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Merge branch 'release_25.1' into dev
# Conflicts: # lib/galaxy/version.py # packages/app/HISTORY.rst # packages/auth/HISTORY.rst # packages/config/HISTORY.rst # packages/data/HISTORY.rst # packages/files/HISTORY.rst # packages/job_execution/HISTORY.rst # packages/job_metrics/HISTORY.rst # packages/meta/HISTORY.rst # packages/navigation/HISTORY.rst # packages/objectstore/HISTORY.rst # packages/schema/HISTORY.rst # packages/selenium/HISTORY.rst # packages/test_api/HISTORY.rst # packages/test_base/HISTORY.rst # packages/test_driver/HISTORY.rst # packages/tool_shed/HISTORY.rst # packages/tool_shed_schema/HISTORY.rst # packages/tool_util/HISTORY.rst # packages/tool_util_models/HISTORY.rst # packages/tours/HISTORY.rst # packages/util/HISTORY.rst # packages/web_apps/HISTORY.rst # packages/web_client/HISTORY.rst # packages/web_framework/HISTORY.rst # packages/web_stack/HISTORY.rst
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‎packages/app/HISTORY.rst‎

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-------------------
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25.1.0 (2025-12-12)
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-------------------
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=========
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Bug fixes
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=========
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* Workaround to numeric sorting in the local portion of tool versions if they are galaxy "build" numbers by `@natefoo <https://github.com/natefoo>`_ in `#13570 <https://github.com/galaxyproject/galaxy/pull/13570>`_
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* Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#20422 <https://github.com/galaxyproject/galaxy/pull/20422>`_
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* Remove decoded ids from job/dataset error report email by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20714 <https://github.com/galaxyproject/galaxy/pull/20714>`_
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* Fix `multiple="true"` data collection map over for shell_command tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20859 <https://github.com/galaxyproject/galaxy/pull/20859>`_
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* Fix default conditional test parameters... by `@jmchilton <https://github.com/jmchilton>`_ in `#20942 <https://github.com/galaxyproject/galaxy/pull/20942>`_
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* Set minimum profile version for expression tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21151 <https://github.com/galaxyproject/galaxy/pull/21151>`_
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* Add Convert characters1 to workflow safe updates by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21160 <https://github.com/galaxyproject/galaxy/pull/21160>`_
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* Bump up minimal tpv version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21166 <https://github.com/galaxyproject/galaxy/pull/21166>`_
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* Add missing more-itertools dependency by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21214 <https://github.com/galaxyproject/galaxy/pull/21214>`_
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* Fix downloading subworkflows without stored workflow by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21223 <https://github.com/galaxyproject/galaxy/pull/21223>`_
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* Fix fastapi package conflict by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21349 <https://github.com/galaxyproject/galaxy/pull/21349>`_
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* Skip mako for rendering tool help by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21428 <https://github.com/galaxyproject/galaxy/pull/21428>`_
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* Fix optional subworkflow input scheduling bug by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21435 <https://github.com/galaxyproject/galaxy/pull/21435>`_
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* Maintain columns on sample sheet map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21436 <https://github.com/galaxyproject/galaxy/pull/21436>`_
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============
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Enhancements
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============
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* Support credentials(secrets/variables) in tool requirements by `@arash77 <https://github.com/arash77>`_ in `#19084 <https://github.com/galaxyproject/galaxy/pull/19084>`_
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* Allow several Galaxy Markdown directives to be embedded. by `@jmchilton <https://github.com/jmchilton>`_ in `#19086 <https://github.com/galaxyproject/galaxy/pull/19086>`_
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* Add tags to output datasets from tool form by `@PlushZ <https://github.com/PlushZ>`_ in `#19225 <https://github.com/galaxyproject/galaxy/pull/19225>`_
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* Implement Sample Sheets by `@jmchilton <https://github.com/jmchilton>`_ in `#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`_
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* Consider collections in on_strings for parameters accepting multiple datasets by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19817 <https://github.com/galaxyproject/galaxy/pull/19817>`_
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* Remove backbone-based charts modules by `@guerler <https://github.com/guerler>`_ in `#19892 <https://github.com/galaxyproject/galaxy/pull/19892>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20139 <https://github.com/galaxyproject/galaxy/pull/20139>`_
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* Remove legacy visualizations by `@guerler <https://github.com/guerler>`_ in `#20173 <https://github.com/galaxyproject/galaxy/pull/20173>`_
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* Split Login and Register, enable OIDC Registration. by `@uwwint <https://github.com/uwwint>`_ in `#20287 <https://github.com/galaxyproject/galaxy/pull/20287>`_
