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

v24.1.2

What's Changed

• [24.1] fix no-op workflow "relabel" shouldn't result in a notification by @ElectronicBlueberry in #18473
• [24.1] Make default_panel_view a _by_host option by @natefoo in #18471
• [24.1] Stabilize test_purge_while_job_running test by @mvdbeek in #18498
• [24.1] Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
• [24.0] Return generic message for password reset email by @ahmedhamidawan in #18479
• [24.1] Backport pod5 datatype by @TomHarrop in #18507
• [23.2] Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510
• [24.0] Follow-up on #18212 by @nsoranzo in #18516
• [24.0] Fix view parameter type in Job index API by @davelopez in #18521
• [24.1] Prevent job submission if input collection element is deleted by @mvdbeek in #18517
• [24.1] Use name instead of ID for displaying object stores + revise user-facing language in UI by @davelopez in #18525
• [24.1] Check if dataset has any data before running provider checks by @mvdbeek in #18526
• [24.1] Strip unicode null from tool stdio by @mvdbeek in #18527
• [24.1] Simplify and fix useDatatypesMapper by @mvdbeek in #18550
• [24.1] Also check dataset.deleted when determining if data can be displayed by @mvdbeek in #18547
• [24.1] Fix map over calculation for runtime inputs by @mvdbeek in #18535
• [24.1] Fix shared caches with extended metadata collection. by @jmchilton in #18520
• [24.1] Fix undo removing all freehand comments by @ElectronicBlueberry in #18557
• [24.1] Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
• [24.1] Apply statsd arg sanitization to all pages by @mvdbeek in #18509
• [24.1] Raise appropriate exception if ldda not found by @mvdbeek in #18569
• [24.1] Fix history changes switch to simple form by @ElectronicBlueberry in #18574
• [24.0] Fix Archive header encoding by @arash77 in #18583
• [24.0] Fix for not-null in 'column_list' object by @hujambo-dunia in #18553
• [23.0] Fix API key reveals on mouse hover by @itisAliRH in #18593
• [24.0] Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
• [24.0] Set minimum weasyprint version by @mvdbeek in #18606
• [24.1] Adjust sentry default config -- drop replay by @dannon in #18622
• [24.1] More datatype deprecation warnings by @mvdbeek in #18612
• [23.0] Fix for Numeric form field to allow Null min/max values in validation methods by @hujambo-dunia in #18585
• [24.1] xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605
• [24.1] Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
• [24.1] Include workflow invocation id in exception logs by @mvdbeek in #18594
• [24.1] Fix invocation view steps scroll bug by @ahmedhamidawan in #18614
• [24.1] Fix resume_paused_jobs if no session provided by @mvdbeek in #18640
• [24.0] Close install model session when request ends by @mvdbeek in #18629
• [24.1] Update h5web by @dannon in #18552
• [24.0] Don't set file size to zero by @mvdbeek in #18653
• [23.2] Strip whitespace when listifying admin users by @jdavcs in #18656
• [24.1] Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
• [24.1] Optimize useInvocationGraph for Invocation view by @ahmedhamidawan in #18663
• [24.0] Improve workflow creating/saving UX by @ahmedhamidawan in #18657
• [24.1] Fix export_remote include/exclude metadata flag by @davelopez in #18659
• [24.0] Remove unnecessary assert for file_size by @davelopez in #18669
• [24.1] Fix h5ad metadata by @nilchia in #18635
• [24.1] Return error when following a link to a non-ready display application by @mvdbeek in #18672
• [24.1] Only load authnz routes when oidc enabled by @mvdbeek in #18683
• [24.1] File source and object store instance api fixes by @mvdbeek in #18685
• [24.0] Fix import all datasets from library folder by @davelopez in #18687
• [24.0] Make sure we set file size also for purged outputs by @mvdbeek in #18681
• [24.1] Fix sorting users in admin by last login by @jdavcs in #18694
• [24.1] Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
• [24.1] Fix upload when current history changes by @davelopez in #18703
• [24.1] Fix output hover for workflow parameter outputs by @mvdbeek in #18720
• [24.1] Fill in missing help for cross product tools. by @jmchilton in #18698
• [24.1] Add error handling in WorkflowInvocationState by @ahmedhamidawan in #18726
• [24.1] Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
• [24.1] Fix invocation grid selenium that fails intermittently by @ahmedhamidawan in #18735
• [24.1] Fix resume paused jobs response handling by @dannon in #18733
• [24.1] Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
• [24.1] Fix datatype validation of newly built collection by @mvdbeek in #18738
• [24.1] Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730
• [24.1] Show items with same hid but different id in history by @ahmedhamidawan in #18689
• [24.0] Fix rules runtime editable by @ElectronicBlueberry in #18741
• [24.1] Fix directory get or create logic by @mvdbeek in #18752
• [24.1] Fix scratch storage modal title by @mvdbeek in #18753
• [24.1] Fix job summary for optional unset job data inputs by @mvdbeek in #18754
• [24.1] Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
• [24.1] Fix infinite rapid polling in useKeyedCache by @mvdbeek in #18756
• [24.0] Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788
• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
• [24.1] Fixing RegisterForm.vue not appending prefix when set. by @mcuaya1 in #18786
• [24.0] Update ENA url in ebi_sra tool by @mvdbeek in #18771
• [24.1] Fix wrong extension on pick data output by @mvdbeek in #18798
• [24.1] Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by @cat-bro in #18784
• [24.1] Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802
• [24.1] Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805
• [24.1] Collect job metrics also when job failed by @mvdbeek in #18809
• [24.1] Fix optional text handling ...

