• freeze (make sticky) header row in tabular files by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/17455
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17541
• [23.2] Fix emission estimates typo by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17543
• Workflow anonymous user buttons by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17537
• add npy datatype by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/17517
• Fixing data_source tools and incrementing tool profile by @wm75 in https://github.com/galaxyproject/galaxy/pull/17515
• has_size assertion: implement size (as synonym for value) by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17490
• Hide wigtobigWig tool by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17328
• Allow for upper case container tags by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17254
• Change default milestone to target 24.1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17549
• Add harmonize collections tool (or whatever other name) by @lldelisle in https://github.com/galaxyproject/galaxy/pull/16662
• Fix test_index_advanced_filter API test re-running by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17547
• Refactor Workflow API routes - Part 1 by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/17463
• Enable workflow buttons right click by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17529
• Enhance Avivator display app to support regular Tiffs by @davelopez in https://github.com/galaxyproject/galaxy/pull/17554
• Add basic TIFF Image visualization by @davelopez in https://github.com/galaxyproject/galaxy/pull/17553
• Add nameeq and genomebuild_eq filters to HistoryFilters by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17389
• Remove virtual scroller from History by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17546
• Update .gitignore by @davelopez in https://github.com/galaxyproject/galaxy/pull/17559
• [23.2] Associate default history with session when creating a new session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17557
• tests: check ftype and decompress interaction by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17545
• Filter out subworkflow invocations by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17558
• Drop plugin-based new user welcome. by @dannon in https://github.com/galaxyproject/galaxy/pull/17568
• add shm_size based on ShmSize by @richard-burhans in https://github.com/galaxyproject/galaxy/pull/17565
• Refactor Workflow Import components by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17495
• Add help text to workflow invocation states by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17569
• Add multiple drag/drop and keyboard accessible selection to HistoryPanel items by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17502
• Add element_identifier and ext to inputs config file export by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17357
• Add support for (fast5.tar).xz binary compressed files by @tuncK in https://github.com/galaxyproject/galaxy/pull/17106
• Update tour testing selector usage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14005
• Feature SBOL datatypes by @guillaume-gricourt in https://github.com/galaxyproject/galaxy/pull/17482
• Make columns types an empty list for empty tabular data by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/13918
• Remove legacy phyloviz, circster and sweepster artifacts by @guerler in https://github.com/galaxyproject/galaxy/pull/17573
• Links to individual invocations. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17566
• [23.2] Account for newlines in CIF Datatype sniffer by @patrick-austin in https://github.com/galaxyproject/galaxy/pull/17582
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17580
• consistently compare profile versions by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16492
• Apply default theme to theme selector by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17583
• Add image_diff comparison method for test output verification using images by @kostrykin in https://github.com/galaxyproject/galaxy/pull/17556
• Add migrations revision identifier for 24.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17589
• [23.2] Fix test_page_encoding and test_collection_explicit_and_implicit integration tests by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17584
• [23.1] Fix ancient bug: incorrect usage of func.coalesce in User model by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17577
• [24.0] Update version to 24.0.rc1 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17591
• [24.0] Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in https://github.com/galaxyproject/galaxy/pull/17294
• [23.2] Fix tool shed webapp by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17597
• [24.0] Extend regex groups in stdio regex matches by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17016
• [24.0] Fix test_oidc_login_existing_user test by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17612
• [23.2] Don't call get_or_create_default_history() twice for invalidated sessions by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17613
• [23.2] Anticipate PendingRollbackError in check_database_connection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17598
• [24.0] Fix bugs relating to history keyboard navigation by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17587
• [24.0] Make latestworkflowuuid optional by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17629
• [24.0] Increase ContentItem clickable area by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17621
• [23.2] Fix switch to history in invocations list by @davelopez in https://github.com/galaxyproject/galaxy/pull/17616
• [24.0] default sort all grid histories the same by @martenson in https://github.com/galaxyproject/galaxy/pull/17635
• [24.0] do not link to invocations for workflow that has never run by @martenson in https://github.com/galaxyproject/galaxy/pull/17626
• [24.0] More efficient change_state queries, maybe fix deadlock by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17632
• [24.0] Fix workflow person validation by @dannon in https://github.com/galaxyproject/galaxy/pull/17636
• [24.0] Make WorkflowInput label, value and uuid optional by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17638
• [23.1] Fix DataResult type by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17639
• [24.0] Prevent 500 for anon /api/invocations by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17640
• Merge 23.2 into 24.0 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17644
• [24.0] Don't fail for anon /api/users request by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17645
• [23.2] Fix tool panel workflow and favorites button bugs by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17634
• [24.0] Don't index tasks without task_uuid by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17646
• [24.0] Add basic model import attribute validation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17628
• [23.2] Yaml nested assertions: fix parsing by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17641
• [24.0] Fix history panel arrow navigate by id bug, add HistoryOperations to HistoryView and prevent item selection in unowned histories by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17648
• [24.0] fix shared item details and initial filters by @martenson in https://github.com/galaxyproject/galaxy/pull/17651
• [23.2] Npz sniffing: do not read the whole file by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17674
• [24.0] Drop release notes webhook by @dannon in https://github.com/galaxyproject/galaxy/pull/17675
• [24.0] Fix contentitem display routing. by @dannon in https://github.com/galaxyproject/galaxy/pull/17687
• [23.2] Assert that at least one file in npz zipfile ends with .npy by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17679
• [23.2] Separate ConnectedValue from RuntimeValue by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17678
• [23.2] Limit new anon histories by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17657
• [24.0] Purge history from history panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17685
• [24.0] Moves archived histories from Masthead to Histories Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/17649
• [24.0] Fix incorrect history item count in histories lists by @davelopez in https://github.com/galaxyproject/galaxy/pull/17714
• [24.0] Fix archived histories tab anonymous access by @davelopez in https://github.com/galaxyproject/galaxy/pull/17719
• [24.0] Improve published histories listing performance in UI by @davelopez in https://github.com/galaxyproject/galaxy/pull/17717
• [24.0] Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17716
• [24.0] Workflow Comment Indexing by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17700
• [24.0] Fix date range popover cutoff in history swtich by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17724
• [24.0] Always display grid pagination on the right by @guerler in https://github.com/galaxyproject/galaxy/pull/17722
• [24.0] Fix Workflow Name Display in WorkflowCard to Prevent Bleeding Over Borders by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17721
• [24.0] Fix Collection Scrolling not showing all items by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17720
• [24.0] fix overflowing and hiding of storage popovers by @martenson in https://github.com/galaxyproject/galaxy/pull/17742
• [24.0] Prevent dragover for item from same history in history panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17761
• [24.0] Fix usage of DISTINCT by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17759
• [24.0] Fix tag sorting by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17753
• [24.0] Fix histories API index_query serialization by @davelopez in https://github.com/galaxyproject/galaxy/pull/17726
• [24.0] Don't require history to calculate anon disk usage by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17765
• [23.1] Handle missing indexer for a dataset by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17736
• [24.0] Fix input parameter step type by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17767
• [24.0] Fix anon user values again by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17772
• [24.0] Revise language around non-private object stores by @martenson in https://github.com/galaxyproject/galaxy/pull/17744
• [24.0] Fix include_nested_invocations parameter use by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17768
• [24.0] change user-facing language from "object store" to "storage location" by @martenson in https://github.com/galaxyproject/galaxy/pull/17763
• [24.0] Add missing fields in histories listings by @davelopez in https://github.com/galaxyproject/galaxy/pull/17775
• [24.0] Grid filtering bug fixes by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17684
• [24.0] Minor log cleanup. by @dannon in https://github.com/galaxyproject/galaxy/pull/17789
• [24.0] Clarify language about the activity bar being beta by @dannon in https://github.com/galaxyproject/galaxy/pull/17790
• [24.0] Swap history dropdown from using the tiny caret to faBars. by @dannon in https://github.com/galaxyproject/galaxy/pull/17791
• [24.0] Avoid showing a shareable URL with the default slug/username. by @dannon in https://github.com/galaxyproject/galaxy/pull/17788
• [24.0] Use hg clone --stream to clone repos by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17786
• [24.0] Fix visualization activity plugin list images by @dannon in https://github.com/galaxyproject/galaxy/pull/17792
• [24.0] Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17777
• [24.0] Defer job attributes that are usually not needed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17795
• [24.0] Prompt user to change default history permissions... by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17782
• [24.0] Restore histories API behavior for keys query parameter by @davelopez in https://github.com/galaxyproject/galaxy/pull/17779
• [24.0] Fix new default history creation when in remote or single user mode by @dannon in https://github.com/galaxyproject/galaxy/pull/17796
• [24.0] Fix anonymous user create, run and import workflows by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/17776
• [24.0] Fix history filters taking up space in GridList by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17652
• [24.0] Fix source history update_time being updated when importing a public history by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17728
• [24.0] Fix change_datatype PJA for dynamic collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17803
• [24.0] Fix datasets API custom keys encoding by @davelopez in https://github.com/galaxyproject/galaxy/pull/17793
• [24.0] Return published histories first in displaybyusernameandslug by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17808
• [24.0] Improve Shift+Click select in history panel and add it for ContentItem selector checkboxes as well by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17762
• [24.0] Datasets list anonymous access and history link fixes. by @dannon in https://github.com/galaxyproject/galaxy/pull/17756
• [24.0] remove link to non existent page from Data menu by @martenson in https://github.com/galaxyproject/galaxy/pull/17816
• [24.0] Show full Data menu when in single user mode. by @dannon in https://github.com/galaxyproject/galaxy/pull/17815
• [23.2] Backport of #17796 by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17824
• [24.0] Simplify nested collection joins by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17817
• [23.0] Fix excessive memory usage for npz files by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17828
• [24.0] Fix very slow user data table query by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17830
• [24.0] Update db revision 24.0 release tags by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17834
• [24.0] Fix optional types in Help Forum API by @davelopez in https://github.com/galaxyproject/galaxy/pull/17832
• [24.0] Improved error messages for runtime sharing problems. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17794
• [24.0] Minor refactor of query building logic for readability by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17835
• [23.2] Fix error in release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17837
• [24.0] Allow admin to sharpen language about selected object stores. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17806
• [24.0] Fix Help Forum Integration uses Long ID by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17844
• [23.2] Proxy Access-Control-* headers when using x-accel-redirect by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17842
• [24.0] Fix incorrect miscinfo 'fix this' display by @dannon in https://github.com/galaxyproject/galaxy/pull/17851
• [23.2] Fix user login when duplicate UserRoleAssociation exists by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17854
• [24.0] Fix Multi-History status bar reactivity by @davelopez in https://github.com/galaxyproject/galaxy/pull/17812
• [24.0] Embed fix by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17852
• [24.0] Fix activity bar unreachable in some pages by @davelopez in https://github.com/galaxyproject/galaxy/pull/17860
• [24.0] Fix tool panel loading delay by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17847
• [24.0] Embed download fix by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17861
• [24.0] wait for config to load with user prefs options by @martenson in https://github.com/galaxyproject/galaxy/pull/17865
• [23.1] Normalize extensions when loading tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17868
• [24.0] Record missing outputs as test errors by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17874
• [24.0] Ignore user data table errors for now by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17880
• [24.0] 24.0 release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17610
• [24.0] Fix archived histories mixing with active in histories list by @davelopez in https://github.com/galaxyproject/galaxy/pull/17856
• [24.0] Add more last minute PRs to release notes by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17887

New Contributors

• @jozh2008 made their first contribution in https://github.com/galaxyproject/galaxy/pull/17161
• @PlushZ made their first contribution in https://github.com/galaxyproject/galaxy/pull/17327
• @guillaume-gricourt made their first contribution in https://github.com/galaxyproject/galaxy/pull/17482

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.2.1...v24.0.0

- Python
Published by jdavcs about 2 years ago

galaxy - v.23.2.1

What's Changed

• [23.2] Drop empty section by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17386
• [23.2] Fix notification badge delay by @davelopez in https://github.com/galaxyproject/galaxy/pull/17349
• [23.2] Fix upload modal loses its content when closed by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17338
• [23.2] Respect upstream_gzip setting when streaming dataset collection archive by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17400
• [23.2] Ignore empty lines in packagesbydep_dag file when building packages by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17395
• [23.0] Fix uploading of docs for release_NN.N branches by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17404
• [23.1] Set webdav file source to use temp files by default by @davelopez in https://github.com/galaxyproject/galaxy/pull/17388
• [23.2] Cleanup versions, formatting in setup.cfg, HISTORY.rst in all packages by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17414
• [23.2] Fix target history when uploading files by @davelopez in https://github.com/galaxyproject/galaxy/pull/17431
• [23.0] Update python-multipart to 0.0.7 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17429
• [23.2] Fix workflow report markdown editor toolbox becoming non-responsive. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17427
• [23.1] Encode tool link consistently by @davelopez in https://github.com/galaxyproject/galaxy/pull/17426
• [23.2] add a test for multi input element when hda and dces are mixed together by @martenson in https://github.com/galaxyproject/galaxy/pull/17419
• [23.1] Fix history bulk operations menu conditions by @davelopez in https://github.com/galaxyproject/galaxy/pull/17433
• [23.0] Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17384
• [23.2] Backport model store fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17439
• [23.0] Fix bug: true >> True by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17446
• More defensive access of extra props in filesources by @nuwang in https://github.com/galaxyproject/galaxy/pull/17445
• [23.0] Fix datasetStore.saveDatasets bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17448
• [23.1] Fix history bulk operations menu (part 2) by @davelopez in https://github.com/galaxyproject/galaxy/pull/17456
• [23.1] Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17459
• [23.2] Build param dict before creating entrypoint by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17440
• [23.2] Fix creating new erronous workflow can produce multiple empty workflows by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17406
• Merge release23.1 into release23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17471
• [23.2] Fix auto-select of file name in upload (Backport of #17466) by @davelopez in https://github.com/galaxyproject/galaxy/pull/17477
• [23.2] Set metadata states on dataset association, not dataset by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17474
• [23.2] Remove two print statements by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17480
• [23.2] Fix succces typo by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17481
• [23.2] Fix merge by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17491
• [23.2] Add magres datatype by @martenson in https://github.com/galaxyproject/galaxy/pull/17499
• [23.2] Provide working routes.url_for every ASGI request by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17497