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* Empower Users to More Pragmatically Import Datasets & Collections From Tables by `@jmchilton <https://github.com/jmchilton>`_ in `#20288 <https://github.com/galaxyproject/galaxy/pull/20288>`_
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* Switch Default Visualization Endpoint to script, migrate to YAML by `@guerler <https://github.com/guerler>`_ in `#20303 <https://github.com/galaxyproject/galaxy/pull/20303>`_
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* Add short term storage expiration indicator to history items by `@davelopez <https://github.com/davelopez>`_ in `#20332 <https://github.com/galaxyproject/galaxy/pull/20332>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20347 <https://github.com/galaxyproject/galaxy/pull/20347>`_
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* Install Visualization plugins as self-contained packages by `@guerler <https://github.com/guerler>`_ in `#20348 <https://github.com/galaxyproject/galaxy/pull/20348>`_
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* Prepare ``ToolBox.dynamic_tool_to_tool()`` for CWL formats by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20364 <https://github.com/galaxyproject/galaxy/pull/20364>`_
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* Install visualizations directly to static path, avoid duplication by `@guerler <https://github.com/guerler>`_ in `#20372 <https://github.com/galaxyproject/galaxy/pull/20372>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20383 <https://github.com/galaxyproject/galaxy/pull/20383>`_
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* Type annotation fixes for mypy 1.16.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20424 <https://github.com/galaxyproject/galaxy/pull/20424>`_
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* Implement dataset source requested transformations. by `@jmchilton <https://github.com/jmchilton>`_ in `#20435 <https://github.com/galaxyproject/galaxy/pull/20435>`_
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* Add username_key setting to configure python-social-auth OIDC by `@marius-mather <https://github.com/marius-mather>`_ in `#20497 <https://github.com/galaxyproject/galaxy/pull/20497>`_
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* Remove deprecated tool document cache by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20510 <https://github.com/galaxyproject/galaxy/pull/20510>`_
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* Fixes for invocation import. by `@jmchilton <https://github.com/jmchilton>`_ in `#20528 <https://github.com/galaxyproject/galaxy/pull/20528>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20537 <https://github.com/galaxyproject/galaxy/pull/20537>`_
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* Decode OIDC access token as part of authentication pipeline by `@marius-mather <https://github.com/marius-mather>`_ in `#20547 <https://github.com/galaxyproject/galaxy/pull/20547>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20577 <https://github.com/galaxyproject/galaxy/pull/20577>`_
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* Display the Galaxy Citation within the Export Tool References List by `@mschatz <https://github.com/mschatz>`_ in `#20584 <https://github.com/galaxyproject/galaxy/pull/20584>`_
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* Implement Data Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#20592 <https://github.com/galaxyproject/galaxy/pull/20592>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20601 <https://github.com/galaxyproject/galaxy/pull/20601>`_
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* Add a "Debug" (email report) tab to Workflow Invocations by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20624 <https://github.com/galaxyproject/galaxy/pull/20624>`_
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* Clean up code from pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20642 <https://github.com/galaxyproject/galaxy/pull/20642>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20653 <https://github.com/galaxyproject/galaxy/pull/20653>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20680 <https://github.com/galaxyproject/galaxy/pull/20680>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20699 <https://github.com/galaxyproject/galaxy/pull/20699>`_
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* Improve cli and slurmcli runner traceability for job status and failure reasons by `@selten <https://github.com/selten>`_ in `#20717 <https://github.com/galaxyproject/galaxy/pull/20717>`_
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* Refactor Files Sources Framework for stronger typing using pydantic models by `@davelopez <https://github.com/davelopez>`_ in `#20728 <https://github.com/galaxyproject/galaxy/pull/20728>`_
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* Hierarchical display collection dataset states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20731 <https://github.com/galaxyproject/galaxy/pull/20731>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20732 <https://github.com/galaxyproject/galaxy/pull/20732>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20753 <https://github.com/galaxyproject/galaxy/pull/20753>`_
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* Consolidate visualization mako, avoid user agent styles by `@guerler <https://github.com/guerler>`_ in `#20760 <https://github.com/galaxyproject/galaxy/pull/20760>`_
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* Add configfiles support and various enhancements for user defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20761 <https://github.com/galaxyproject/galaxy/pull/20761>`_
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* Drop old load_workflow controller method, use API by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20774 <https://github.com/galaxyproject/galaxy/pull/20774>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20779 <https://github.com/galaxyproject/galaxy/pull/20779>`_
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* Add Hugging Face 🤗 file source and user-defined template by `@davelopez <https://github.com/davelopez>`_ in `#20805 <https://github.com/galaxyproject/galaxy/pull/20805>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20812 <https://github.com/galaxyproject/galaxy/pull/20812>`_