v24.1.1

What's Changed

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

New Contributors

• @laperlej made their first contribution in #18459

Full Changelog: v24.1...v24.1.1

v24.0.3

What's Changed

• [24.0] Backport OIDC schema fix by @mvdbeek in #18111
• [23.2] Allow purge query param, deprecate purge body param by @mvdbeek in #18105
• [24.0] Fix switching between nested collection elements by @mvdbeek in #18115
• [24.0] Fix deprecated deprecated argument by @mvdbeek in #18119
• [24.0] Ignore AdminRequired and RegisteredUserRequired Sentry events by @mvdbeek in #18118
• [24.0] Include traceback when logging email PJA exception by @mvdbeek in #18122
• [24.0] Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123
• [24.0] Don't log exception if cancelled slurm job doesn't have stderr file by @mvdbeek in #18121
• [24.0] Raise exception if collection elements missing during download by @jdavcs in #18094
• [24.0] Fix and unify axios error handling by @mvdbeek in #18112
• [24.0] Fix activity bar touch events on iOS devices by @mvdbeek in #18109
• [24.0] Fix vanishing connections on workflow upgrade by @ElectronicBlueberry in #18107
• [24.0] Fix listing possibly untitled records in Invenio Plugin by @davelopez in #18130
• [24.0] Don't commit in DeleteIntermediatesAction by @mvdbeek in #18131
• [24.0] Fix data default values not getting added to history by @mvdbeek in #18132
• [24.0] Fix undefined reading 'produces_entry_points' TypeError by @ahmedhamidawan in #18141
• [24.0] Fix config access in StorageManager by @dannon in #18143
• [24.0] Fix Legacy HTML page view by @mvdbeek in #18145
• [24.0] Delay tool form rendering until config is loaded by @mvdbeek in #18151
• [24.0] Raise RequestParameterInvalidException when url is invalid by @mvdbeek in #18155
• [24.0] Drop redundant error message by @mvdbeek in #18156
• [24.0] Fix error message when accessing restricted Zenodo records by @davelopez in #18169
• [24.0] Downgrade count lines error to warning by @mvdbeek in #18175
• [24.0] Emit warning when user-cancelled job already complete by @mvdbeek in #18178
• [24.0] Fix typos in create release documentation page by @jdavcs in #18181
• [24.0] Fix on success redirect by @mvdbeek in #18187
• [24.0] Fix Edit Dataset UI when there is an error retrieving the dataset by @davelopez in #18188
• [24.0] Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190
• [24.0] Fix make all histories private with immutable histories by @davelopez in #18200
• [24.0] Remove legacy code, reference to sqlalchemy migrate by @jdavcs in #18202
• [24.0] Fix submitted value in workflow run form if data is constrained by tag filter by @mvdbeek in #18193
• [24.0] Add string cast for dbkey / genome_build by @mvdbeek in #18207
• [24.0] Include stack when reporting delete error by @mvdbeek in #18208
• [24.0] Replace Multiselect selectLabel with icons in FormSelect by @ahmedhamidawan in #18194
• [24.0] Fix pca 3d rendering of tabular files and visualization error handling in general by @mvdbeek in #18211
• [24.0] Don't fail metadata if we only have an extra output files dir by @mvdbeek in #18179
• [24.0] Add GenericItem error handling by @ahmedhamidawan in #18203
