History ------- .. to_doc --------- 26.1.dev0 --------- ------------------- 25.1.2 (2026-03-09) ------------------- ========= Bug fixes ========= * Add missing enable_beta_tool_formats config option by `@bernt-matthias `_ in `#21190 `_ * Properly parse build info from requirement info by `@bernt-matthias `_ in `#21481 `_ * Fix private dataset sharing error handling by `@davelopez `_ in `#21689 `_ * Add selenium test and fix inline images in workflow report tables by `@mvdbeek `_ in `#21698 `_ * Fix route to workflow editor with version does not load expected version by `@ahmedhamidawan `_ in `#21711 `_ * Fix database migration error from 25.0 > 25.1 by `@jdavcs `_ in `#21737 `_ * Fix npm trusted publishing in 25.1 release workflow by `@dannon `_ in `#21747 `_ * Make galaxy-web-apps package compatible with latest FastAPI by `@nsoranzo `_ in `#21753 `_ * Fix disable_local_accounts displays register link by `@davelopez `_ in `#21764 `_ * Fix help forum integration by `@davelopez `_ in `#21773 `_ * Fix workflow rename modal is not reactive to prop changes by `@ahmedhamidawan `_ in `#21785 `_ * Fix tag dropdown not closing on outside click, and not selecting in Safari by `@mvdbeek `_ in `#21797 `_ * Make database heartbeat more robust (backport) by `@mvdbeek `_ in `#21812 `_ * Allow workflow download with missing file source references by `@mvdbeek `_ in `#21814 `_ * Fix AWS Batch monitor crash, delete copied monitor method by `@mvdbeek `_ in `#21818 `_ * Fix form number negative handling by `@davelopez `_ in `#21819 `_ * Fix tool credentials on containerized (Singularity/Docker) destinations by `@arash77 `_ in `#21821 `_ * Pin setuptools<82 for galaxy-files package - Backport #21824 by `@nsoranzo `_ in `#21826 `_ * Add `builtin_converters` section to integrated tool panel by `@ahmedhamidawan `_ in `#21838 `_ * Fix Galaxy UI nesting in data manager job info view by `@mvdbeek `_ in `#21840 `_ * Fix output dataset permission guessing by `@mvdbeek `_ in `#21862 `_ * Fix loading non-tool files from watched tool directories by `@mvdbeek `_ in `#21880 `_ * Fix credential validation logic in tool form component by `@itisAliRH `_ in `#21889 `_ * Ensure markdown elements do not render if argument is undefined by `@ahmedhamidawan `_ in `#21908 `_ * Fix "Create New" in workflow editor not resetting editor state by `@ahmedhamidawan `_ in `#21918 `_ * Enforce storage quota for Celery-based data fetch jobs by `@mvdbeek `_ in `#21941 `_ * Fix optional parameter persisting ``NO_REPLACEMENT`` sentinel when not provided by `@mvdbeek `_ in `#21964 `_ * Fix recording duplicate workflow_request_input_step_parameter rows by `@mvdbeek `_ in `#21980 `_ * Fix AttributeError when requesting invalid metadata file by `@mvdbeek `_ in `#21985 `_ * Fix NoReplacement handling in workflow callback_helper by `@mvdbeek `_ in `#21994 `_ * Fix pick_value output inheriting hidden state from input datasets by `@mvdbeek `_ in `#21995 `_ ============ Enhancements ============ * Add Deacon idx format by `@SantaMcCloud `_ in `#21632 `_ * Add amnis cif flow cytometry data type by `@bernt-matthias `_ in `#21829 `_ ============= 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 `_ * Record input parameter invocation inputs by `@mvdbeek `_ in `#21452 `_ * Remove ref and polish release-drafter workflow by `@ahmedhamidawan `_ in `#21467 `_ * Maintain column definitions on map over by `@mvdbeek `_ in `#21468 `_ * Add missing test file for sig datatype by `@SaimMomin12 `_ in `#21473 `_ * Remove `release-drafter` workflow and add a release config file to improve generated notes by `@ahmedhamidawan `_ in `#21478 `_ * 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 `_ * Fix subworkflow runs for disconnected required inputs with defaults by `@mvdbeek `_ in `#21488 `_ * change locuszoom package version to 0.0.7 by `@elmedjadjirayane `_ in `#21494 `_ * Pin release prebuilt client package exactly by `@dannon `_ in `#21498 `_ * Usability fixes for sample sheet selection. by `@jmchilton `_ in `#21503 `_ * Fix exception message to enable debugging of missing dataset issue. by `@jmchilton `_ in `#21504 `_ * Fix type annotation for invocation report ``errors`` field by `@mvdbeek `_ in `#21508 `_ * Add missing dependencies to ``galaxy-files`` package by `@nsoranzo `_ in `#21518 `_ * Filter out failed_metadata HDAs from job cache by `@mvdbeek `_ in `#21544 `_ * Fix pulsar with ``rewrite_parameters: false`` by `@mvdbeek `_ in `#21557 `_ * Fix job cache collection copy by `@mvdbeek `_ in `#21558 `_ * Show "Expires today" instead of "Expires soon" in Expiration Warning by `@mvdbeek `_ in `#21560 `_ * Use quotes for Galaxy citation bibtex by `@bernt-matthias `_ in `#21563 `_ * Supports Dataverse file access via both persistent and database IDs by `@davelopez `_ in `#21569 `_ * Fix passing user id to preferences by `@guerler `_ in `#21576 `_ * Fix Pulsar with ``default_file_action: none`` by `@mvdbeek `_ in `#21578 `_ * Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by `@jmchilton `_ in `#21584 `_ * Add belated deprecation of Python 3.9 support by `@nsoranzo `_ in `#21598 `_ * Fix loading of credentials when associated tools are missing by `@arash77 `_ in `#21599 `_ * Fix race condition in workflow collection populated state check by `@mvdbeek `_ in `#21613 `_ * Harden Dataverse integration by `@davelopez `_ in `#21624 `_ * Add split paired or unpaired tool to sample tool conf by `@bernt-matthias `_ in `#21647 `_ * Fix secret credential editing and add clear button by `@itisAliRH `_ in `#21650 `_ * Fix condor typo by `@gsaudade99 `_ in `#21651 `_ * Fix HTCondor runner unwatching jobs when stopping containers by `@kysrpex `_ in `#21656 `_ * Fix data manager .loc file selection logic by `@jdavcs `_ in `#21664 `_ * Fixes storage management check for anonymous users by `@davelopez `_ in `#21680 `_ * Resets selection filter when loading dialog by `@davelopez `_ in `#21681 `_ * Fixes duplicated entries in "share with individual users" component by `@davelopez `_ in `#21683 `_ * Simplify docker build, use node as specified in requirements by `@mvdbeek `_ in `#21695 `_ * Remove Discover Tools button in the workflow tool panel by `@ahmedhamidawan `_ in `#21697 `_ * Fix option propagation for workflow inputs connected to multiple subworkflows by `@mvdbeek `_ in `#21712 `_ * Fix collection job state not preserved during history export/import by `@mvdbeek `_ in `#21716 `_ * Add missing filter_failed_collection_1.1.0.xml tool by `@mvdbeek `_ in `#21719 `_ * Strip inline comments in conditional requirements by `@mvdbeek `_ in `#21720 `_ * Exclude node_modules at all depths in Docker builds by `@mvdbeek `_ in `#21721 `_ ============ Enhancements ============ * add new datatype for kmindex index data by `@Smeds `_ in `#21429 `_ * Add sample sheet support to many database operation tools by `@mvdbeek `_ in `#21465 `_ * Add Sourmash sig new datatype by `@SaimMomin12 `_ in `#21469 `_ * Add new jupyter version by `@bgruening `_ in `#21531 `_ * Adds object_expires_after_days example usage to sample config by `@davelopez `_ in `#21547 `_ * Add tool credentials system documentation and schema updates by `@arash77 `_ in `#21561 `_ * Add a few datatypes from the digital humanities domain by `@bgruening `_ in `#21596 `_ * Add new datatype pg and hg for pangenomics by `@SaimMomin12 `_ in `#21620 `_ * Add database operation tool to convert sample sheets to list collections by `@mvdbeek `_ in `#21625 `_ * Add new datatypes required for VG tool by `@SaimMomin12 `_ in `#21644 `_ * Document security considerations for using secrets by `@bernt-matthias `_ in `#21654 `_ ============= Other changes ============= * Update 25.1 release notes with config changes by `@ahmedhamidawan `_ in `#21444 `_ * Fix 25.1 release month on user facing notes by `@ahmedhamidawan `_ in `#21450 `_ * Fix sample_sheet column display by `@mvdbeek `_ in `#21457 `_ * Merge 25.1 into master by `@ahmedhamidawan `_ in `#21482 `_ * Improve tempdir cleanup in integration tests by `@mvdbeek `_ in `#21520 `_ ------------------- 25.1.0 (2025-12-12) ------------------- ========= Bug fixes ========= * Workaround to numeric sorting in the local portion of tool versions if they are galaxy "build" numbers by `@natefoo `_ in `#13570 `_ * Change wording of the client side storage handling by `@bgruening `_ in `#19815 `_ * Check for ``format="input"`` as well as ``format="auto"`` in datatype linter by `@bernt-matthias `_ in `#20177 `_ * Add missing galaxy slots and memory tool by `@mvdbeek `_ in `#20262 `_ * Fix a transiently failing API test. by `@jmchilton `_ in `#20278 `_ * Fix test timeout in k8s ``test_slots_and_memory`` test by `@mvdbeek `_ in `#20284 `_ * Fix memory and slots test by `@mvdbeek `_ in `#20291 `_ * Add built visualizations path to .gitignore by `@guerler `_ in `#20355 `_ * Remove 8 year old note that points at a non-existent subdomain by `@scottcain `_ in `#20361 `_ * Restore Nora by `@guerler `_ in `#20387 `_ * Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by `@dependabot[bot] `_ in `#20422 `_ * Fix client build, set create_time by `@mvdbeek `_ in `#20445 `_ * Update mulled_containers.rst by `@ccoulombe `_ in `#20446 `_ * Fix transient selenium error when adding collection input. by `@jmchilton `_ in `#20460 `_ * Collection API related spelling fix. by `@jmchilton `_ in `#20470 `_ * Fix alembic down_revision for trigger replacement migration by `@mvdbeek `_ in `#20501 `_ * Add a merge migration, revert previous edit by `@jdavcs `_ in `#20507 `_ * Update core.history tour by `@pavanvidem `_ in `#20576 `_ * Add missing cleanup table by `@jdavcs `_ in `#20594 `_ * Fix UI Bug - don't allow checking deferred for local files. by `@jmchilton `_ in `#20609 `_ * Require user for visualizations create endpoint by `@guerler `_ in `#20615 `_ * Use store to cache step jobs summary by `@ahmedhamidawan `_ in `#20638 `_ * Fix typo in lib/galaxy/config/sample/job_conf.sample.yml: enviroment --> environment by `@blankenberg `_ in `#20652 `_ * Remove select and deselect labels from visualization select field by `@guerler `_ in `#20665 `_ * Fix assertion on python version by `@ccoulombe `_ in `#20696 `_ * Remove decoded ids from job/dataset error report email by `@ahmedhamidawan `_ in `#20714 `_ * Fix various collection descriptions in history panel. by `@jmchilton `_ in `#20736 `_ * Various client unit test fixes and cleanup. by `@jmchilton `_ in `#20752 `_ * More client unit test clean up. by `@jmchilton `_ in `#20755 `_ * More cleanup for Jest output. by `@jmchilton `_ in `#20769 `_ * Fix anndata metadata by `@nilchia `_ in `#20778 `_ * Fix Switch to history link click actions and add extensive jests by `@ahmedhamidawan `_ in `#20783 `_ * Fix visualization installs by `@dannon `_ in `#20788 `_ * Only show breadcrumb when on history permissions route (not in sharing view) by `@ahmedhamidawan `_ in `#20800 `_ * Fix Ipynb datatype sniffer and add unit tests. by `@ksuderman `_ in `#20811 `_ * Ignore yaml and json in prettier pre-commit hook by `@mvdbeek `_ in `#20823 `_ * Bump requirement of directory converters by `@bernt-matthias `_ in `#20834 `_ * Fix lint error in `WorkflowRunSuccess` by `@ahmedhamidawan `_ in `#20837 `_ * Fix `multiple="true"` data collection map over for shell_command tools by `@mvdbeek `_ in `#20859 `_ * Fix test in ``configfile_user_defined.yml`` by `@nsoranzo `_ in `#20873 `_ * Likely fix for transiently failing published histories test. by `@jmchilton `_ in `#20890 `_ * Update requirements of sort1 tool by `@nsoranzo `_ in `#20892 `_ * Avoid overscroll behavior by `@guerler `_ in `#20908 `_ * Bump codecov/codecov-action from 3 to 5 by `@dependabot[bot] `_ in `#20920 `_ * Extract: do not use common prefix dir by `@bernt-matthias `_ in `#20929 `_ * Fix default conditional test parameters... by `@jmchilton `_ in `#20942 `_ * Fix JupyterLite History Identifier Retrieval Without Dataset by `@guerler `_ in `#20971 `_ * Apply overscroll behavior setting to html by `@guerler `_ in `#20975 `_ * Ensure that conversion_key is defined by `@guerler `_ in `#20984 `_ * Tsc fixes and pin by `@dannon `_ in `#20985 `_ * Fix jest tests -- wait for async calls in grid list by `@dannon `_ in `#20986 `_ * Fix comp1 / test_subworkflow_map_over_data_column by `@mvdbeek `_ in `#20992 `_ * Save IGV locus and improve error handling by `@guerler `_ in `#20996 `_ * Fix content wrapping in cards and preference title by `@guerler `_ in `#21009 `_ * Fix horizontal scrolling w/ GButton in input-group-append by `@dannon `_ in `#21025 `_ * Fix GCS file source to handle virtual directories without marker objects by `@dannon `_ in `#21051 `_ * Fix Huggingface timestamp parsing when `last_commit` is missing by `@davelopez `_ in `#21072 `_ * Allow cors on data and tool landing pages by `@mvdbeek `_ in `#21078 `_ * Fix invocation export dataset exclusion by `@davelopez `_ in `#21091 `_ * Fix copy export download link for old exports by `@davelopez `_ in `#21094 `_ * Test and fix CORS on exceptions by `@mvdbeek `_ in `#21105 `_ * Fix invalid invocation tab handling and unify disabled tab components by `@ahmedhamidawan `_ in `#21115 `_ * Fix shift+click range select not working in history list by `@ahmedhamidawan `_ in `#21117 `_ * Restore job.get_param_values by `@mvdbeek `_ in `#21130 `_ * Improve _touch_collection_update_time_cte performance by `@mvdbeek `_ in `#21134 `_ * Fix type annotation in test_run_workflow_use_cached_job_implicit_conv… by `@mvdbeek `_ in `#21138 `_ * Use corepack to link yarn into $VIRTUALENV/bin by `@mvdbeek `_ in `#21140 `_ * Pin Ansible version by `@ksuderman `_ in `#21141 `_ * Remove invocation view connection animations by `@ahmedhamidawan `_ in `#21145 `_ * Mark user creation API endpoint as admin-only by `@mvdbeek `_ in `#21149 `_ * Set minimum profile version for expression tools by `@mvdbeek `_ in `#21151 `_ * Fix subworkflow editing by `@mvdbeek `_ in `#21159 `_ * Add Convert characters1 to workflow safe updates by `@mvdbeek `_ in `#21160 `_ * Use yarn instead of npx to use pinned openapi-typescript by `@mvdbeek `_ in `#21164 `_ * Bump up minimal tpv version by `@mvdbeek `_ in `#21166 `_ * Fix proxy endpoint encoding by `@davelopez `_ in `#21169 `_ * Enable drag-and-drop of collection elements in IGV by `@guerler `_ in `#21173 `_ * Save build date to GITHUB_OUTPUT by `@ksuderman `_ in `#21181 `_ * Don't show the "view sheet" button for non-sample sheet collections. by `@jmchilton `_ in `#21191 `_ * Allow collection builder to be invoked consecutively by `@ahmedhamidawan `_ in `#21193 `_ * Add Hyphy Vision Result Viewer by `@guerler `_ in `#21196 `_ * Don't create extra watchers when switching tabs by `@natefoo `_ in `#21197 `_ * Drop single 'pair' from standard upload UI, preferring lists, or lists of pairs as options for user by `@dannon `_ in `#21200 `_ * Assorted workbook upload fixes. by `@jmchilton `_ in `#21203 `_ * Wrap ontology card in tool discovery view below list view selector by `@ahmedhamidawan `_ in `#21212 `_ * Add missing more-itertools dependency by `@nsoranzo `_ in `#21214 `_ * Fix downloading subworkflows without stored workflow by `@mvdbeek `_ in `#21223 `_ * Fix href for tool links by `@mvdbeek `_ in `#21232 `_ * Apply tool test timeout only once by `@bernt-matthias `_ in `#21246 `_ * Fix workbook download link by `@jmchilton `_ in `#21261 `_ * Fixes download for restricted Zenodo records by `@davelopez `_ in `#21274 `_ * Update the mulled.py script to check json output by `@nilchia `_ in `#21276 `_ * Prevent duplicate `current_history_json` calls by `@ahmedhamidawan `_ in `#21282 `_ * Prevent duplicate fetches for full workflow in invocation view by `@ahmedhamidawan `_ in `#21284 `_ * Add a rate limiter to the API client factory by `@ahmedhamidawan `_ in `#21286 `_ * Fix keyed cache fetching over and over if fetched value is 0 by `@ahmedhamidawan `_ in `#21293 `_ * Fix invocations scroll list cards to show update time by `@ahmedhamidawan `_ in `#21294 `_ * Set `create_time` as the default time for sorting/display for invocations by `@ahmedhamidawan `_ in `#21314 `_ * Fix `TERMINAL_STATES` array has a duplicate state by `@ahmedhamidawan `_ in `#21342 `_ * Force correct client build by `@mvdbeek `_ in `#21346 `_ * Fix fastapi package conflict by `@mvdbeek `_ in `#21349 `_ * Backport smoke-test and pr jobs from dev branch by `@ksuderman `_ in `#21350 `_ * Use anaconda API to find package download URL by `@nsoranzo `_ in `#21360 `_ * Fix database revision tags by `@jdavcs `_ in `#21377 `_ * Use a new format tox environment in lint GitHub action by `@nsoranzo `_ in `#21419 `_ * Skip mako for rendering tool help by `@mvdbeek `_ in `#21428 `_ * Fix optional subworkflow input scheduling bug by `@mvdbeek `_ in `#21435 `_ * Maintain columns on sample sheet map over by `@mvdbeek `_ in `#21436 `_ ============ Enhancements ============ * Don't serialize view of item in delete/purge request by `@mvdbeek `_ in `#18732 `_ * Support credentials(secrets/variables) in tool requirements by `@arash77 `_ in `#19084 `_ * Allow several Galaxy Markdown directives to be embedded. by `@jmchilton `_ in `#19086 `_ * Add tags to output datasets from tool form by `@PlushZ `_ in `#19225 `_ * Implement Sample Sheets by `@jmchilton `_ in `#19305 `_ * Refactor and use `ScrollList` component in more places by `@mvdbeek `_ in `#19318 `_ * User preferences redesign by `@itisAliRH `_ in `#19658 `_ * Refactor Object Store Selection Modals UI by `@itisAliRH `_ in `#19697 `_ * Consider collections in on_strings for parameters accepting multiple datasets by `@bernt-matthias `_ in `#19817 `_ * Remove backbone-based charts modules by `@guerler `_ in `#19892 `_ * Add `selectedItems` composable by `@ahmedhamidawan `_ in `#19973 `_ * Update Python dependencies by `@galaxybot `_ in `#20139 `_ * Remove legacy visualizations by `@guerler `_ in `#20173 `_ * Add rerun.io web viewer by `@guerler `_ in `#20202 `_ * Selenium tests for various 24.2 features. by `@jmchilton `_ in `#20215 `_ * Update Javascript package licenses to MIT by `@mr-c `_ in `#20264 `_ * Split Login and Register, enable OIDC Registration. by `@uwwint `_ in `#20287 `_ * Empower Users to More Pragmatically Import Datasets & Collections From Tables by `@jmchilton `_ in `#20288 `_ * Update GitHub workflows to use PostgreSQL 17 image by `@nsoranzo `_ in `#20292 `_ * Switch Default Visualization Endpoint to script, migrate to YAML by `@guerler `_ in `#20303 `_ * Add short term storage expiration indicator to history items by `@davelopez `_ in `#20332 `_ * Update Python dependencies by `@galaxybot `_ in `#20347 `_ * Install Visualization plugins as self-contained packages by `@guerler `_ in `#20348 `_ * Add LocusZoom Visualization by `@elmedjadjirayane `_ in `#20354 `_ * Refactor CollectionDescription component props to use HDCASummary by `@davelopez `_ in `#20356 `_ * Update create_time field to be required in history content items by `@davelopez `_ in `#20357 `_ * Prepare ``ToolBox.dynamic_tool_to_tool()`` for CWL formats by `@nsoranzo `_ in `#20364 `_ * Install visualizations directly to static path, avoid duplication by `@guerler `_ in `#20372 `_ * Update Python dependencies by `@galaxybot `_ in `#20383 `_ * Use full page width in reports and pages by `@guerler `_ in `#20384 `_ * Workflow Graph Search by `@ElectronicBlueberry `_ in `#20390 `_ * History CitationsList export improvements by `@dannon `_ in `#20402 `_ * Enhance citations page by `@davelopez `_ in `#20408 `_ * Base Implementation of GFormInput by `@ElectronicBlueberry `_ in `#20418 `_ * Type annotation fixes for mypy 1.16.0 by `@nsoranzo `_ in `#20424 `_ * Allow larger viz in pages by `@guerler `_ in `#20427 `_ * Implement dataset source requested transformations. by `@jmchilton `_ in `#20435 `_ * Add username_key setting to configure python-social-auth OIDC by `@marius-mather `_ in `#20497 `_ * Test case for using URL-based workflow inputs with implicit conversions. by `@jmchilton `_ in `#20509 `_ * Remove deprecated tool document cache by `@nsoranzo `_ in `#20510 `_ * Fixes for invocation import. by `@jmchilton `_ in `#20528 `_ * Update Python dependencies by `@galaxybot `_ in `#20537 `_ * Decode OIDC access token as part of authentication pipeline by `@marius-mather `_ in `#20547 `_ * Add Dataverse template by `@davelopez `_ in `#20551 `_ * Update Python dependencies by `@galaxybot `_ in `#20577 `_ * Display the Galaxy Citation within the Export Tool References List by `@mschatz `_ in `#20584 `_ * Add recent downloads page for STS requests by `@davelopez `_ in `#20585 `_ * Implement Data Landing Requests by `@jmchilton `_ in `#20592 `_ * Update Python dependencies by `@galaxybot `_ in `#20601 `_ * Improve BreadcrumbHeading and add unit tests by `@itisAliRH `_ in `#20618 `_ * Remove vue-tsc diff comparison from CI by `@dannon `_ in `#20620 `_ * Add a "Debug" (email report) tab to Workflow Invocations by `@ahmedhamidawan `_ in `#20624 `_ * Clean up code from pyupgrade by `@nsoranzo `_ in `#20642 `_ * Update location of latest tpv shared db by `@nuwang `_ in `#20651 `_ * Update Python dependencies by `@galaxybot `_ in `#20653 `_ * Add markdown hint to schema by `@bgruening `_ in `#20654 `_ * Update tiffviewer visualization to version 0.0.3 by `@davelopez `_ in `#20658 `_ * Improve GCard visibility handling and type definitions by `@itisAliRH `_ in `#20663 `_ * Removes `entries` from purged filter label in history grid by `@guerler `_ in `#20664 `_ * Unify History export UX using wizard by `@davelopez `_ in `#20666 `_ * Sort collection dialog by HID descending. by `@jmchilton `_ in `#20674 `_ * Update Python dependencies by `@galaxybot `_ in `#20680 `_ * Fix resource watcher composable race condition by `@davelopez `_ in `#20690 `_ * Add special case for BAM files in RStudio by `@bgruening `_ in `#20692 `_ * Add `fsspec` base implementation for File Source plugins by `@davelopez `_ in `#20698 `_ * Update Python dependencies by `@galaxybot `_ in `#20699 `_ * Add more info to inheritance chain by `@arash77 `_ in `#20701 `_ * History Components Navigation/Heading Improvements by `@itisAliRH `_ in `#20702 `_ * Improve cli and slurmcli runner traceability for job status and failure reasons by `@selten `_ in `#20717 `_ * Attempt to reuse previously materialized datasets by `@mvdbeek `_ in `#20718 `_ * Make workflow invocation tabs routable by `@ahmedhamidawan `_ in `#20719 `_ * Drop ucsc test server from sample build sites by `@mvdbeek `_ in `#20723 `_ * Refactor Files Sources Framework for stronger typing using pydantic models by `@davelopez `_ in `#20728 `_ * Hierarchical display collection dataset states by `@mvdbeek `_ in `#20731 `_ * Update Python dependencies by `@galaxybot `_ in `#20732 `_ * Fix Client Linting Run Error by `@itisAliRH `_ in `#20734 `_ * Add embed-compatible view for galaxy pages by `@dannon `_ in `#20737 `_ * Make invocations panel reactive using the invocation store by `@ahmedhamidawan `_ in `#20738 `_ * New History List Using GCard by `@itisAliRH `_ in `#20744 `_ * Change Advanced Tool Search to a Tool Discovery View by `@ahmedhamidawan `_ in `#20747 `_ * Update Python dependencies by `@galaxybot `_ in `#20753 `_ * Consolidate visualization mako, avoid user agent styles by `@guerler `_ in `#20760 `_ * Add configfiles support and various enhancements for user defined tools by `@mvdbeek `_ in `#20761 `_ * Fix WorkflowComment tests warnings by `@davelopez `_ in `#20762 `_ * A production data types checklist to aid creating/reviewing new data types by `@jmchilton `_ in `#20768 `_ * Fail Jest tests on warn/error console logging. by `@jmchilton `_ in `#20770 `_ * Modernize and Refactor Tour components by `@ahmedhamidawan `_ in `#20771 `_ * Increase wait time (retry) in UCSC data source test by `@davelopez `_ in `#20772 `_ * Drop old load_workflow controller method, use API by `@mvdbeek `_ in `#20774 `_ * Apply eslint fixes by `@mvdbeek `_ in `#20775 `_ * Allow fine-grained selection of included files in Invocation Export Wizard by `@davelopez `_ in `#20776 `_ * Stabilize client build after client-dev-server by `@davelopez `_ in `#20777 `_ * Update Python dependencies by `@galaxybot `_ in `#20779 `_ * Remove Backbone from UI bootstrap initialization by `@guerler `_ in `#20786 `_ * Adapt S3 file source to fsspec by `@davelopez `_ in `#20794 `_ * Remove Backbone dependency from webhook wrappers by `@guerler `_ in `#20797 `_ * Fix fsspec fs path handling by `@davelopez `_ in `#20799 `_ * Add Hugging Face 🤗 file source and user-defined template by `@davelopez `_ in `#20805 `_ * Refactor MESSAGES constant in FileSourceTypeSpan.vue by `@davelopez `_ in `#20806 `_ * Fix new linting errors in unit test mounts by `@davelopez `_ in `#20807 `_ * Update Python dependencies by `@galaxybot `_ in `#20812 `_ * Enable data label column selection in basic Plotly plots and add heatmap by `@guerler `_ in `#20813 `_ * Upgrade Prettier 3 by `@dannon `_ in `#20815 `_ * Update 2 docs pages by `@nsoranzo `_ in `#20824 `_ * Add small improvements for running CWL tools by `@nsoranzo `_ in `#20826 `_ * Bump jspdf from 2.5.1 to 3.0.2 in /client by `@dependabot[bot] `_ in `#20828 `_ * Migrate icon defs in CollectionOperations.vue to best practices. by `@jmchilton `_ in `#20829 `_ * Update pytest to v8 by `@nsoranzo `_ in `#20838 `_ * Modernize tools in the filters/ dir by `@natefoo `_ in `#20840 `_ * Update Python dependencies by `@galaxybot `_ in `#20841 `_ * Update Integration tests by `@nsoranzo `_ in `#20844 `_ * Allow adding extra steps to the default pipeline of the OIDC authentication by `@marius-mather `_ in `#20845 `_ * Use a streaming based parser (ijson) when setting metadata for biom1 files. by `@ksuderman `_ in `#20851 `_ * Support remote file source hashes by `@davelopez `_ in `#20853 `_ * Various Container Execution Enhancements (including GCP Batch support) by `@jmchilton `_ in `#20862 `_ * Update maf tools with profiles, required_files, and requirements. by `@natefoo `_ in `#20865 `_ * Add support for hierarchical module systems in lmod + module dependency resolvers by `@t1mk1k `_ in `#20866 `_ * Replace tour_generator webhook with internal API and frontend by `@ahmedhamidawan `_ in `#20868 `_ * Update Python dependencies by `@galaxybot `_ in `#20869 `_ * Improve type annotation for job runners and ``InteractiveToolManager`` by `@nsoranzo `_ in `#20871 `_ * Add axt and maf to auto_compressed_types by `@richard-burhans `_ in `#20875 `_ * Drop Python helper script from sort1 tool by `@nsoranzo `_ in `#20876 `_ * Update JupyterLite version to 0.6.4 by `@guerler `_ in `#20877 `_ * Add visualization navigation guard by `@dannon `_ in `#20881 `_ * Add main tool CI tests by `@nsoranzo `_ in `#20884 `_ * Bump vite from 6.3.5 to 6.3.6 in /client-api by `@dependabot[bot] `_ in `#20885 `_ * Set default option to make datasets accessible only to individual users when sharing histories with particular users by `@davelopez `_ in `#20886 `_ * Refactor sharing logic for unified type handling by `@davelopez `_ in `#20888 `_ * Replace deprecated ``codecs.open()`` by `@nsoranzo `_ in `#20891 `_ * Small cleanup of tool execution code. by `@jmchilton `_ in `#20899 `_ * Update Python dependencies by `@galaxybot `_ in `#20905 `_ * Add Multiple Sequence Alignment Viewer 2.0 by `@guerler `_ in `#20907 `_ * Improve Invocation View step display by `@ahmedhamidawan `_ in `#20912 `_ * Allow creation of visualizations without dataset by `@guerler `_ in `#20914 `_ * Enable dependabot version updates for GitHub actions by `@nsoranzo `_ in `#20915 `_ * Add support for picking ``from_work_dir`` directory by `@mvdbeek `_ in `#20916 `_ * Include format in internal json model by `@mvdbeek `_ in `#20917 `_ * Bump docker/login-action from 2 to 3 by `@dependabot[bot] `_ in `#20918 `_ * Bump docker/build-push-action from 4 to 6 by `@dependabot[bot] `_ in `#20919 `_ * Bump actions/setup-node from 4 to 5 by `@dependabot[bot] `_ in `#20921 `_ * Bump docker/setup-buildx-action from 2 to 3 by `@dependabot[bot] `_ in `#20922 `_ * Add tool to add nesting level to collection by `@bernt-matthias `_ in `#20926 `_ * Update Python dependencies by `@galaxybot `_ in `#20930 `_ * Make jupyterlite default visualization for ipynb by `@guerler `_ in `#20931 `_ * Allow addressing user defined tools in job config by `@mvdbeek `_ in `#20932 `_ * Wire up and test resource requirement via tpv by `@mvdbeek `_ in `#20936 `_ * Bump actions/checkout from 4 to 5 by `@dependabot[bot] `_ in `#20937 `_ * Bump peter-evans/create-pull-request from 6 to 7 by `@dependabot[bot] `_ in `#20938 `_ * Bump docker/metadata-action from 4 to 5 by `@dependabot[bot] `_ in `#20939 `_ * Bump actions/setup-python from 5 to 6 by `@dependabot[bot] `_ in `#20940 `_ * Bump actions/github-script from 7 to 8 by `@dependabot[bot] `_ in `#20941 `_ * Adds IGV.js Visualization by `@guerler `_ in `#20943 `_ * Add a dedicated `ToolFormTags` component for tool form output tags by `@ahmedhamidawan `_ in `#20945 `_ * Limit admin requirement of selected tool data api endpoints by `@guerler `_ in `#20949 `_ * Add resource docs and tweak tool source schema title generation by `@mvdbeek `_ in `#20951 `_ * Allow specifying a command for determining a docker host port by `@natefoo `_ in `#20953 `_ * Allow sending and tracking landing request origin by `@mvdbeek `_ in `#20957 `_ * Track landing request with invocation by `@mvdbeek `_ in `#20960 `_ * Use nodejs-wheel to install node by `@mvdbeek `_ in `#20963 `_ * Move tours schema to schema directory (to fix package structure) by `@ahmedhamidawan `_ in `#20965 `_ * Update Python dependencies by `@galaxybot `_ in `#20968 `_ * Log task execution errors with log.exception by `@mvdbeek `_ in `#20970 `_ * Bump actions/labeler from 5 to 6 by `@dependabot[bot] `_ in `#20976 `_ * Simplify plugin staging with explicit clean step by `@dannon `_ in `#20983 `_ * Bump vitessce to 3.8.2 by `@guerler `_ in `#21003 `_ * Update Python dependencies by `@galaxybot `_ in `#21005 `_ * Fix and migrate HIV-TRACE to Charts Visualization Framework by `@guerler `_ in `#21006 `_ * Add README and update the minimal visualization example by `@guerler `_ in `#21007 `_ * Add freq.json datatype subclass by `@guerler `_ in `#21012 `_ * Bump up total-perspective-vortex dependency by `@mvdbeek `_ in `#21014 `_ * Fix GCard Layout and White Spaces by `@itisAliRH `_ in `#21026 `_ * Add Keyboard Navigation to History Lists by `@itisAliRH `_ in `#21035 `_ * Add 2 net utilities to the min image by `@afgane `_ in `#21085 `_ * Use workflow-style payload in data landing request by `@mvdbeek `_ in `#21107 `_ * Release notes by `@ahmedhamidawan `_ in `#21162 `_ * Add Release Drafter GitHub Action integration by `@dannon `_ in `#21195 `_ * Tighter API for tool run tagging. by `@jmchilton `_ in `#21210 `_ * Makes "set as current" the primary action in history list by `@davelopez `_ in `#21233 `_ * Optimize /api/invocations/steps/{step_id} by `@mvdbeek `_ in `#21249 `_ * [igv] Allow selection of genomes from history fasta/2bit by `@guerler `_ in `#21269 `_ * Update tool profile version for credentials by `@davelopez `_ in `#21273 `_ * New datatype addition: HAL by `@SaimMomin12 `_ in `#21379 `_ * Add PNTS datatype for 3D Tiles Point Cloud by `@kgerb `_ in `#21414 `_ * A