History ------- .. to_doc --------- 26.1.dev0 --------- ------------------- 25.1.2 (2026-03-09) ------------------- ========= Bug fixes ========= * Fix private dataset sharing error handling by `@davelopez `_ in `#21689 `_ * Fix database migration error from 25.0 > 25.1 by `@jdavcs `_ in `#21737 `_ * Make database heartbeat more robust (backport) by `@mvdbeek `_ in `#21812 `_ * Fix recording duplicate workflow_request_input_step_parameter rows by `@mvdbeek `_ in `#21980 `_ ============= Other changes ============= * Fix worker segfault in gunicorn preload mode on OSX by `@mvdbeek `_ in `#21837 `_ ------------------- 25.1.1 (2026-02-03) ------------------- ========= Bug fixes ========= * Sample sheet column fix by `@mvdbeek `_ in `#21446 `_ * Maintain column definitions on map over by `@mvdbeek `_ in `#21468 `_ * Add missing test file for sig datatype by `@SaimMomin12 `_ in `#21473 `_ * Do not update a user's update_time when an admin archives (and purges) a history by `@natefoo `_ in `#21484 `_ * Add missing ending newline to test.sig test data file by `@nsoranzo `_ in `#21485 `_ * Usability fixes for sample sheet selection. by `@jmchilton `_ in `#21503 `_ * Fix exception message to enable debugging of missing dataset issue. by `@jmchilton `_ in `#21504 `_ * Add missing dependencies to ``galaxy-files`` package by `@nsoranzo `_ in `#21518 `_ * Fix job cache collection copy by `@mvdbeek `_ in `#21558 `_ * Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by `@jmchilton `_ in `#21584 `_ * Fix race condition in workflow collection populated state check by `@mvdbeek `_ in `#21613 `_ * Fix collection job state not preserved during history export/import by `@mvdbeek `_ in `#21716 `_ ============ Enhancements ============ * Add Sourmash sig new datatype by `@SaimMomin12 `_ in `#21469 `_ * Add database operation tool to convert sample sheets to list collections by `@mvdbeek `_ in `#21625 `_ ------------------- 25.1.0 (2025-12-12) ------------------- ========= Bug fixes ========= * Fix alembic down_revision for trigger replacement migration by `@mvdbeek `_ in `#20501 `_ * Add a merge migration, revert previous edit by `@jdavcs `_ in `#20507 `_ * Add missing cleanup table by `@jdavcs `_ in `#20594 `_ * Fix anndata metadata by `@nilchia `_ in `#20778 `_ * Fix Ipynb datatype sniffer and add unit tests. by `@ksuderman `_ in `#20811 `_ * Bump requirement of directory converters by `@bernt-matthias `_ in `#20834 `_ * Extract: do not use common prefix dir by `@bernt-matthias `_ in `#20929 `_ * Ensure that conversion_key is defined by `@guerler `_ in `#20984 `_ * Fix invocation export dataset exclusion by `@davelopez `_ in `#21091 `_ * Restore job.get_param_values by `@mvdbeek `_ in `#21130 `_ * Improve _touch_collection_update_time_cte performance by `@mvdbeek `_ in `#21134 `_ * Assorted workbook upload fixes. by `@jmchilton `_ in `#21203 `_ * Fix database revision tags by `@jdavcs `_ in `#21377 `_ * Maintain columns on sample sheet map over by `@mvdbeek `_ in `#21436 `_ ============ Enhancements ============ * Support credentials(secrets/variables) in tool requirements by `@arash77 `_ in `#19084 `_ * Implement Sample Sheets by `@jmchilton `_ in `#19305 `_ * Empower Users to More Pragmatically Import Datasets & Collections From Tables by `@jmchilton `_ in `#20288 `_ * Add short term storage expiration indicator to history items by `@davelopez `_ in `#20332 `_ * Type annotation fixes for mypy 1.16.0 by `@nsoranzo `_ in `#20424 `_ * Implement dataset source requested transformations. by `@jmchilton `_ in `#20435 `_ * Remove deprecated tool document cache by `@nsoranzo `_ in `#20510 `_ * Decode OIDC access token as part of authentication pipeline by `@marius-mather `_ in `#20547 `_ * Implement Data Landing Requests by `@jmchilton `_ in `#20592 `_ * Clean up code from pyupgrade by `@nsoranzo `_ in `#20642 `_ * Update Python dependencies by `@galaxybot `_ in `#20680 `_ * Attempt to reuse previously materialized datasets by `@mvdbeek `_ in `#20718 `_ * Refactor Files Sources Framework for stronger typing using pydantic models by `@davelopez `_ in `#20728 `_ * Hierarchical display collection dataset states by `@mvdbeek `_ in `#20731 `_ * Use a streaming based parser (ijson) when setting metadata for biom1 files. by `@ksuderman `_ in `#20851 `_ * Improve type annotation for job runners and ``InteractiveToolManager`` by `@nsoranzo `_ in `#20871 `_ * Update Python dependencies by `@galaxybot `_ in `#20905 `_ * Allow sending and tracking landing request origin by `@mvdbeek `_ in `#20957 `_ * Track landing request with invocation by `@mvdbeek `_ in `#20960 `_ * Optimize /api/invocations/steps/{step_id} by `@mvdbeek `_ in `#21249 `_ * A better way to designate config_watcher by `@jdavcs `_ in `#21426 `_ ============= Other changes ============= * Small tweaks and cleanup from sample sheets branch by `@jmchilton `_ in `#20229 `_ * Merge `release_25.0` into `dev` by `@davelopez `_ in `#20484 `_ * Merge release_25.0 into dev by `@davelopez `_ in `#20490 `_ * Sample Sheet Bug Fixes around Preserving Collection Metadata by `@jmchilton `_ in `#20749 `_ * Add tool_id and tool_version column to tool_landing_request table by `@mvdbeek `_ in `#20795 `_ * Add 25.1 migration tags by `@ahmedhamidawan `_ in `#21017 `_ * Restore .get_metadata function by `@mvdbeek `_ in `#21045 `_ * Fix forward merge by `@mvdbeek `_ in `#21307 `_ * Fix db revision tags by `@mvdbeek `_ in `#21442 `_ ------------------- 25.0.4 (2025-11-18) ------------------- ========= Bug fixes ========= * Add safetensors datatype by `@nilchia `_ in `#20754 `_ * Skip sam metadata if we have too many references by `@mvdbeek `_ in `#20820 `_ * Backport of #20984 by `@davelopez `_ in `#20994 `_ * Backport fix anndata datatype update by `@nilchia `_ in `#21111 `_ * Create new datasets when creating skipped database operation tool outputs by `@mvdbeek `_ in `#21142 `_ * Fix optional param unset in RO-Crate export by `@davelopez `_ in `#21192 `_ ============ Enhancements ============ * Add Auspice JSON datatype by `@pvanheus `_ in `#20466 `_ * Add SpatialData datatype by `@nilchia `_ in `#21000 `_ * Use job cache also for implicit conversions by `@mvdbeek `_ in `#21021 `_ * support ZARR v3 for Spatialdata dt by `@nilchia `_ in `#21265 `_ ------------------- 25.0.3 (2025-09-23) ------------------- ========= Bug fixes ========= * Ensure that workflow invocations are persisted with state by `@mvdbeek `_ in `#20784 `_ * Fix password reset functionality for lowercase emails by `@jdavcs `_ in `#20801 `_ * Drop eager argument from invocation related methods by `@mvdbeek `_ in `#20863 `_ * Use ``populated_optimized`` when serializing collection by `@mvdbeek `_ in `#20872 `_ * Speed up ``ImplicitCollectionJobs.job_list`` by `@mvdbeek `_ in `#20887 `_ * Add LDDA purged property by `@mvdbeek `_ in `#20895 `_ * Avoid potential race condition in replacement_for_connection by `@mvdbeek `_ in `#20909 `_ * Fix sessionless tag creation by `@mvdbeek `_ in `#20925 `_ ============ Enhancements ============ * Fix DOCX detection and add PPTX support by `@arash77 `_ in `#20827 `_ * Add HiC datatype by `@abretaud `_ in `#20874 `_ ============= Other changes ============= * Undo accidental push by `@bernt-matthias `_ in `#20854 `_ * Merge 25.0 into dev by `@ahmedhamidawan `_ in `#20911 `_ ------------------- 25.0.2 (2025-08-13) ------------------- ========= Bug fixes ========= * Remove ``num_unique_values`` tiff metadata element by `@mvdbeek `_ in `#20464 `_ * Propagate cached job output replacement to copies of outputs by `@mvdbeek `_ in `#20553 `_ * Fix deferred datasets in multiple dataset parameters. by `@jmchilton `_ in `#20650 `_ * Add `num_unique_values` tiff metadata element, fixed by `@kostrykin `_ in `#20669 `_ ============ Enhancements ============ * Improve workflow monitor loop times by `@mvdbeek `_ in `#20522 `_ * Pairtool updated format and sniffers by `@Smeds `_ in `#20634 `_ * Add support for M4A audio files by `@arash77 `_ in `#20667 `_ ------------------- 25.0.1 (2025-06-20) ------------------- ========= Bug fixes ========= * Pin isa-rwval 0.10.11, drop conditional import handling by `@natefoo `_ in `#20527 `_ ------------------- 25.0.0 (2025-06-18) ------------------- ========= Bug fixes ========= * Better handling of public pages and workflows authored by deleted users by `@jdavcs `_ in `#19394 `_ * Alternative `format_source` fix by `@mvdbeek `_ in `#19395 `_ * Use ``id`` entity attribute when setting ``exampleOfWork`` property by `@nsoranzo `_ in `#19396 `_ * Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by `@jdavcs `_ in `#19620 `_ * Fix Galaxy ignoring job object_store_id for quota check by `@bernt-matthias `_ in `#19854 `_ * Fix various mypy issues around mapped attributes by `@mvdbeek `_ in `#19883 `_ * More fixes to `FormData` drag and drop and typing by `@ahmedhamidawan `_ in `#19900 `_ * Use lower case extension for setting datatype in data discovery by `@bernt-matthias `_ in `#19954 `_ * Add new line to vtpascii test file by `@guerler `_ in `#20051 `_ * Fix certain cases of collection parameter handling during workflow execution. by `@jmchilton `_ in `#20152 `_ * Update tabular_csv.py to use less memory in tsv->csv conversion by `@cat-bro `_ in `#20187 `_ * Fix tool-provided metadata for CONVERTER_tar_to_directory by `@mr-c `_ in `#20260 `_ * Log invalid vault paths by `@mvdbeek `_ in `#20363 `_ * Update triggers by `@jdavcs `_ in `#20425 `_ * Fix copying of job metrics for cached jobs by `@mvdbeek `_ in `#20436 `_ * Dataset Display and Preferred Viz fixes by `@dannon `_ in `#20439 `_ * Recreate triggers by `@jdavcs `_ in `#20491 `_ ============ Enhancements ============ * Workflow Editor Activity Bar by `@ElectronicBlueberry `_ in `#18729 `_ * Add author and tools details in RO-Crate by `@Marie59 `_ in `#18820 `_ * Extend image metadata by `@kostrykin `_ in `#18951 `_ * Implement tool markdown reports. by `@jmchilton `_ in `#19054 `_ * Let file sources choose a path for uploaded files by `@kysrpex `_ in `#19154 `_ * Calculate hash for new non-deferred datasets when finishing a job by `@nsoranzo `_ in `#19181 `_ * Fix UP031 errors - Part 1 by `@nsoranzo `_ in `#19194 `_ * Fix UP031 errors - Part 4 by `@nsoranzo `_ in `#19235 `_ * Fix UP031 errors - Part 5 by `@nsoranzo `_ in `#19282 `_ * Fix UP031 errors - Part 6 by `@nsoranzo `_ in `#19314 `_ * Misc fixes 202412 by `@nsoranzo `_ in `#19341 `_ * Type annotation fixes for mypy 1.14.0 by `@nsoranzo `_ in `#19372 `_ * Empower Users to Build More Kinds of Collections, More Intelligently by `@jmchilton `_ in `#19377 `_ * SQLAlchemy 2.0 follow-up by `@jdavcs `_ in `#19388 `_ * Set safe default extraction filter for tar archives by `@nsoranzo `_ in `#19406 `_ * Remove transaction helper by `@jdavcs `_ in `#19407 `_ * Prevent users from reusing a banned email after account is purged by `@jdavcs `_ in `#19413 `_ * Add IGB display support for CRAM files by `@paige-kulzer `_ in `#19428 `_ * Add User-Defined Tools by `@mvdbeek `_ in `#19434 `_ * Type annotation improvements by `@nsoranzo `_ in `#19485 `_ * Update Python dependencies by `@galaxybot `_ in `#19567 `_ * Expand workflow metadata for readme. by `@jmchilton `_ in `#19591 `_ * Format code with black 25.1.0 by `@nsoranzo `_ in `#19625 `_ * Type annotation improvements by `@nsoranzo `_ in `#19642 `_ * Generate correct types for Dataset source transformations on backend. by `@jmchilton `_ in `#19666 `_ * Drop support for Python 3.8 by `@nsoranzo `_ in `#19685 `_ * Define simple models for job messages. by `@jmchilton `_ in `#19688 `_ * Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 1 by `@nsoranzo `_ in `#19706 `_ * Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 2 by `@nsoranzo `_ in `#19726 `_ * Add bigbed to bed converter and tests by `@d-callan `_ in `#19787 `_ * Update Python dependencies by `@galaxybot `_ in `#19816 `_ * Populate image metadata without allocating memory for the entire