• [24.0] Backport #18197 by @nsoranzo in #18212
• [24.0] Use config_section to distinguish between galaxy and ts or other apps by @jdavcs in #18215
• [24.0] Prevent anonymous and inactive users from running workflows by @ahmedhamidawan in #18192
• [24.0] Restrict job_files access to jobs that are not terminal by @mvdbeek in #18217
• [24.0] Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214
• [24.0] do not expand datasets that are known to be inaccessible by @martenson in #17818
• [24.0] Raise RequestParameterInvalidException if url can't be verified by @mvdbeek in #18230
• [24.0] Don't set dataset peek for errored jobs by @mvdbeek in #18231
• [24.0] Decrease log level for expected visualization errors by @mvdbeek in #18229
• [24.0] Raise appropriate exception if accessing deleted input file by @mvdbeek in #18223
• [24.0] Reset content-length for unhandled exceptions by @mvdbeek in #18233
• [24.0] Fix element serialization for collections that aren't populated yet by @mvdbeek in #18235
• [24.0] Fix userOwnsHistory conditions by @davelopez in #18243
• [23.1] Minor fix to enable external hgweb process by @mvdbeek in #18256
• [24.0] Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250
• [23.1] Add missing TS migration by @jdavcs in #18267
• [23.2] Add hgweb_repo_prefix attribute to TestToolShedConfig by @nsoranzo in #18268
• [24.0] Format with black by @nsoranzo in #18273
• [24.0] Transparently open compressed files in DatasetDataProvider by @mvdbeek in #18248
• [24.0] Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249
• [24.0] Fix Invenio credentials handling by @davelopez in #18255
• [23.1] Add revision tags for TS migration in 23.1 by @jdavcs in #18271
• [24.0] Only log error if deleting directory really failed by @mvdbeek in #18236
• [24.0] Don't attempt to download purged datasets by @mvdbeek in #18278
• [24.0] Set page importable to false when serializing by @mvdbeek in #18263
• [24.0] Fix first_dataset_element type hint by @mvdbeek in #18284
• [23.2] Add toolshed database revision tags for 23.2 by @jdavcs in #18293
• [24.0] Add TS db revision tags for 24.0 by @jdavcs in #18294
• [24.0] Use correct link for log in or register in Copy Modal by @davelopez in #18289
• [24.0] Redirect anonymous users to home when importing public histories by @davelopez in #18286
• [24.0] Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283
• [24.0] Move tool shed specific driver function to tool_shed.test by @mvdbeek in #18296
• [24.0] Don't serialize display application links for deleted datasets by @mvdbeek in #18307
• [23.1] More fixes for running the TS with external hgweb by @mvdbeek in #18279
• Merge 23.1 into 23.2 by @mvdbeek in #18320
• [23.2] Fix integration tests by @mvdbeek in #18326
• [23.2] Fix tool_shed package unit tests by @mvdbeek in #18327
• [23.2] Fix one more tool shed unit test by @mvdbeek in #18328
• [23.1] Make toolshed repo permissions world-readable by @mvdbeek in #18332
• [24.0] Downgrade doi fetch error to debug by @mvdbeek in #18330
• [24.0] Fix users API serialization when listing users by @davelopez in #18329
• [23.2] Skip new history creation if user is anonymous and login is required by @mvdbeek in #18319
• [24.0] Fix seek in slurm memo...