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.2...v23.2.1

- Python
Published by jdavcs over 2 years ago

galaxy - v23.1.0

Release notes

Galaxy 23.1.0 was released on 25th of September 2023

user highlight release notes full release notes

What's Changed

list of all merged PRs

* Version 23.1.dev by @dannon in https://github.com/galaxyproject/galaxy/pull/15353 * Towards decoupling datatypes and model by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15186 * Fix bad auto-merge of dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15386 * vueify formUpload with composition API by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15409 * Bump ua-parser-js from 0.7.31 to 0.7.33 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/15425 * Outline Deployment Tests by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15420 * Drop defineEmits import from FormUpload by @dannon in https://github.com/galaxyproject/galaxy/pull/15450 * Prettier targeting refinements by @dannon in https://github.com/galaxyproject/galaxy/pull/15449 * Move database access code out of tool_util by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15467 * Follow up to #15186 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15388 * Make serving address more visible in console by @davelopez in https://github.com/galaxyproject/galaxy/pull/15468 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15492 * Stricter typescript config by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15311 * Create ToolSuccess route and refactor component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15484 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15498 * Use connection instead of session for ItemGrabber by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15496 * Implement initial tool/wf test assertions module for JSON data. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15494 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15435 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15511 * Various Tool Shed Cleanup by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15247 * xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15534 * Add basic selenium test for shared histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/15538 * Phylocanvas rebuild by @dannon in https://github.com/galaxyproject/galaxy/pull/15521 * Move TS to Alembic by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15509 * Add new release tags to manage_toolshed_db.sh script by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15542 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15546 * Use sentry-fastapi integration, expose sampling rate by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15550 * Merge release_23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15566 * Updating build-related dependencies, static cleanup. by @dannon in https://github.com/galaxyproject/galaxy/pull/15527 * Have prettier use a cache. by @dannon in https://github.com/galaxyproject/galaxy/pull/15575 * QUnit elimination by @dannon in https://github.com/galaxyproject/galaxy/pull/15452 * Update browserslist and exclusions, linting. by @dannon in https://github.com/galaxyproject/galaxy/pull/15524 * Drop workflow exports to myexperiment.org by @dannon in https://github.com/galaxyproject/galaxy/pull/15576 * Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/15517 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15581 * add missing f for f-string by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15584 * Fix jest tests run on CI by @davelopez in https://github.com/galaxyproject/galaxy/pull/15588 * Handle "email_from" config option consistently, as per schema description by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15557 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15594 * Bump undici from 5.14.0 to 5.19.1 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/15609 * Alternatively allow double quotation marks in search filters by @guerler in https://github.com/galaxyproject/galaxy/pull/15606 * Update database_heartbeat for SA 2.0 compatibility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15611 * Unify url handling with filesources by @nuwang in https://github.com/galaxyproject/galaxy/pull/15497 * Explore tool remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/15510 * Update supports_skip_locked, supports_returning for SA 2.0 compatibility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15633 * Fix call to `docker_cached_container_description` by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15598 * Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15643 * Changes to match latest playbook by @nuwang in https://github.com/galaxyproject/galaxy/pull/15647 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15652 * Install singularity in the integration GitHub workflow by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/14922 * Unpin Beaker requirement by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15665 * Fix for new style conda packages by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15446 * Add transactional state to JobHandlerStopQueue by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15671 * Add transactional state to workflow scheduling manager by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15683 * Drop model mapping unit tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15669 * Minor hid display tweak by @dannon in https://github.com/galaxyproject/galaxy/pull/15662 * Remove DELETED_NEW job state from code base by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15690 * Empower Users to Select Storage Destination by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14073 * update the admin activation docs by @martenson in https://github.com/galaxyproject/galaxy/pull/15670 * Follow up on object store selection PR. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15654 * Use chevrons instead of eye for showing expandable/collapsible sections by @dannon in https://github.com/galaxyproject/galaxy/pull/15688 * Update selenium hid text assertion by @dannon in https://github.com/galaxyproject/galaxy/pull/15691 * Verify that activation and reset emails are properly generated by @guerler in https://github.com/galaxyproject/galaxy/pull/15681 * Cleanup API schema for dropping deleted_new by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15708 * Merge release_23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15711 * Tweaks to new object store and quota APIs by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15709 * Use Animation Frame in Workflow Editor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15725 * Fix Enums in API docs by @davelopez in https://github.com/galaxyproject/galaxy/pull/15740 * Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15713 * More object store documentation. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15707 * Fix occasional package problems related to dependencies. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15734 * Merge conflicting db migration branches into one by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15771 * fix premature return in user API by @martenson in https://github.com/galaxyproject/galaxy/pull/15781 * Implement some initial object store selection end-to-end tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15785 * Add API test and refactor code for related:hid history filter by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15786 * Quota source labelling bug fixes and improvements by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15795 * Enable ``strict_equality`` mypy option by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15808 * Add selenium test for history Related filter by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15720 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15809 * Convert more of the object store selection client to TypeScript. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15783 * Add Storage Management API by @davelopez in https://github.com/galaxyproject/galaxy/pull/15295 * Fix/Enhance recalculate disk usage API endpoint by @davelopez in https://github.com/galaxyproject/galaxy/pull/15739 * Add ensureDefined assertion utility by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15834 * Convert utilities to typescript by @dannon in https://github.com/galaxyproject/galaxy/pull/15718 * [PROCEDURES] Add Laila as a committer by @dannon in https://github.com/galaxyproject/galaxy/pull/15789 * Fix log message by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15838 * merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/15830 * Enable no-throw-literal eslint rule by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15849 * Migrate to MyST-Parser for Markdown docs by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15844 * Utils refactor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15837 * [PROCEDURES] Remove jxtx from committers list. by @dannon in https://github.com/galaxyproject/galaxy/pull/15790 * Drop use_legacy_history from config by @dannon in https://github.com/galaxyproject/galaxy/pull/15861 * Fix masthead element padding and improve brand text contrast by @guerler in https://github.com/galaxyproject/galaxy/pull/15689 * Adding onFocus and onBlur functionality to editing the history name by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15853 * merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/15854 * Move @types/d3 to dev dependencies by @davelopez in https://github.com/galaxyproject/galaxy/pull/15864 * Fix anonymous user uploads when vault is configured by @tchaussepiedifb in https://github.com/galaxyproject/galaxy/pull/15858 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15564 * Fix WorkflowDisplay error message handling by @dannon in https://github.com/galaxyproject/galaxy/pull/15865 * Fix information popovers when displaying object stores for selection. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15867 * Fix filesource file url support by @nuwang in https://github.com/galaxyproject/galaxy/pull/15794 * Initial end-to-end tests for separate quota sources per object store by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15800 * Allow typescript unit testing with navigation YAML. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15784 * Enable per-destination ``container_resolver_config_file`` by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15884 * Add StatesInfo component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15745 * Allow pending inputs in some collection operation tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15892 * Exclude tests from TypeScript compilation by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15900 * Merge 23.0 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15902 * Advanced tool search result tweaks by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15908 * ci: show test classes with non standard names by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15886 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15920 * Fix Multi-History infinite loading loop. by @dannon in https://github.com/galaxyproject/galaxy/pull/15931 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15890 * Update release notes footer by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15941 * Introducing the Activity Bar, initial concept and layout by @guerler in https://github.com/galaxyproject/galaxy/pull/14802 * Summarize long Workflow annotations in WorkflowList by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15925 * Migrate user and user flags stores to Pinia by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15938 * Make container builders use mamba by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15953 * Update locale.js by @undergone2345 in https://github.com/galaxyproject/galaxy/pull/15963 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15958 * Build container with nodejs by @ksuderman in https://github.com/galaxyproject/galaxy/pull/15979 * Migrate history store to pinia by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15108 * Add text-break to wrap long published titles by @guerler in https://github.com/galaxyproject/galaxy/pull/15980 * Fix Activity Bar toggle reactivity by @davelopez in https://github.com/galaxyproject/galaxy/pull/15988 * Convert legacy side panels to flex-compatible panels by @guerler in https://github.com/galaxyproject/galaxy/pull/15935 * Emit filterText to HistoryPanel from historyStore by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15926 * Drop database views by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15876 * Add suggested Training material to Tool Form by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15628 * Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15811 * Improve display chunk generation for BAMs by @wm75 in https://github.com/galaxyproject/galaxy/pull/15972 * Fetcher Mock utility by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15992 * Add alter_column migration utility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16009 * Mock fetcher followup by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16011 * Export tool citations configurable message by @minh-biocommons in https://github.com/galaxyproject/galaxy/pull/15998 * Fix for link pop-up window/toaster after Data Library to History import by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16008 * Fix nullable deleted column in API Keys table by @davelopez in https://github.com/galaxyproject/galaxy/pull/15956 * reorganize user menu for consistency by @martenson in https://github.com/galaxyproject/galaxy/pull/15994 * remove inherited title from masthead dropdown items by @martenson in https://github.com/galaxyproject/galaxy/pull/15995 * minor tooltip and UI client changes by @martenson in https://github.com/galaxyproject/galaxy/pull/16017 * Fix pasting file fails if text starts with `file ` by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16023 * Add option to create list for all datasets in a history to dropdown by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15947 * Refactor badge parsing/serialization/typing for reuse. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15987 * Allow importing a workflow from a shared URL by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15903 * Code cleanups from ruff and pyupgrade by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16035 * Change confusing pulsar logs message by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16038 * Object store badges spelling fixes. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16028 * Refactor integration tests to create utility for setting up a database vault. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16027 * 12875/form drilldown vue conversion by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15813 * Another round of easy tool shed cleanup. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15540 * implement admin jobs filtering by @martenson in https://github.com/galaxyproject/galaxy/pull/16020 * Add support for visualizing HDF5 datasets. by @jarrah42 in https://github.com/galaxyproject/galaxy/pull/15394 * Add missing fields to HistorySummary schema model by @davelopez in https://github.com/galaxyproject/galaxy/pull/16041 * Gitignore update by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16046 * Fixes the parcel2 build for hdf5 viz when using node18. by @dannon in https://github.com/galaxyproject/galaxy/pull/16047 * New history selector with quick actions by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16040 * Vendorise ``packaging.versions.LegacyVersion`` by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16058 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15942 * Show backend search errors in hist panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15874 * Change release note icon by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16049 * Rename object stores in config. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16029 * Migrate job metrics store and component to use pinia and composition api by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16056 * Deprecate tools/evolution by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15656 * Use jsdom-worker instead of mock by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16064 * Use Filtering class to get and set filter texts by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15996 * Drop `UserHistories` provider by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15993 * External Login Flow: Redirect users if account already exists by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15019 * Ensure that unselected checkbox inputs emit null instead of an empty array by @guerler in https://github.com/galaxyproject/galaxy/pull/16059 * Fix font-awesome library types by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16068 * unify workflows grid components by @martenson in https://github.com/galaxyproject/galaxy/pull/16045 * Remove legacy form fields from parameter factory by @guerler in https://github.com/galaxyproject/galaxy/pull/15983 * Updated doc and tests for attribute value filter by @tuncK in https://github.com/galaxyproject/galaxy/pull/15929 * Add create_foreign_key migration utility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16077 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16086 * Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16080 * Vueify Select field by @guerler in https://github.com/galaxyproject/galaxy/pull/16010 * Merge release_23.0 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16088 * Fix and test startup with Python 3.11 on macOS by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16082 * Refactor a few client object store components by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16051 * Use automated naming convention to generate indexes and constraints in database by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16089 * Fix minor Switch to History bug in `HistoryView` by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16095 * Use `_.+` for unused variables by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16098 * Attempt to fix mypy check by @davelopez in https://github.com/galaxyproject/galaxy/pull/16103 * De-duplicate code around object store caches. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16108 * Improve robustness of collection edit E2E test. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16092 * Workflow Editor Infinite Grid with Landmark-Lines by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16097 * Workflow Connections Dynamic Radius by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16102 * Fix resetting metadata on many repositories at once via the shed API by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14906 * Allow HEAD request for requesting metadata files by @martenson in https://github.com/galaxyproject/galaxy/pull/16113 * Add hdf4 datatype by @TheoMathurin in https://github.com/galaxyproject/galaxy/pull/16105 * Merge branch 'release_23.0' into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16118 * Place admin panel section data into computed prop by @guerler in https://github.com/galaxyproject/galaxy/pull/16115 * De-duplication and improvements to the in-process object store cache monitor by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16111 * Dataset chunking tests (and small fixes) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16069 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16123 * Add Storage Dashboard visualizations for histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/14820 * add required_files to the tag list for linting by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16129 * Upgraded to new multiselect Tags component for Workflows, DatasetList, Attributes by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/15225 * Fix : Ignore error messages for admin created accounts by @jvanbraekel in https://github.com/galaxyproject/galaxy/pull/16132 * Add count support for listing filters by @davelopez in https://github.com/galaxyproject/galaxy/pull/16075 * Selenium test for displaying workflows with problems in pages. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16085 * [webhook/gtn] Expand query selector list to encompass 'a' by @hexylena in https://github.com/galaxyproject/galaxy/pull/16100 * Disable invalid link for anonymous users. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16147 * Improve histories and datasets immutability checks by @davelopez in https://github.com/galaxyproject/galaxy/pull/16143 * When writing test error debug directories, create a 'latest' symlink. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16148 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16149 * Refactor caching object stores ahead of adding task-based store. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16144 * Integrate accessibility testing into Selenium testing by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16122 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16153 * Add option to see invocations related to a history by @martenson in https://github.com/galaxyproject/galaxy/pull/16136 * Documents use of k8s_extra_job_envs in job_conf sample advanced by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15110 * Migrate display applications API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16156 * Improve robustness of collection upload tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16093 * Move axe-selenium-python to dev dependencies by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16162 * FITS data format by @volodymyrss in https://github.com/galaxyproject/galaxy/pull/15905 * Scope pinned histories by user ID by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16142 * Fix linting of FITS datatype code by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16169 * Fix eslint / ts overrides by @dannon in https://github.com/galaxyproject/galaxy/pull/16166 * Updates MGnify interactive tool to v1.1.0 by @SandyRogers in https://github.com/galaxyproject/galaxy/pull/16179 * Accessibility fixes for workflows, login, and registration. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16146 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16182 * Record input datasets and collections at full parameter path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15978 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16186 * Merge ``Target`` class with ``CondaTarget`` by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16181 * Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16197 * Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16198 * Add WorkflowBox to Activity bar Side Panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15944 * Hide Activity Bar for anonymous users by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16200 * Remove various fallback behaviors by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16199 * Add Processing for Custom Icons by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16157 * Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16208 * Drop TS unit mapping tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16206 * adjust grid sharing indicators by @martenson in https://github.com/galaxyproject/galaxy/pull/16163 * Update carbon emissions calculations explanation page styling by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16192 * FITS file visualization plugin by @francoismg in https://github.com/galaxyproject/galaxy/pull/16187 * Ensure session is request-scoped for legacy endpoints by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16207 * Add Repository owner field to ToolSearch by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16061 * End-to-end tests for new user welcome. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16158 * Improved Cache Monitoring for Object Stores by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16110 * Merge 23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16228 * Fixes initial state of select all checkbox by @guerler in https://github.com/galaxyproject/galaxy/pull/16217 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16227 * Allow user customization of the activity bar by @guerler in https://github.com/galaxyproject/galaxy/pull/16184 * Handle appending to a results file that does not exists. by @ksuderman in https://github.com/galaxyproject/galaxy/pull/16233 * Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15421 * Initial e2e test for history storage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16221 * tool_util: switch to mambaforge on non-32bit; add arm64 support by @mr-c in https://github.com/galaxyproject/galaxy/pull/16223 * Protection against problematic boolean parameters. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15493 * Add slack error reporting plugin by @hexylena in https://github.com/galaxyproject/galaxy/pull/15025 * Adding fuzzy search functionality to front end search by @tcollins2011 in https://github.com/galaxyproject/galaxy/pull/15855 * allow anon access for api/datasets/get_content_as_text by @martenson in https://github.com/galaxyproject/galaxy/pull/16226 * Allow users to create new activity bar items by @guerler in https://github.com/galaxyproject/galaxy/pull/16196 * Replace bootstrap_history.py with galaxy-release-util by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16231 * Fix some drs handling issues by @nuwang in https://github.com/galaxyproject/galaxy/pull/15777 * Don't error on missing parameters or unused parameters in UI controllers by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16246 * Selenium type fixes and annotations. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16242 * Add Galaxy Notification System by @davelopez in https://github.com/galaxyproject/galaxy/pull/15663 * Show search in `HistoryView` by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16225 * Selenium test for page history links. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16222 * Refine activity bar dragging behavior by @guerler in https://github.com/galaxyproject/galaxy/pull/16245 * Paginate History Store by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16084 * e2e test for workflow license selector by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16243 * Marginally more storage management selenium coverage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16263 * Adjust notifications activity item by @guerler in https://github.com/galaxyproject/galaxy/pull/16265 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16267 * Add History Archival feature by @davelopez in https://github.com/galaxyproject/galaxy/pull/16003 * Add interactive tools activity by @guerler in https://github.com/galaxyproject/galaxy/pull/16266 * Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/16255 * Small test decorator improvements. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16220 * read job_conf directly from `config_dir` instead of computing it again from `config_file` by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15596 * Container resolvers: add docs, typing and tests by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15614 * bring grids for (published) pages on par with workflows by @martenson in https://github.com/galaxyproject/galaxy/pull/16209 * Add zipped mongodb and genenotebook datatypes by @abretaud in https://github.com/galaxyproject/galaxy/pull/16173 * Reset autocommit to True (temporarily) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16283 * OIDC tokens by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/15300 * Display Tags in Workflow Editor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16282 * Fix and Improve Workflow Editor Panning by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16178 * E2E Tests for Edit Dataset Attributes Page by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16224 * Decompress history data for testing assertions by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15085 * Bump msal version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16285 * Fixes for two framework test tools by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15483 * Expose additional beaker caching backends by @claudiofr in https://github.com/galaxyproject/galaxy/pull/15349 * Bump default milestone to 23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16287 * Merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16289 * Set Initial Filter for Paired List Collection Creator Based on Initial Elements by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16279 * Improve container resolver documentation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16280 * Update version to 23.1.rc1 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16292 * [23.1] Update 23.1 release tags for migration scripts by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16294 * [23.1] Open latest version of tool from tool panel link by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16290 * [23.1] Fix recalculate_quota throug kombu message by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16299 * [23.1] handle prefix in dataset contents properly by @martenson in https://github.com/galaxyproject/galaxy/pull/16301 * [23.1] Fix form builder value handling by @guerler in https://github.com/galaxyproject/galaxy/pull/16304 * [23.1] Fix ordering of data libraries from API by @martenson in https://github.com/galaxyproject/galaxy/pull/16300 * [23.1] qualify querying for an api-key by @martenson in https://github.com/galaxyproject/galaxy/pull/16320 * [23.1] Remove pin on ``packaging`` in packages by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16322 * [23.1] Fix tool remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/16311 * [23.1] Fix 'news' webhook to account for the RC one more time. by @dannon in https://github.com/galaxyproject/galaxy/pull/16328 * [23.1] Filter deleted keys from api_keys relationship by @dannon in https://github.com/galaxyproject/galaxy/pull/16321 * [23.1] Makefile-based setting of NODE_OPTIONS for client build by @dannon in https://github.com/galaxyproject/galaxy/pull/16324 * [23.1] Refactor workflow store to be more reliable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16334 * [23.1] Include workflow invocations in default activity by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16338 * [23.1] Sanitize substring in matchingTerm by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16351 * [23.1] Make tags in public histories read-only by @davelopez in https://github.com/galaxyproject/galaxy/pull/16348 * [23.1] Improve help text for conditional workflow step by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16355 * [23.1] Hide conditionally skipped output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16356 * [23.1] Fix invocation progress bar for skipped and deleted jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16365 * [23.1] Fix workflow invocation detail reactivity by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16369 * [23.1] Add missing singularity_no_mount prop parsing by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16367 * [23.1] Disable console instead of dropping by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16372 * [23.1] Fix Nested Tool Panel Labels by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16376 * [23.1] Fix disk usage recalculation for distributed object stores by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16380 * [23.1] Add message showing console disable/enable, along with instructions o… by @dannon in https://github.com/galaxyproject/galaxy/pull/16401 * [23.1] Fix histories count by @davelopez in https://github.com/galaxyproject/galaxy/pull/16400 * [23.1] Job cache fixes for DCEs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16384 * [23.1] Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16421 * [23.1] Fix toolform creator by @dannon in https://github.com/galaxyproject/galaxy/pull/16419 * [23.1] For display (only) allow control+click for new window opening by @dannon in https://github.com/galaxyproject/galaxy/pull/16432 * [23.1] Fix webhook release note seen pin by @dannon in https://github.com/galaxyproject/galaxy/pull/16446 * [23.1] Fix multi-broadcast overlap by @davelopez in https://github.com/galaxyproject/galaxy/pull/16444 * [23.1] Fix error_reports linting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16465 * [23.1] Swap datatype&convert tab to a static 'datatypes' tab. by @dannon in https://github.com/galaxyproject/galaxy/pull/16466 * [23.1] Fix history items repeated search bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16452 * [23.1] Fix Storage Dashboard missing archived histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16473 * [23.1] Restore resolution of Conda environments generated from non-lowercase package names by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16474 * [23.1] Add missing archived filter in saved histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16475 * [23.1] use router instead of hard links for certain page urls by @martenson in https://github.com/galaxyproject/galaxy/pull/16297 * [23.1] Fix tagging component for anonymous users by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16481 * [23.1] Bump bx-python to 0.10.0 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16484 * [23.1] Remove blinking animation from icons by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16471 * [23.1] Fix up unit tests for local use by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16483 * [23.1] Fix tags ownership by @davelopez in https://github.com/galaxyproject/galaxy/pull/16339 * [23.1] Make ToolBox v-b-tooltip.hover directives noninteractive by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16506 * [23.1] Fix `ToolBoxWorkflow` search delay bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16505 * [23.1] Fix history item states help display to apply same styling attributes by @dannon in https://github.com/galaxyproject/galaxy/pull/16500 * [23.1] H5web updates by @dannon in https://github.com/galaxyproject/galaxy/pull/16509 * [23.1] Fix for Accessibility, on Workflows List page Tooltip by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16520 * [23.1] fix font-weight disparity between browsers by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16515 * [23.0] Fix upload paramfile handling (for real user setups) by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16504 * [23.1] Fix double-encoding notification content by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16530 * [23.1] Exclude selenium version with broken type hints by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16531 * [23.1] Restore tmp mounting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16533 * [23.1] Run through tmp_dir_creation_statement only once by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16529 * [23.1] Limit tool document cache to tool configs with explicit cache path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16537 * [22.01] Fix up tox.ini by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16567 * [23.0] Add missing unit-coverage environment by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16570 * [23.0] Fix dataset collection url in workflow reports by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16571 * [23.0] Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16569 * [23.0] Fix incorrect ASGI request host by @davelopez in https://github.com/galaxyproject/galaxy/pull/16574 * [22.01] Fix incorrect ASGI request host by @davelopez in https://github.com/galaxyproject/galaxy/pull/16575 * [23.1] Fix shared item notification link by @davelopez in https://github.com/galaxyproject/galaxy/pull/16581 * [23.0] Fix conditional step evaluation with datasets in repeats by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16584 * [23.1] Don't use ``docker run`` --user flag on OSX by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16573 * [23.1] Ignore errors with user-set job resources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16579 * [23.0] Don't read request body into memory by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16585 * [23.0] Fix extra files path handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16541 * [23.1] Bump minimum tpv version to 2.3.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16597 * [23.1] make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16594 * [23.1] Fix replacement parameters for subworkflows. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16592 * [23.0] Fixes for extra files handling and cached object stores by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16595 * [23.1] Drop expunge_all() call in WebTransactionRequest by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16606 * [23.1] Drop RecursiveMiddleware by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16605 * [23.1] Fix `multiple` remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/16542 * [23.1] Optimize getting current user session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16604 * [23.1] Backport tool mem fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16601 * [23.1] Only reindex tool search once after forking by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16611 * [23.1] Fix Published Pages and Pages view showing same content by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16614 * [23.1] Remove render.py script from iSEE by @neoformit in https://github.com/galaxyproject/galaxy/pull/16616 * [23.1] Reload toolbox after forking when using `--preload` by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16620 * [22.01] Passing Identifier for div to Write the Chart Panel to by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16598 * [23.1] Account for expires/expires_in when refreshing token by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16621 * [23.0] Allow the legacy DELETE dataset endpoint to accept any string for the history_id by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16593 * [23.1] Make datatype edit default value a string instead of list of strings by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16591 * [23.0] Don't fail invocation message without dependent_workflow_step_id by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16628 * [23.1] Fixes for conditional subworkflow steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16632 * [23.0] Lazy load tool data tables in celery worker by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16640 * [23.1] Fix nested conditional workflow steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16641 * [23.1] Make sort_collection tool require terminal datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16661 * [23.1] xsd: allow name attribute of test collections by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16663 * [23.1] Fix expression evaluation for nested state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16656 * [23.0] Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer by @simonbray in https://github.com/galaxyproject/galaxy/pull/16659 * [22.05] Switch to upstream setup-chromedriver action by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16669 * [23.1] Push to object store even if ``set_meta`` fails by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16667 * [23.1] Ensure Job belongs to current SA session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16655 * [23.1] Login/Register fixes by @dannon in https://github.com/galaxyproject/galaxy/pull/16652 * [23.1] Fix regex validation for global inline flags by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16683 * [23.1] Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16678 * [23.1] Only show 'edit' on published pages when viewer is the owner. by @dannon in https://github.com/galaxyproject/galaxy/pull/16680 * [23.1] Update galaxyproject/charts utilizing visualizations by @dannon in https://github.com/galaxyproject/galaxy/pull/16674 * [23.1] Fix closed transaction error on galaxy startup/check jobs by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16687 * [23.1] FileInput no longer accept 'U' in the file mode by @bgruening in https://github.com/galaxyproject/galaxy/pull/16704 * [23.1] List extra files only for terminal datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16705 * [23.0] Update pulsar client library to 0.15.5 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16701 * [23.1] Fix legend not scrollable in storage overview charts by @davelopez in https://github.com/galaxyproject/galaxy/pull/16703 * [23.1] Add missing join condition in job search by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16710 * [23.1] Fix job search query by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16714 * [23.1] Fix collection id encoding by @davelopez in https://github.com/galaxyproject/galaxy/pull/16718 * [23.1] Fix unittest mocks to support us checking geturl() by @dannon in https://github.com/galaxyproject/galaxy/pull/16726 * [23.1] Fix allowlist deserialization in file sources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16729 * [23.1] Workaround for XML nodes of job resource parameters losing their children by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16728 * [23.1] force wrap long parameter names in the workflow form by @martenson in https://github.com/galaxyproject/galaxy/pull/16732 * [23.1] prevent toolbox scrollbar by @martenson in https://github.com/galaxyproject/galaxy/pull/16734 * [23.1] Copy the collection contents by default when copying a collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16717 * [23.1] 23.1 Release Notes by @dannon in https://github.com/galaxyproject/galaxy/pull/16329