image content by `@kostrykin `_ in `#19830 `_ * Add mandatory RO-Crate metadata when exporting by `@elichad `_ in `#19846 `_ * Improve type annotations of ``ModelPersistenceContext`` and derived classes by `@nsoranzo `_ in `#19852 `_ * Drop old galaxy_session records by `@jdavcs `_ in `#19872 `_ * Clarify is_active method usage for Python Social Auth in Galaxy by `@dannon `_ in `#19899 `_ * Drop old job metrics by `@jdavcs `_ in `#19936 `_ * Allow PathLike parameters in ``make_fast_zipfile()`` by `@nsoranzo `_ in `#19955 `_ * Add type hints around collection copying and job things by `@mvdbeek `_ in `#19961 `_ * Job cache allow different names when possible by `@mvdbeek `_ in `#19962 `_ * Improve type annotation of tool parameter wrapping by `@nsoranzo `_ in `#19991 `_ * Implement dataset collection support in workflow landing requests by `@mvdbeek `_ in `#20004 `_ * Enable ``warn_redundant_casts`` mypy option and drop redundant casts by `@nsoranzo `_ in `#20008 `_ * Add vitesscejson datatype by `@guerler `_ in `#20027 `_ * Add VTK Visualization Toolkit Plugin by `@guerler `_ in `#20028 `_ * Add DOI to workflow metadata by `@jdavcs `_ in `#20033 `_ * Add sample datasets for visualizations by `@guerler `_ in `#20046 `_ * Add docx datatype by `@bgruening `_ in `#20055 `_ * Add flac audio format by `@bgruening `_ in `#20057 `_ * Improve type annotation of `galaxy.util` submodules by `@nsoranzo `_ in `#20104 `_ * Add specific datatypes for Cytoscape and Kepler.gl by `@guerler `_ in `#20117 `_ * Visualization-First Display functionality by `@dannon `_ in `#20190 `_ * Improve type annotation of ``galaxy.model.dataset_collections`` by `@nsoranzo `_ in `#20194 `_ * Improve performance of job cache query by `@mvdbeek `_ in `#20319 `_ * DatasetView and Card Polish by `@dannon `_ in `#20342 `_ ============= Other changes ============= * Merge 24.2 into dev by `@ahmedhamidawan `_ in `#19933 `_ * Fix copying job output from discovered outputs by `@mvdbeek `_ in `#19999 `_ * Add 25.0 migration tags by `@ahmedhamidawan `_ in `#20265 `_ * Rename vitessce_json file_ext to vitessce.json by `@mvdbeek `_ in `#20473 `_ ------------------- 24.2.4 (2025-06-17) ------------------- ========= Bug fixes ========= * Reduce default framework tool test timeout to 60 seconds by `@mvdbeek `_ in `#19819 `_ * Try to recover from recurring activation link error by `@jdavcs `_ in `#19844 `_ * Check if index exists before creating by `@jdavcs `_ in `#19873 `_ * Let pysam use extra threads available in job by `@mvdbeek `_ in `#19917 `_ * Handle special charater in raw SQL by `@jdavcs `_ in `#19925 `_ * Use ``make_fast_zipfile`` directly by `@mvdbeek `_ in `#19947 `_ * Job cache backports by `@mvdbeek `_ in `#20078 `_ * Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING` by `@natefoo `_ in `#20209 `_ * Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by `@natefoo `_ in `#20239 `_ * Make response header values strings by `@mvdbeek `_ in `#20475 `_ * Link workflow invocation outputs upon importing invocation by `@mvdbeek `_ in `#20485 `_ * Make optional edam-ontology in datatypes registry optional by `@natefoo `_ in `#20492 `_ ============ Enhancements ============ * Bump up max_peek_size to 50MB by `@mvdbeek `_ in `#19823 `_ ------------------- 24.2.3 (2025-03-16) ------------------- ========= Bug fixes ========= * Fix private role name performance issue by `@jdavcs `_ in `#19679 `_ * Fix anndata metadata setting for data with integer indexes by `@mvdbeek `_ in `#19774 `_ * Fix parameter model constructions with leading underscores, fixes converter linting by `@mvdbeek `_ in `#19790 `_ ============ Enhancements ============ * Add rDock prm datatype by `@nsoranzo `_ in `#19783 `_ ------------------- 24.2.2 (2025-03-08) ------------------- ========= Bug fixes ========= * Fix recording transform action name. by `@jmchilton `_ in `#19672 `_ ============ Enhancements ============ * Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek `_ in `#19694 `_ ============= Other changes ============= * Backport #19620 by `@nsoranzo `_ in `#19725 `_ ------------------- 24.2.1 (2025-02-28) ------------------- ========= Bug fixes ========= * Set content-type to text/plain if dataset not safe by `@mvdbeek `_ in `#19563 `_ * Fail request explicitly when sqlite provider used on non-sqlite file by `@mvdbeek `_ in `#19630 `_ * Fix various bugs around tool data table bundles by `@mvdbeek `_ in `#19659 `_ ------------------- 24.2.0 (2025-02-11) ------------------- ========= Bug fixes ========= * Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs `_ in `#18196 `_ * Raise Message Exception when displaying binary data by `@mvdbeek `_ in `#18503 `_ * Fixes for errors reported by mypy 1.11.0 by `@nsoranzo `_ in `#18608 `_ * Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo `_ in `#18755 `_ * Fix migration data fixes tests by `@jdavcs `_ in `#18885 `_ * Fix backend role sharing bug by `@jdavcs `_ in `#18942 `_ * Add merge migration to merge 2 heads by `@jdavcs `_ in `#19163 `_ * Record implicitly converted dataset as input dataset by `@mvdbeek `_ in `#19301 `_ * Fix quota usage with user object stores by `@davelopez `_ in `#19323 `_ * Fix workflows with optional non-default parameter input by `@mvdbeek `_ in `#19332 `_ * Fix importing shared workflows with deeply nested subworkflows by `@mvdbeek `_ in `#19335 `_ * Backport fix from #19396 by `@nsoranzo `_ in `#19399 `_ * Prevent cycling through failing conversion jobs in trackster by `@mvdbeek `_ in `#19494 `_ * Fix extracting workflows from purged and deleted histories by `@mvdbeek `_ in `#19525 `_ * Fix error message when subworkflow input connection missing by `@mvdbeek `_ in `#19526 `_ * Fix admin cancel job message not being displayed to the user by `@davelopez `_ in `#19537 `_ * Add tool_id index on job table by `@mvdbeek `_ in `#19543 `_ * Update 24.2 db revision tags by `@jdavcs `_ in `#19550 `_ * Provide guidance in case of deadlock during db migration by `@jdavcs `_ in `#19551 `_ * Fix job paused on user defined object store by `@davelopez `_ in `#19578 `_ * Handle isatools dependency by `@jdavcs `_ in `#19582 `_ ============ Enhancements ============ * Experimental galactic wizard by `@dannon `_ in `#15860 `_ * Improve usability of Directory datatype by `@wm75 `_ in `#17614 `_ * Update Python dependencies by `@galaxybot `_ in `#18226 `_ * Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton `_ in `#18272 `_ * More data access tests, some refactoring and cleanup by `@jdavcs `_ in `#18312 `_ * Update Python dependencies by `@galaxybot `_ in `#18406 `_ * Add pod5 datatype by `@TomHarrop `_ in `#18419 `_ * Prepare for NumPy 2.0 by `@nsoranzo `_ in `#18422 `_ * Add unique constraints to the email and username fields in the galaxy_user table by `@jdavcs `_ in `#18493 `_ * Improvements for K8S deployment (especially ITs) by `@almahmoud `_ in `#18514 `_ * Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo `_ in `#18773 `_ * Handle compressed content in dataset preview for all sequence classes by `@PlushZ `_ in `#18776 `_ * Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs `_ in `#18777 `_ * Workflow Landing Requests by `@jmchilton `_ in `#18807 `_ * Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo `_ in `#18811 `_ * Refactor migration testing setup code by `@jdavcs `_ in `#18886 `_ * Allow setting a few global defaults for file source plugin types. by `@jmchilton `_ in `#18909 `_ * Type annotations and fixes by `@nsoranzo `_ in `#18911 `_ * Add filter null collection operation tool by `@mvdbeek `_ in `#18928 `_ * Fix extra files path type hint by `@davelopez `_ in `#18958 `_ * Decouple user email from role name by `@jdavcs `_ in `#18966 `_ * Optimize to_history_dataset_association in create_datasets_from_library_folder by `@arash77 `_ in `#18970 `_ * Workflow landing improvements by `@mvdbeek `_ in `#18979 `_ * Allow recovering a normalized version of workflow request state from API by `@jmchilton `_ in `#18985 `_ * Add some Zarr-based datatypes by `@davelopez `_ in `#19040 `_ * Run installed Galaxy with no config and a simplified entry point by `@natefoo `_ in `#19050 `_ * Annotate ``DatasetAssociationManager`` as generic type by `@nsoranzo `_ in `#19063 `_ * Move TRS import into WorkflowContentManager by `@mvdbeek `_ in `#19070 `_ * Allow deferred datasets to behave as URIs by `@davelopez `_ in `#19077 `_ * Better cleanup of sharing roles on user purge by `@jdavcs `_ in `#19096 `_ * Add XML based `vtk` datatype by `@tStehling `_ in `#19104 `_ * Access public history in job cache / job search by `@mvdbeek `_ in `#19108 `_ * Always validate hashes when provided by `@nsoranzo `_ in `#19110 `_ * Enable specifying dataset hash in test jobs by `@mvdbeek `_ in `#19113 `_ * Enhance UTF-8 support for filename handling in downloads by `@arash77 `_ in `#19161 `_ * Backport of Workflow Editor Activity Bar by `@dannon `_ in `#19212 `_ * Fix default value handling for parameters connected to required parameters by `@mvdbeek `_ in `#19219 `_ ============= Other changes ============= * Merge 24.1 by `@jdavcs `_ in `#18386 `_ * Format dev to fix linting. by `@jmchilton `_ in `#18860 `_ * Add 24.2 migration tags by `@jdavcs `_ in `#19169 `_ * Fix type annotations for pysam 0.23.0 by `@nsoranzo `_ in `#19571 `_ ------------------- 24.1.4 (2024-12-11) ------------------- ========= Bug fixes ========= * Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ in `#18428 `_ * Improve workflow-related exception reporting by `@mvdbeek `_ in `#18447 `_ * Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ * Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ * Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ * Also check dataset.deleted when determining if data can be displayed by `@mvdbeek `_ in `#18547 `_ * Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ * Fix h5ad metadata by `@nilchia `_ in `#18635 `_ * Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ * Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ * Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ * Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ * Make pylibmagic import optional by `@mvdbeek `_ in `#18813 `_ * Ignore converted datasets in invalid input states by `@mvdbeek `_ in `#18850 `_ * Fix discovered outputs with directory metadata and distributed object by `@mvdbeek `_ in `#18855 `_ * Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ * Fix wrong final state when init_from is used by `@mvdbeek `_ in `#18871 `_ * Fix history import when parent_hda not serialized by `@mvdbeek `_ in `#18873 `_ * Limit max number of items in dataproviders by `@mvdbeek `_ in `#18881 `_ * Allow cors in biom and q2view display applications by `@mvdbeek `_ in `#18890 `_ * Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek `_ in `#18976 `_ * Optimize/fix sqlite hid update statement by `@mvdbeek `_ in `#19106 `_ * Prefer auto-decompressed datatype when picking conversion target by `@mvdbeek `_ in `#19162 `_ * Fix various invocation export issues by `@mvdbeek `_ in `#19215 `_ * Fix bad merge conflict resolution by `@nsoranzo `_ in `#19297 `_ ============= Other changes ============= * Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ ------------------- 24.1.3 (2024-10-25) ------------------- ========= Bug fixes ========= * Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ in `#18428 `_ * Improve workflow-related exception reporting by `@mvdbeek `_ in `#18447 `_ * Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ * Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ * Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ * Also check dataset.deleted when determining if data can be displayed by `@mvdbeek `_ in `#18547 `_ * Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ * Fix h5ad metadata by `@nilchia `_ in `#18635 `_ * Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ * Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ * Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ * Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ * Make pylibmagic import optional by `@mvdbeek `_ in `#18813 `_ * Ignore converted datasets in invalid input states by `@mvdbeek `_ in `#18850 `_ * Fix discovered outputs with directory metadata and distributed object by `@mvdbeek `_ in `#18855 `_ * Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ * Fix wrong final state when init_from is used by `@mvdbeek `_ in `#18871 `_ * Fix history import when parent_hda not serialized by `@mvdbeek `_ in `#18873 `_ * Limit max number of items in dataproviders by `@mvdbeek `_ in `#18881 `_ * Allow cors in biom and q2view display applications by `@mvdbeek `_ in `#18890 `_ * Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek `_ in `#18976 `_ ============= Other changes ============= * Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ ------------------- 24.1.2 (2024-09-25) ------------------- ========= Bug fixes ========= * Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ * Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ * Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ * Also check dataset.deleted when determining if data can be displayed by `@mvdbeek `_ in `#18547 `_ * Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ * Fix h5ad metadata by `@nilchia `_ in `#18635 `_ * Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ * Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ * Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ * Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ * Make pylibmagic import optional by `@mvdbeek `_ in `#18813 `_ * Ignore converted datasets in invalid input states by `@mvdbeek `_ in `#18850 `_ * Fix discovered outputs with directory metadata and distributed object by `@mvdbeek `_ in `#18855 `_ * Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ * Fix wrong final state when init_from is used by `@mvdbeek `_ in `#18871 `_ * Fix history import when parent_hda not serialized by `@mvdbeek `_ in `#18873 `_ ============= Other changes ============= * Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ ------------------- 24.1.1 (2024-07-02) ------------------- ========= Bug fixes ========= * Fix syntax for SA2.0 by `@jdavcs `_ in `#17663 `_ * Fix empty usernames in database + bug in username generation by `@jdavcs `_ in `#18379 `_ * Fix `input_step_parameters` missing values that don't have a label by `@ahmedhamidawan `_ in `#18405 `_ * Improve workflow-related exception reporting by `@mvdbeek `_ in `#18447 `_ ============ Enhancements ============ * Enable all-vs-all collection analysis patterns. by `@jmchilton `_ in `#17366 `_ * Visualizing workflow runs with an invocation graph view by `@ahmedhamidawan `_ in `#17413 `_ * Better display of estimated line numbers and add number of columns for tabular by `@bernt-matthias `_ in `#17492 `_ * Enable storage management by object store by `@jmchilton `_ in `#17500 `_ * Set minimal metadata also for empty bed datasets by `@wm75 `_ in `#17586 `_ * Type annotation improvements by `@nsoranzo `_ in `#17601 `_ * Type annotation and CWL-related improvements by `@nsoranzo `_ in `#17630 `_ * Update Python dependencies by `@galaxybot `_ in `#17653 `_ * Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#17654 `_ * SQLAlchemy 2.0 by `@jdavcs `_ in `#17778 `_ * Outline use of type_annotation_map to fix mypy issues by `@jmchilton `_ in `#17902 `_ * Add `email` notifications channel by `@davelopez `_ in `#17914 `_ * Model edits and bug fixes by `@jdavcs `_ in `#17922 `_ * Model typing and SA2.0 follow-up by `@jdavcs `_ in `#17958 `_ * Enable ``warn_unused_ignores`` mypy option by `@nsoranzo `_ in `#17991 `_ * Add galaxy to user agent by `@mvdbeek `_ in `#18003 `_ * Refactor galaxy.files plugin loading + config handling. by `@jmchilton `_ in `#18049 `_ * Add stronger type annotations in file sources + refactoring by `@davelopez `_ in `#18050 `_ * Add support for additional media types by `@arash77 `_ in `#18054 `_ * Update Python dependencies by `@galaxybot `_ in `#18063 `_ * Enable flake8-implicit-str-concat ruff rules by `@nsoranzo `_ in `#18067 `_ * Script for deleting userless histories from database + testing + drop unused model testing code by `@jdavcs `_ in `#18079 `_ * Add Net datatype by `@martenson `_ in `#18080 `_ * 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 `_ * Update db revision 24.1 release tags by `@jdavcs `_ in `#18183 `_ * Tighten axt sniffer by `@martenson `_ in `#18204 `_ * More structured indexing for user data objects. by `@jmchilton `_ in `#18291 `_ ============= Other changes ============= * Chore: remove repetitive words by `@tianzedavid `_ in `#18076 `_ * Fix import broken with forward merge by `@mvdbeek `_ in `#18152 `_ ------------------- 24.0.3 (2024-06-28) ------------------- ========= Bug fixes ========= * Downgrade count lines error to warning by `@mvdbeek `_ in `#18175 `_ * Don't set dataset peek for errored jobs by `@mvdbeek `_ in `#18231 `_ * Transparently open compressed files in DatasetDataProvider by `@mvdbeek `_ in `#18248 `_ * Raise exception when extracting dataset from collection without datasets by `@mvdbeek `_ in `#18249 `_ * Set page importable to false when serializing by `@mvdbeek `_ in `#18263 `_ * Fix first_dataset_element type hint by `@mvdbeek `_ in `#18284 `_ * Do not copy purged outputs to object store by `@mvdbeek `_ in `#18342 `_ * Fix user's private role can be missing by `@davelopez `_ in `#18381 `_ * Assign default ``data`` extension on discovered collection output by `@mvdbeek `_ in `#18389 `_ ============= Other changes ============= * Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek `_ in `#18428 `_ ------------------- 24.0.2 (2024-05-07) ------------------- No recorded changes since last release ------------------- 24.0.1 (2024-05-02) ------------------- ========= Bug fixes ========= * Always serialize element_count and populated when listing contents by `@mvdbeek `_ in `#17890 `_ * Fix deadlock that can occur when changing job state by `@mvdbeek `_ in `#17896 `_ * Fix tool form building if select filters from unavailable dataset metadata by `@mvdbeek `_ in `#17930 `_ * Fix ``InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands.`` by `@mvdbeek `_ in `#17932 `_ * Never fail dataset serialization if display_peek fails by `@mvdbeek `_ in `#17937 `_ * Fix output datatype when uncompressing a dataset with incorrect datatype by `@nsoranzo `_ in `#17944 `_ * Use or copy StoredWorkflow when copying step by `@mvdbeek `_ in `#17988 `_ * Raise ``MessageException`` when report references invalid workflow output by `@mvdbeek `_ in `#18009 `_ * Fix tag regex pattern by `@jdavcs `_ in `#18025 `_ * Fix History Dataset Association creation so that hid is always set by `@mvdbeek `_ in `#18036 `_ * Fix history export with missing dataset hids by `@davelopez `_ in `#18052 `_ * Fix comments lost on import by `@ElectronicBlueberry `_ in `#18060 `_ * Fix history update time after bulk operation by `@davelopez `_ in `#18068 `_ ------------------- 24.0.0 (2024-04-02) ------------------- ========= Bug fixes ========= * Fix for converter tests by `@bernt-matthias `_ in `#17188 `_ * correct dbkey for minerva display app by `@hexylena `_ in `#17196 `_ * Fix invocation serialization if no state was set by `@mvdbeek `_ in `#17278 `_ * Fix quotas ID encoding by `@davelopez `_ in `#17335 `_ * Fix model store exports that include implicit conversions. by `@jmchilton `_ in `#17346 `_ * Fix bug: create new PSAAssociation if not in database by `@jdavcs `_ in `#17516 `_ * Fix social_core methods by `@jdavcs `_ in `#17530 `_ * Fix ancient bug: incorrect usage of func.coalesce in User model by `@jdavcs `_ in `#17577 `_ * Account for newlines in CIF Datatype sniffer by `@patrick-austin `_ in `#17582 `_ * Anticipate PendingRollbackError in ``check_database_connection`` by `@mvdbeek `_ in `#17598 `_ * Add basic model import attribute validation by `@mvdbeek `_ in `#17628 `_ * More efficient change_state queries, maybe fix deadlock by `@mvdbeek `_ in `#17632 `_ * Npz sniffing: do not read the whole file by `@bernt-matthias `_ in `#17672 `_ * Assert that at least one file in npz zipfile ends with .npy by `@mvdbeek `_ in `#17679 `_ * Workflow Comment Indexing by `@ElectronicBlueberry `_ in `#17700 `_ * Fix source history update_time being updated when importing a public history by `@jmchilton `_ in `#17728 `_ * Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek `_ in `#17777 `_ * Defer job attributes that are usually not needed by `@mvdbeek `_ in `#17795 `_ * Fix change_datatype PJA for dynamic collections by `@mvdbeek `_ in `#17803 `_ * Simplify nested collection joins by `@mvdbeek `_ in `#17817 `_ * Fix very slow user data table query by `@mvdbeek `_ in `#17830 `_ * Update db revision 24.0 release tags by `@jdavcs `_ in `#17834 `_ * Minor refactor of query building logic for readability by `@jdavcs `_ in `#17835 `_ * Fix user login when duplicate UserRoleAssociation exists by `@mvdbeek `_ in `#17854 `_ ============ Enhancements ============ * Make columns types an empty list for empty tabular data by `@bernt-matthias `_ in `#13918 `_ * port invocation API to fastapi by `@martenson `_ in `#16707 `_ * SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs `_ in `#16932 `_ * Python 3.8 as minimum by `@mr-c `_ in `#16954 `_ * Expose more tool information / navigability in UI. by `@jmchilton `_ in `#17105 `_ * Add support for (fast5.tar).xz binary compressed files by `@tuncK `_ in `#17106 `_ * SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs `_ in `#17122 `_ * Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs `_ in `#17132 `_ * Create pydantic model for the return of show operation - get: `/api/jobs/{job_id}` by `@heisner-tillman `_ in `#17153 `_ * Much simpler default dataset permissions for typical users. by `@jmchilton `_ in `#17166 `_ * Add future=True flag to SA engine by `@jdavcs `_ in `#17174 `_ * Add future=True flag to SA session by `@jdavcs `_ in `#17179 `_ * Vueifiy History Grids by `@guerler `_ in `#17219 `_ * Convert sample object store configuration to YAML and support configuring inline by `@natefoo `_ in `#17222 `_ * Migrate models to pydantic 2 by `@mvdbeek `_ in `#17262 `_ * API endpoint that allows "changing" the objectstore for "safe" scenarios. by `@jmchilton `_ in `#17329 `_ * Enable ``warn_unreachable`` mypy option by `@mvdbeek `_ in `#17365 `_ * Fix type annotation of code using XML etree by `@nsoranzo `_ in `#17367 `_ * Add explicit cache_ok attribute to JSONType subclass by `@mvdbeek `_ in `#17376 `_ * More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo `_ in `#17381 `_ * Update to black 2024 stable style by `@nsoranzo `_ in `#17391 `_ * Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek `_ in `#17435 `_ * UI for "relocating" a dataset to a new object store (when safe) by `@jmchilton `_ in `#17437 `_ * Allow filtering history datasets by object store ID and quota source. by `@jmchilton `_ in `#17460 `_ * Faster FASTA and FASTQ metadata setting by `@bernt-matthias `_ in `#17462 `_ * Feature SBOL datatypes by `@guillaume-gricourt `_ in `#17482 `_ * Display workflow invocation counts. by `@jmchilton `_ in `#17488 `_ * add npy datatype by `@astrovsky01 `_ in `#17517 `_ * Enhance Avivator display app to support regular Tiffs by `@davelopez `_ in `#17554 `_ * Update Python dependencies by `@galaxybot `_ in `#17580 `_ * Add migrations revision identifier for 24.0 by `@jdavcs `_ in `#17589 `_ ------------------- 23.2.1 (2024-02-21) ------------------- ========= Bug fixes ========= * Rename to_dict to populate in FormDefintion to fix bug by `@jdavcs `_ in `#16553 `_ * MINERVA display application: enable cors, add for tabular by `@hexylena `_ in `#16737 `_ * Use AlignedSegment.to_string by `@mvdbeek `_ in `#16803 `_ * Ruff and flake8 fixes by `@nsoranzo `_ in `#16884 `_ * prep for updated h5py and typos by `@mr-c `_ in `#16963 `_ * Fix