better way to designate config_watcher by `@jdavcs `_ in `#21426 `_ * Optionally include column headers in sample sheet file by `@mvdbeek `_ in `#21439 `_ ============= Other changes ============= * Small tweaks and cleanup from sample sheets branch by `@jmchilton `_ in `#20229 `_ * Version 25.1.dev by `@ahmedhamidawan `_ in `#20268 `_ * Merge `release_25.0` into `dev` by `@davelopez `_ in `#20484 `_ * Merge release_25.0 into dev by `@davelopez `_ in `#20490 `_ * Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by `@dependabot[bot] `_ in `#20591 `_ * Bump linkifyjs from 4.1.1 to 4.3.2 in /client by `@dependabot[bot] `_ in `#20707 `_ * 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 `_ * Implement bare-bones view of sample sheet collections as sheet. by `@jmchilton `_ in `#20798 `_ * Fix webpack dev server detection by `@mvdbeek `_ in `#20822 `_ * Fix optional numeric column definitions for sample sheets. by `@jmchilton `_ in `#20830 `_ * Validate sample sheet column definitions in workflow definitions on backend. by `@jmchilton `_ in `#20880 `_ * Bump axios from 1.8.2 to 1.12.0 in /client by `@dependabot[bot] `_ in `#20906 `_ * Merge 25.0 into dev by `@ahmedhamidawan `_ in `#20911 `_ * Bump default milestone to 26.0 by `@ahmedhamidawan `_ in `#20946 `_ * Add 25.1 migration tags by `@ahmedhamidawan `_ in `#21017 `_ * Update version to 25.1.rc1 by `@ahmedhamidawan `_ in `#21019 `_ * Restore .get_metadata function by `@mvdbeek `_ in `#21045 `_ * Fix ``TOOL_WITH_SHELL_COMMAND`` import source by `@mvdbeek `_ in `#21070 `_ * Drop fastapi extra dep from sentry-sdk by `@mvdbeek `_ in `#21156 `_ * Resolve possible symlink before establishing tool file location by `@mvdbeek `_ in `#21175 `_ * 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 `_ * Fix select field cut off in dataset view by `@ahmedhamidawan `_ in `#20947 `_ * Check for expiration in refresh token dictionary by `@jdavcs `_ in `#20954 `_ * Deactivate user file source on unknown error by `@mvdbeek `_ in `#20962 `_ * Don't create workflow outputs to recover input parameter outputs by `@mvdbeek `_ in `#20980 `_ * Fix ``test_multiple_decorators`` unit test for FastAPI 0.118.0 by `@nsoranzo `_ in `#20982 `_ * Fix PUT /api/workflows for user defined tools by `@mvdbeek `_ in `#20987 `_ * Backport of #20984 by `@davelopez `_ in `#20994 `_ * Improves zip file type detection for uploads under windows by `@caroott `_ in `#20999 `_ * Store pulsar job prep error messages by `@mvdbeek `_ in `#21013 `_ * Require OK datasets for filtering empty datasets by `@bernt-matthias `_ in `#21023 `_ * Fix `InvalidRequestError` when saving workflow step with dynamic tool by `@mvdbeek `_ in `#21056 `_ * Fix has_size assertion by `@bernt-matthias `_ in `#21081 `_ * Run landing request state through validator by `@mvdbeek `_ in `#21087 `_ * Fix workflow run form input restrictions by `@mvdbeek `_ in `#21095 `_ * Backport fix anndata datatype update by `@nilchia `_ in `#21111 `_ * Prefix download link by `@martenson `_ in `#21112 `_ * Create new datasets when creating skipped database operation tool outputs by `@mvdbeek `_ in `#21142 `_ * Fix workflow landing rendering if public query param not provided by `@mvdbeek `_ in `#21165 `_ * Fix optional param unset in RO-Crate export by `@davelopez `_ in `#21192 `_ * Fix MIME type for LAZ datatype by `@kysrpex `_ in `#21202 `_ * Fix refresh token expiration retrieval logic by `@nuwang `_ in `#21213 `_ * Fix direct tool execution not using the latest version by `@jmchilton `_ in `#21240 `_ * Fix proxy url validation for non-printable characters by `@davelopez `_ in `#21280 `_ * Swap to NPM trusted publishing for prebuilt client by `@dannon `_ in `#21290 `_ ============ 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 `_ * Add LAS and LAZ file format by `@bgruening `_ in `#21049 `_ * New datatype addition: gam for vg toolkit by `@SaimMomin12 `_ in `#21096 `_ * Harden proxy redirect validation by `@davelopez `_ in `#21185 `_ * support ZARR v3 for Spatialdata dt by `@nilchia `_ in `#21265 `_ ============= Other changes ============= * New datatype addition: beast.trees datatype by `@SaimMomin12 `_ in `#21055 `_ * Add display_in_upload to LAZ and LAS by `@bgruening `_ in `#21060 `_ * Backport `Fix proxy endpoint encoding` by `@davelopez `_ in `#21184 `_ ------------------- 25.0.3 (2025-09-23) ------------------- ========= Bug fixes ========= * Cascade newly created windows in window manager by `@guerler `_ in `#20780 `_ * Remove ``packages/meta/requirements.txt`` by `@nsoranzo `_ in `#20782 `_ * Ensure that workflow invocations are persisted with state by `@mvdbeek `_ in `#20784 `_ * Fix password reset functionality for lowercase emails by `@jdavcs `_ in `#20801 `_ * Fix token refresh bug (cilogon) by `@jdavcs `_ in `#20821 `_ * Disable Run Tool button when there are errors by `@ahmedhamidawan `_ in `#20839 `_ * Update Celery section in admin docs by `@jdavcs `_ in `#20856 `_ * Drop eager argument from invocation related methods by `@mvdbeek `_ in `#20863 `_ * Improve dataset collection fetch performance in the invocation view by `@ahmedhamidawan `_ in `#20870 `_ * Use ``populated_optimized`` when serializing collection by `@mvdbeek `_ in `#20872 `_ * Fix role.description bug by `@jdavcs `_ in `#20883 `_ * Speed up ``ImplicitCollectionJobs.job_list`` by `@mvdbeek `_ in `#20887 `_ * Bump up integration test k8s version by `@mvdbeek `_ in `#20889 `_ * Make check for existing user in custos_authnz.py case insensitive by `@cat-bro `_ in `#20893 `_ * 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 `_ * Fix collection element sorting in extended_metadata by `@mvdbeek `_ in `#20928 `_ ============ Enhancements ============ * Render Tool Descriptions in Markdown in TRS imports by `@itisAliRH `_ in `#20814 `_ * Fix DOCX detection and add PPTX support by `@arash77 `_ in `#20827 `_ * Include galaxy user agent in data source tools by `@mvdbeek `_ in `#20836 `_ * 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 `_ * Bump up python for for pulsar package tests by `@mvdbeek `_ in `#20521 `_ * Update Gravity to 1.0.8 by `@natefoo `_ in `#20523 `_ * Prevent DCE collections from being renamed by `@ahmedhamidawan `_ in `#20534 `_ * Use venv instead of virtualenv in package `make setup-venv` by `@natefoo `_ in `#20536 `_ * Move definition of ``DatasetCollectionDescriptionT`` before its use by `@nsoranzo `_ in `#20539 `_ * Fix docs versioning by `@nsoranzo `_ in `#20542 `_ * Fix restricting user defined tool input datasets extensions by `@mvdbeek `_ in `#20545 `_ * Fix description and metadata of some packages by `@nsoranzo `_ in `#20546 `_ * Fix activity bar reordering persistence by `@dannon `_ in `#20550 `_ * Fix PDF preview functionality in dataset view by `@dannon `_ in `#20552 `_ * Propagate cached job output replacement to copies of outputs by `@mvdbeek `_ in `#20553 `_ * Fix workflow invocation report pdf generate by `@itisAliRH `_ in `#20558 `_ * Fix Storage Dashboard Link to Dataset Details by `@itisAliRH `_ in `#20565 `_ * Upgrade requests-unixsocket for requests compatibility by `@natefoo `_ in `#20566 `_ * Don't assume cwd = job directory when running prepare dirs by `@natefoo `_ in `#20571 `_ * Fix planemo serve, need user list by `@mvdbeek `_ in `#20575 `_ * Fix apply rules ownership check by `@mvdbeek `_ in `#20582 `_ * Don't fail volume mount construction for tools without tool directory by `@mvdbeek `_ in `#20593 `_ * Prevent importing workflows with invalid step UUID by `@davelopez `_ in `#20596 `_ * Fix workflow loading error handling by `@davelopez `_ in `#20597 `_ * Do not set attribute on a namedtuple by `@jdavcs `_ in `#20599 `_ * Constraint conditional `redis` version to allow only minor updates by `@davelopez `_ in `#20603 `_ * fix Admin job limit query by `@martenson `_ in `#20626 `_ * Correct visualization response schema by `@guerler `_ in `#20627 `_ * Ignore webob http exceptions for logging purposes by `@mvdbeek `_ in `#20630 `_ * Fix HistoryDatasetAsTable by `@mvdbeek `_ in `#20636 `_ * Fix bug: tool output file may be overwritten by Runner's multi work t… by `@jianzuoyi `_ in `#20639 `_ * Fix IntersectionObserver updates when replacing items by `@davelopez `_ in `#20646 `_ * Fix optional unspecified input to conditional step by `@mvdbeek `_ in `#20647 `_ * Avoid postgres truncation of aliases and labels by `@mvdbeek `_ in `#20649 `_ * Fix deferred datasets in multiple dataset parameters. by `@jmchilton `_ in `#20650 `_ * Fix empty default Optionals for tool_shed_repositories API. by `@jmchilton `_ in `#20656 `_ * Remove content from ``packages/meta/requirements.txt`` by `@nsoranzo `_ in `#20662 `_ * Add `num_unique_values` tiff metadata element, fixed by `@kostrykin `_ in `#20669 `_ * Bump up pulsar dependency to 0.15.9 by `@mvdbeek `_ in `#20672 `_ * Fix invocation header by `@qchiujunhao `_ in `#20676 `_ * Fix scratchbook display by `@dannon `_ in `#20684 `_ * Fix Invenio file downloads for published records with draft by `@davelopez `_ in `#20685 `_ * Input linter: add missing attribute to `sort_by` by `@bernt-matthias `_ in `#20693 `_ * Fix dataset serializers and response models by `@arash77 `_ in `#20694 `_ * Add username filter to published pages grid by `@ahmedhamidawan `_ in `#20703 `_ * Fix parameter models for optional color params. by `@jmchilton `_ in `#20705 `_ * Prevent negative offset in historyStore handleTotalCountChange by `@davelopez `_ in `#20708 `_ * Fix click to edit link by `@mvdbeek `_ in `#20710 `_ * Fix ``test_base_image_for_targets`` mulled test to use mzmine by `@nsoranzo `_ in `#20713 `_ * DatasetView Header - fixes text wrapping issues on small screens by `@dannon `_ in `#20721 `_ * Update galaxy-release-util by `@mvdbeek `_ in `#20727 `_ * Fix maximum workflow invocation duration test by `@mvdbeek `_ in `#20729 `_ * Remove base_dir from zip in make_fast_zipfile by `@davelopez `_ in `#20739 `_ * fix config for nginx in docs by `@martenson `_ in `#20757 `_ ============ Enhancements ============ * add fasta.bz2 as auto_compressed type by `@bernt-matthias `_ in `#20496 `_ * Add redis conditional dependency by `@davelopez `_ in `#20502 `_ * Improve workflow monitor loop times by `@mvdbeek `_ in `#20522 `_ * Add datatype for LexicMap index by `@Smeds `_ in `#20586 `_ * Clarify how to separate job and workflow scheduling by `@mvdbeek `_ in `#20625 `_ * Add mzMLb and MBI datatypes by `@chambm `_ in `#20632 `_ * Pairtool updated format and sniffers by `@Smeds `_ in `#20634 `_ * Add support for M4A audio files by `@arash77 `_ in `#20667 `_ ============= Other changes ============= * Require user for visualizations create endpoint by `@mvdbeek `_ in `#20629 `_ * Merge 24.2 into 25.0 by `@ahmedhamidawan `_ in `#20681 `_ ------------------- 25.0.1 (2025-06-20) ------------------- ========= Bug fixes ========= * Fix single data element identifier to be a regular string by `@mvdbeek `_ in `#20438 `_ * Relax validation of XML test assertion parsing by `@mvdbeek `_ in `#20511 `_ * Add id-token: write for npm publishing by `@mvdbeek `_ in `#20519 `_ * Do not expose user info to non authenticated users by `@bernt-matthias `_ in `#20524 `_ * names of package extras cannot contain underscores by `@mr-c `_ in `#20525 `_ * Pin isa-rwval 0.10.11, drop conditional import handling by `@natefoo `_ in `#20527 `_ * Fix import of ``galaxy.tool_util.cwl`` module by `@nsoranzo `_ in `#20529 `_ * Fix `galaxy-config` script, move install to `galaxy-dependencies` in app package by `@natefoo `_ in `#20531 `_ ============ Enhancements ============ * Bump gravity dependency to 1.1.0 by `@mvdbeek `_ in `#20520 `_ * Update the dev package build and install script by `@natefoo `_ in `#20526 `_ ============= Other changes ============= * Merge Release 25.0 into the master branch by `@ahmedhamidawan `_ in `#20514 `_ * Fixes for static handling and the web_client package by `@natefoo `_ in `#20516 `_ * Fix link in user release notes by `@bgruening `_ in `#20518 `_ * Bump Gravity to 1.1.1 by `@natefoo `_ in `#20533 `_ ------------------- 25.0.0 (2025-06-18) ------------------- ========= Bug fixes ========= * Stabilize HistoryView.test.js by `@jmchilton `_ in `#19165 `_ * Cleanup Jest Test Output (part 2) by `@jmchilton `_ in `#19178 `_ * Fix Pesky warning with PersistentTaskProgressMonitorAlert.test.ts by `@ElectronicBlueberry `_ in `#19180 `_ * Cleanup Jest Test Output (part 3) by `@jmchilton `_ in `#19185 `_ * Cleanup Jest Test Output (part 4) by `@jmchilton `_ in `#19186 `_ * Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by `@dependabot[bot] `_ in `#19189 `_ * Don't calculate dataset hash for datasets in non-OK state by `@nsoranzo `_ in `#19191 `_ * Cleanup test output console for tool panel tests. by `@jmchilton `_ in `#19210 `_ * Update Vizarr package version to 0.1.6 by `@davelopez `_ in `#19228 `_ * Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by `@dependabot[bot] `_ in `#19233 `_ * Use ``resource_path()`` to access datatypes_conf.xml.sample as a package resource by `@nsoranzo `_ in `#19331 `_ * Require importlib-resources also for Python 3.9-3.11 by `@nsoranzo `_ in `#19358 `_ * Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by `@dependabot[bot] `_ in `#19369 `_ * Node 22 unreachable fixes by `@mvdbeek `_ in `#19378 `_ * 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 `_ * Display email activation help only if user activation is enabled by `@jdavcs `_ in `#19402 `_ * Prevent negative offset by `@jdavcs `_ in `#19409 `_ * Avoid using custos refresh tokens which are expired by `@martenson `_ in `#19411 `_ * Fix wrong id in test_combined_mapping_and_subcollection_mapping by `@mvdbeek `_ in `#19481 `_ * Fix preferred object store id reactivity by `@ElectronicBlueberry `_ in `#19491 `_ * Fix wrong URI written to `ExportObjectResultMetadata` when exporting histories to eLabFTW by `@kysrpex `_ in `#19541 `_ * Fix `test_mulled_build.py::test_mulled_build_files_cli` with `use_mamba=True` by `@kysrpex `_ in `#19545 `_ * Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by `@jdavcs `_ in `#19620 `_ * Update eLabFTW file source template docs by `@kysrpex `_ in `#19632 `_ * Fix more vue tsc indicated type issues by `@jmchilton `_ in `#19650 `_ * Yet More Vue Typing Error Fixes by `@jmchilton `_ in `#19680 `_ * Fix incorrect type in tool_util.deps and fix package structure. by `@jmchilton `_ in `#19702 `_ * Add linter argument to linter report function calls by `@bernt-matthias `_ in `#19708 `_ * Refactor tool panel handling, resolve transiently failing jest test by `@guerler `_ in `#19733 `_ * Jest Cleanup (Part 5) by `@jmchilton `_ in `#19743 `_ * Use fissix also when python3-lib2to3 is not installed by `@nsoranzo `_ in `#19749 `_ * Fix setting env and tags on resubmission by `@bernt-matthias `_ in `#19753 `_ * Revise consistently failing edam tool panel view test. by `@jmchilton `_ in `#19762 `_ * Add missing tool test file by `@jmchilton `_ in `#19763 `_ * Bump axios from 1.7.4 to 1.8.2 in /client by `@dependabot[bot] `_ in `#19773 `_ * Fix wording of API doc string by `@bernt-matthias `_ in `#19776 `_ * Add better `WorkflowSummary` type by `@ahmedhamidawan `_ in `#19779 `_ * Fix workflow run graph non input steps not appearing bug by `@ahmedhamidawan `_ in `#19781 `_ * Update webdav user file source template help text by `@sanjaysrikakulam `_ in `#19784 `_ * HelpText improvements (content, sizing) and WorkflowInvocationHeader tweaks. by `@dannon `_ in `#19792 `_ * Remove unused (define* - compiler macro) imports from TextEditor.vue by `@dannon `_ in `#19793 `_ * Fix Selenium workflow tests not updating param type properly. by `@jmchilton `_ in `#19810 `_ * Fix Galaxy ignoring job object_store_id for quota check by `@bernt-matthias `_ in `#19854 `_ * Cleanup circular dependencies around utils.ts. by `@jmchilton `_ in `#19857 `_ * Remove circular dependency around user store. by `@jmchilton `_ in `#19859 `_ * Move some store types out into own file to reduce circular dependencies. by `@jmchilton `_ in `#19860 `_ * Fix most new vue typescript errors discovered in #19851 by `@jmchilton `_ in `#19862 `_ * Create rucio.cfg from inside Rucio objectstore by `@SergeyYakubov `_ in `#19863 `_ * Fix broken optimisation introduced in #19852 by `@nsoranzo `_ in `#19871 `_ * 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 FA Component (w/svg) instead of span+font in RunWorkflow header by `@dannon `_ in `#19901 `_ * Change wording in the google drive user file source template by `@sanjaysrikakulam `_ in `#19927 `_ * Move `FormBoolean` back to `FormElement` field in workflow run form by `@ahmedhamidawan `_ in `#19938 `_ * Fix ``test_in_directory`` on osx by `@mvdbeek `_ in `#19943 `_ * Fix adding tags popup closing logic on focus out by `@itisAliRH `_ in `#19950 `_ * Use lower case extension for setting datatype in data discovery by `@bernt-matthias `_ in `#19954 `_ * Fix ownership check in history contents update route by `@mvdbeek `_ in `#19969 `_ * Remove hgv_sift from tool_conf.xml.sample by `@natefoo `_ in `#19972 `_ * Unwind more client dependencies at top of stack. by `@jmchilton `_ in `#19983 `_ * Fix `keyedCache` never allowing multiple fetches by `@ahmedhamidawan `_ in `#20020 `_ * Pass host url to visualizations by `@guerler `_ in `#20022 `_ * Also chown R lib in RStudio BioC tool by `@natefoo `_ in `#20025 `_ * Add new line to vtpascii test file by `@guerler `_ in `#20051 `_ * Fix linting with markdown in tool help by `@bgruening `_ in `#20058 `_ * Update breadcrumb item 'to' type for better routing support by `@itisAliRH `_ in `#20065 `_ * Always render Outputs tab in invocation view by `@ahmedhamidawan `_ in `#20073 `_ * Remove collapse invocations panel on mouseleave feature by `@ahmedhamidawan `_ in `#20074 `_ * Bump http-proxy-middleware from 2.0.7 to 2.0.9 in /client by `@dependabot[bot] `_ in `#20086 `_ * Fix `test_workflow_run` export selenium by `@ahmedhamidawan `_ in `#20089 `_ * Fix and migrate Drawrna by `@guerler `_ in `#20102 `_ * Add hid to selection field in visualization creation form by `@guerler `_ in `#20108 `_ * Remove only the Docker images specific for the test by `@nsoranzo `_ in `#20109 `_ * Fixes for GButtons with disabled state by `@ahmedhamidawan `_ in `#20121 `_ * Sort visualization datasets by hid by `@guerler `_ in `#20123 `_ * Wait for Gbutton to become enabled by `@mvdbeek `_ in `#20131 `_ * Allow deferred and ok state datasets for vis by `@guerler `_ in `#20143 `_ * Fix certain cases of collection parameter handling during workflow execution. by `@jmchilton `_ in `#20152 `_ * Yaml parser fixes part2 by `@mvdbeek `_ in `#20162 `_ * Fix tapis module typing errors by `@jdavcs `_ in `#20175 `_ * Use ``backports.zoneinfo`` in ``job_metrics`` package under Python <3.9 by `@nsoranzo `_ in `#20178 `_ * Update tabular_csv.py to use less memory in tsv->csv conversion by `@cat-bro `_ in `#20187 `_ * Corrects header levels in Visualization Help Markdown by `@guerler `_ in `#20199 `_ * Move UnprivilegedToolResponse into api by `@mvdbeek `_ in `#20207 `_ * Package fixes by `@nsoranzo `_ in `#20208 `_ * Fix NFDI auth by `@bgruening `_ in `#20217 `_ * Fix next milestone by `@martenson `_ in `#20219 `_ * Group Tool Versions in IT Panel by `@dannon `_ in `#20244 `_ * Fix vue-tsc issue in ParameterStep by `@dannon `_ in `#20245 `_ * Replace Bootstrap Popover with Popper wrapper by `@guerler `_ in `#20246 `_ * Fix tool-provided metadata for CONVERTER_tar_to_directory by `@mr-c `_ in `#20260 `_ * Fix theme selector by `@guerler `_ in `#20275 `_ * Fix interactive activity highlighting by `@guerler `_ in `#20276 `_ * Fix inconsistent header sizes by `@guerler `_ in `#20277 `_ * Add non-dev httpx dependency by `@mvdbeek `_ in `#20281 `_ * Remove duplicated job id in job success view by `@ahmedhamidawan `_ in `#20289 `_ * Skip multiple pasted URLs when checking for remote Zip by `@davelopez `_ in `#20300 `_ * Fix masthead logo height by `@guerler `_ in `#20302 `_ * Increase proxy API robustness by validating URL before use by `@davelopez `_ in `#20311 `_ * Rerun workflows for the correct version/instance by `@ahmedhamidawan `_ in `#20313 `_ * Avoid displaying dataset tab view in window manager by `@guerler `_ in `#20317 `_ * Fix display urls by `@dannon `_ in `#20318 `_ * Fix workflow bookmark filtering by `@davelopez `_ in `#20325 `_ * Add test for workflow instance download fix by `@ahmedhamidawan `_ in `#20326 `_ * Add basic validation to workflow creator attribute by `@jdavcs `_ in `#20328 `_ * Fix broken admin navigation option and add missing menu items by `@dannon `_ in `#20333 `_ * Error on duplicate labels by `@ElectronicBlueberry `_ in `#20335 `_ * Small UI fixes for ag-grid based rule grid. by `@jmchilton `_ in `#20358 `_ * Fix selection issue when adding tags to workflows in bulk by `@davelopez `_ in `#20362 `_ * Log invalid vault paths by `@mvdbeek `_ in `#20363 `_ * Remove redundant badge when creating collection from upload by `@ahmedhamidawan `_ in `#20367 `_ * Make invocation errors more compact by `@ahmedhamidawan `_ in `#20369 `_ * Generate a tenant-unique UID for tapis. by `@dannon `_ in `#20370 `_ * Use router to route to creating a new file source by `@ahmedhamidawan `_ in `#20374 `_ * Fix radio button options in CopyModal by `@davelopez `_ in `#20378 `_ * Fix conda_link to use platform.machine() for architecture detection by `@chrisagrams `_ in `#20381 `_ * Fix create file source button, show only at root by `@davelopez `_ in `#20385 `_ * Force Monaco into a separate bundle by `@dannon `_ in `#20396 `_ * Prevent waiting for history item state to be ok in uploader by `@ahmedhamidawan `_ in `#20397 `_ * Fix toolshed-installed tool icons by `@dannon `_ in `#20399 `_ * Add job config variable for singularity `--contain` by `@bernt-matthias `_ in `#20400 `_ * Fix form select input sorting by `@davelopez `_ in `#20401 `_ * Bug fix: allow any collection type in FormCollectionType. by `@jmchilton `_ in `#20403 `_ * Fixes for the admin jobs interface by `@martenson `_ in `#20405 `_ * Fix $app attribute access in cheetah templates by `@mvdbeek `_ in `#20414 `_ * Fix job rerun with tool version change by `@mvdbeek `_ in `#20417 `_ * Update pulsar-galaxy-lib to 0.15.8 by `@mvdbeek `_ in `#20419 `_ * Update triggers by `@jdavcs `_ in `#20425 `_ * Fix workflow logo URL not being persisted. by `@jmchilton `_ in `#20428 `_ * Fix css alignment styling of login page by `@ahmedhamidawan `_ in `#20429 `_ * Add user-facing explanation for legacy workflow run form usage by `@ahmedhamidawan `_ in `#20431 `_ * Upgrade tensorflow conditional dependency version to 2.15.1 by `@cat-bro `_ in `#20434 `_ * Fix copying of job metrics for cached jobs by `@mvdbeek `_ in `#20436 `_ * Dataset Display and Preferred Viz fixes by `@dannon `_ in `#20439 `_ * Wrap Tool and Workflow run headers properly by `@ahmedhamidawan `_ in `#20440 `_ * Fix inconsistent styling in List Collection Builder selector by `@ahmedhamidawan `_ in `#20442 `_ * Fix add button is enabled when empty tag list by `@davelopez `_ in `#20443 `_ * Set ``GALAXY_CONFIG_FILE`` env var if starting handler with `-c` by `@mvdbeek `_ in `#20449 `_ * Fix pagination state in FilesDialog by `@davelopez `_ in `#20452 `_ * Data Libraries - persist number of entries displayed in folders by `@dannon `_ in `#20455 `_ * Fix multiple remote file upload to collection creator by `@ahmedhamidawan `_ in `#20456 `_ * Bug fix: paired_or_unpaired also endswith paired. by `@jmchilton `_ in `#20458 `_ * Fix bug with handling compressed file names while auto-pairing. by `@jmchilton `_ in `#20459 `_ * Fix dataset error button not using router by `@ahmedhamidawan `_ in `#20472 `_ * Don't fit workflow if it doesn't have steps by `@mvdbeek `_ in `#20480 `_ * Remove rename modal from List Collection Creator by `@ahmedhamidawan `_ in `#20487 `_ * Use DatasetAsImage component for DatasetView image display by `@dannon `_ in `#20488 `_ * Recreate triggers by `@jdavcs `_ in `#20491 `_ * Allow workflow description to show full text by `@davelopez `_ in `#20500 `_ ============ Enhancements ============ * Dynamic options: add data table filter by `@bernt-matthias `_ in `#12941 `_ * Run the tool working dir backup/restore on Pulsar by `@natefoo `_ in `#16696 `_ * Strip galaxy filename annotation on upload by `@GomeChas `_ in `#18561 `_ * Isolate singularity containers more thoroughly for better reproducibility. by `@rhpvorderman `_ in `#18628 `_ * Upgrade bundled/requested node version to 22.15.0 by `@dannon `_ in `#18710 `_ * 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 `_ * Avoid persisting credentials on checkout step of the Github actions by `@arash77 `_ in `#19089 `_ * Let file sources choose a path for uploaded files by `@kysrpex `_ in `#19154 `_ * Move heatmap visualization to new script endpoint by `@guerler `_ in `#19176 `_ * Calculate hash for new non-deferred datasets when finishing a job by `@nsoranzo `_ in `#19181 `_ * Update Python dependencies by `@galaxybot `_ in `#19190 `_ * Move phylocanvas to script entry point by `@guerler `_ in `#19193 `_ * Fix UP031 errors - Part 1 by `@nsoranzo `_ in `#19194 `_ * Drop thumbs up reaction as pull request approval method by `@nsoranzo `_ in `#19202 `_ * Fix UP031 errors - Part 2 by `@nsoranzo `_ in `#19204 `_ * Add plotly.js by `@guerler `_ in `#19206 `_ * Switch h5web to script endpoint by `@guerler `_ in `#19211 `_ * Update visualizations to latest charts package by `@guerler `_ in `#19213 `_ * Fix UP031 errors - Part 3 by `@nsoranzo `_ in `#19218 `_ * Add Vitessce Viewer by `@guerler `_ in `#19227 `_ * Fix UP031 errors - Part 4 by `@nsoranzo `_ in `#19235 `_ * Explicitly add cwl-utils to dependencies by `@nsoranzo `_ in `#19257 `_ * Refactor for better reuse of workflow parameter type constants by `@nsoranzo `_ in `#19260 `_ * Fix UP031 errors - Part 5 by `@nsoranzo `_ in `#19282 `_ * Workflow Run Form Enhancements by `@ahmedhamidawan `_ in `#19294 `_ * Minor drag style adjustment for activities by `@guerler `_ in `#19299 `_ * Extract and typescript-ify datatype selection in wfeditor. by `@jmchilton `_ in `#19304 `_ * Migrate WF Collection Input Form Definition to Client Side by `@jmchilton `_ in `#19313 `_ * Fix UP031 errors - Part 6 by `@nsoranzo `_ in `#19314 `_ * eLabFTW integration via Galaxy file source by `@kysrpex `_ in `#19319 `_ * Update pydantic to 2.10.3 by `@nsoranzo `_ in `#19326 `_ * Add workflow selection and bulk actions by `@itisAliRH `_ in `#19336 `_ * Refactor and add tests for Popovers by `@guerler `_ in `#19337 `_ * Use popper wrapper for help text popover by `@guerler `_ in `#19340 `_ * Misc fixes 202412 by `@nsoranzo `_ in `#19341 `_ * Rework some form components for reuse. by `@jmchilton `_ in `#19347 `_ * Hide outdated visualizations from visualizations activity panel by `@guerler `_ in `#19353 `_ * Update Python dependencies by `@galaxybot `_ in `#19366 `_ * Add Dataverse RDM repository integration by `@KaiOnGitHub `_ in `#19367 `_ * Type annotation fixes for mypy 1.14.0 by `@nsoranzo `_ in `#19372 `_ * Make conditional discriminators literals instead of generic string/bool by `@mvdbeek `_ in `#19374 `_ * Empower Users to Build More Kinds of Collections, More Intelligently by `@jmchilton `_ in `#19377 `_ * Remove apptainer-version pin by `@nsoranzo `_ in `#19380 `_ * Clarify that extra_scopes is sometimes non-optional by `@martenson `_ in `#19385 `_ * SQLAlchemy 2.0 follow-up by `@jdavcs `_ in `#19388 `_ * Documentation around highlighting PRs for release notes. by `@jmchilton `_ in `#19390 `_ * Change galaxy system user uid for K8s image by `@afgane `_ in `#19403 `_ * Gulp build improvements, update. by `@dannon `_ in `#19405 `_ * 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 `_ * Irods objectstore templates by `@pauldg `_ in `#19415 `_ * Update Python dependencies by `@galaxybot `_ in `#19418 `_ * Enable cloning subworkflows by `@ElectronicBlueberry `_ in `#19420 `_ * Allow controlling strict channel priority in mulled-build by `@bernt-matthias `_ in `#19425 `_ * Add IGB display support for CRAM files by `@paige-kulzer `_ in `#19428 `_ * Document `$__user_name__` by `@bernt-matthias `_ in `#19433 `_ * Add User-Defined Tools by `@mvdbeek `_ in `#19434 `_ * Type annotations improvements by `@nsoranzo `_ in `#19442 `_ * Handles S3 listing errors by `@itisAliRH `_ in `#19446 `_ * Improve asynchronous tasks error handling and reporting by `@davelopez `_ in `#19448 `_ * Reset invocation export wizard after completion by `@davelopez `_ in `#19449 `_ * Workflow Editor Auto Zoom by `@ElectronicBlueberry `_ in `#19451 `_ * Update main citation to 2024 community paper by `@nsoranzo `_ in `#19453 `_ * Add test that verifies workflow source_metadata is preserved on landing claim by `@mvdbeek `_ in `#19454 `_ * Update Python dependencies by `@galaxybot `_ in `#19464 `_ * Type annotation improvements by `@nsoranzo `_ in `#19485 `_ * Add eLabFTW file source from file source templates by `@kysrpex `_ in `#19493 `_ * Update Python dependencies by `@galaxybot `_ in `#19510 `_ * Remote File Sources and Storage Locations redesign by `@itisAliRH `_ in `#19521 `_ * Support setting and displaying timezone with the core metrics plugin by `@natefoo `_ in `#19527 `_ * Allow to send notifications when Admins cancel jobs by `@davelopez `_ in `#19547 `_ * Add config options for tool dependency installs by `@afgane `_ in `#19565 `_ * Update Python dependencies by `@galaxybot `_ in `#19567 `_ * Remove tags used by `@ElectronicBlueberry `_ in `#19576 `_ * Support setting masthead height in a theme by `@ksuderman `_ in `#19581 `_ * Expand workflow metadata for readme. by `@jmchilton `_ in `#19591 `_ * Add vue-tsc baseline comparison to client-lint workflow by `@dannon `_ in `#19593 `_ * Add failed jobs working directory cleanup as a celery periodic task by `@sanjaysrikakulam `_ in `#19594 `_ * Enhance OpenAI Chat Integration by `@uwwint `_ in `#19612 `_ * Add InvenioRDM file source template by `@davelopez `_ in `#19619 `_ * Use discriminated unions in object stores and file source template configs by `@davelopez `_ in `#19621 `_ * Use correct `plugin_kind` in user file sources by `@davelopez `_ in `#19622 `_ * Update Python dependencies by `@galaxybot `_ in `#19623 `_ * Format code with black 25.1.0 by `@nsoranzo `_ in `#19625 `_ * Add Zenodo file source template by `@davelopez `_ in `#19638 `_ * Type annotation improvements by `@nsoranzo `_ in `#19642 `_ * Workflow landing request - collapse activity bar by default. by `@dannon `_ in `#19652 `_ * Enhance ListHeader Component for Reusability by `@itisAliRH `_ in `#19655 `_ * Add Breadcrumb Heading Component by `@itisAliRH `_ in `#19656 `_ * Mention default values for truevalue and falsevalue by `@pvanheus `_ in `#19657 `_ * Update test_create_dataset_in_subfolder to check for the dataset presence by `@davelopez `_ in `#19660 `_ * Relax job status check in test_delete_user_cancel_all_jobs by `@davelopez `_ in `#19661 `_ * Refactor dependencies for tool output actions. by `@jmchilton `_ in `#19662 `_ * More Vue Typescript Fixes by `@jmchilton `_ in `#19663 `_ * Click to edit history name in `HistoryPanel` by `@ahmedhamidawan `_ in `#19665 `_ * Generate correct types for Dataset source transformations on