galaxy-data 26.0.1.dev0__tar.gz → 26.1.0__tar.gz

galaxy_data-26.1.0/HISTORY.rst

@@ -0,0 +1,1205 @@
+History
+-------
+
+.. to_doc
+
+-------------------
+26.1.0 (2026-08-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Make database heartbeat more robust by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21734 <https://github.com/galaxyproject/galaxy/pull/21734>`_
+* Fix tag duplication when copying datasets/collections between histories by `@dannon <https://github.com/dannon>`_ in `#22109 <https://github.com/galaxyproject/galaxy/pull/22109>`_
+* Fix more paired_or_unpaired collection issues by `@jmchilton <https://github.com/jmchilton>`_ in `#22170 <https://github.com/galaxyproject/galaxy/pull/22170>`_
+* Fix Hashicorp Vault 2.0 non-canonical path rejection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22530 <https://github.com/galaxyproject/galaxy/pull/22530>`_
+* Skip missing history item ids in job exports by `@guerler <https://github.com/guerler>`_ in `#22563 <https://github.com/galaxyproject/galaxy/pull/22563>`_
+* Merge 26.0 into dev (CI-clean rebase of #22749) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22753 <https://github.com/galaxyproject/galaxy/pull/22753>`_
+* Fix tag creation self-deadlock under SQLite by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22846 <https://github.com/galaxyproject/galaxy/pull/22846>`_
+* Handle existing rows in tool_source during db migration by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22870 <https://github.com/galaxyproject/galaxy/pull/22870>`_
+* Always attempt to build tool request for new API endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22894 <https://github.com/galaxyproject/galaxy/pull/22894>`_
+* Fix legacy DatabaseVault secrets canonical key migration by `@davelopez <https://github.com/davelopez>`_ in `#22942 <https://github.com/galaxyproject/galaxy/pull/22942>`_
+* Hide generated headers for tabular previews by `@qchiujunhao <https://github.com/qchiujunhao>`_ in `#22947 <https://github.com/galaxyproject/galaxy/pull/22947>`_
+* Keep the standalone SSE monitor out of the control-queue routing table by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22958 <https://github.com/galaxyproject/galaxy/pull/22958>`_
+* Include hidden intermediates in workflow extraction summary (#22967) by `@jmchilton <https://github.com/jmchilton>`_ in `#22970 <https://github.com/galaxyproject/galaxy/pull/22970>`_
+* Fix storage operation column types (Database migration) by `@davelopez <https://github.com/davelopez>`_ in `#23032 <https://github.com/galaxyproject/galaxy/pull/23032>`_
+* Update spatialdata datatype by `@nilchia <https://github.com/nilchia>`_ in `#23087 <https://github.com/galaxyproject/galaxy/pull/23087>`_
+* Bound memory use in h5grove structured content endpoint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23089 <https://github.com/galaxyproject/galaxy/pull/23089>`_
+* Fix Workflow.copy() dropping readme, help, logo_url and doi by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23117 <https://github.com/galaxyproject/galaxy/pull/23117>`_
+* Fix fasta preview rendering for sequences larger than 100 KB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23163 <https://github.com/galaxyproject/galaxy/pull/23163>`_
+* Use a thread-safe libmagic handle when sniffing datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#23200 <https://github.com/galaxyproject/galaxy/pull/23200>`_
+
+============
+Enhancements
+============
+
+* Show persistent best practice results in workflow editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19546 <https://github.com/galaxyproject/galaxy/pull/19546>`_
+* Various YAML Tool Hardening and Progress toward Tool State Goals by `@jmchilton <https://github.com/jmchilton>`_ in `#21828 <https://github.com/galaxyproject/galaxy/pull/21828>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21853 <https://github.com/galaxyproject/galaxy/pull/21853>`_
+* Drop use of pkg_resources by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21858 <https://github.com/galaxyproject/galaxy/pull/21858>`_
+* Use (also) case-insensitive comparison for user email by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21885 <https://github.com/galaxyproject/galaxy/pull/21885>`_
+* Add ASCII Raster (.asc) datatype by `@tStehling <https://github.com/tStehling>`_ in `#21937 <https://github.com/galaxyproject/galaxy/pull/21937>`_
+* Migrate Python packages to \`src\` layout and pure namespace packages by `@mr-c <https://github.com/mr-c>`_ in `#21977 <https://github.com/galaxyproject/galaxy/pull/21977>`_
