galaxyproject/galaxy v24.1

on GitHub

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 @dannon in #16983
• Visualizing workflow runs with an invocation graph view by @ahmedhamidawan in #17413
• Consolidate Visualization container, avoid using default iframe by @guerler in #18016
• Make urgent notifications mandatory by @davelopez in #17975
• Add Attributes section to Edit Collection view as well by @ahmedhamidawan in #18071
• Fix toolbar header z-index by @itisAliRH in #18084
• Ensure history update_time is set when exporting by @davelopez in #18086
• Chore: remove repetitive words by @tianzedavid in #18076
• Add Net datatype by @martenson in #18080
• Add a button that filters out a tool section in the tool panel by @ahmedhamidawan in #18034
• Dynamic tool fixes by @dcore94 in #18085
• Overhaul Azure storage infrastructure. by @jmchilton in #18087
• Fix AWS object store for us-east-2 by @jmchilton in #18100
• Tests and bugfixes for cloudbridge object store. by @jmchilton in #18099
• Hide bookmark toggle on deleted workflows by @itisAliRH in #18103
• Update Python dependencies by @galaxybot in #18095
• Automatically bind galaxy_data_manager_data_path in containers by @bernt-matthias in #17596
• Workflow editor item selection by @ElectronicBlueberry in #17615
• Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106
• [24.0] Backport OIDC schema fix by @mvdbeek in #18111
• [23.2] Allow purge query param, deprecate purge body param by @mvdbeek in #18105
• Fairly critical fix for #18087 by @jmchilton in #18110
• [24.0] Fix switching between nested collection elements by @mvdbeek in #18115
• [24.0] Fix deprecated deprecated argument by @mvdbeek in #18119
• Add vue sentry integration by @mvdbeek in #18120
• [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
• Add datasets/collections filter to history panel filters by @ahmedhamidawan in #18039
• Drop "?" (Help) from DatasetActions list by @dannon in #18124
• [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
• Revises handling of warnings in the workflow run form by @guerler in #18126
• [24.0] Fix data default values not getting added to history by @mvdbeek in #18132
• Workflow preview improvements by @itisAliRH in #18108
• Enable all-vs-all collection analysis patterns. by @jmchilton in #17366
• Tool linter: check for leaf nodes with unstripped text content by @bernt-matthias in #17656
• Fix permissions for temporary upload file for API uploads by @bernt-matthias in #17850
• Document syntax for accessing nested parameters in change_format - when tags by @bernt-matthias in #18018
• Mailing list wording tweaks by @dannon in #17867
• Update s3fs dependency. by @jmchilton in #18135
• Script for deleting userless histories from database + testing + drop unused model testing code by @jdavcs in #18079
• [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
• Fix import broken with forward merge by @mvdbeek in #18152
• [24.0] Delay tool form rendering until config is loaded by @mvdbeek in #18151
• Only include tool stdout/stderr in HDA info by @natefoo in #16730
• [24.0] Raise RequestParameterInvalidException when url is invalid by @mvdbeek in #18155
• More unit testing for object store stuff. by @jmchilton in #18136
• [24.0] Drop redundant error message by @mvdbeek in #18156
• Update Python dependencies by @galaxybot in #18125
• Display DOIs in Archived Histories by @davelopez in #18134
• Addition of release process doc by @dannon in #17680
• [24.0] Fix error message when accessing restricted Zenodo records by @davelopez in #18169
• Small refinements and fixes to new release process doc by @nsoranzo in #18170
• Add onedata objectstore by @bwalkowi in #17540
• Change InvocationsList into a grid using GridList by @ahmedhamidawan in #18088
• Add support for additional media types by @arash77 in #18054
• [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
• Fix boto3-stubs typecheck dependency by @nsoranzo in #18173
• Add an Invocations Panel for the Invocations activity by @ahmedhamidawan in #18137
• Enhance form drilldown by @hujambo-dunia in #18074
• Merge 24.0 into dev by @mvdbeek in #18177
• Set minimal metadata also for empty bed datasets by @wm75 in #17586
• De-duplication of onedata objectstore code. by @jmchilton in #18174
• Add galaxy to user agent by @mvdbeek in #18003
• Add message to Invocations panel for no invocations by @ahmedhamidawan in #18180
• Empower users to bring their own storage and file sources by @jmchilton in #18127
• Harden User Object Store and File Source Creation by @jmchilton in #18172
• [24.0] Fix typos in create release documentation page by @jdavcs in #18181
• Update db revision 24.1 release tags by @jdavcs in #18183
• [24.1] Move activity panel go to button to top by @ahmedhamidawan in #18182
• [24.1] Update version to 24.1.rc1 by @jdavcs in #18184
• [24.0] Fix on success redirect by @mvdbeek in #18187
• Add pagination support to Files Source plugins by @davelopez in #18059
• [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
• [24.1] Fix selection highlight in Files Dialog when using items provider by @davelopez in #18201
• [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
• [24.1] Fix file source search query with empty string value by @davelopez in #18191
• [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
• [24.1] Revert some requests import changes by @nsoranzo in #18199
• [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
• Merge 24.0 into 24.1 by @mvdbeek in #18239
• [24.1] Tighten axt sniffer by @martenson in #18204
• [24.1] Drop restriction to switch to immutable histories by @davelopez in #18234
• [24.1] Allow bookmarking public workflows by @itisAliRH in #18247
• [24.1] Change ActivityPanel go to button to primary by @ahmedhamidawan in #18244