cardinality violation error: subquery returns multiple results by `@jdavcs `_ in `#17224 `_ * Fix Display Application link generation by `@mvdbeek `_ in `#17227 `_ * Display application fixes and tests by `@mvdbeek `_ in `#17233 `_ * Rollback invalidated transaction by `@jdavcs `_ in `#17280 `_ * Set metadata states on dataset association, not dataset by `@mvdbeek `_ in `#17474 `_ * Provide working routes.url_for every ASGI request by `@mvdbeek `_ in `#17497 `_ ============ Enhancements ============ * Implement default locations for data and collection parameters. by `@jmchilton `_ in `#14955 `_ * Display beginning of non-text files as text instead of triggering a download by `@SergeyYakubov `_ in `#15447 `_ * Tool Shed 2.0 by `@jmchilton `_ in `#15639 `_ * Limit number of celery task executions per second per user by `@claudiofr `_ in `#16232 `_ * Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek `_ in `#16252 `_ * Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs `_ in `#16264 `_ * Update Python dependencies by `@galaxybot `_ in `#16409 `_ * Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs `_ in `#16431 `_ * SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs `_ in `#16434 `_ * Update Python dependencies by `@galaxybot `_ in `#16436 `_ * Implement datatype upload warnings by `@jmchilton `_ in `#16564 `_ * Support new genome browser chain file format by `@claudiofr `_ in `#16576 `_ * Workflow Comments 💬 by `@ElectronicBlueberry `_ in `#16612 `_ * Bump samtools converters by `@bernt-matthias `_ in `#16668 `_ * Misc. edits/refactorings to session handling by `@jdavcs `_ in `#16712 `_ * SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs `_ in `#16724 `_ * Migrate `collection elements` store to Pinia by `@davelopez `_ in `#16725 `_ * Reset autocommit to False by `@jdavcs `_ in `#16745 `_ * Drop legacy server-side search by `@jdavcs `_ in `#16755 `_ * Optimize iteration in DatasetInstance model + SA2.0 fix by `@jdavcs `_ in `#16776 `_ * Migrate a part of the jobs API to Fast API by `@heisner-tillman `_ in `#16778 `_ * Replace file_name property with get_file_name function by `@SergeyYakubov `_ in `#16783 `_ * Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu `_ in `#16795 `_ * Allow partial matches in workflow name tag search and search all tags for unquoted query by `@ahmedhamidawan `_ in `#16860 `_ * Vueify Visualizations Grid by `@guerler `_ in `#16892 `_ * Standardize to W3C naming for color. by `@dannon `_ in `#16949 `_ * Move and re-use persist_extra_files by `@mvdbeek `_ in `#16955 `_ * Fix invocation report to target correct workflow version. by `@jmchilton `_ in `#17008 `_ * optimize object store cache operations by `@SergeyYakubov `_ in `#17025 `_ * Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek `_ in `#17342 `_ * Add magres datatype by `@martenson `_ in `#17499 `_ ============= Other changes ============= * Merge 23.1 into dev by `@mvdbeek `_ in `#16534 `_ * Merge release_23.1 into dev by `@mvdbeek `_ in `#16768 `_ * Create db head merge revision. by `@dannon `_ in `#16838 `_ * merge release_23.1 into dev by `@martenson `_ in `#16933 `_ * Minor clarification/typo fix in datatypes.data by `@dannon `_ in `#16993 `_ * Fix `.file_name` access in merge forward by `@mvdbeek `_ in `#17097 `_ * Backport model store fixes by `@mvdbeek `_ in `#17439 `_ * Fix succces typo by `@mvdbeek `_ in `#17481 `_ ------------------- 23.1.4 (2024-01-04) ------------------- ========= Bug fixes ========= * Fix User.current_galaxy_session by `@mvdbeek `_ in `#17232 `_ ============= Other changes ============= * Backport #17188: Fix for converter tests by `@mvdbeek `_ in `#17231 `_ ------------------- 23.1.3 (2023-12-01) ------------------- ========= Bug fixes ========= * Add missing optional description field, fixes ephemeris data library example by `@mvdbeek `_ in `#17116 `_ ------------------- 23.1.2 (2023-11-29) ------------------- ========= Bug fixes ========= * Skip change_datatype things if we're not actually changing the extension by `@mvdbeek `_ in `#16931 `_ * Fix copying metadata to copied job outputs by `@mvdbeek `_ in `#17007 `_ * Update tar_to_directory dependency by `@mvdbeek `_ in `#17009 `_ * Assert that ``DatasetCollectioElement`` has an associated object by `@mvdbeek `_ in `#17071 `_ * Fix input dates in notifications: consider timezone offset by `@davelopez `_ in `#17088 `_ * Allow relative URLs in broadcasts action links by `@davelopez `_ in `#17093 `_ ============ Enhancements ============ * Improve invocation error reporting by `@mvdbeek `_ in `#16917 `_ * Add support for larch datatypes by `@patrick-austin `_ in `#17080 `_ ------------------- 23.1.1 (2023-10-23) ------------------- ========= Bug fixes ========= * Fix bad auto-merge of dev. by `@jmchilton `_ in `#15386 `_ * Merge conflicting db migration branches into one by `@jdavcs `_ in `#15771 `_ * Enable ``strict_equality`` mypy option by `@nsoranzo `_ in `#15808 `_ * Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by `@jdavcs `_ in `#15811 `_ * Fix anonymous user uploads when vault is configured by `@tchaussepiedifb `_ in `#15858 `_ * Fix nullable deleted column in API Keys table by `@davelopez `_ in `#15956 `_ * Attempt to fix mypy check by `@davelopez `_ in `#16103 `_ * Ensure session is request-scoped for legacy endpoints by `@jdavcs `_ in `#16207 `_ * Reset autocommit to True (temporarily) by `@jdavcs `_ in `#16283 `_ * Update 23.1 release tags for migration scripts by `@jdavcs `_ in `#16294 `_ * Fix form builder value handling by `@guerler `_ in `#16304 `_ * Fix tags ownership by `@davelopez `_ in `#16339 `_ * Fix disk usage recalculation for distributed object stores by `@mvdbeek `_ in `#16380 `_ * Job cache fixes for DCEs by `@mvdbeek `_ in `#16384 `_ * Fix histories count by `@davelopez `_ in `#16400 `_ * Fix double-encoding notification content by `@mvdbeek `_ in `#16530 `_ * Optimize getting current user session by `@mvdbeek `_ in `#16604 `_ * Fixes for conditional