v25.0.2

What's Changed

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

New Contributors

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

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

v25.0.1

What's Changed

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

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

v25.0.0

What's Changed

• Stabilize HistoryView.test.js by @jmchilton in #19165
• Fix Pesky warning with PersistentTaskProgressMonitorAlert.test.ts by @ElectronicBlueberry in #19180
• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181
• Cleanup Jest Test Output (part 2) by @jmchilton in #19178
• Dynamic options: add data table filter by @bernt-matthias in #12941
• Cleanup Jest Test Output (part 3) by @jmchilton in #19185
• Don't calculate dataset hash for datasets in non-OK state by @nsoranzo in #19191
• Fix UP031 errors - Part 1 by @nsoranzo in #19194
• Cleanup Jest Test Output (part 4) by @jmchilton in #19186
• Extend image metadata by @kostrykin in #18951
• Move phylocanvas to script entry point by @guerler in #19193
• Move heatmap visualization to new script endpoint by @guerler in #19176
• Fix UP031 errors - Part 2 by @nsoranzo in #19204
• Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot in #19189
• Workflow Editor Activity Bar by @ElectronicBlueberry in #18729
• Add plotly.js by @guerler in #19206
• Switch h5web to script endpoint by @guerler in #19211
• Update visualizations to latest charts package by @guerler in #19213
• Fix UP031 errors - Part 3 by @nsoranzo in #19218
• Cleanup test output console for tool panel tests. by @jmchilton in #19210
• Update Vizarr package version to 0.1.6 by @davelopez in #19228
• Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot in #19233
• Fix UP031 errors - Part 4 by @nsoranzo in #19235
• Explicitly add cwl-utils to dependencies by @nsoranzo in #19257
• Merge 24.2 into dev by @jmchilton in #19240
• Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260
• [PROCEDURES] Drop thumbs up reaction as pull request approval method by @nsoranzo in #19202
• Fix UP031 errors - Part 5 by @nsoranzo in #19282
• Merge 24.2 into dev. by @jmchilton in #19273
• Merge latest 24.2 into dev. by @jmchilton in #19290
• Minor drag style adjustment for activities by @guerler in #19299
• Fix UP031 errors - Part 6 by @nsoranzo in #19314
• Update pydantic to 2.10.3 by @nsoranzo in #19326
• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331
• Extract and typescript-ify datatype selection in wfeditor. by @jmchilton in #19304
• Refactor and add tests for Popovers by @guerler in #19337
• Misc fixes 202412 by @nsoranzo in #19341
• Use popper wrapper for help text popover by @guerler in #19340
• Update Python dependencies by @galaxybot in #19190
• Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in #19358
• Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot in #19369
• Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372
• Node 22 unreachable fixes by @mvdbeek in #19378
• Make conditional discriminators literals instead of generic string/bool by @mvdbeek in #19374
• Remove apptainer-version pin by @nsoranzo in #19380
• SQLAlchemy 2.0 follow-up by @jdavcs in #19388
• Use id entity attribute when setting exampleOfWork property by @nsoranzo in #19396
• Update Python dependencies by @galaxybot in #19366
• Display email activation help only if user activation is enabled by @jdavcs in #19402
• Prevent negative offset by @jdavcs in #19409
• Update Python dependencies by @galaxybot in #19418
• Set safe default extraction filter for tar archives by @nsoranzo in #19406
• Let file sources choose a path for uploaded files by @kysrpex in #19154
• Enable cloning subworkflows by @ElectronicBlueberry in #19420
• Merge Release 24.2 into dev by @ahmedhamidawan in #19443
• Add Vitessce Viewer by @guerler in #19227
• Type annotations improvements by @nsoranzo in #19442
• Alternative format_source fix by @mvdbeek in #19395
• Update main citation to 2024 community paper by @nsoranzo in #19453
• Reset invocation export wizard after completion by @davelopez in #19449
• Remove transaction helper by @jdavcs in #19407
• Update Python dependencies by @galaxybot in #19464
• Document $__user_name__ by @bernt-matthias in #19433
• Improve asynchronous tasks error handling and reporting by @davelopez in #19448
• Workflow Editor Auto Zoom by @ElectronicBlueberry in #19451
• Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394
• Avoid using custos refresh tokens which are expired by @martenson in #19411
• Handles S3 listing errors by @itisAliRH in #19446
• Add test that verifies workflow source_metadata is preserved on landing claim by @mvdbeek in #19454
• eLabFTW integration via Galaxy file source by @kysrpex in #19319
• Add Dataverse RDM repository integration by @KaiOnGitHub in #19367
• Type annotation improvements by @nsoranzo in #19485
• Fix wrong id in test_combined_mapping_and_subcollection_mapping by @mvdbeek in #19481
• Fix preferred object store id reactivity by @ElectronicBlueberry in #19491
• Add author and tools details in RO-Crate by @Marie59 in #18820
• Add workflow selection and bulk actions by @itisAliRH in #19336
• Update Python dependencies by @galaxybot in #19510
• Prevent users from reusing a banned email after account is purged by @jdavcs in #19413
• Fix wrong URI written to ExportObjectResultMetadata when exporting histories to eLabFTW by @kysrpex in #19541
• Fix package versions by @jdavcs in #19566
• Update Python dependencies by @galaxybot in #19567
• Add IGB display support for CRAM files by @paige-kulzer in #19428
• Change galaxy system user uid for K8s image by @afgane in #19403
• Merge 24.2 into dev by @jdavcs in #19590
• Hide outdated visualizations from visualizations activity panel by @guerler in #19353
• Add vue-tsc baseline comparison to client-lint workflow by @dannon in #19593
• Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594
• Add eLabFTW file source from file source templates by @kysrpex in #19493
• Update Python dependencies by @galaxybot in https://github.com/galaxyproject/galaxy/...