New Contributors

• @tchaussepiedifb made their first contribution in https://github.com/galaxyproject/galaxy/pull/15858
• @undergone2345 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15963
• @minh-biocommons made their first contribution in https://github.com/galaxyproject/galaxy/pull/15998
• @jarrah42 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15394
• @TheoMathurin made their first contribution in https://github.com/galaxyproject/galaxy/pull/16105
• @volodymyrss made their first contribution in https://github.com/galaxyproject/galaxy/pull/15905
• @tcollins2011 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15855

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.5...v23.1

- Python
Published by martenson over 2 years ago

galaxy - v23.2.0

Release notes

Galaxy 23.2.0 was released on 30th of January 2024

user highlight release notes full release notes

What's Changed

list of all merged PRs

* Version 23.2.dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16293 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16305 * Add Python string formatting best practices by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16312 * Drop (admin only) userskeys controller by @dannon in https://github.com/galaxyproject/galaxy/pull/16318 * Client import sorting by @dannon in https://github.com/galaxyproject/galaxy/pull/16345 * Merge 23.1->dev by @dannon in https://github.com/galaxyproject/galaxy/pull/16361 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16360 * Add carbon emissions admin configuration options by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16307 * Replace Persistedstate Pinia Plugin with User-Scoped Composable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16371 * Exclude auto-generated schema file from labeler by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16378 * Display beginning of non-text files as text instead of triggering a download by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/15447 * Bump semver from 5.7.1 to 5.7.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16388 * Merge release_23.1 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16393 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16389 * Standardize, lint vue component name casing. by @dannon in https://github.com/galaxyproject/galaxy/pull/16398 * Update carbon emissions methodology page to match current feature spe… by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16392 * Limit number of celery task executions per second per user by @claudiofr in https://github.com/galaxyproject/galaxy/pull/16232 * Disable verbose parso logging in db_shell.py by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16410 * Refactor FilesDialog services to use Fetcher by @davelopez in https://github.com/galaxyproject/galaxy/pull/16414 * Bump word-wrap from 1.2.3 to 1.2.4 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16417 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16409 * Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16264 * Fix SA2.0 syntax in scripts/helper.py, fix ancient bug by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16425 * Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16430 * Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16431 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16436 * Prepare Uploader Vueification by removing jQuery by @guerler in https://github.com/galaxyproject/galaxy/pull/16408 * Fix labeler for UI UX labels by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16456 * Never consider `_galaxy_` conda env as unused by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16460 * Force makefile client targets to use .venv-shipped node if it exists by @dannon in https://github.com/galaxyproject/galaxy/pull/16462 * pin fs.dropboxfs to >=1 by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16451 * Migrate some Remote Files Export components to composition API + TS by @davelopez in https://github.com/galaxyproject/galaxy/pull/16391 * Bump tough-cookie from 4.1.2 to 4.1.3 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16385 * Add new datatype: STL by @TanguyGen in https://github.com/galaxyproject/galaxy/pull/16478 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16485 * Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15825 * Migrate cloud API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16296 * Re-add missing type guard by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16486 * Rename MetadataEqualsValidator by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16489 * Test that object store cache file gets updated by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16493 * Migrate a part of the users API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16341 * Make it obvious that `WorkflowInvocationStep` is clickable/expandable by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16507 * Add framework test for profile behavior of `format="input"` by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15482 * Update interactivetool_mgnify_notebook to v1.2.2 by @SandyRogers in https://github.com/galaxyproject/galaxy/pull/16517 * Migrate configuration store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16514 * Scope Workflow Stores to Workflow ID by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16523 * Fix and update visualization plugins by @mahendrapaipuri in https://github.com/galaxyproject/galaxy/pull/16119 * Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16534 * Move database access code out of ``galaxy.util`` by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16526 * Document that required text parameters need a validator by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16538 * Published Workflow Sharing Page Overhaul by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16510 * Refactor FilesDialog + Remote Files API schema improvements by @davelopez in https://github.com/galaxyproject/galaxy/pull/16420 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16521 * Vueify Data Uploader by @guerler in https://github.com/galaxyproject/galaxy/pull/16472 * Make form repeat blocks reordarable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/14892 * Remove unnecessary check: item cannot be None by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16550 * add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools by @khaled196 in https://github.com/galaxyproject/galaxy/pull/16503 * Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16553 * Add uploader test cases, consolidate payload processing by @guerler in https://github.com/galaxyproject/galaxy/pull/16554 * Fix: serialize `tool_shed_urls` directly from the API by @davelopez in https://github.com/galaxyproject/galaxy/pull/16561 * Drop syncConfigToGalaxy by @davelopez in https://github.com/galaxyproject/galaxy/pull/16562 * Add support for CILogon deployments in different regions than the US by @uwwint in https://github.com/galaxyproject/galaxy/pull/16490 * Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16536 * Support new genome browser chain file format by @claudiofr in https://github.com/galaxyproject/galaxy/pull/16576 * Run eslint autofix as a part of client format when using Makefile by @dannon in https://github.com/galaxyproject/galaxy/pull/16586 * Implement datatype upload warnings by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16564 * Remove xml remnant in sample yml job conf by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16609 * Add Invenio RDM repository integration by @davelopez in https://github.com/galaxyproject/galaxy/pull/16381 * Make tool id searchable in side panel search by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16543 * Explicitly document default of multiple by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16625 * Run poetry under Python 3.8 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16638 * Fix dependency update GitHub workflow by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16639 * Switch out conditional requirement parser by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16636 * Vueify _fieldDialog by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16236 * Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16649 * Ensure Job belongs to current SA session by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16647 * cwl testing: use the proposed 1.2.1 CWL conformance tests. by @mr-c in https://github.com/galaxyproject/galaxy/pull/16658 * Add scroll pagination and username filter to `HistoryPublishedList` by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16642 * Bump samtools converters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16668 * Clarify documentation on how to build a job runner by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16665 * Enhance disk quota usage summary by @davelopez in https://github.com/galaxyproject/galaxy/pull/16670 * History MultiView drag-drop on history picker creates new history by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16644 * Create `GDateTime` component by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16622 * Notifications admin panel by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16278 * Fix notifications icon not showing in Masthead by @davelopez in https://github.com/galaxyproject/galaxy/pull/16679 * Fix flaky test timing issue in DiskUsageSummary component by @davelopez in https://github.com/galaxyproject/galaxy/pull/16685 * Include `regex` when linting validators by @davelopez in https://github.com/galaxyproject/galaxy/pull/16684 * Minor: Fix import warning by @davelopez in https://github.com/galaxyproject/galaxy/pull/16692 * Skip node installation for ``check_indexes`` tests by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16694 * Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16691 * Vueify Tool Form Data Selector by @guerler in https://github.com/galaxyproject/galaxy/pull/16578 * Enhance task monitor composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/16695 * Misc. edits/refactorings to session handling by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16712 * Migrate `dataset` store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16709 * Enhance Short Term Storage Composable by @davelopez in https://github.com/galaxyproject/galaxy/pull/16711 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16577 * force wrap long parameter names in the workflow form by @martenson in https://github.com/galaxyproject/galaxy/pull/16731 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16735 * Update build_a_job_runner.rst by @maikenp in https://github.com/galaxyproject/galaxy/pull/16673 * SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16434 * Reset autocommit to False by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16745 * Account for shared usage between TS and galaxy apps by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16746 * Selective bold text by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16748 * Migrate `collection elements` store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16725 * Don't copy collection elements in ``test_dataset_collection_hide_originals`` by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16747 * Change Sentry error reporting plug-in by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16686 * Drop legacy server-side search by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16755 * Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in https://github.com/galaxyproject/galaxy/pull/16762 * Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in https://github.com/galaxyproject/galaxy/pull/16690 * provide specific example for API docs - tags by @martenson in https://github.com/galaxyproject/galaxy/pull/16769 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16770 * Fix large gap between labels and form elements by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16753 * Tool Shed 2.0 by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15639 * Fix selenium selector for collections by @davelopez in https://github.com/galaxyproject/galaxy/pull/16754 * Initial bug fixes for tool shed 2. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16787 * SA2.0 fixes for TS2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16791 * Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16768 * Fix duplicate key eslint error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16810 * Use AlignedSegment.to_string by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16803 * Fix shed unit test by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16811 * Add ClientSearchMiss Sentry Capture by @dannon in https://github.com/galaxyproject/galaxy/pull/16789 * Fix package version handling for initial minor releases by @dannon in https://github.com/galaxyproject/galaxy/pull/16743 * move the email and username redacting from the role loop by @martenson in https://github.com/galaxyproject/galaxy/pull/16805 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16807 * Optimize iteration in DatasetInstance model + SA2.0 fix by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16776 * Another batch of SA2.0 edits in TS 2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16799 * Fix collection drilling by @davelopez in https://github.com/galaxyproject/galaxy/pull/16819 * Add Time Format to ``Generated with Galaxy {{ version }} on {{ time }} UTC`` statement by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16757 * Migrate `collection attributes` store to Pinia by @davelopez in https://github.com/galaxyproject/galaxy/pull/16752 * Adjust tz inclusion in workflow reports by @dannon in https://github.com/galaxyproject/galaxy/pull/16835 * Create db head merge revision. by @dannon in https://github.com/galaxyproject/galaxy/pull/16838 * Refactor dataset services by @davelopez in https://github.com/galaxyproject/galaxy/pull/16839 * Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16848 * Create reusable `FilterMenu` with advanced options by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16522 * chore: fix typos by @afuetterer in https://github.com/galaxyproject/galaxy/pull/16851 * Improve collection items scrolling by @davelopez in https://github.com/galaxyproject/galaxy/pull/16738 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16853 * Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16739 * SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16724 * Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16833 * Remove remaining legacy backbone form input elements by @guerler in https://github.com/galaxyproject/galaxy/pull/16834 * Fix bug in SQLAlchemy statement by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16881 * Bump @babel/traverse from 7.18.11 to 7.23.2 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16874 * Drop unused HistoryContentManager code and related tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16882 * Ruff and flake8 fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16884 * Fix bug in SA statement: desc() applied to column, not statement by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16887 * Use vue modal instead of global backbone modal in user preferences by @guerler in https://github.com/galaxyproject/galaxy/pull/16830 * Update help in relabel_from_file.xml by @lldelisle in https://github.com/galaxyproject/galaxy/pull/16891 * Tool Shed 2.0 fixes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16825 * Restore ToolsApi and create new api route for new panel structure by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16872 * Update cellxgene interactive tool to 1.1.1 by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15313 * MINERVA display application: enable cors, add for tabular by @hexylena in https://github.com/galaxyproject/galaxy/pull/16737 * Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16758 * Toolshed client build separation by @dannon in https://github.com/galaxyproject/galaxy/pull/15000 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16896 * Refactor/OIDC custos by @uwwint in https://github.com/galaxyproject/galaxy/pull/16497 * Add parameter name to validation errors by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15440 * Update client dependencies. by @dannon in https://github.com/galaxyproject/galaxy/pull/16867 * Bump undici from 5.19.1 to 5.26.5 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/16897 * Fix selenium selector for Workflow Run warnings by @davelopez in https://github.com/galaxyproject/galaxy/pull/16908 * Fix link to mercurial tip in tool shed 2.0. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16895 * Fix navigation error in tool shed tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16902 * Fix type annotation of ``lib/tool_shed/test/functional/`` by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16901 * Refactor client API packages by @davelopez in https://github.com/galaxyproject/galaxy/pull/16847 * Fix subtle bug in listify function + simplify list munging by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16904 * Convert `historyItemsStore` to ts+composition by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16873 * Update datatypes_conf.xml.sample with docx type by @yvanlebras in https://github.com/galaxyproject/galaxy/pull/16713 * Fix import in historyItemsStore.ts by @davelopez in https://github.com/galaxyproject/galaxy/pull/16916 * Allow partial matches in workflow name tag search and search all tags for unquoted query by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16860 * Enable some flake8-logging-format rules in ruff by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16915 * Fix GQL infinite scrolling in tool shed. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16914 * merge release_23.1 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16933 * Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16940 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16939 * Fix select parameter doesn't show parameter name in UI by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16942 * Change `api/tool_panel` to `api/tool_panels/...` by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16928 * Remove record access handling for Invenio RDM plugin by @davelopez in https://github.com/galaxyproject/galaxy/pull/16900 * Workflow Comments 💬 by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16612 * Allow switching histories from Storage Dashboard Visualizations by @davelopez in https://github.com/galaxyproject/galaxy/pull/16945 * Standardize to W3C naming for color. by @dannon in https://github.com/galaxyproject/galaxy/pull/16949 * Publish tool shed frontend to npm. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16924 * Allow to permanently delete non-deleted items in Storage Dashboard Visualizations by @davelopez in https://github.com/galaxyproject/galaxy/pull/16944 * Add helper to get dataset or collection via ``src`` and ``id`` by @mr-c in https://github.com/galaxyproject/galaxy/pull/16953 * Move and re-use persist_extra_files by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16955 * Enhance Invenio RDM integration by @davelopez in https://github.com/galaxyproject/galaxy/pull/16964 * Remove sentry.py from mypy exclusions. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16959 * Augment pgcleanup to allow periodically deleting old datasets. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16340 * Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16672 * Allow non-optional integer/float params without value attribute by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16966 * prep for updated h5py and typos by @mr-c in https://github.com/galaxyproject/galaxy/pull/16963 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16978 * Implement default locations for data and collection parameters. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14955 * Expose Workflow Checkpoint in Workflow Reports by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16760 * Fix maf_thread_for_species.py by @lldelisle in https://github.com/galaxyproject/galaxy/pull/16971 * Fix rendering of an empty page by @dannon in https://github.com/galaxyproject/galaxy/pull/16985 * Implement instance URLs in Galaxy markdown. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16675 * Minor clarification/typo fix in datatypes.data by @dannon in https://github.com/galaxyproject/galaxy/pull/16993 * Workflow Embed by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16657 * Remove "Create Workflow" form and allow workflow creation in editor by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16938 * Replace file_name property with get_file_name function by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/16783 * Fixes for job metrics Galaxy markdown component. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16994 * Merge 23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17000 * SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16852 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17011 * Update API tool_panels route conditions by @dannon in https://github.com/galaxyproject/galaxy/pull/16991 * Upgrade job manager's index_query method to SA2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17020 * Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16252 * Show current tool panel view name on top of tool panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17021 * Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in https://github.com/galaxyproject/galaxy/pull/16795 * Remove eventHub custom module, swap to appropriate alternatives. by @dannon in https://github.com/galaxyproject/galaxy/pull/17037 * Restyle Vue Multiselect and Adapt Option Order by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17015 * Change Broadcast Notifications Style by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17032 * Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17038 * Open `HistoryStorageOverview` in center panel from `HistoryPanel` by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17043 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17050 * Vueify Visualizations Grid by @guerler in https://github.com/galaxyproject/galaxy/pull/16892 * optimize object store cache operations by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/17025 * Upgrade axios to 1.6.2 by @dannon in https://github.com/galaxyproject/galaxy/pull/17053 * Quote singularity env parameters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17055 * Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17056 * Use debounce instead of timeout utility by @guerler in https://github.com/galaxyproject/galaxy/pull/17057 * Disable conda_auto_init in embedded pulsar test cases by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17061 * Fix testing of the galaxy-tool-shed package by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17062 * Migrate a part of the jobs API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16778 * Fix typescript warning for grid list operation by @guerler in https://github.com/galaxyproject/galaxy/pull/17065 * Migrate groups API to fastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/17051 * Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17069 * New select component for selecting a large amount of options by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17059 * Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/17084 * Merge release_23.1 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17086 * Add docs for tool panel and panel view administration by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17078 * Migrate ItemTags API to FastAPI by @arash77 in https://github.com/galaxyproject/galaxy/pull/17064 * [PROCEDURES] Add Ahmed as a committer by @dannon in https://github.com/galaxyproject/galaxy/pull/17017 * Use eventbus to emit route request in grid list by @guerler in https://github.com/galaxyproject/galaxy/pull/17070 * Fix for fits_image_viewer visualization plugin by @francoismg in https://github.com/galaxyproject/galaxy/pull/17002 * Enhance Global Drag-and-Drop feature for Upload component by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16995 * Make job state param optional again by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17077 * Prevent excessive `api/tool_panels` calls by keeping views in store by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17039 * Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/17018 * [EGD 2023 Cofest] Galaxy help forum integration by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16798 * Allow relative URLs in broadcasts action links by @davelopez in https://github.com/galaxyproject/galaxy/pull/17042 * Fix invocation report to target correct workflow version. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17008 * Visually indicate currently viewed/edited dataset by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16859 * Make notification message input multi-line by @davelopez in https://github.com/galaxyproject/galaxy/pull/17091 * Enhance Notification Broadcasts Admin Panel by @davelopez in https://github.com/galaxyproject/galaxy/pull/17090 * Add EGI Check-in as OIDC authentication option by @enolfc in https://github.com/galaxyproject/galaxy/pull/16782 * [23.2] Update version to 23.2.rc1 by @dannon in https://github.com/galaxyproject/galaxy/pull/17095 * [23.2] Fix `.file_name` access in merge forward by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17097 * [23.2] Disable admin notifications management if notifications are disabled in config by @davelopez in https://github.com/galaxyproject/galaxy/pull/17114 * [23.2] Tool panel views overflow bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17112 * [23.2] Fix hid/elementindex for collection displays by @dannon in https://github.com/galaxyproject/galaxy/pull/17110 * [23.2] Fix CSS issue affecting all dropdown menus by @davelopez in https://github.com/galaxyproject/galaxy/pull/17124 * [23.2] Expose file_name property in DatasetFilenameWrapper by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17107 * [23.2] Fix job search when ``command_version`` is None by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17129 * [23.2] Enhance xsd schema and allow simpler assertion lists by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17134 * [23.2] Make payload optional again for create tag API by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17144 * [23.2] Fix select option appears for single select by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17146 * [23.2] Support configuring job metrics inline, update documentation by @natefoo in https://github.com/galaxyproject/galaxy/pull/17178 * [23.2] Add rerun and show details buttons in expanded collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17182 * [23.2] Fix job destination extra params by @dannon in https://github.com/galaxyproject/galaxy/pull/17186 * [23.2] Add support for Cgroupsv2 by @natefoo in https://github.com/galaxyproject/galaxy/pull/17169 * [23.2] Fix tools missing in panel bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17192 * [23.2] Disable Workflow Report and Generate PDF buttons unless workflow is successful by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/17149 * [23.2] Fix Multiselect in BModal overflows out of view bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17197 * [23.2] Fix `ToolSearch` bug for `StaticToolPanelView`s by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17213 * [23.2] Fix categories in ToolShed repo create API by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/17218 * [23.2] Fix cardinality violation error: subquery returns multiple results by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17224 * [23.2] Remove `SingleItemSelector` deselect label, fix history filters hidden on smaller screen by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/17199 * [23.2] Fix job parameter display by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17226 * [23.2] Fix Display Application link generation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17227 * [23.2] Display application fixes and tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17233 * [23.1] Add back 1.1.0 version of Filtering1 tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16883 * [23.2] Tagging component performance improvements by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17253 * [23.1] Add binary datatypes for intermediate output of fastk tools by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/17265 * [23.1] Remove duplicates when copying sections for tool panel view by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17117 * [23.1] Fix ``to_cwl`` for nested collections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17276 * [23.2] Rollback invalidated transaction by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17280 * [23.1] Always copy datasets in collection builder modals by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17268 * [23.2] Install newer celery on python 3.8+ by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17309 * [23.2] Discard sqlalchemy session after task completion by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17317 * [23.2] Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17315 * [23.2] Scope session for job runner monitor loop by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17319 * [23.1] Enable job resubmissions in k8s runner by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15238 * Revert "[23.1] Enable job resubmissions in k8s runner" by @nuwang in https://github.com/galaxyproject/galaxy/pull/17323 * [23.2] Improve Embed Performance by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17326 * [23.2] Fix Subworkflow Edit Button by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/17330 * [23.1] Disable tag editing on non-owned Pages by @davelopez in https://github.com/galaxyproject/galaxy/pull/17337 * [23.2] Initial release notes for 23.2 by @dannon in https://github.com/galaxyproject/galaxy/pull/17259 * [23.2] Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17342 * Merge 23.1 into 23.2 by @davelopez in https://github.com/galaxyproject/galaxy/pull/17343 * [23.2] Ensure release notes include all PRs added during the freeze by re-running the release note bootstrapping by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17344 * [23.2] make release titles consistent by @martenson in https://github.com/galaxyproject/galaxy/pull/17341 * [23.2] Write to a temp filename in posix file source plugin by @natefoo in https://github.com/galaxyproject/galaxy/pull/17350 * [23.2] Always store multi select data input values in fixed order by @guerler in https://github.com/galaxyproject/galaxy/pull/17352 * [23.2] Add latest PRs to release by @jdavcs in https://github.com/galaxyproject/galaxy/pull/17383 * [23.2] Fix the purge historyless HDAs pgcleanup action by @natefoo in https://github.com/galaxyproject/galaxy/pull/17382