• [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
• [24.1] Merge 24.0 into 24.1 by @jdavcs in #18270
• [23.2] Add hgweb_repo_prefix attribute to TestToolShedConfig by @nsoranzo in #18268
• [24.0] Format with black by @nsoranzo in #18273
• [24.1] Fix handler: access to result row items changed in SA2.0 by @jdavcs in #18274
• [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
• [24.1] Fix history export error handling by @davelopez in #18251
• [23.1] Add revision tags for TS migration in 23.1 by @jdavcs in #18271
• [24.1] Remove linter for unstripped text content for tool xml leaves by @bernt-matthias in #18252
• [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
• [24.1] Fix "label updated" popup triggers too often by @ElectronicBlueberry in #18303
• [24.1] Fix various packages' issues by @nsoranzo in #18301
• [24.1] Adds pinia to manually mounted vue components by @guerler in #18299
• [24.0] Don't serialize display application links for deleted datasets by @mvdbeek in #18307
• [24.1] Fix non-history items drag&drop into histories by @davelopez in #18308
• [24.1] Small bug fixes for user data plugins by @jmchilton in #18246
• [24.1] Backport Qiskit Jupyter Notebook update to 24.1 by @natefoo in #18310
• [24.1] Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in #18305
• Fix the link to the carbon config by @bgruening in #18314
• [24.1] Display error message if not an image in reports by @davelopez in #18309
• [24.1] Fix pinia in manually mounted components by @davelopez in #18315
• [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
• [24.1] Filter data dialog entries by dataset state, only display ok state by @guerler in #18313
• [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
• [24.1] Disable state filter for collections in HistoryFilters by @ahmedhamidawan in #18324
• [23.2] Skip new history creation if user is anonymous and login is required by @mvdbeek in #18319
• [24.1] Fix word bleeding in modals, sharing page and history rename by @itisAliRH in #18306
• [24.1] Rebuild Galaxy config by @bgruening in #18325
• [24.1] Update parcel-built visualizations to use parcel v2 by @dannon in #18311
• [24.0] Fix seek in slurm memory check by @mvdbeek in #18338
• [24.1] Fix typing issue in reused variable by @davelopez in #18344
• [24.1] Fix visualizations compatible dataset filtering by @davelopez in #18343
• [24.0] Fix authentication error for anonymous users querying jobs by @davelopez in #18333
• Fix #18316 (anonymous file sources) by @jmchilton in #18352
• [24.1] Merge 24.0 into 24.1 by @jdavcs in #18353
• [23.2] Allow DCE as outer input to to_cwl by @mvdbeek in #18349
• [24.1] More structured indexing for user data objects. by @jmchilton in #18291
• [24.0] Fix anonymous user job retrieval logic by @davelopez in #18358
• [24.1] Fix check for anonymous by @jdavcs in #18364
• [24.1] Merge 24.0 into 24.1 by @jdavcs in #18365
• [24.0] Do not copy purged outputs to object store by @mvdbeek in #18342
• [24.1] Add copy link to published workflow in WorkflowCard by @itisAliRH in #18370
• [24.0] Sanitize FormElement error messages by @mvdbeek in #18377
• [24.0] Drop unnecessary escaping for workflow name and annotation by @mvdbeek in #18376
• [24.0] Fix user's private role can be missing by @davelopez in #18381
• [24.0] Make sure that all Linter subclasses are imported for listing them by @bernt-matthias in #18339
• [24.1] Allow running and editing workflows for specific versions by @ahmedhamidawan in #18378
• [24.0] Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348
• [24.0] Fix null inputs in database operation tools by @mvdbeek in #18385
• [24.1] Fix empty usernames in database + bug in username generation by @jdavcs in #18379
• [24.1] Fix duplicated requests when browsing files sources with pagination by @davelopez in #18387
• [24.1] Fix dataset details polling re-render by @itisAliRH in #18388
• [24.0] Fix workflow editor tool form scroll memory by @ElectronicBlueberry in #18390
• [24.1] Onedada object store and files source stability fixes by @bwalkowi in #18372
• [24.1] Merge 24.0 into 24.1 by @jdavcs in #18393
• [24.1] Reset current page when browsing sub-folders in FilesSources by @davelopez in #18395
• [24.0] Fix update group API payload model by @davelopez in #18374
• [24.0] Allow in_range validator for selects by @bernt-matthias in #18403
• [24.0] Fix invocation step_job_summary for new collections by @mvdbeek in #18402
• [24.0] Fix get_accessible_job if called without session by @mvdbeek in #18400
• [24.1] Ensure datatypes match on dragging elements into FormData by @mvdbeek in #18410
• [24.0] Fix collection map over status for dragged collections by @mvdbeek in #18416
• [24.0] Serialize purged flag for datasets in collections by @davelopez in #18420
• [24.1] Add TypedDict for JobsSummary by @mvdbeek in #18418
• [24.0] Really allow in-range validator for txt by @bernt-matthias in #18411
• [24.0] Assign default data extension on discovered collection output by @mvdbeek in #18389
• [24.1] Fix workflow tags initialisation in workflow editor by @itisAliRH in #18396
• [24.1] Fix input_step_parameters missing values that don't have a label by @ahmedhamidawan in #18405
• [24.0] Minor linting cleanup by @mvdbeek in #18421
• [24.1] Pin pydantic to >=2.7.4 by @nsoranzo in #18423
• [24.1] Release notes by @jdavcs in #18218
• [24.1] Add latest PRs to release notes by @jdavcs in #18424

New Contributors

• @martin-g made their first contribution in #17693
• @tianzedavid made their first contribution in #18076
• @dcore94 made their first contribution in #18085
• @Edmontosaurus made their first contribution in #18106
• @bwalkowi made their first contribution in #17540

Full Changelog: v24.0.2...v24.1