v24.2.4

What's Changed

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

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

v24.2.3

What's Changed

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

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

v24.2.2

What's Changed

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

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

v24.2.1

What's Changed

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

Full Changelog: v24.2.0...v24.2.1

v24.2.0

What's Changed

• Update version to 24.2.dev by @jdavcs in #18185
• Change default milestone to target 24.2 by @jdavcs in #18186
• Update versions of GitHub actions by @nsoranzo in #18197
• Play nice with password managers by @martenson in #18206
• Drop "Send to cloud" tool and associated cloudauthz code by @jdavcs in #18196
• Merge 24.0, 24.1 into dev by @mvdbeek in #18288
• new edits and now using a docker image with qiskit1.0 by @thepineapplepirate in #18225
• Update Python dependencies by @galaxybot in #18226
• Fix loading error for built in tool sift by @bernt-matthias in #18357
• Merge latest 24.1 into dev. by @jmchilton in #18360
• More data access tests, some refactoring and cleanup by @jdavcs in #18312
• Update GPU JupyterLab tool by @anuprulez in #18220
• Merge 24.1 by @jdavcs in #18386
• [24.1] Fix Object store empty list alert by @itisAliRH in #18413
• Bump ws from 8.11.0 to 8.17.1 in /client by @dependabot in #18417
• Prepare for NumPy 2.0 by @nsoranzo in #18422
• Add pod5 datatype by @TomHarrop in #18419
• [PROCEDURES] Minor adjustments to SECURITY.md to reflect that we call yearly releases LTS by @dannon in #18171
• Minor additions to release process by @bernt-matthias in #18450
• Masthead Revision by @guerler in #17927
• Updates the About Page by @guerler in #18461
• Update plausible script name in mako templates by @sanjaysrikakulam in #18458
• Move workflow preview to primary link for workflows card list -- easi… by @dannon in #18463
• Fix some deprecations by @nsoranzo in #18433
• Fixed Podman 5 issue in sample job config file by @sveinugu in #18439
• Fix Workflow Preview Selenium Test Error by @itisAliRH in #18483
• Workflow Card Buttons Refactors [GCC2024_COFEST] by @itisAliRH in #18465
• Stray small changes from structured_tool_state branch. by @jmchilton in #18453
• Move Workflow List Files to New Location [GCC2024_COFEST] by @itisAliRH in #18466
• Update package dev versions by @jdavcs in #18489
• Moves Libraries from Masthead to Activity Bar by @guerler in #18468
• Update Python dependencies by @galaxybot in #18406
• Raise Message Exception when displaying binary data by @mvdbeek in #18503
• [PROCEDURES] remove davebx from committers list by @martenson in #18452
• Add missing version in the file sources and object store templates by @sanjaysrikakulam in #18497
• Improve invocation export UI by @davelopez in #18512
• Fix "worklfow" typo here and there by @abretaud in #18523
• Update openapi-typescript dependency to version 6.7.6 by @davelopez in #18519
• Minor config documentation enhancements by @bgruening in #18499
• Mixed enhancements from CWL branch by @nsoranzo in #18539
• Update Python dependencies by @galaxybot in #18505
• Adds an option to restore activity bar defaults by @guerler in #18469
• Fix some Toolshed 2.0 development paper-cuts by @davelopez in #18538