v24.1

What's Changed

• Update version to 24.1.dev by @jdavcs in #17592
• Add colabfold tar file datatype by @astrovsky01 in #17567
• Bump es5-ext from 0.10.62 to 0.10.63 in /client by @dependabot in #17555
• Enables activity bar by default by @guerler in #17531
• Adding object store plugin for Rucio by @SergeyYakubov in #17156
• Better display of estimated line numbers and add number of columns for tabular by @bernt-matthias in #17492
• Bump yaml from 2.1.1 to 2.3.4 in /client by @dependabot in #17125
• Add test and doc showing how dynamic selects are used by @bernt-matthias in #16885
• Unpin social-auth-core dependency by @nsoranzo in #17607
• Type annotation improvements by @nsoranzo in #17601
• Type annotation and CWL-related improvements by @nsoranzo in #17630
• Code cleanups from ruff and pyupgrade by @nsoranzo in #17654
• Modernization and cleanup of job state related client code. by @jmchilton in #17593
• Npz sniffing: do not read the whole file by @bernt-matthias in #17672
• Login components refactors by @itisAliRH in #17564
• Fix syntax for SA2.0 by @jdavcs in #17663
• Tool linter: check for valid bio.tools entries by @bernt-matthias in #17655
• Update Python dependencies by @galaxybot in #17653
• Collections common refactors by @itisAliRH in #17571
• Add content assertion XML tags for test output verification using images by @kostrykin in #17581
• Add browser and operating system info to issue template by @ElectronicBlueberry in #17696
• Issue #17631: Make it possible to use custom invfile.lua if needed by @martin-g in #17693
• remove reference to a non-existent component by @martenson in #17686
• Activity bar preference handling fixes. by @dannon in #17701
• Fix bug in image_util.py by @kostrykin in #17749
• Fix bug in galaxy.xsd by @kostrykin in #17752
• Fix bug in assert_has_image_n_labels by @kostrykin in #17754
• Add carbon_intensity.csv to package by @nuwang in #17748
• Bump follow-redirects from 1.15.4 to 1.15.6 in /client by @dependabot in #17766
• Update Python dependencies by @galaxybot in #17764
• Add support for floating point TIFF files in verification of image-based tool outputs by @kostrykin in #17797
• Datasets refactors by @itisAliRH in #17799
• Bump webpack-dev-middleware from 5.3.3 to 5.3.4 in /client by @dependabot in #17820
• Merge release_24.0 -> dev by @dannon in #17833
• Fix odd object store exception by @jmchilton in #17810
• Update Python dependencies by @galaxybot in #17819
• Bump express from 4.18.1 to 4.19.2 in /client by @dependabot in #17840
• Fixes for mapping workflow labels to markdown dialogs. by @jmchilton in #17424
• Add tool linting for valid EDAM terms by @bernt-matthias in #17839
• Enable storage management by object store by @jmchilton in #17500
• Update Python dependencies by @galaxybot in #17870
• Remove duplicate tool panel insertion, rely on activity bar by @guerler in #17872
• Update labels in Markdown editor when workflow labels change. by @jmchilton in #17863
• [24.0] Fix release notes images and videos by @jdavcs in #17889