New Contributors

• @TanguyGen made their first contribution in https://github.com/galaxyproject/galaxy/pull/16478
• @khaled196 made their first contribution in https://github.com/galaxyproject/galaxy/pull/16503
• @sebastian-schaaf made their first contribution in https://github.com/galaxyproject/galaxy/pull/16762
• @lopiola made their first contribution in https://github.com/galaxyproject/galaxy/pull/16690
• @afuetterer made their first contribution in https://github.com/galaxyproject/galaxy/pull/16851
• @arash77 made their first contribution in https://github.com/galaxyproject/galaxy/pull/17051
• @enolfc made their first contribution in https://github.com/galaxyproject/galaxy/pull/16782

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.4...v23.2

- Python
Published by martenson over 2 years ago

galaxy - v23.1.4

What's Changed

• [23.1] Properly clear session on OIDC logout by @guerler in https://github.com/galaxyproject/galaxy/pull/17120
• [23.0] Assert that tus uploader instance has URL by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17133
• [23.1] Fix workflow index total matches counting by @davelopez in https://github.com/galaxyproject/galaxy/pull/17176
• [23.1] Fix url_for in tool error reports by @davelopez in https://github.com/galaxyproject/galaxy/pull/17210
• [23.1] Fix User.currentgalaxysession by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17232
• [23.1] Backport #17188: Fix for converter tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17231
• [23.1] Separate collection and non-collection data element by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17236

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.3...v23.1.4

- Python
Published by mvdbeek over 2 years ago

galaxy - v23.1.3

What's Changed

• [23.1] Allow re-click of display with force reloading if already on the route. by @dannon in https://github.com/galaxyproject/galaxy/pull/17111
• [23.1] Add missing optional description field, fixes ephemeris data library example by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17116

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.2...v23.1.3

- Python
Published by mvdbeek over 2 years ago

galaxy - v23.1.2

What's Changed

• [23.1] Fix History item deletion/undeletion reactivity with filter and ToolForm input field by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16889
• [23.1] Fix unbound runner variable when there is an error in the job config by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16906
• [23.1] Provide error message instead of internal server error by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16905
• [23.1] Fix missing grep input in sort1 tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16910
• [23.1] Improve invocation error reporting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16917
• [23.1] Fix library import from path linking files by @davelopez in https://github.com/galaxyproject/galaxy/pull/16919
• [23.1] Test link data with extended metadata by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16921
• [23.1] Skip change_datatype things if we're not actually changing the extension by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16931
• [23.1] Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16937
• [23.1] Add execute back to published workflows list by @dannon in https://github.com/galaxyproject/galaxy/pull/16934
• [23.1] Include owner's annotation when exporting workflow by @dannon in https://github.com/galaxyproject/galaxy/pull/16930
• [23.1] Fix discarded dataset ordering in Storage Dashboard by @davelopez in https://github.com/galaxyproject/galaxy/pull/16929
• [23.1] Backport Fix select parameter doesn't show parameter name in UI by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16943
• [23.1] Adds biii as supported xref reference type by @kostrykin in https://github.com/galaxyproject/galaxy/pull/16952
• [23.1] Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16961
• [23.1] Workaround issue in Routes by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16981
• [23.1] Backport Fix mafthreadfor_species.py by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16989
• [23.1] Empty page render fix - backport by @dannon in https://github.com/galaxyproject/galaxy/pull/16992
• [23.1] Client publication by @dannon in https://github.com/galaxyproject/galaxy/pull/16999
• [23.1] Don't store job in JobIO instance attributes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16965
• [23.1] Fix copying metadata to copied job outputs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17007
• [23.1] Update tartodirectory dependency by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17009
• [23.0] Upgrade minimum conda to be compatible with latest conda-build by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/17013
• [23.1] Change log level for duplicate data table entries to warning by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16988
• [23.1] Fix duplicated tools in tool panel view section copying by @jmchilton in https://github.com/galaxyproject/galaxy/pull/17036
• [23.1] Fix filtering of active broadcasts for admins by @davelopez in https://github.com/galaxyproject/galaxy/pull/17049
• [23.1] Prevent workflow submission with missing input values by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17048
• [23.0] Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17067
• [23.1] Remove rollback from __check_jobs_at_startup by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17085
• [23.1] Assert that DatasetCollectioElement has an associated object by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17071
• [23.1] Fix input dates in notifications: consider timezone offset by @davelopez in https://github.com/galaxyproject/galaxy/pull/17088
• [23.1] Add HEAD route to job_files endpoint by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17072
• [23.1] Add support for larch datatypes by @patrick-austin in https://github.com/galaxyproject/galaxy/pull/17080
• [23.1] Allow relative URLs in broadcasts action links by @davelopez in https://github.com/galaxyproject/galaxy/pull/17093
• [23.1] Implement missing upload for S3 file sources by @davelopez in https://github.com/galaxyproject/galaxy/pull/17100
• [23.1] Fix web_apps dependencies by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17099
• [23.1] Ensure that plugin build hash actually has a git hash to compare with… by @dannon in https://github.com/galaxyproject/galaxy/pull/17104
• [23.1] Set correct tool_path for packaged galaxy by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/17102

New Contributors

• @kostrykin made their first contribution in https://github.com/galaxyproject/galaxy/pull/16952