• Add errors fast api by @arash77 in #18093
• Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in #18524
• Fix MessageException handling in get_edit by @mvdbeek in #18529
• Fix bugs in tool shed tool API. by @jmchilton in #18558
• Improvements to Tool Test Parsing by @jmchilton in #18560
• Improve datasets permissions API schema typing by @davelopez in #18563
• Add task expiration to persistent task monitor by @davelopez in #18551
• Drop unused datasets controller methods by @mvdbeek in #18568
• Group tool templating exceptions in sentry by @mvdbeek in #18570
• Add a new version of the production s3fs file source template with the writable configuration variable added by @sanjaysrikakulam in #18575
• Consistent type imports, fixes and linting. by @dannon in #18589
• Tighten user notification API response types by @davelopez in #18599
• Move history multiview item actions to top by @ahmedhamidawan in #18265
• Improve update user API payload schema by @davelopez in #18602
• More tool test typing. by @jmchilton in #18590
• Record container id and type in core job metrics by @mvdbeek in #18579
• Bump requirejs from 2.3.6 to 2.3.7 in /client by @dependabot in #18610
• Implement Declarative Testing for Workflow Behaviors by @jmchilton in #18542
• [24.1] Fix collection type drag and drop validation by @mvdbeek in #18623
• Improve update history payload schema by @davelopez in #18618
• Rev pinned gxformat2. by @jmchilton in #18624
• Fixes for errors reported by mypy 1.11.0 by @nsoranzo in #18608
• Improve typing for archived histories API schema by @davelopez in #18586
• Remove unused functions in dataset managers by @jmchilton in #18631
• Reduce unnecessary requests when browsing tool repositories in Admin Panel by @davelopez in #18632
• Refactor FolderTopBar to TypeScript by @itisAliRH in #18488
• Bug fix for invalid duplicate id in function test tools. by @jmchilton in #18644
• Handle output parsing when tool is not available for tool-centric API. by @jmchilton in #18643
• Enable verbatimModuleSyntax, fix jest usage by @dannon in #18595
• Improve types around User in schema and client by @davelopez in #18645
• Rip repository_registry out of tool shed 2.0 by @jmchilton in #18647
• Another shot at tool shed API fixes by @jmchilton in #18646
• Better Typing for Tool Execution Plumbing by @jmchilton in #18626
• Undo stack UI by @ElectronicBlueberry in #18548
• Restore interactive tools watcher by @guerler in #18581
• Parameter Model Improvements by @jmchilton in #18641
• [PROCEDURES] Add Alireza to committers group by @nsoranzo in #18613
• Improve accept header API schema by @davelopez in #18668
• Another round of parameter model improvements. by @jmchilton in #18673
• De-couple XML from tool interface for test collections. by @jmchilton in #18676
• Allow connecting text param into data column parameter by @mvdbeek in #18674
• Update mercurial by @mvdbeek in #18686
• Restore repository update in the tool shed 2.0. by @jmchilton in #18655
• Update ExportToRemoteModal.vue to use TypeScript by @davelopez in #18706
• Upgrade openapi-typescript to 7.0.2 + swap to openapi-fetch by @davelopez in #18532
• Fix "Latest Updates" order in t...

v24.1.4

What's Changed

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

Full Changelog: v24.1.3...v24.1.4

v24.1.3

What's Changed

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

Full Changelog: v24.1.2...v24.1.3