• SQLAlchemy 2.0 by @jdavcs in #17778
• Add pin_labels attribute for image_diff comparison method by @kostrykin in #17866
• Disable published item copy button when editing slug by @martenson in #17888
• Enable managing object store usage within a history. by @jmchilton in #17853
• Rename JupyTool to something more searchable (i.e. JupyterLab which includes the substring Jupyter) by @hexylena in #17849
• Collection components refactors by @itisAliRH in #17647
• Bump undici from 5.28.3 to 5.28.4 in /client by @dependabot in #17905
• Fix client types around history items by @davelopez in #17924
• Update config docs about Celery by @davelopez in #17918
• Workflow editor undo/redo by @ElectronicBlueberry in #17774
• Update Python dependencies by @galaxybot in #17923
• Consolidates data dialog components by @guerler in #17802
• merge 24.0 to dev by @martenson in #17942
• Add admin activity to activity bar by @guerler in #17877
• Replace sample Celery result_backend in config by @davelopez in #17949
• Use typed API client for reporting job errors. by @jmchilton in #17969
• Model edits and bug fixes by @jdavcs in #17922
• Drop unused workflow controller methods by @mvdbeek in #17974
• Model typing and SA2.0 follow-up by @jdavcs in #17958
• Dataset information refactors by @itisAliRH in #17804
• Error reporting unit tests by @jmchilton in #17968
• Outline use of type_annotation_map to fix mypy issues by @jmchilton in #17902
• Adds pages to the activity bar by @guerler in #17925
• Revises visualizations activity by @guerler in #17931
• Enable warn_unused_ignores mypy option by @nsoranzo in #17991
• Add email notifications channel by @davelopez in #17914
• Implement a page object accessibility dialog by @jmchilton in #17225
• Update Python dependencies by @galaxybot in #17982
• Add tags to data dialog display, restores update_time and extension columns by @guerler in #17992
• Make celery fixture available in framework tests by @mvdbeek in #18020
• Add some admin facing docs on data tables by @bernt-matthias in #17585
• Add section divider to activity bar, fix click handler by @guerler in #18007
• Ensures that the activity bar is not shown when use_panels is set to false by @guerler in #17926
• Refactor convert HistoryExport component to Typescript by @davelopez in #18028
• Add Zenodo integration by @davelopez in #18022
• Tweak export records UI by @davelopez in #18038
• More typing in galaxy.files. by @jmchilton in #18037
• Remove deprecated BCO export endpoint by @martenson in #16645
• Update Python dependencies by @galaxybot in #18035
• Refactor galaxy.files plugin loading + config handling. by @jmchilton in #18049
• Fix (I think) a transiently failing selenium error. by @jmchilton in #18065
• Update Python dependencies by @galaxybot in #18063
• Add stronger type annotations in file sources + refactoring by @davelopez in #18050
• Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067
• Persistent toggle sections of job info by @dan...