subworkflow steps by `@mvdbeek `_ in `#16632 `_ * Copy the collection contents by default when copying a collection by `@mvdbeek `_ in `#16717 `_ * Fix allowlist deserialization in file sources by `@mvdbeek `_ in `#16729 `_ * Fix workflow output display without label by `@mvdbeek `_ in `#16749 `_ * Fix and prevent persisting null file_size by `@mvdbeek `_ in `#16855 `_ * Fix workflow import losing tool_version by `@mvdbeek `_ in `#16869 `_ * Remove more flushes in database operation tools by `@mvdbeek `_ in `#16875 `_ * Fix join condition for nested collection query by `@mvdbeek `_ in `#16880 `_ ============ Enhancements ============ * Empower Users to Select Storage Destination by `@jmchilton `_ in `#14073 `_ * Add Storage Dashboard visualizations for histories by `@davelopez `_ in `#14820 `_ * Towards decoupling datatypes and model by `@jdavcs `_ in `#15186 `_ * Add Storage Management API by `@davelopez `_ in `#15295 `_ * OIDC tokens by `@SergeyYakubov `_ in `#15300 `_ * Expose additional beaker caching backends by `@claudiofr `_ in `#15349 `_ * Follow up to #15186 by `@jdavcs `_ in `#15388 `_ * Add support for visualizing HDF5 datasets. by `@jarrah42 `_ in `#15394 `_ * Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs `_ in `#15421 `_ * Update Python dependencies by `@galaxybot `_ in `#15435 `_ * Unify url handling with filesources by `@nuwang `_ in `#15497 `_ * Move TS to Alembic by `@jdavcs `_ in `#15509 `_ * Update Python dependencies by `@galaxybot `_ in `#15564 `_ * Update database_heartbeat for SA 2.0 compatibility by `@jdavcs `_ in `#15611 `_ * Update supports_skip_locked, supports_returning for SA 2.0 compatibility by `@jdavcs `_ in `#15633 `_ * Add Galaxy Notification System by `@davelopez `_ in `#15663 `_ * Drop model mapping unit tests by `@jdavcs `_ in `#15669 `_ * Add transactional state to workflow scheduling manager by `@jdavcs `_ in `#15683 `_ * Remove DELETED_NEW job state from code base by `@jdavcs `_ in `#15690 `_ * Fix/Enhance recalculate disk usage API endpoint by `@davelopez `_ in `#15739 `_ * Drop database views by `@jdavcs `_ in `#15876 `_ * Update Python dependencies by `@galaxybot `_ in `#15890 `_ * FITS data format by `@volodymyrss `_ in `#15905 `_ * Improve display chunk generation for BAMs by `@wm75 `_ in `#15972 `_ * Add History Archival feature by `@davelopez `_ in `#16003 `_ * Add alter_column migration utility by `@jdavcs `_ in `#16009 `_ * Code cleanups from ruff and pyupgrade by `@nsoranzo `_ in `#16035 `_ * Add missing fields to HistorySummary schema model by `@davelopez `_ in `#16041 `_ * Dataset chunking tests (and small fixes) by `@jmchilton `_ in `#16069 `_ * Add create_foreign_key migration utility by `@jdavcs `_ in `#16077 `_ * Refactor models enums to eliminate schema dependency on model layer. by `@jmchilton `_ in `#16080 `_ * Use automated naming convention to generate indexes and constraints in database by `@jdavcs `_ in `#16089 `_ * Add zipped mongodb and genenotebook datatypes by `@abretaud `_ in `#16173 `_ * Drop workarounds for old ro-crate-py and docutils versions by `@mvdbeek `_ in `#16198 `_ * bring grids for (published) pages on par with workflows by `@martenson `_ in `#16209 `_ * Add Visium datatype for squidpy and spatialomics tools by `@astrovsky01 `_ in `#16255 `_ * Filter deleted keys from api_keys relationship by `@dannon `_ in `#16321 `_ * Increase `CustosAuthnzToken.external_user_id` column size by `@davelopez `_ in `#16818 `_ ============= Other changes ============= * Follow up on object store selection PR. by `@jmchilton `_ in `#15654 `_ * Fix Enums in API docs by `@davelopez `_ in `#15740 `_ * merge release_23.0 into dev by `@martenson `_ in `#15830 `_ * Fix linting of FITS datatype code by `@mvdbeek `_ in `#16169 `_ * backport of pysam tostring by `@martenson `_ in `#16822 `_ ------------------- 23.0.6 (2023-10-23) ------------------- ========= Bug fixes ========= * Fix extra files path handling by `@mvdbeek `_ in `#16541 `_ * Don't fail invocation message without dependent_workflow_step_id by `@mvdbeek `_ in `#16628 `_ ------------------- 23.0.5 (2023-07-29) ------------------- ========= Bug fixes ========= * Copy when_expression when copying workflow step by `@mvdbeek `_ in `#16377 `_ ------------------- 23.0.4 (2023-06-30) ------------------- No recorded changes since last release ------------------- 23.0.3 (2023-06-26) ------------------- No recorded changes since last release ------------------- 23.0.2 (2023-06-13) ------------------- No recorded changes since last release ------------------- 23.0.1 (2023-06-08) ------------------- ========= Bug fixes ========= * Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek `_ in `#15744 `_ * Fix folder listing via file browser by `@mvdbeek `_ in `#15950 `_ * Fix RO-crate invocation export with complex collections by `@davelopez `_ in `#15971 `_ * Backport Improve display chunk generation for BAMs by `@mvdbeek `_ in `#16007 `_ * Ensure history export contains all expected datasets by `@davelopez `_ in `#16013 `_ * Various fixes to path prefix handling by `@mvdbeek `_ in `#16033 `_ * Fix dataype_change not updating HDCA update_time by `@mvdbeek `_ in `#16099 `_ * Fix mypy error due to alembic 1.11.0 by `@nsoranzo `_ in `#16104 `_ * Fix extended metadata file size handling by `@mvdbeek `_ in `#16109 `_ * Fix implicit converters with optional parameters by `@mvdbeek `_ in `#16133 `_ * Make ``ctx_rev`` optional in InstalledToolShedRepository response model by `@dannon `_ in `#16139 `_ * Fix optional fields being validated as missing in ts api by `@jmchilton `_ in `#16141 `_ * Support ro crate 0.8.0 and 0.7.0 by `@mvdbeek `_ in `#16193 `_ * Verify existence of default value attribute for user forms fields by `@guerler `_ in `#16205 `_ ------------------- 20.9.0 (2020-10-15) ------------------- * First release from the 20.09 branch of Galaxy. ------------------- 20.5.0 (2020-07-04) ------------------- * First release from the 20.05 branch of Galaxy.