+* Improve celery rate limit and concurrency handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22189 <https://github.com/galaxyproject/galaxy/pull/22189>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#22206 <https://github.com/galaxyproject/galaxy/pull/22206>`_
+* Test against psycopg3 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22210 <https://github.com/galaxyproject/galaxy/pull/22210>`_
+* Show file size for CRAM datasets and in download tooltip by `@dannon <https://github.com/dannon>`_ in `#22273 <https://github.com/galaxyproject/galaxy/pull/22273>`_
+* Add Hashicorp Vault token renewal support by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22281 <https://github.com/galaxyproject/galaxy/pull/22281>`_
+* Search and paginate user and roles api by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22311 <https://github.com/galaxyproject/galaxy/pull/22311>`_
+* Add sheet_names metadata to XLSX datatype by `@Anthony96pi <https://github.com/Anthony96pi>`_ in `#22327 <https://github.com/galaxyproject/galaxy/pull/22327>`_
+* Galaxy Notebooks: Persistent Narrative for Human-AI Collaborative Science in Galaxy by `@jmchilton <https://github.com/jmchilton>`_ in `#22361 <https://github.com/galaxyproject/galaxy/pull/22361>`_
+* Clean up legacy SQLAlchemy patterns that emit deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22462 <https://github.com/galaxyproject/galaxy/pull/22462>`_
+* Clean up Pydantic v2 deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22463 <https://github.com/galaxyproject/galaxy/pull/22463>`_
+* Clean up remaining deprecation warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22473 <https://github.com/galaxyproject/galaxy/pull/22473>`_
+* Mark History.jobs relationship as viewonly by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22474 <https://github.com/galaxyproject/galaxy/pull/22474>`_
+* Server-Sent Events for history + notification updates by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22513 <https://github.com/galaxyproject/galaxy/pull/22513>`_
+* Fix display of BAMs with large headers by `@wm75 <https://github.com/wm75>`_ in `#22516 <https://github.com/galaxyproject/galaxy/pull/22516>`_
+* Speed up integration tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22538 <https://github.com/galaxyproject/galaxy/pull/22538>`_
+* Overhaul and synchronize collection type algebra verbs by `@jmchilton <https://github.com/jmchilton>`_ in `#22565 <https://github.com/galaxyproject/galaxy/pull/22565>`_
+* Use now() wrapper instead of datetime.now() by `@bgruening <https://github.com/bgruening>`_ in `#22579 <https://github.com/galaxyproject/galaxy/pull/22579>`_
+* Add bulk dataset storage migration by `@davelopez <https://github.com/davelopez>`_ in `#22606 <https://github.com/galaxyproject/galaxy/pull/22606>`_
+* Improve type annotation of workflow management methods by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22637 <https://github.com/galaxyproject/galaxy/pull/22637>`_
+* Paginate /api/tools/{tool_id}/build history options by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22643 <https://github.com/galaxyproject/galaxy/pull/22643>`_
+* Enhance workflow extraction by IDs with deduplication and UI improvements by `@jmchilton <https://github.com/jmchilton>`_ in `#22706 <https://github.com/galaxyproject/galaxy/pull/22706>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Respect workflow object store preference for mapped step outputs  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22409 <https://github.com/galaxyproject/galaxy/pull/22409>`_
+* Avoid premature commit when copying MetadataFile by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22422 <https://github.com/galaxyproject/galaxy/pull/22422>`_
+* Fix testing, publishing and dependencies of packages by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22445 <https://github.com/galaxyproject/galaxy/pull/22445>`_
+* Fix \`get_structure\` when it is passed a DCE with nested elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22453 <https://github.com/galaxyproject/galaxy/pull/22453>`_
+* Enforce file source access during dataset materialization by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22486 <https://github.com/galaxyproject/galaxy/pull/22486>`_
+* Fix sample sheet upload without sample-sheet-specific columns  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22488 <https://github.com/galaxyproject/galaxy/pull/22488>`_
+* Truncate dataset name in export arcname to avoid OSError by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22518 <https://github.com/galaxyproject/galaxy/pull/22518>`_
+* Catch end of file error when reading corrupted tabular dataset by `@guerler <https://github.com/guerler>`_ in `#22523 <https://github.com/galaxyproject/galaxy/pull/22523>`_