v24.0.2

What's Changed

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

Full Changelog: v24.0.1...v24.0.2

v24.0.1

What's Changed

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

New Contributors

• @SaimMomin12 made their first contribution in #17875
• @natwhitaker made their first contribution in #17971

Full Changelog: v24.0.0...v24.0.1

v24.0.0

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

What's Changed

• Version 23.3.dev by @dannon in #17096
• Python 3.8 as minimum by @mr-c in #16954
• SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932
• Add history items display state for collections/lists with failed or new populated_state by @ahmedhamidawan in #16996
• Dataset Display : force reload on subsequent clicks. by @dannon in #16982
• Remove web framework dependency from tools by @davelopez in #17058
• Bump @adobe/css-tools from 4.3.1 to 4.3.2 in /client by @dependabot in #17115
• Vueify Admin User Grid by @guerler in #17030
• Update Python dependencies by @galaxybot in #17123
• SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by @jdavcs in #17122
• Vueify Admin Roles Grid by @guerler in #17118
• Migrate job destination parameters store to Pinia by @davelopez in #17119
• Vueify Admin Groups Grid by @guerler in #17126
• Migrate dataset extra files store to Pinia by @davelopez in #17145
• Vueify Admin Forms and Quota grids by @guerler in #17141
• Don't require admin user to list /api/tool_data by @jozh2008 in #17161
• Update Python dependencies by @galaxybot in #17157
• Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132
• Add keyedCache composable by @davelopez in #17148
• Replace discouraged Mambaforge with Miniforge3 by @nsoranzo in #17177
• Qiskit in galaxy by @thepineapplepirate in #17170
• Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter by @jdavcs in #17184
• Add future=True flag to SA engine by @jdavcs in #17174
• Add future=True flag to SA session by @jdavcs in #17179
• Convert dataset path destination store to composable by @davelopez in #17175
• Clarify the meaning of lexical sorting of discovered datasets by @bernt-matthias in #17190
• Update DatasetError.vue to fix broken link by @jennaj in #17193
• Fix for converter tests by @bernt-matthias in #17188
• xsd: reorder choices for permissive boolean by @bernt-matthias in #17187
• Accept any number of arguments to the secret decoder ring by @natefoo in #17191
• correct dbkey for minerva display app by @hexylena in #17196
• Update Python dependencies by @galaxybot in #17201
• Bump default milestone to 24.0 by @mvdbeek in #17211
• Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in #17153
• Reload built-in converters on toolbox reload by @bernt-matthias in #17209
• Improve links to Hub, Matrix and WGs in CONTRIBUTING.md by @nsoranzo in #17221
• Add a3m datatype by @astrovsky01 in #17217
• Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216
• Vendorize fastapi-utls.cbv by @jdavcs in #17205
• Migrate workflow invocation store to Pinia by @davelopez in #17203
• Update Python dependencies by @galaxybot in #17230
• Expose more tool information / navigability in UI. by @jmchilton in #17105
• Implement Galaxy Markdown directive history_dataset_as_table. by @jmchilton in #16681
• port invocation API to fastapi by @martenson in #16707
• Update Python dependencies by @galaxybot in #17235
• Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977
• Reuse test instance during non-integration tests by @mvdbeek in #17234
• Workflow node connector improvements by @ElectronicBlueberry in #17240
• Build and cache galaxy client for selenium and startup tests by @mvdbeek in #17239
• tus wants a json response from v2.0.0 by @mira-miracoli in #17246
• Update Python dependencies by @galaxybot in #17247
• Add missing re-usable commit-id output by @mvdbeek in #17248
• Update CONTRIBUTORS.md with new email address for Jeremy Goecks by @jgoecks in #17255
• Make flex panel drag handle more obvious by @ElectronicBlueberry in #17113
• Bump follow-redirects from 1.15.1 to 1.15.4 in /client by @dependabot in #17260
• Migrate models to pydantic 2 by @mvdbeek in #17262
• Optional Reply-to SMTP header in tool error reports by @neoformit in #17243
• Fixes for output discovery by @bernt-matthias in #17266
• Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222
• Fix invocation serialization if no state was set by @mvdbeek in #17278
• Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979
• Render Useful Markdown Components for Mapped Over Steps by @jmchilton in #17198
• Workflow node connector improvements followup by @ElectronicBlueberry in #17244
• Vueifiy History Grids by @guerler in #17219
• Add OIDC backend configuration schema and validation by @uwwint in #17274
• Fix Workflow Comment Model for Pydantic 2 by @ElectronicBlueberry in #17296
• Improve ModelManager type hints by @mvdbeek in #17299
• Fix any type for tool_data_file_path by @mvdbeek in #17293
• Package tests fixes by @nsoranzo in #17301
• Follow-up on #17274 and #17262 by @nsoranzo in #17302
• Scoped Store Refactor and Store Composition Refactor by @ElectronicBlueberry in #17304
• Refactor two of the missing invocation routes to FastAPI by @heisner-tillman in #17237
• Allow job files to consume TUS uploads by @jmchilton in #17242
• Rollback invalidated transaction: catch them earlier by @jdavcs in #17312
• Make Workflow Editor Toolbar Toggleable by @ElectronicBlueberry in #17297
• Enable job resubmissions in k8s runner by @nuwang in #17324
• Adjust Flex Panel Drag Handle and Collapse Button by @ElectronicBlueberry in #17298
• Add accepted extensions to form data input by @ElectronicBlueberry in #17238
• Overhaul Galaxy Markdown Help by @jmchilton in #17228
• Document SQLAlchemy session lifespan by @mvdbeek in #17322
• add documentation for data source tool by @PlushZ in #17327
• [23.2] fix s3fs templating by @bgruening in #17311
• Add support for Python 3.12 by @tuncK in #16796
• Fix quotas ID encoding by @davelopez in #17335
• Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340
• Port HistoryPanel component to composition API and typescript by @Renni771 in #17318
• Merge 23.2 into dev by @jdavcs in ...