backend. by `@jmchilton `_ in `#19666 `_ * Remove unused(?) data_dialog form element type. by `@jmchilton `_ in `#19669 `_ * Add webdavclient3 to conditional-requirements.txt by `@bgruening `_ in `#19671 `_ * Update Python dependencies by `@galaxybot `_ in `#19682 `_ * Drop support for Python 3.8 by `@nsoranzo `_ in `#19685 `_ * Define simple models for job messages. by `@jmchilton `_ in `#19688 `_ * Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. by `@jaidevjoshi83 `_ in `#19689 `_ * Add forgotten linter test by `@bernt-matthias `_ in `#19690 `_ * Fix MarkdownDialog types by `@davelopez `_ in `#19703 `_ * Move RequiredAppT back into galaxy packages. by `@jmchilton `_ in `#19704 `_ * Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 1 by `@nsoranzo `_ in `#19706 `_ * Improved simplicity and isolation in transiently failing test. by `@jmchilton `_ in `#19709 `_ * Update RStudio IT by `@afgane `_ in `#19711 `_ * Speedup mulled build test by `@bernt-matthias `_ in `#19712 `_ * Update TypeScript version to 5.7.3 by `@davelopez `_ in `#19713 `_ * Augments popper wrapper, add click and escape handler by `@guerler `_ in `#19717 `_ * Move vega wrapper to shared common directory and add error handler by `@guerler `_ in `#19718 `_ * Move Markdown components to subdirectory for modularity by `@guerler `_ in `#19719 `_ * Rucio templates by `@SergeyYakubov `_ in `#19720 `_ * Preserve workflow labels in final invocation reports by `@guerler `_ in `#19721 `_ * ToolShed 2.1 - Various bugfixes and enhancements. by `@jmchilton `_ in `#19722 `_ * Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 2 by `@nsoranzo `_ in `#19726 `_ * Update Python dependencies by `@galaxybot `_ in `#19727 `_ * Add a script to reorganize tool data based on the new layout for genomic Data Managers by `@natefoo `_ in `#19728 `_ * Move history watcher and minor fixes by `@guerler `_ in `#19732 `_ * Fix Tours and add tooltips to history items by `@guerler `_ in `#19734 `_ * Show workflow help (and readme?) in run form by `@ahmedhamidawan `_ in `#19736 `_ * Enhance breadcrumb navigation UX in small screen sizes by `@itisAliRH `_ in `#19737 `_ * ToolShed2 - Add more context when navigating between tools an repositories. by `@jmchilton `_ in `#19738 `_ * Improvements to package decomposition. by `@jmchilton `_ in `#19759 `_ * Add cell-based markdown editor for pages by `@guerler `_ in `#19769 `_ * Rename tool "Citations" to "References" by `@nsoranzo `_ in `#19770 `_ * Update Python dependencies by `@galaxybot `_ in `#19772 `_ * Add visualization framework interface to cell-based markdown editor by `@guerler `_ in `#19775 `_ * Allow overriding datatypes for planemo lint by `@selten `_ in `#19780 `_ * Introduce reusable GCard component for unified card layout by `@itisAliRH `_ in `#19785 `_ * Add history sharing and accessibility management view by `@ahmedhamidawan `_ in `#19786 `_ * Add bigbed to bed converter and tests by `@d-callan `_ in `#19787 `_ * xsd: use CollectionType for collections in tests by `@bernt-matthias `_ in `#19802 `_ * Update Python dependencies by `@galaxybot `_ in `#19816 `_ * Workflow Run Form Enhancements follow up by `@ahmedhamidawan `_ in `#19825 `_ * More user feedback in FormRulesEdit (for Apply Rules tool) by `@jmchilton `_ in `#19827 `_ * Use direct icon references in FormSelectMany.vue. by `@jmchilton `_ in `#19829 `_ * Populate image metadata without allocating memory for the entire image content by `@kostrykin `_ in `#19830 `_ * Syntactic sugar to ease TPV configuration. by `@jmchilton `_ in `#19834 `_ * Improve markdown editor modularity and structure by `@guerler `_ in `#19835 `_ * Add mandatory RO-Crate metadata when exporting by `@elichad `_ in `#19846 `_ * Enable lazy loading for ace-builds by `@ElectronicBlueberry `_ in `#19847 `_ * Add basic support for icons in tools by `@davelopez `_ in `#19850 `_ * Webpack build performance improvements by `@dannon `_ in `#19851 `_ * Improve type annotations of ``ModelPersistenceContext`` and derived classes by `@nsoranzo `_ in `#19852 `_ * Client circular dependency check by `@dannon `_ in `#19858 `_ * Migrate from Prism to Monaco for ToolSource display. by `@dannon `_ in `#19861 `_ * Drop old galaxy_session records by `@jdavcs `_ in `#19872 `_ * Update Python dependencies by `@galaxybot `_ in `#19874 `_ * Add Tapis auth support by `@dannon `_ in `#19887 `_ * Make preferences drop down available in single user deployments by `@ksuderman `_ in `#19888 `_ * Clarify is_active method usage for Python Social Auth in Galaxy by `@dannon `_ in `#19899 `_ * FITS Graph Viewer - script name tweak. by `@dannon `_ in `#19902 `_ * Improve docs for output filters by `@bernt-matthias `_ in `#19904 `_ * Various styling improvements to Workflow Run and Invocation views by `@ahmedhamidawan `_ in `#19905 `_ * Overhaul workflow runtime settings display. by `@dannon `_ in `#19906 `_ * Allow embedding vitessce visualizations by `@mvdbeek `_ in `#19909 `_ * Replace backend-based page creation controller endpoint by `@guerler `_ in `#19914 `_ * Remove unnecessary code duplications by `@nsoranzo `_ in `#19921 `_ * Migrate Page editing controller endpoint to API by `@guerler `_ in `#19923 `_ * RStudio IT updates to work on .org by `@afgane `_ in `#19924 `_ * Update Python dependencies by `@galaxybot `_ in `#19929 `_ * Show pre-populated landing data values in workflow run form by `@ahmedhamidawan `_ in `#19935 `_ * Drop old job metrics by `@jdavcs `_ in `#19936 `_ * Fix local import in ``__resolvers_dict`` by `@mvdbeek `_ in `#19944 `_ * First steps of bootstrap replacement by `@ElectronicBlueberry `_ in `#19946 `_ * Decrease sentry_sdk.errors log level to INFO by `@natefoo `_ in `#19951 `_ * Allow PathLike parameters in ``make_fast_zipfile()`` by `@nsoranzo `_ in `#19955 `_ * Add link to view history on dataset info page by `@natefoo `_ in `#19956 `_ * Allow resizing Visualizations in Markdown editor by `@guerler `_ in `#19958 `_ * Add share button for invocations by `@ahmedhamidawan `_ in `#19959 `_ * Add type hints around collection copying and job things by `@mvdbeek `_ in `#19961 `_ * Job cache allow different names when possible by `@mvdbeek `_ in `#19962 `_ * Button replacement batch 1 by `@ElectronicBlueberry `_ in `#19963 `_ * Update Python dependencies by `@galaxybot `_ in `#19964 `_ * Adds a trimInputs prop to FormGeneric to trim string values on submit. by `@dannon `_ in `#19971 `_ * Add Katex Equation rendering plugin to Markdown Editor by `@guerler `_ in `#19988 `_ * Allow different AI providers (as long as they are openai compatible) by `@uwwint `_ in `#19989 `_ * Button replacement batch 2 by `@ElectronicBlueberry `_ in `#19990 `_ * Improve type annotation of tool parameter wrapping by `@nsoranzo `_ in `#19991 `_ * Add Niivue viewer by `@guerler `_ in `#19995 `_ * IT Activity Panel by `@dannon `_ in `#19996 `_ * Selenium test cases for running workflow from form upload. by `@jmchilton `_ in `#19997 `_ * Update Python dependencies by `@galaxybot `_ in `#19998 `_ * Restore Visualization insertion options in Reports Editor by `@guerler `_ in `#20000 `_ * Implement dataset collection support in workflow landing requests by `@mvdbeek `_ in `#20004 `_ * Add kepler.gl visualization by `@guerler `_ in `#20005 `_ * Enable ``warn_redundant_casts`` mypy option and drop redundant casts by `@nsoranzo `_ in `#20008 `_ * Update vitessce version by `@mvdbeek `_ in `#20016 `_ * Merge Inputs/Parameters and Outputs/Collections Tabs by `@ahmedhamidawan `_ in `#20019 `_ * Show workflow README in split view next to the form inputs by `@ahmedhamidawan `_ in `#20026 `_ * Add vitesscejson datatype by `@guerler `_ in `#20027 `_ * Add VTK Visualization Toolkit Plugin by `@guerler `_ in `#20028 `_ * Move README to center panel in workflow editor by `@ahmedhamidawan `_ in `#20029 `_ * Add help text popovers for workflow runtime settings by `@ahmedhamidawan `_ in `#20031 `_ * Add rerun option for workflows by `@ahmedhamidawan `_ in `#20032 `_ * Add DOI to workflow metadata by `@jdavcs `_ in `#20033 `_ * Add support for Markdown help text in visualizations by `@guerler `_ in `#20043 `_ * Add sample datasets for visualizations by `@guerler `_ in `#20046 `_ * Add ZIP explorer to import individual files from local or remote ZIP archives by `@davelopez `_ in `#20054 `_ * Add docx datatype by `@bgruening `_ in `#20055 `_ * Add markdown datatype by `@bgruening `_ in `#20056 `_ * Add flac audio format by `@bgruening `_ in `#20057 `_ * Client refactorings ahead of #19377. by `@jmchilton `_ in `#20059 `_ * Add rd datatype by `@richard-burhans `_ in `#20060 `_ * GLink implementation by `@ElectronicBlueberry `_ in `#20063 `_ * GCard Full Description by `@itisAliRH `_ in `#20064 `_ * Enhance Storage Dashboard Selected Item UI by `@itisAliRH `_ in `#20070 `_ * Add activity panel width to local storage by `@ahmedhamidawan `_ in `#20072 `_ * Hide non-functional and replaced visualizations (e.g. Nora, MSA) by `@guerler `_ in `#20077 `_ * Flexible mapping from collection parameter types to collection builder components. by `@jmchilton `_ in `#20082 `_ * Route to creating a new file source in remote file browser modal by `@ahmedhamidawan `_ in `#20084 `_ * Use visualization dropdown solely for examples by `@guerler `_ in `#20094 `_ * Set node version to 22.13.0 by `@davelopez `_ in `#20095 `_ * Update Python dependencies by `@galaxybot `_ in `#20096 `_ * Adds Example Datasets and Help Text for Visualizations by `@guerler `_ in `#20097 `_ * Enhance external login interface styling by `@ahmedhamidawan `_ in `#20100 `_ * Add Molstar by `@guerler `_ in `#20101 `_ * Improve type annotation of `galaxy.util` submodules by `@nsoranzo `_ in `#20104 `_ * Add alignment.js for multiple sequence alignment rendering by `@guerler `_ in `#20110 `_ * Add specific datatypes for Cytoscape and Kepler.gl by `@guerler `_ in `#20117 `_ * Run integration tests on latest Ubuntu by `@nsoranzo `_ in `#20118 `_ * Add role creation form by `@guerler `_ in `#20119 `_ * Migrate Transition Systems Visualization by `@guerler `_ in `#20125 `_ * Add logo, description and help for aequatus by `@guerler `_ in `#20128 `_ * Drop now unused controller method by `@mvdbeek `_ in `#20129 `_ * Add updated PCA plot by `@guerler `_ in `#20140 `_ * Browse multiple trees in phylocanvas by `@guerler `_ in `#20141 `_ * Add more metadata, esp `infer_from` to datatypes configuration by `@bgruening `_ in `#20142 `_ * Show job ids on job success by `@ahmedhamidawan `_ in `#20145 `_ * Additional type hints for ``toolbox.get_tool`` / ``toolbox.has_tool`` by `@mvdbeek `_ in `#20150 `_ * Create working dir output outside of tool evaluator by `@mvdbeek `_ in `#20153 `_ * Improved rule builder display for non-nested lists (most of them). by `@jmchilton `_ in `#20156 `_ * Revise transiently failing data source test. by `@jmchilton `_ in `#20157 `_ * Yaml parser fixes and improvements (part 1) by `@mvdbeek `_ in `#20158 `_ * Fix remaining vue-tsc errors by `@dannon `_ in `#20163 `_ * Add three AAI providers by `@martenson `_ in `#20165 `_ * Add replacement_dataset option to collection filter tools by `@simonbray `_ in `#20166 `_ * Implement file source to integrate Galaxy with RSpace by `@kysrpex `_ in `#20167 `_ * G modal implementation by `@ElectronicBlueberry `_ in `#20168 `_ * Add client package by `@natefoo `_ in `#20171 `_ * Add JupyterLite by `@guerler `_ in `#20174 `_ * Standalone Galaxy API Client Package by `@dannon `_ in `#20181 `_ * Add visualization test data by `@nilchia `_ in `#20183 `_ * Bump vega from 5.30.0 to 5.32.0 in /client by `@mvdbeek `_ in `#20188 `_ * Visualization-First Display functionality by `@dannon `_ in `#20190 `_ * Improve type annotation of ``galaxy.model.dataset_collections`` by `@nsoranzo `_ in `#20194 `_ * Have `make dist` in the web_client package build the client by `@natefoo `_ in `#20195 `_ * Add plotly 6.0.1 to JupyterLite by `@guerler `_ in `#20201 `_ * Enable visualizations for anonymous user by `@guerler `_ in `#20210 `_ * Migrate ChiraViz by `@guerler `_ in `#20214 `_ * Display invocation inputs and outputs in workflow report by `@mvdbeek `_ in `#20222 `_ * Use TUS streaming and remove redundant IndexDB temp store in Zip Explorer by `@davelopez `_ in `#20226 `_ * Add more descriptions to custom tool source schema by `@mvdbeek `_ in `#20266 `_ * Improve handling of very large files in Tabulator by `@guerler `_ in `#20271 `_ * Touch up Dataset View by `@guerler `_ in `#20290 `_ * Improve performance of job cache query by `@mvdbeek `_ in `#20319 `_ * Remove type import side-effects by `@ElectronicBlueberry `_ in `#20321 `_ * Enable retrieving contents from extra file paths when request contains leading `/` by `@mvdbeek `_ in `#20336 `_ * DatasetView and Card Polish by `@dannon `_ in `#20342 `_ * Release notes by `@ahmedhamidawan `_ in `#20386 `_ * Deprecate ``enable_tool_document_cache`` by `@nsoranzo `_ in `#20433 `_ * Update tiffviewer to latest version supporting more formats by `@davelopez `_ in `#20457 `_ * Add Aladin as standard FITS viewer by `@bgruening `_ in `#20465 `_ * Add molstar as default viewer for some molecule formats by `@bgruening `_ in `#20467 `_ * Add ``/api/datasets/{dataset_id}/extra_files/raw/{filename:path}`` by `@mvdbeek `_ in `#20468 `_ ============= Other changes ============= * Merge 24.2 into dev. by `@jmchilton `_ in `#19273 `_ * Fix package versions by `@jdavcs `_ in `#19566 `_ * Merge 24.2 into dev by `@jdavcs `_ in `#19590 `_ * Bump @babel/runtime-corejs3 from 7.23.2 to 7.26.10 in /client by `@dependabot[bot] `_ in `#19788 `_ * Rebuild API schema for latest dev. by `@jmchilton `_ in `#19789 `_ * Make job cache generally available by `@dannon `_ in `#19798 `_ * Fix workflow license component typing by `@guerler `_ in `#19878 `_ * Fix import and update_page type signature by `@mvdbeek `_ in `#19932 `_ * Merge 24.2 into dev by `@ahmedhamidawan `_ in `#19933 `_ * Log controller exceptions by `@natefoo `_ in `#19974 `_ * Fix copying job output from discovered outputs by `@mvdbeek `_ in `#19999 `_ * Add env var to skip CircularDependencyPlugin in development mode by `@dannon `_ in `#20038 `_ * Bump h11 from 0.14.0 to 0.16.0 in /lib/galaxy/dependencies by `@dependabot[bot] `_ in `#20088 `_ * Fix formatting in webapp and client/install.py by `@dannon `_ in `#20185 `_ * Bump default milestone to 25.1 by `@mvdbeek `_ in `#20189 `_ * Bump axios from 1.7.4 to 1.8.2 in /client by `@dependabot[bot] `_ in `#20205 `_ * Bug fixes around wizard usage. by `@jmchilton `_ in `#20224 `_ * Bug fix - allow file drops into PasteData widget. by `@jmchilton `_ in `#20232 `_ * Only show custom tool editor in activity bar settings when user has access by `@mvdbeek `_ in `#20247 `_ * Fix job rerun for dynamic tools by `@mvdbeek `_ in `#20259 `_ * Add 25.0 migration tags by `@ahmedhamidawan `_ in `#20265 `_ * Update version to 25.0.rc1 by `@ahmedhamidawan `_ in `#20267 `_ * Bug fix - auto-pairing step not connected to collection builder in wizard. by `@jmchilton `_ in `#20345 `_ * Fix minor IT panel/display issues by `@dannon `_ in `#20404 `_ * Rename vitessce_json file_ext to vitessce.json by `@mvdbeek `_ in `#20473 `_ ------------------- 24.2.4 (2025-06-17) ------------------- ========= Bug fixes ========= * Fix #19515 - invalid citation handling changed with 24.2. by `@jmchilton `_ in `#19716 `_ * Fix collection builder input states by `@mvdbeek `_ in `#19797 `_ * Reduce default framework tool test timeout to 60 seconds by `@mvdbeek `_ in `#19819 `_ * Backport #19810: Fix workflow param tests not updating param type. by `@mvdbeek `_ in `#19820 `_ * Fix various job concurrency limit issues by `@mvdbeek `_ in `#19824 `_ * Do not reorder options in FormSelect component when multiselect disabled by `@jdavcs `_ in `#19837 `_ * Decode/encode FormDirectory paths to allow spaces (and other characters) by `@ahmedhamidawan `_ in `#19841 `_ * Try to recover from recurring activation link error by `@jdavcs `_ in `#19844 `_ * Add spacing between workflow author and invocation count by `@ahmedhamidawan `_ in `#19849 `_ * Fix default ordering of items sorted by name by `@jdavcs `_ in `#19853 `_ * Handle directories with percents directories with export_remote.xml. by `@jmchilton `_ in `#19865 `_ * Fix drag and drop for dataset collection elements by `@ahmedhamidawan `_ in `#19866 `_ * Don't collect unnamed outputs twice in extended metadata mode by `@mvdbeek `_ in `#19868 `_ * Check if index exists before creating by `@jdavcs `_ in `#19873 `_ * Lazy-load invocation step jobs as needed by `@mvdbeek `_ in `#19877 `_ * Fix tabular metadata setting on pulsar with remote metadata by `@mvdbeek `_ in `#19891 `_ * Skip ``data_meta`` filter in run form by `@mvdbeek `_ in `#19895 `_ * Drop unused alembic-utils from galaxy-data package requirements by `@nsoranzo `_ in `#19896 `_ * Fix duplicate extensions for data inputs by `@ahmedhamidawan `_ in `#19903 `_ * Skip implicit HDA conversions in DataToolParameter options by `@davelopez `_ in `#19911 `_ * Fix duplicate entries when using drag and drop in multiple mode by `@davelopez `_ in `#19913 `_ * Let pysam use extra threads available in job by `@mvdbeek `_ in `#19917 `_ * Handle special charater in raw SQL by `@jdavcs `_ in `#19925 `_ * Report TestCaseValidation as linter error for 24.2 and above by `@bernt-matthias `_ in `#19928 `_ * Better interactive tool entry point query by `@mvdbeek `_ in `#19942 `_ * Drop unnecessary job cache job subquery by `@mvdbeek `_ in `#19945 `_ * Use ``make_fast_zipfile`` directly by `@mvdbeek `_ in `#19947 `_ * Fix attempt restriction on multiple connections by `@mvdbeek `_ in `#19948 `_ * Fix various parameter validation issues. by `@jmchilton `_ in `#19949 `_ * Sort intersected options by `@mvdbeek `_ in `#19953 `_ * Do not print OIDC access tokens to the logs by `@kysrpex `_ in `#19966 `_ * Renew OIDC access tokens using valid refresh tokens by `@kysrpex `_ in `#19967 `_ * Fix bug in psa-authnz redirect handling by `@dannon `_ in `#19968 `_ * Add missing job state history entry for queued state by `@mvdbeek `_ in `#19977 `_ * Restrict job cache to terminal jobs (and other fixes) by `@mvdbeek `_ in `#19978 `_ * Do not display default labels obscuring selectable options in a vue-multiselect component by `@jdavcs `_ in `#19981 `_ * Fix dynamic filter option access when building command line by `@mvdbeek `_ in `#19982 `_ * Always set copy_elements to true by `@mvdbeek `_ in `#19985 `_ * ChatGXY Error Handling by `@dannon `_ in `#19987 `_ * Ensure job states are fetched in invocation view by `@ahmedhamidawan `_ in `#20010 `_ * Renew access tokens from PSA using valid refresh tokens by `@kysrpex `_ in `#20040 `_ * Fix edit permission for datasets delete button in storage dashboard overview by location by `@itisAliRH `_ in `#20066 `_ * Job cache backports by `@mvdbeek `_ in `#20078 `_ * Fix `mulled-search --destination quay`, add index reuse by `@natefoo `_ in `#20107 `_ * Fix edam selenium test by `@mvdbeek `_ in `#20134 `_ * Skip ``param_value`` filter if ref value is runtime value by `@mvdbeek `_ in `#20144 `_ * Fix ``DataCollectionParameterModel`` factory by `@mvdbeek `_ in `#20164 `_ * Fix invocation failure dataset reference by `@mvdbeek `_ in `#20200 `_ * 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 `_ * Fall back to name in job summary if no input label given by `@mvdbeek `_ in `#20258 `_ * Fix WF Run RO-Crate logo width in Firefox by `@davelopez `_ in `#20305 `_ * Fix searching roles in admin UI by `@jdavcs `_ in `#20394 `_ * Skip validation of expression.json input in workflow parameter validator by `@mvdbeek `_ in `#20412 `_ * Fix unit tests returning values by `@nsoranzo `_ in `#20413 `_ * Fix ``mull_targets()`` with mamba 2.x by `@nsoranzo `_ in `#20416 `_ * Make response header values strings by `@mvdbeek `_ in `#20475 `_ * Fix legacy get_metadata_file controller route by `@mvdbeek `_ in `#20477 `_ * Prevent running datatype autodetect on purged datasets by `@mvdbeek `_ in `#20479 `_ * 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 `_ * Point install_requires at requirements.txt file by `@mvdbeek `_ in `#19864 `_ * Fix Invenio file source downloads not working with some Invenio instances by `@davelopez `_ in `#19930 `_ * Update selectable object stores after adding or editing them by `@davelopez `_ in `#19992 `_ ============= Other changes ============= * Backport parts of #19659 by `@bernt-matthias `_ in `#19805 `_ * Remove unused client route for standalone wizard interface by `@dannon `_ in `#19836 `_ * Publish pre-built client with (point-)release by `@mvdbeek `_ in `#19879 `_ * Update dev package version in meta package by `@natefoo `_ in `#20159 `_ ------------------- 19.9.0 (2019-11-21) ------------------- * Initial import from dev branch of Galaxy during 19.09 development cycle.