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* Update pytest to v8 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20838 <https://github.com/galaxyproject/galaxy/pull/20838>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20841 <https://github.com/galaxyproject/galaxy/pull/20841>`_
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* Allow adding extra steps to the default pipeline of the OIDC authentication by `@marius-mather <https://github.com/marius-mather>`_ in `#20845 <https://github.com/galaxyproject/galaxy/pull/20845>`_
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* Use a streaming based parser (ijson) when setting metadata for biom1 files. by `@ksuderman <https://github.com/ksuderman>`_ in `#20851 <https://github.com/galaxyproject/galaxy/pull/20851>`_
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* Various Container Execution Enhancements (including GCP Batch support) by `@jmchilton <https://github.com/jmchilton>`_ in `#20862 <https://github.com/galaxyproject/galaxy/pull/20862>`_
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* Replace tour_generator webhook with internal API and frontend by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20868 <https://github.com/galaxyproject/galaxy/pull/20868>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20869 <https://github.com/galaxyproject/galaxy/pull/20869>`_
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* Improve type annotation for job runners and ``InteractiveToolManager`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20871 <https://github.com/galaxyproject/galaxy/pull/20871>`_
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* Replace deprecated ``codecs.open()`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20891 <https://github.com/galaxyproject/galaxy/pull/20891>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20905 <https://github.com/galaxyproject/galaxy/pull/20905>`_
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* Allow creation of visualizations without dataset by `@guerler <https://github.com/guerler>`_ in `#20914 <https://github.com/galaxyproject/galaxy/pull/20914>`_
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* Add support for picking ``from_work_dir`` directory by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20916 <https://github.com/galaxyproject/galaxy/pull/20916>`_
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* Add tool to add nesting level to collection by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20926 <https://github.com/galaxyproject/galaxy/pull/20926>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20930 <https://github.com/galaxyproject/galaxy/pull/20930>`_
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* Allow addressing user defined tools in job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20932 <https://github.com/galaxyproject/galaxy/pull/20932>`_
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* Wire up and test resource requirement via tpv by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20936 <https://github.com/galaxyproject/galaxy/pull/20936>`_
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* Limit admin requirement of selected tool data api endpoints by `@guerler <https://github.com/guerler>`_ in `#20949 <https://github.com/galaxyproject/galaxy/pull/20949>`_
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* Add resource docs and tweak tool source schema title generation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20951 <https://github.com/galaxyproject/galaxy/pull/20951>`_
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* Allow sending and tracking landing request origin by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20957 <https://github.com/galaxyproject/galaxy/pull/20957>`_
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* Use nodejs-wheel to install node by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20963 <https://github.com/galaxyproject/galaxy/pull/20963>`_
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* Move tours schema to schema directory (to fix package structure) by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20965 <https://github.com/galaxyproject/galaxy/pull/20965>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20968 <https://github.com/galaxyproject/galaxy/pull/20968>`_
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* Log task execution errors with log.exception by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20970 <https://github.com/galaxyproject/galaxy/pull/20970>`_
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* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21005 <https://github.com/galaxyproject/galaxy/pull/21005>`_
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* Bump up total-perspective-vortex dependency by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21014 <https://github.com/galaxyproject/galaxy/pull/21014>`_
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* Tighter API for tool run tagging. by `@jmchilton <https://github.com/jmchilton>`_ in `#21210 <https://github.com/galaxyproject/galaxy/pull/21210>`_
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* Optimize /api/invocations/steps/{step_id} by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21249 <https://github.com/galaxyproject/galaxy/pull/21249>`_
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* Optionally include column headers in sample sheet file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21439 <https://github.com/galaxyproject/galaxy/pull/21439>`_
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=============
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Other changes
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=============
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* Merge `release_25.0` into `dev` by `@davelopez <https://github.com/davelopez>`_ in `#20484 <https://github.com/galaxyproject/galaxy/pull/20484>`_
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* Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by `@dependabot[bot] <https://github.com/dependabot[bot]>`_ in `#20591 <https://github.com/galaxyproject/galaxy/pull/20591>`_
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* Sample Sheet Bug Fixes around Preserving Collection Metadata by `@jmchilton <https://github.com/jmchilton>`_ in `#20749 <https://github.com/galaxyproject/galaxy/pull/20749>`_
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* Validate sample sheet column definitions in workflow definitions on backend. by `@jmchilton <https://github.com/jmchilton>`_ in `#20880 <https://github.com/galaxyproject/galaxy/pull/20880>`_