v.23.2.1

What's Changed

• [23.2] Drop empty section by @jdavcs in #17386
• [23.2] Fix notification badge delay by @davelopez in #17349
• [23.2] Fix upload modal loses its content when closed by @ahmedhamidawan in #17338
• [23.2] Respect upstream_gzip setting when streaming dataset collection archive by @mvdbeek in #17400
• [23.2] Ignore empty lines in packages_by_dep_dag file when building packages by @jdavcs in #17395
• [23.0] Fix uploading of docs for release_NN.N branches by @nsoranzo in #17404
• [23.1] Set webdav file source to use temp files by default by @davelopez in #17388
• [23.2] Cleanup versions, formatting in setup.cfg, HISTORY.rst in all packages by @jdavcs in #17414
• [23.2] Fix target history when uploading files by @davelopez in #17431
• [23.0] Update python-multipart to 0.0.7 by @nsoranzo in #17429
• [23.2] Fix workflow report markdown editor toolbox becoming non-responsive. by @jmchilton in #17427
• [23.1] Encode tool link consistently by @davelopez in #17426
• [23.2] add a test for multi input element when hda and dces are mixed together by @martenson in #17419
• [23.1] Fix history bulk operations menu conditions by @davelopez in #17433
• [23.0] Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in #17384
• [23.2] Backport model store fixes by @mvdbeek in #17439
• [23.0] Fix bug: true >> True by @jdavcs in #17446
• More defensive access of extra props in filesources by @nuwang in #17445
• [23.0] Fix datasetStore.saveDatasets bug by @ahmedhamidawan in #17448
• [23.1] Fix history bulk operations menu (part 2) by @davelopez in #17456
• [23.1] Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @mvdbeek in #17459
• [23.2] Build param dict before creating entrypoint by @mvdbeek in #17440
• [23.2] Fix creating new erronous workflow can produce multiple empty workflows by @ahmedhamidawan in #17406
• Merge release_23.1 into release_23.2 by @mvdbeek in #17471
• [23.2] Fix auto-select of file name in upload (Backport of #17466) by @davelopez in #17477
• [23.2] Set metadata states on dataset association, not dataset by @mvdbeek in #17474
• [23.2] Remove two print statements by @bernt-matthias in #17480
• [23.2] Fix succces typo by @mvdbeek in #17481
• [23.2] Fix merge by @jdavcs in #17491
• [23.2] Add magres datatype by @martenson in #17499
• [23.2] Provide working routes.url_for every ASGI request by @mvdbeek in #17497