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.1.1...v23.1.2

- Python
Published by mvdbeek over 2 years ago

galaxy - v23.1.1

What's Changed

• Version 23.1.dev by @dannon in https://github.com/galaxyproject/galaxy/pull/15353
• Towards decoupling datatypes and model by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15186
• Fix bad auto-merge of dev. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15386
• vueify formUpload with composition API by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15409
• Bump ua-parser-js from 0.7.31 to 0.7.33 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/15425
• Outline Deployment Tests by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15420
• Drop defineEmits import from FormUpload by @dannon in https://github.com/galaxyproject/galaxy/pull/15450
• Prettier targeting refinements by @dannon in https://github.com/galaxyproject/galaxy/pull/15449
• Move database access code out of tool_util by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15467
• Follow up to #15186 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15388
• Make serving address more visible in console by @davelopez in https://github.com/galaxyproject/galaxy/pull/15468
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15492
• Stricter typescript config by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15311
• Create ToolSuccess route and refactor component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15484
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15498
• Use connection instead of session for ItemGrabber by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15496
• Implement initial tool/wf test assertions module for JSON data. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15494
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15435
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15511
• Various Tool Shed Cleanup by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15247
• xsd: add multiple to the list of attributes for all parameter types deriving from select by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15534
• Add basic selenium test for shared histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/15538
• Phylocanvas rebuild by @dannon in https://github.com/galaxyproject/galaxy/pull/15521
• Move TS to Alembic by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15509
• Add new release tags to managetoolsheddb.sh script by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15542
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15546
• Use sentry-fastapi integration, expose sampling rate by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15550
• Merge release_23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15566
• Updating build-related dependencies, static cleanup. by @dannon in https://github.com/galaxyproject/galaxy/pull/15527
• Have prettier use a cache. by @dannon in https://github.com/galaxyproject/galaxy/pull/15575
• QUnit elimination by @dannon in https://github.com/galaxyproject/galaxy/pull/15452
• Update browserslist and exclusions, linting. by @dannon in https://github.com/galaxyproject/galaxy/pull/15524
• Drop workflow exports to myexperiment.org by @dannon in https://github.com/galaxyproject/galaxy/pull/15576
• Added title on anchor tag on keyboard Focus for W3C Accessibility Compliance by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/15517
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15581
• add missing f for f-string by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15584
• Fix jest tests run on CI by @davelopez in https://github.com/galaxyproject/galaxy/pull/15588
• Handle "email_from" config option consistently, as per schema description by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15557
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15594
• Bump undici from 5.14.0 to 5.19.1 in /client by @dependabot in https://github.com/galaxyproject/galaxy/pull/15609
• Alternatively allow double quotation marks in search filters by @guerler in https://github.com/galaxyproject/galaxy/pull/15606
• Update database_heartbeat for SA 2.0 compatibility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15611
• Unify url handling with filesources by @nuwang in https://github.com/galaxyproject/galaxy/pull/15497
• Explore tool remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/15510
• Update supportsskiplocked, supports_returning for SA 2.0 compatibility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15633
• Fix call to docker_cached_container_description by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15598
• Wrap checkjobsat_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15643
• Changes to match latest playbook by @nuwang in https://github.com/galaxyproject/galaxy/pull/15647
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15652
• Install singularity in the integration GitHub workflow by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/14922
• Unpin Beaker requirement by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15665
• Fix for new style conda packages by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15446
• Add transactional state to JobHandlerStopQueue by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15671
• Add transactional state to workflow scheduling manager by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15683
• Drop model mapping unit tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15669
• Minor hid display tweak by @dannon in https://github.com/galaxyproject/galaxy/pull/15662
• Remove DELETED_NEW job state from code base by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15690
• Empower Users to Select Storage Destination by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14073
• update the admin activation docs by @martenson in https://github.com/galaxyproject/galaxy/pull/15670
• Follow up on object store selection PR. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15654
• Use chevrons instead of eye for showing expandable/collapsible sections by @dannon in https://github.com/galaxyproject/galaxy/pull/15688
• Update selenium hid text assertion by @dannon in https://github.com/galaxyproject/galaxy/pull/15691
• Verify that activation and reset emails are properly generated by @guerler in https://github.com/galaxyproject/galaxy/pull/15681
• Cleanup API schema for dropping deleted_new by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15708
• Merge release_23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15711
• Tweaks to new object store and quota APIs by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15709
• Use Animation Frame in Workflow Editor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15725
• Fix Enums in API docs by @davelopez in https://github.com/galaxyproject/galaxy/pull/15740
• Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15713
• More object store documentation. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15707
• Fix occasional package problems related to dependencies. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15734
• Merge conflicting db migration branches into one by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15771
• fix premature return in user API by @martenson in https://github.com/galaxyproject/galaxy/pull/15781
• Implement some initial object store selection end-to-end tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15785
• Add API test and refactor code for related:hid history filter by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15786
• Quota source labelling bug fixes and improvements by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15795
• Enable strict_equality mypy option by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15808
• Add selenium test for history Related filter by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15720
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15809
• Convert more of the object store selection client to TypeScript. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15783
• Add Storage Management API by @davelopez in https://github.com/galaxyproject/galaxy/pull/15295
• Fix/Enhance recalculate disk usage API endpoint by @davelopez in https://github.com/galaxyproject/galaxy/pull/15739
• Add ensureDefined assertion utility by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15834
• Convert utilities to typescript by @dannon in https://github.com/galaxyproject/galaxy/pull/15718
• [PROCEDURES] Add Laila as a committer by @dannon in https://github.com/galaxyproject/galaxy/pull/15789
• Fix log message by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15838
• merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/15830
• Enable no-throw-literal eslint rule by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15849
• Migrate to MyST-Parser for Markdown docs by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15844
• Utils refactor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15837
• [PROCEDURES] Remove jxtx from committers list. by @dannon in https://github.com/galaxyproject/galaxy/pull/15790
• Drop uselegacyhistory from config by @dannon in https://github.com/galaxyproject/galaxy/pull/15861
• Fix masthead element padding and improve brand text contrast by @guerler in https://github.com/galaxyproject/galaxy/pull/15689
• Adding onFocus and onBlur functionality to editing the history name by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15853
• merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/15854
• Move @types/d3 to dev dependencies by @davelopez in https://github.com/galaxyproject/galaxy/pull/15864
• Fix anonymous user uploads when vault is configured by @tchaussepiedifb in https://github.com/galaxyproject/galaxy/pull/15858
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15564
• Fix WorkflowDisplay error message handling by @dannon in https://github.com/galaxyproject/galaxy/pull/15865
• Fix information popovers when displaying object stores for selection. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15867
• Fix filesource file url support by @nuwang in https://github.com/galaxyproject/galaxy/pull/15794
• Initial end-to-end tests for separate quota sources per object store by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15800
• Allow typescript unit testing with navigation YAML. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15784
• Enable per-destination container_resolver_config_file by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15884
• Add StatesInfo component by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15745
• Allow pending inputs in some collection operation tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15892
• Exclude tests from TypeScript compilation by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15900
• Merge 23.0 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15902
• Advanced tool search result tweaks by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15908
• ci: show test classes with non standard names by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15886
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15920
• Fix Multi-History infinite loading loop. by @dannon in https://github.com/galaxyproject/galaxy/pull/15931
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15890
• Update release notes footer by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/15941
• Introducing the Activity Bar, initial concept and layout by @guerler in https://github.com/galaxyproject/galaxy/pull/14802
• Summarize long Workflow annotations in WorkflowList by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15925
• Migrate user and user flags stores to Pinia by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15938
• Make container builders use mamba by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15953
• Update locale.js by @undergone2345 in https://github.com/galaxyproject/galaxy/pull/15963
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15958
• Build container with nodejs by @ksuderman in https://github.com/galaxyproject/galaxy/pull/15979
• Migrate history store to pinia by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15108
• Add text-break to wrap long published titles by @guerler in https://github.com/galaxyproject/galaxy/pull/15980
• Fix Activity Bar toggle reactivity by @davelopez in https://github.com/galaxyproject/galaxy/pull/15988
• Convert legacy side panels to flex-compatible panels by @guerler in https://github.com/galaxyproject/galaxy/pull/15935
• Emit filterText to HistoryPanel from historyStore by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15926
• Drop database views by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15876
• Add suggested Training material to Tool Form by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15628
• Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15811
• Improve display chunk generation for BAMs by @wm75 in https://github.com/galaxyproject/galaxy/pull/15972
• Fetcher Mock utility by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15992
• Add alter_column migration utility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16009
• Mock fetcher followup by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16011
• Export tool citations configurable message by @minh-biocommons in https://github.com/galaxyproject/galaxy/pull/15998
• Fix for link pop-up window/toaster after Data Library to History import by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16008
• Fix nullable deleted column in API Keys table by @davelopez in https://github.com/galaxyproject/galaxy/pull/15956
• reorganize user menu for consistency by @martenson in https://github.com/galaxyproject/galaxy/pull/15994
• remove inherited title from masthead dropdown items by @martenson in https://github.com/galaxyproject/galaxy/pull/15995
• minor tooltip and UI client changes by @martenson in https://github.com/galaxyproject/galaxy/pull/16017
• Fix pasting file fails if text starts with file by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16023
• Add option to create list for all datasets in a history to dropdown by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15947
• Refactor badge parsing/serialization/typing for reuse. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15987
• Allow importing a workflow from a shared URL by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15903
• Code cleanups from ruff and pyupgrade by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16035
• Change confusing pulsar logs message by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16038
• Object store badges spelling fixes. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16028
• Refactor integration tests to create utility for setting up a database vault. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16027
• 12875/form drilldown vue conversion by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/15813
• Another round of easy tool shed cleanup. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15540
• implement admin jobs filtering by @martenson in https://github.com/galaxyproject/galaxy/pull/16020
• Add support for visualizing HDF5 datasets. by @jarrah42 in https://github.com/galaxyproject/galaxy/pull/15394
• Add missing fields to HistorySummary schema model by @davelopez in https://github.com/galaxyproject/galaxy/pull/16041
• Gitignore update by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16046
• Fixes the parcel2 build for hdf5 viz when using node18. by @dannon in https://github.com/galaxyproject/galaxy/pull/16047
• New history selector with quick actions by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16040
• Vendorise packaging.versions.LegacyVersion by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16058
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/15942
• Show backend search errors in hist panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15874
• Change release note icon by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16049
• Rename object stores in config. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16029
• Migrate job metrics store and component to use pinia and composition api by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16056
• Deprecate tools/evolution by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15656
• Use jsdom-worker instead of mock by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16064
• Use Filtering class to get and set filter texts by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15996
• Drop UserHistories provider by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15993
• External Login Flow: Redirect users if account already exists by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15019
• Ensure that unselected checkbox inputs emit null instead of an empty array by @guerler in https://github.com/galaxyproject/galaxy/pull/16059
• Fix font-awesome library types by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16068
• unify workflows grid components by @martenson in https://github.com/galaxyproject/galaxy/pull/16045
• Remove legacy form fields from parameter factory by @guerler in https://github.com/galaxyproject/galaxy/pull/15983
• Updated doc and tests for attribute value filter by @tuncK in https://github.com/galaxyproject/galaxy/pull/15929
• Add createforeignkey migration utility by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16077
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16086
• Refactor models enums to eliminate schema dependency on model layer. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16080
• Vueify Select field by @guerler in https://github.com/galaxyproject/galaxy/pull/16010
• Merge release_23.0 into dev by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16088
• Fix and test startup with Python 3.11 on macOS by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16082
• Refactor a few client object store components by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16051
• Use automated naming convention to generate indexes and constraints in database by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16089
• Fix minor Switch to History bug in HistoryView by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16095
• Use _.+ for unused variables by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16098
• Attempt to fix mypy check by @davelopez in https://github.com/galaxyproject/galaxy/pull/16103
• De-duplicate code around object store caches. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16108
• Improve robustness of collection edit E2E test. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16092
• Workflow Editor Infinite Grid with Landmark-Lines by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16097
• Workflow Connections Dynamic Radius by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16102
• Fix resetting metadata on many repositories at once via the shed API by @jmchilton in https://github.com/galaxyproject/galaxy/pull/14906
• Allow HEAD request for requesting metadata files by @martenson in https://github.com/galaxyproject/galaxy/pull/16113
• Add hdf4 datatype by @TheoMathurin in https://github.com/galaxyproject/galaxy/pull/16105
• Merge branch 'release_23.0' into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16118
• Place admin panel section data into computed prop by @guerler in https://github.com/galaxyproject/galaxy/pull/16115
• De-duplication and improvements to the in-process object store cache monitor by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16111
• Dataset chunking tests (and small fixes) by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16069
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16123
• Add Storage Dashboard visualizations for histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/14820
• add required_files to the tag list for linting by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16129
• Upgraded to new multiselect Tags component for Workflows, DatasetList, Attributes by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/15225
• Fix : Ignore error messages for admin created accounts by @jvanbraekel in https://github.com/galaxyproject/galaxy/pull/16132
• Add count support for listing filters by @davelopez in https://github.com/galaxyproject/galaxy/pull/16075
• Selenium test for displaying workflows with problems in pages. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16085
• [webhook/gtn] Expand query selector list to encompass 'a' by @hexylena in https://github.com/galaxyproject/galaxy/pull/16100
• Disable invalid link for anonymous users. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16147
• Improve histories and datasets immutability checks by @davelopez in https://github.com/galaxyproject/galaxy/pull/16143
• When writing test error debug directories, create a 'latest' symlink. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16148
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16149
• Refactor caching object stores ahead of adding task-based store. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16144
• Integrate accessibility testing into Selenium testing by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16122
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16153
• Add option to see invocations related to a history by @martenson in https://github.com/galaxyproject/galaxy/pull/16136
• Documents use of k8sextrajobenvs in jobconf sample advanced by @pcm32 in https://github.com/galaxyproject/galaxy/pull/15110
• Migrate display applications API to Fast API by @heisner-tillman in https://github.com/galaxyproject/galaxy/pull/16156
• Improve robustness of collection upload tests. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16093