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* Drop fastapi extra dep from sentry-sdk by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21156 <https://github.com/galaxyproject/galaxy/pull/21156>`_
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* Resolve possible symlink before establishing tool file location by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21175 <https://github.com/galaxyproject/galaxy/pull/21175>`_
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25.0.4 (2025-11-18)
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25.0.4 (2025-11-18)
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-------------------
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=========
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Bug fixes
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=========
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* Fix typo in lib/galaxy/config/sample/job_conf.sample.yml: enviroment --> environment by `@blankenberg <https://github.com/blankenberg>`_ in `#20652 <https://github.com/galaxyproject/galaxy/pull/20652>`_
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============
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Enhancements
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============
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* Implement Sample Sheets by `@jmchilton <https://github.com/jmchilton>`_ in `#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`_
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* Add rerun.io web viewer by `@guerler <https://github.com/guerler>`_ in `#20202 <https://github.com/galaxyproject/galaxy/pull/20202>`_
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* Split Login and Register, enable OIDC Registration. by `@uwwint <https://github.com/uwwint>`_ in `#20287 <https://github.com/galaxyproject/galaxy/pull/20287>`_
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* Add LocusZoom Visualization by `@elmedjadjirayane <https://github.com/elmedjadjirayane>`_ in `#20354 <https://github.com/galaxyproject/galaxy/pull/20354>`_
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* Remove deprecated tool document cache by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20510 <https://github.com/galaxyproject/galaxy/pull/20510>`_
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* Decode OIDC access token as part of authentication pipeline by `@marius-mather <https://github.com/marius-mather>`_ in `#20547 <https://github.com/galaxyproject/galaxy/pull/20547>`_
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* Display the Galaxy Citation within the Export Tool References List by `@mschatz <https://github.com/mschatz>`_ in `#20584 <https://github.com/galaxyproject/galaxy/pull/20584>`_
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* Clean up code from pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20642 <https://github.com/galaxyproject/galaxy/pull/20642>`_
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* Update location of latest tpv shared db by `@nuwang <https://github.com/nuwang>`_ in `#20651 <https://github.com/galaxyproject/galaxy/pull/20651>`_
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* Allow adding extra steps to the default pipeline of the OIDC authentication by `@marius-mather <https://github.com/marius-mather>`_ in `#20845 <https://github.com/galaxyproject/galaxy/pull/20845>`_
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* Various Container Execution Enhancements (including GCP Batch support) by `@jmchilton <https://github.com/jmchilton>`_ in `#20862 <https://github.com/galaxyproject/galaxy/pull/20862>`_
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* Replace tour_generator webhook with internal API and frontend by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20868 <https://github.com/galaxyproject/galaxy/pull/20868>`_
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* Add axt and maf to auto_compressed_types by `@richard-burhans <https://github.com/richard-burhans>`_ in `#20875 <https://github.com/galaxyproject/galaxy/pull/20875>`_
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* Add Multiple Sequence Alignment Viewer 2.0 by `@guerler <https://github.com/guerler>`_ in `#20907 <https://github.com/galaxyproject/galaxy/pull/20907>`_
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* Add tool to add nesting level to collection by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20926 <https://github.com/galaxyproject/galaxy/pull/20926>`_
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* Make jupyterlite default visualization for ipynb by `@guerler <https://github.com/guerler>`_ in `#20931 <https://github.com/galaxyproject/galaxy/pull/20931>`_
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* Allow addressing user defined tools in job config by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20932 <https://github.com/galaxyproject/galaxy/pull/20932>`_
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* Allow specifying a command for determining a docker host port by `@natefoo <https://github.com/natefoo>`_ in `#20953 <https://github.com/galaxyproject/galaxy/pull/20953>`_
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* Add freq.json datatype subclass by `@guerler <https://github.com/guerler>`_ in `#21012 <https://github.com/galaxyproject/galaxy/pull/21012>`_
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* New datatype addition: HAL by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21379 <https://github.com/galaxyproject/galaxy/pull/21379>`_
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* Add PNTS datatype for 3D Tiles Point Cloud by `@kgerb <https://github.com/kgerb>`_ in `#21414 <https://github.com/galaxyproject/galaxy/pull/21414>`_
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=============
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Other changes
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=============
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* Merge `release_25.0` into `dev` by `@davelopez <https://github.com/davelopez>`_ in `#20484 <https://github.com/galaxyproject/galaxy/pull/20484>`_
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1255
-------------------
1356
25.0.4 (2025-11-18)
1457
-------------------

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