Full Changelog: v23.2...v23.2.1

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 #16293
• Update Python dependencies by @galaxybot in #16305
• Add Python string formatting best practices by @nsoranzo in #16312
• Drop (admin only) userskeys controller by @dannon in #16318
• Client import sorting by @dannon in #16345
• Merge 23.1->dev by @dannon in #16361
• Update Python dependencies by @galaxybot in #16360
• Add carbon emissions admin configuration options by @Renni771 in #16307
• Replace Persistedstate Pinia Plugin with User-Scoped Composable by @ElectronicBlueberry in #16371
• Exclude auto-generated schema file from labeler by @ElectronicBlueberry in #16378
• Display beginning of non-text files as text instead of triggering a download by @SergeyYakubov in #15447
• Bump semver from 5.7.1 to 5.7.2 in /client by @dependabot in #16388
• Merge release_23.1 into dev by @nsoranzo in #16393
• Update Python dependencies by @galaxybot in #16389
• Standardize, lint vue component name casing. by @dannon in #16398
• Update carbon emissions methodology page to match current feature spe… by @Renni771 in #16392
• Limit number of celery task executions per second per user by @claudiofr in #16232
• Disable verbose parso logging in db_shell.py by @mvdbeek in #16410
• Refactor FilesDialog services to use Fetcher by @davelopez in #16414
• Bump word-wrap from 1.2.3 to 1.2.4 in /client by @dependabot in #16417
• Update Python dependencies by @galaxybot in #16409
• Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264
• Fix SA2.0 syntax in scripts/helper.py, fix ancient bug by @jdavcs in #16425
• Merge release_23.1 into dev by @mvdbeek in #16430
• Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431
• Update Python dependencies by @galaxybot in #16436
• Prepare Uploader Vueification by removing jQuery by @guerler in #16408
• Fix labeler for UI UX labels by @ElectronicBlueberry in #16456
• Never consider _galaxy_ conda env as unused by @bernt-matthias in #16460
• Force makefile client targets to use .venv-shipped node if it exists by @dannon in #16462
• pin fs.dropboxfs to >=1 by @bernt-matthias in #16451
• Migrate some Remote Files Export components to composition API + TS by @davelopez in #16391
• Bump tough-cookie from 4.1.2 to 4.1.3 in /client by @dependabot in #16385
• Add new datatype: STL by @TanguyGen in #16478
• Update Python dependencies by @galaxybot in #16485
• Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825
• Migrate cloud API to Fast API by @heisner-tillman in #16296
• Re-add missing type guard by @mvdbeek in #16486
• Rename MetadataEqualsValidator by @bernt-matthias in #16489
• Test that object store cache file gets updated by @mvdbeek in #16493
• Migrate a part of the users API to Fast API by @heisner-tillman in #16341
• Make it obvious that WorkflowInvocationStep is clickable/expandable by @ahmedhamidawan in #16507
• Add framework test for profile behavior of format="input" by @bernt-matthias in #15482
• Update interactivetool_mgnify_notebook to v1.2.2 by @SandyRogers in #16517
• Migrate configuration store to Pinia by @davelopez in #16514
• Scope Workflow Stores to Workflow ID by @ElectronicBlueberry in #16523
• Fix and update visualization plugins by @mahendrapaipuri in #16119
• Merge 23.1 into dev by @mvdbeek in #16534
• Move database access code out of galaxy.util by @jdavcs in #16526
• Document that required text parameters need a validator by @bernt-matthias in #16538
• Published Workflow Sharing Page Overhaul by @ElectronicBlueberry in #16510
• Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420
• Update Python dependencies by @galaxybot in #16521
• Vueify Data Uploader by @guerler in #16472
• Make form repeat blocks reordarable by @ElectronicBlueberry in #14892
• Remove unnecessary check: item cannot be None by @jdavcs in #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 #16503
• Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in #16553
• Add uploader test cases, consolidate payload processing by @guerler in #16554
• Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561
• Drop syncConfigToGalaxy by @davelopez in #16562
• Add support for CILogon deployments in different regions than the US by @uwwint in #16490
• Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536
• Support new genome browser chain file format by @claudiofr in #16576
• Run eslint autofix as a part of client format when using Makefile by @dannon in #16586
• Implement datatype upload warnings by @jmchilton in #16564
• Remove xml remnant in sample yml job conf by @bernt-matthias in #16609
• Add Invenio RDM repository integration by @davelopez in #16381
• Make tool id searchable in side panel search by @ahmedhamidawan in #16543
• Explicitly document default of multiple by @bernt-matthias in #16625
• Run poetry under Python 3.8 by @nsoranzo in #16638
• Fix dependency update GitHub workflow by @nsoranzo in #16639
• Switch out conditional requirement parser by @mvdbeek in #16636
• Vueify _fieldDialog by @assuntad23 in #16236
• Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar by @nsoranzo in #16649
• Ensure Job belongs to current SA session by @jdavcs in #16647
• cwl testing: use the proposed 1.2.1 CWL conformance tests. by @mr-c in #16658
• Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642
• Bump samtools converters by @bernt-matthias in #16668
• Clarify documentation on how to build a job runner by @jdavcs in #16665
• Enhance disk quota usage summary by @davelopez in #16670
• History MultiView drag-drop on history picker creates new history by @ahmedhamidawan in #16644
• Create GDateTime component by @itisAliRH in https://github.com/g...