• Move axe-selenium-python to dev dependencies by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16162
• FITS data format by @volodymyrss in https://github.com/galaxyproject/galaxy/pull/15905
• Scope pinned histories by user ID by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16142
• Fix linting of FITS datatype code by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16169
• Fix eslint / ts overrides by @dannon in https://github.com/galaxyproject/galaxy/pull/16166
• Updates MGnify interactive tool to v1.1.0 by @SandyRogers in https://github.com/galaxyproject/galaxy/pull/16179
• Accessibility fixes for workflows, login, and registration. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16146
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16182
• Record input datasets and collections at full parameter path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15978
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16186
• Merge Target class with CondaTarget by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16181
• Merge 23.0 into dev by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16197
• Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16198
• Add WorkflowBox to Activity bar Side Panel by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15944
• Hide Activity Bar for anonymous users by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16200
• Remove various fallback behaviors by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16199
• Add Processing for Custom Icons by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16157
• Fix "database is locked" error (occurring in the context of workflow testing under SQLite) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16208
• Drop TS unit mapping tests by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16206
• adjust grid sharing indicators by @martenson in https://github.com/galaxyproject/galaxy/pull/16163
• Update carbon emissions calculations explanation page styling by @Renni771 in https://github.com/galaxyproject/galaxy/pull/16192
• FITS file visualization plugin by @francoismg in https://github.com/galaxyproject/galaxy/pull/16187
• Ensure session is request-scoped for legacy endpoints by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16207
• Add Repository owner field to ToolSearch by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16061
• End-to-end tests for new user welcome. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16158
• Improved Cache Monitoring for Object Stores by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16110
• Merge 23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16228
• Fixes initial state of select all checkbox by @guerler in https://github.com/galaxyproject/galaxy/pull/16217
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16227
• Allow user customization of the activity bar by @guerler in https://github.com/galaxyproject/galaxy/pull/16184
• Handle appending to a results file that does not exists. by @ksuderman in https://github.com/galaxyproject/galaxy/pull/16233
• Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in https://github.com/galaxyproject/galaxy/pull/15421
• Initial e2e test for history storage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16221
• tool_util: switch to mambaforge on non-32bit; add arm64 support by @mr-c in https://github.com/galaxyproject/galaxy/pull/16223
• Protection against problematic boolean parameters. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/15493
• Add slack error reporting plugin by @hexylena in https://github.com/galaxyproject/galaxy/pull/15025
• Adding fuzzy search functionality to front end search by @tcollins2011 in https://github.com/galaxyproject/galaxy/pull/15855
• allow anon access for api/datasets/getcontentas_text by @martenson in https://github.com/galaxyproject/galaxy/pull/16226
• Allow users to create new activity bar items by @guerler in https://github.com/galaxyproject/galaxy/pull/16196
• Replace bootstrap_history.py with galaxy-release-util by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16231
• Fix some drs handling issues by @nuwang in https://github.com/galaxyproject/galaxy/pull/15777
• Don't error on missing parameters or unused parameters in UI controllers by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16246
• Selenium type fixes and annotations. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16242
• Add Galaxy Notification System by @davelopez in https://github.com/galaxyproject/galaxy/pull/15663
• Show search in HistoryView by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16225
• Selenium test for page history links. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16222
• Refine activity bar dragging behavior by @guerler in https://github.com/galaxyproject/galaxy/pull/16245
• Paginate History Store by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16084
• e2e test for workflow license selector by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16243
• Marginally more storage management selenium coverage. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16263
• Adjust notifications activity item by @guerler in https://github.com/galaxyproject/galaxy/pull/16265
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/pull/16267
• Add History Archival feature by @davelopez in https://github.com/galaxyproject/galaxy/pull/16003
• Add interactive tools activity by @guerler in https://github.com/galaxyproject/galaxy/pull/16266
• Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in https://github.com/galaxyproject/galaxy/pull/16255
• Small test decorator improvements. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16220
• read jobconf directly from `configdirinstead of computing it again fromconfig_file` by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15596
• Container resolvers: add docs, typing and tests by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15614
• bring grids for (published) pages on par with workflows by @martenson in https://github.com/galaxyproject/galaxy/pull/16209
• Add zipped mongodb and genenotebook datatypes by @abretaud in https://github.com/galaxyproject/galaxy/pull/16173
• Reset autocommit to True (temporarily) by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16283
• OIDC tokens by @SergeyYakubov in https://github.com/galaxyproject/galaxy/pull/15300
• Display Tags in Workflow Editor by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16282
• Fix and Improve Workflow Editor Panning by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16178
• E2E Tests for Edit Dataset Attributes Page by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16224
• Decompress history data for testing assertions by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15085
• Bump msal version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16285
• Fixes for two framework test tools by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15483
• Expose additional beaker caching backends by @claudiofr in https://github.com/galaxyproject/galaxy/pull/15349
• Bump default milestone to 23.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16287
• Merge release_23.0 into dev by @martenson in https://github.com/galaxyproject/galaxy/pull/16289
• Set Initial Filter for Paired List Collection Creator Based on Initial Elements by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16279
• Improve container resolver documentation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16280
• Update version to 23.1.rc1 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16292
• [23.1] Update 23.1 release tags for migration scripts by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16294
• [23.1] Open latest version of tool from tool panel link by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16290
• [23.1] Fix recalculate_quota throug kombu message by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16299
• [23.1] handle prefix in dataset contents properly by @martenson in https://github.com/galaxyproject/galaxy/pull/16301
• [23.1] Fix form builder value handling by @guerler in https://github.com/galaxyproject/galaxy/pull/16304
• [23.1] Fix ordering of data libraries from API by @martenson in https://github.com/galaxyproject/galaxy/pull/16300
• [23.1] qualify querying for an api-key by @martenson in https://github.com/galaxyproject/galaxy/pull/16320
• [23.1] Remove pin on packaging in packages by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16322
• [23.1] Fix tool remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/16311
• [23.1] Fix 'news' webhook to account for the RC one more time. by @dannon in https://github.com/galaxyproject/galaxy/pull/16328
• [23.1] Filter deleted keys from api_keys relationship by @dannon in https://github.com/galaxyproject/galaxy/pull/16321
• [23.1] Makefile-based setting of NODE_OPTIONS for client build by @dannon in https://github.com/galaxyproject/galaxy/pull/16324
• [23.1] Refactor workflow store to be more reliable by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16334
• [23.1] Include workflow invocations in default activity by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16338
• [23.1] Sanitize substring in matchingTerm by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16351
• [23.1] Make tags in public histories read-only by @davelopez in https://github.com/galaxyproject/galaxy/pull/16348
• [23.1] Improve help text for conditional workflow step by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16355
• [23.1] Hide conditionally skipped output by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16356
• [23.1] Fix invocation progress bar for skipped and deleted jobs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16365
• [23.1] Fix workflow invocation detail reactivity by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16369
• [23.1] Add missing singularitynomount prop parsing by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16367
• [23.1] Disable console instead of dropping by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16372
• [23.1] Fix Nested Tool Panel Labels by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16376
• [23.1] Fix disk usage recalculation for distributed object stores by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16380
• [23.1] Add message showing console disable/enable, along with instructions o… by @dannon in https://github.com/galaxyproject/galaxy/pull/16401
• [23.1] Fix histories count by @davelopez in https://github.com/galaxyproject/galaxy/pull/16400
• [23.1] Job cache fixes for DCEs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16384
• [23.1] Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16421
• [23.1] Fix toolform creator by @dannon in https://github.com/galaxyproject/galaxy/pull/16419
• [23.1] For display (only) allow control+click for new window opening by @dannon in https://github.com/galaxyproject/galaxy/pull/16432
• [23.1] Fix webhook release note seen pin by @dannon in https://github.com/galaxyproject/galaxy/pull/16446
• [23.1] Fix multi-broadcast overlap by @davelopez in https://github.com/galaxyproject/galaxy/pull/16444
• [23.1] Fix error_reports linting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16465
• [23.1] Swap datatype&convert tab to a static 'datatypes' tab. by @dannon in https://github.com/galaxyproject/galaxy/pull/16466
• [23.1] Fix history items repeated search bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16452
• [23.1] Fix Storage Dashboard missing archived histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16473
• [23.1] Restore resolution of Conda environments generated from non-lowercase package names by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16474
• [23.1] Add missing archived filter in saved histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16475
• [23.1] use router instead of hard links for certain page urls by @martenson in https://github.com/galaxyproject/galaxy/pull/16297
• [23.1] Fix tagging component for anonymous users by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16481
• [23.1] Bump bx-python to 0.10.0 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16484
• [23.1] Remove blinking animation from icons by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/16471
• [23.1] Fix up unit tests for local use by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16483
• [23.1] Fix tags ownership by @davelopez in https://github.com/galaxyproject/galaxy/pull/16339
• [23.1] Make ToolBox v-b-tooltip.hover directives noninteractive by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16506
• [23.1] Fix ToolBoxWorkflow search delay bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16505
• [23.1] Fix history item states help display to apply same styling attributes by @dannon in https://github.com/galaxyproject/galaxy/pull/16500
• [23.1] H5web updates by @dannon in https://github.com/galaxyproject/galaxy/pull/16509
• [23.1] Fix for Accessibility, on Workflows List page Tooltip by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16520
• [23.1] fix font-weight disparity between browsers by @hujambo-dunia in https://github.com/galaxyproject/galaxy/pull/16515
• [23.1] Fix double-encoding notification content by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16530
• [23.1] Exclude selenium version with broken type hints by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16531
• [23.1] Restore tmp mounting by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16533
• [23.1] Run through tmpdircreation_statement only once by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16529
• [23.1] Limit tool document cache to tool configs with explicit cache path by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16537
• [23.1] Fix shared item notification link by @davelopez in https://github.com/galaxyproject/galaxy/pull/16581
• [23.1] Don't use docker run --user flag on OSX by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16573
• [23.1] Ignore errors with user-set job resources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16579
• [23.1] Bump minimum tpv version to 2.3.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16597
• [23.1] make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16594
• [23.1] Fix replacement parameters for subworkflows. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16592
• [23.1] Drop expunge_all() call in WebTransactionRequest by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16606
• [23.1] Drop RecursiveMiddleware by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16605
• [23.1] Fix multiple remote test data by @davelopez in https://github.com/galaxyproject/galaxy/pull/16542
• [23.1] Optimize getting current user session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16604
• [23.1] Backport tool mem fixes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16601
• [23.1] Only reindex tool search once after forking by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16611
• [23.1] Fix Published Pages and Pages view showing same content by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16614
• [23.1] Remove render.py script from iSEE by @neoformit in https://github.com/galaxyproject/galaxy/pull/16616
• [23.1] Reload toolbox after forking when using --preload by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16620
• [23.1] Account for expires/expires_in when refreshing token by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16621
• [23.1] Make datatype edit default value a string instead of list of strings by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16591
• [23.1] Fixes for conditional subworkflow steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16632
• [23.1] Fix nested conditional workflow steps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16641
• [23.1] Make sort_collection tool require terminal datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16661
• [23.1] xsd: allow name attribute of test collections by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16663
• [23.1] Fix expression evaluation for nested state by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16656
• [23.1] Push to object store even if set_meta fails by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16667
• [23.1] Ensure Job belongs to current SA session by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16655
• [23.1] Login/Register fixes by @dannon in https://github.com/galaxyproject/galaxy/pull/16652
• [23.1] Fix regex validation for global inline flags by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16683
• [23.1] Fix metadata setting in extended metadata + outputstoworking_directory mode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16678
• [23.1] Only show 'edit' on published pages when viewer is the owner. by @dannon in https://github.com/galaxyproject/galaxy/pull/16680
• [23.1] Update galaxyproject/charts utilizing visualizations by @dannon in https://github.com/galaxyproject/galaxy/pull/16674
• [23.1] Fix closed transaction error on galaxy startup/check jobs by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16687
• [23.1] FileInput no longer accept 'U' in the file mode by @bgruening in https://github.com/galaxyproject/galaxy/pull/16704
• [23.1] List extra files only for terminal datasets by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16705
• [23.1] Fix legend not scrollable in storage overview charts by @davelopez in https://github.com/galaxyproject/galaxy/pull/16703
• [23.1] Add missing join condition in job search by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16710
• [23.1] Fix job search query by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16714
• [23.1] Fix collection id encoding by @davelopez in https://github.com/galaxyproject/galaxy/pull/16718
• [23.1] Fix unittest mocks to support us checking geturl() by @dannon in https://github.com/galaxyproject/galaxy/pull/16726
• [23.1] Fix allowlist deserialization in file sources by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16729
• [23.1] Workaround for XML nodes of job resource parameters losing their children by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16728
• [23.1] force wrap long parameter names in the workflow form by @martenson in https://github.com/galaxyproject/galaxy/pull/16732
• [23.1] prevent toolbox scrollbar by @martenson in https://github.com/galaxyproject/galaxy/pull/16734
• [23.1] Copy the collection contents by default when copying a collection by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16717
• [23.1] 23.1 Release Notes by @dannon in https://github.com/galaxyproject/galaxy/pull/16329
• [23.1] Fix workflow output display without label by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16749
• [23.1] Add deprecation notice for api/search by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16756
• [23.1] Add missing requirements to perl tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16763
• [23.1] Don't allow empty selection on required select field by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16759
• [23.1] Fix public archived histories not importable by @davelopez in https://github.com/galaxyproject/galaxy/pull/16766
• [23.1] Fix ItemOwnerShipException in tag removal by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16773
• [23.1] Allow importing history with same name as original history by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16741
• [23.1] Fix short ids in tool panel views. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16800
• [23.1] Disable button in CopyModal for histories when copying history by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16793
• [23.1] move history and tool panel tooltips out of the way by @martenson in https://github.com/galaxyproject/galaxy/pull/16808
• [23.1] Fix tool panel views for versionless tool ids by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16809
• [23.1] Fix parameter display in job info page for tools with sections by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16821
• [23.1] move the email and username redacting from the role loop by @martenson in https://github.com/galaxyproject/galaxy/pull/16820
• [23.1] backport of pysam tostring by @martenson in https://github.com/galaxyproject/galaxy/pull/16822
• [23.1] Increase CustosAuthnzToken.external_user_id column size by @davelopez in https://github.com/galaxyproject/galaxy/pull/16818
• [23.1] Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16829
• [23.1] Fix up local tool version handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16836
• [23.1] Exclude onopened and onclosed from watcher events by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16850
• [23.1] Specify uid for the k8s image by @afgane in https://github.com/galaxyproject/galaxy/pull/16844
• [23.1] Fix and prevent persisting null file_size by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16855
• [23.1] Fix safe update version handling in run form by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16865
• [23.1] Fix workflow import losing tool_version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16869
• [23.1] Allow referring to steps by label only in markdown editor by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16861
• [23.1] Remove more flushes in database operation tools by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16875
• [23.1] Fix tag ownership check by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16877
• [23.1] Fix join condition for nested collection query by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16880
• [23.1] Fix delete collection + elements by @davelopez in https://github.com/galaxyproject/galaxy/pull/16879

New Contributors

• @tchaussepiedifb made their first contribution in https://github.com/galaxyproject/galaxy/pull/15858
• @undergone2345 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15963
• @minh-biocommons made their first contribution in https://github.com/galaxyproject/galaxy/pull/15998
• @jarrah42 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15394
• @tuncK made their first contribution in https://github.com/galaxyproject/galaxy/pull/15929
• @TheoMathurin made their first contribution in https://github.com/galaxyproject/galaxy/pull/16105
• @volodymyrss made their first contribution in https://github.com/galaxyproject/galaxy/pull/15905
• @francoismg made their first contribution in https://github.com/galaxyproject/galaxy/pull/16187
• @tcollins2011 made their first contribution in https://github.com/galaxyproject/galaxy/pull/15855

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.6...v23.1.1

- Python
Published by mvdbeek over 2 years ago

galaxy - v23.0.6

What's Changed

• [23.0] Fix upload paramfile handling (for real user setups) by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16504
• [22.01] Fix up tox.ini by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16567
• [23.0] Add missing unit-coverage environment by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16570
• [23.0] Fix dataset collection url in workflow reports by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16571
• [23.0] Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16569
• [23.0] Fix incorrect ASGI request host by @davelopez in https://github.com/galaxyproject/galaxy/pull/16574
• [22.01] Fix incorrect ASGI request host by @davelopez in https://github.com/galaxyproject/galaxy/pull/16575
• [23.0] Fix conditional step evaluation with datasets in repeats by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16584
• [23.0] Don't read request body into memory by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16585
• [23.0] Fix extra files path handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16541
• [23.0] Fixes for extra files handling and cached object stores by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16595
• [22.01] Passing Identifier for div to Write the Chart Panel to by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16598
• [23.0] Allow the legacy DELETE dataset endpoint to accept any string for the history_id by @assuntad23 in https://github.com/galaxyproject/galaxy/pull/16593
• [23.0] Don't fail invocation message without dependentworkflowstep_id by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16628
• [23.0] Lazy load tool data tables in celery worker by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16640
• [23.0] Force __DUPLICATE_FILE_TO_COLLECTION__ 'size' param to integer by @simonbray in https://github.com/galaxyproject/galaxy/pull/16659
• [22.05] Switch to upstream setup-chromedriver action by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16669
• [23.0] Update pulsar client library to 0.15.5 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16701
• [23.0] Fix RE for new version scheme in doc/source/conf.versioning.py by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16765
• [23.0] Show MessageException in invocation UI by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16772
• [23.0] Fix create/install commands for conda 23.9.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16831

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.5...v23.0.6

- Python
Published by mvdbeek over 2 years ago

galaxy - v23.0.5

What's Changed

• [22.05] Slugify username received from oidc by @nuwang in https://github.com/galaxyproject/galaxy/pull/16251
• [23.0] Don't attempt to call a bool when using mem-self handler assignment. by @natefoo in https://github.com/galaxyproject/galaxy/pull/16359
• [23.0] Fix dataset create time convert by @itisAliRH in https://github.com/galaxyproject/galaxy/pull/15329
• [23.0] Minor bug fix for default mail templates by @neoformit in https://github.com/galaxyproject/galaxy/pull/16362
• [23.0] Fix display of named tags in mako by @davelopez in https://github.com/galaxyproject/galaxy/pull/16368
• [23.0] Fix active step display in workflow editor side panel by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16364
• [23.0] Copy when_expression when copying workflow step by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16377
• [23.0] Pin black version to 23.3.0 in workflow action by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16390
• [23.0] Don't always install node in the virtualenv by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16395
• [23.0] Fix test discovery in vscode by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16413
• [23.0] Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16403
• [23.0] Allow duplicate labels in linter if outputs contain filters by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15933
• [23.0] Media player fix issue 16415 by @bdwheele in https://github.com/galaxyproject/galaxy/pull/16443
• [23.0] Fix static file serving for robots.txt and favicon.ico when using per_host settings by @mira-miracoli in https://github.com/galaxyproject/galaxy/pull/16459
• [22.05] Bump version of chromedriver setup action by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16461
• [23.0] Fixes for (gitlab) error reporting by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16424
• [23.0] Fix filtering of disabled user preferences in UI by @davelopez in https://github.com/galaxyproject/galaxy/pull/16464
• [23.0] Fix parsing tool metadata from bio.tools by @kysrpex in https://github.com/galaxyproject/galaxy/pull/16449
• [23.0] Adjust testdatadownload method in GalaxyInteractorApi so an admin user is not required by @simonbray in https://github.com/galaxyproject/galaxy/pull/16482
• [23.0] Linter: fix regex for profile version by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16480

New Contributors

• @bdwheele made their first contribution in https://github.com/galaxyproject/galaxy/pull/16443
• @mira-miracoli made their first contribution in https://github.com/galaxyproject/galaxy/pull/16459

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.4...v23.0.5

- Python
Published by mvdbeek almost 3 years ago

galaxy - v23.0.4

What's Changed

• [23.0] Fix tool recommendations shown in a d3 js tree by @anuprulez in https://github.com/galaxyproject/galaxy/pull/15852
• [23.0] Fix folder access for anonymous user by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16330
• [23.0] Fix default when statement evaluation by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16332
• [23.0] Redact private role name and description when purging user by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16349
• [23.0] Pin pydantic in packages to <2 by @natefoo in https://github.com/galaxyproject/galaxy/pull/16354

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.3...v23.0.4

- Python
Published by natefoo almost 3 years ago

galaxy - v23.0.3

What's Changed

• [23.0] Bump galaxy-release-util version to 0.1.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16241
• [23.0] When importing tool data bundles, use the first loc file for the matching table by @natefoo in https://github.com/galaxyproject/galaxy/pull/16247
• [23.0] Load data tables in Celery worker by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16244
• [23.0] xsd: add missing sep attribute for has_n_columns by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16262
• [23.0] Fix converting Enum value to str for Python 3.11 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16284
• [23.0] Forward port of slugify username received from oidc by @nuwang in https://github.com/galaxyproject/galaxy/pull/16271
• [23.0] Missing init prevents models.py being bundled into tool_util by @nuwang in https://github.com/galaxyproject/galaxy/pull/16308

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.2...v23.0.3

- Python
Published by mvdbeek almost 3 years ago

galaxy - 23.0.2

What's Changed

• [23.0] Fix Text File Busy errors at the source by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16212
• [23.0] Point release deps fixes and docs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16214
• [23.0] Rename galaxy-webapps back to galaxy-web-apps by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16216
• [23.0] Port selenium setup to non-deprecated selenium options by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16215
• [23.0] Don't fail CWL tool parsing when Cheetah not installed by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16219
• [23.0] Allow skipping expect_num_outputs when expect_failure is set in tool test by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/16237
• [23.0] Use galaxy-release-util to upload python packages by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16240
• [22.05] Fix dropbox import to support newer versions by @nuwang in https://github.com/galaxyproject/galaxy/pull/16239

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0.1...v23.0.2

- Python
Published by mvdbeek almost 3 years ago

galaxy - 23.0.1

A note about this release

This is the first Galaxy point release for which all Python packages are published to the Python Package Index. Changes listed here and in the package changelog only include changes made since the v23.0 tag was published and do not include changes made in between the v22.5 and v23.0.1 tags. We will include all changes for future releases going forward and we strive for more frequent point releases.

What's Changed

• [23.0] Fix Toast variant color for errors by @davelopez in https://github.com/galaxyproject/galaxy/pull/15928
• [23.0] Fix defineProps warning in client build. by @dannon in https://github.com/galaxyproject/galaxy/pull/15930
• [22.05] Fix mixed outputstoworking_directory pulsar destinations by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15927
• [23.0] Prevent anonymous access to Storage Dashboard by @davelopez in https://github.com/galaxyproject/galaxy/pull/15934
• [23.0] Update Gravity to 1.0.3 by @natefoo in https://github.com/galaxyproject/galaxy/pull/15939
• [23.0] Add ca_certs option for sentry client by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15943
• [23.0] Fix History Import Bugs by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15923
• [23.0] Fix folder listing via file browser by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15950
• [23.0] Change default watchdog inotify_buffer log level to info by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15967
• [23.0] Fix RO-crate invocation export with complex collections by @davelopez in https://github.com/galaxyproject/galaxy/pull/15971
• [23.0] Fix Webhooks not rendering by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15985
• [23.0] Fix invalid link to "workflows by owner" by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/15986
• [23.0] Fix History filters includes related filter bug by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/15975
• [23.0] Fix history export papercuts by @davelopez in https://github.com/galaxyproject/galaxy/pull/15991
• [23.0] Fix build collection not resetting selection by @davelopez in https://github.com/galaxyproject/galaxy/pull/16005
• [23.0] Backport Improve display chunk generation for BAMs by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16007
• [23.0] Allow setting auto_decompress property in staging interface by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16014
• [23.0] Clarify search behavior in placeholder text in Published Histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16006
• [23.0] Make Expression Tools searchable in ToolBoxWorkflow by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16022
• [23.0] Reports app fixes by @dannon in https://github.com/galaxyproject/galaxy/pull/16015
• [23.0] Workflow connections performance with SVG by @ElectronicBlueberry in https://github.com/galaxyproject/galaxy/pull/16000
• [23.0] Tabular Dataset Display Fixes by @dannon in https://github.com/galaxyproject/galaxy/pull/15970
• [23.0] Backport #16023: Fix pasting file fails if text starts with file by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16024
• [23.0] Ensure history export contains all expected datasets by @davelopez in https://github.com/galaxyproject/galaxy/pull/16013
• [23.0] Add support for launching workflows via Tutorial Mode by @hexylena in https://github.com/galaxyproject/galaxy/pull/15684
• [23.0] Fix gcsfs test discovery by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16039
• [23.0] Install node from setup-node action in more tests by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16043
• [23.0] Replace httpbin service with pytest-httpserver by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16042
• [23.0] Fix case sensitive filtering by name in histories by @davelopez in https://github.com/galaxyproject/galaxy/pull/16036
• [23.0] Various fixes to path prefix handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16033
• [23.0] Update pulsar to 0.15.2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16050
• [23.0] Fix minor error in WorkflowList help modal by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16057
• [23.0] Backport fix pop-up link by @davelopez in https://github.com/galaxyproject/galaxy/pull/16060
• [22.05] Fix assertion linting to not fail on byte suffixes by @bernt-matthias in https://github.com/galaxyproject/galaxy/pull/15873
• [23.0] Anonymous User tool link bug fix by @ahmedhamidawan in https://github.com/galaxyproject/galaxy/pull/16065
• [23.0] Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/15744
• [23.0] merge 22.05 by @martenson in https://github.com/galaxyproject/galaxy/pull/16073
• [23.0] Fix BCO export by updating gxformat2 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16081
• [23.0] Add missing dates for versions that contain changelog entries by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16090
• [23.0] Fix job failure handling when condor indicates job failure by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16096
• [23.0] Fix mypy error due to alembic 1.11.0 by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16104
• [23.0] Fix dataypechange not updating HDCA updatetime by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16099
• [23.0] Don't build Docker image when pushing to release branches by @ksuderman in https://github.com/galaxyproject/galaxy/pull/16055
• [23.0] Fix extended metadata file size handling by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16109
• [23.0] Ignore invalid query params in displaybyusernameandslug by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16117
• [23.0] Extract HDA for codefile validateinput hook by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16120
• [23.0] Backport Improve robustness and abstractions used by collection edit tests. by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16116
• [23.0] Fix sort error when re-running job with DCE collection input by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16126
• [23.0] Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in https://github.com/galaxyproject/galaxy/pull/16137
• [23.0] Fix backbone-based data selector to materialize consistent attribute set by @guerler in https://github.com/galaxyproject/galaxy/pull/15981
• [23.0] Fix related-hid in bulk contents API by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16128
• [23.0] Fix implicit converters with optional parameters by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16133
• [22.05] Fix get_test_from_anaconda() and base_image_for_targets() functions by @nsoranzo in https://github.com/galaxyproject/galaxy/pull/16125
• [23.0] Make ctx_rev optional in InstalledToolShedRepository response model by @dannon in https://github.com/galaxyproject/galaxy/pull/16139
• [23.0] Add script for creating (point) releases by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16076
• [23.0] Converge release process auth discovery. by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16160
• [23.0] Show bug error for failed_meta state by @dannon in https://github.com/galaxyproject/galaxy/pull/16165
• [23.0] Fix test search for mulled container hashes by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16170
• [23.0] Tool filtering fix for label handling by @dannon in https://github.com/galaxyproject/galaxy/pull/16168
• [23.0] Fix optional fields being validated as missing in ts api by @jmchilton in https://github.com/galaxyproject/galaxy/pull/16141
• [23.0] Tool warnings can either be None or a Dictionary but not a String by @guerler in https://github.com/galaxyproject/galaxy/pull/16183
• [23.0] Startup fix when tool removed between reboot by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16175
• [23.0] Make point release script compatible with docutils 0.16 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16190
• [23.0] Support ro crate 0.8.0 and 0.7.0 by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16193
• [23.0] Assert that local branches are up to date in release point script by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16195
• [23.0] Pin minimum tpv version by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/16201
• [23.0] Verify existence of default value attribute for user forms fields by @guerler in https://github.com/galaxyproject/galaxy/pull/16205

Full Changelog: https://github.com/galaxyproject/galaxy/compare/v23.0...v23.0.1

- Python
Published by mvdbeek almost 3 years ago