+* Fix data manager URL for managers with '+' version suffix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22525 <https://github.com/galaxyproject/galaxy/pull/22525>`_
+* update the binary.py for spatialdata so it also works if the file has… by `@nilchia <https://github.com/nilchia>`_ in `#22802 <https://github.com/galaxyproject/galaxy/pull/22802>`_
+
+============
+Enhancements
+============
+
+* Replace per-term joins in workflow search with EXISTS subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22548 <https://github.com/galaxyproject/galaxy/pull/22548>`_
+* add TEI XML datatype by `@bgruening <https://github.com/bgruening>`_ in `#22718 <https://github.com/galaxyproject/galaxy/pull/22718>`_
+
+-------------------
+26.0.0 (2026-04-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Drop down revision for drop_job_params migration by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21122 <https://github.com/galaxyproject/galaxy/pull/21122>`_
+* Create alembic merge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21447 <https://github.com/galaxyproject/galaxy/pull/21447>`_
+* Provide more accurate step hints for failing subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21514 <https://github.com/galaxyproject/galaxy/pull/21514>`_
+* Fix width and height assignment for image metadata using Pillow by `@kostrykin <https://github.com/kostrykin>`_ in `#21554 <https://github.com/galaxyproject/galaxy/pull/21554>`_
+* Avoid slash duplication in display application urls by `@guerler <https://github.com/guerler>`_ in `#21809 <https://github.com/galaxyproject/galaxy/pull/21809>`_
+* Fix redirect upon impersonation by `@guerler <https://github.com/guerler>`_ in `#21810 <https://github.com/galaxyproject/galaxy/pull/21810>`_
+* Fix dataset collection tag duplication when copying a history by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21984 <https://github.com/galaxyproject/galaxy/pull/21984>`_
+* Fix AttributeError serializing implicit output collections during job prep by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22034 <https://github.com/galaxyproject/galaxy/pull/22034>`_
+* Fix ``preferred_object_store_id`` not respected for discovered outputs with extended metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22056 <https://github.com/galaxyproject/galaxy/pull/22056>`_
+* Fix TypeError when column_names metadata is None by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22057 <https://github.com/galaxyproject/galaxy/pull/22057>`_
+* Fail job gracefully when output name exceeds 255 character DB limit by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22059 <https://github.com/galaxyproject/galaxy/pull/22059>`_
+* Fix nested collection query performance by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22119 <https://github.com/galaxyproject/galaxy/pull/22119>`_
+* Fix CardinalityViolation in nested collection ARRAY walk scalar subqueries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22123 <https://github.com/galaxyproject/galaxy/pull/22123>`_
+* Use skip_locked also when updating collection  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22133 <https://github.com/galaxyproject/galaxy/pull/22133>`_
+* Fix redundant empty collection elements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22154 <https://github.com/galaxyproject/galaxy/pull/22154>`_
+* Don't fail on probable delete race by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22183 <https://github.com/galaxyproject/galaxy/pull/22183>`_
+* Back port collection fixes from #22170. by `@jmchilton <https://github.com/jmchilton>`_ in `#22193 <https://github.com/galaxyproject/galaxy/pull/22193>`_
+* Optimize dataset get_edit API by deferring expensive role queries by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22232 <https://github.com/galaxyproject/galaxy/pull/22232>`_
+* Batch-prefetch HDCA job_state_summary in history contents listing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22256 <https://github.com/galaxyproject/galaxy/pull/22256>`_
+* Sequence datatypes: only read first character per line for setting metadata by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#22276 <https://github.com/galaxyproject/galaxy/pull/22276>`_
+* Fix slow get_private_role_user_emails_dict query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22307 <https://github.com/galaxyproject/galaxy/pull/22307>`_
+* Fix timestamp parsing in job import/export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22372 <https://github.com/galaxyproject/galaxy/pull/22372>`_
+* Ensure ``x-content-truncated`` header is string by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22386 <https://github.com/galaxyproject/galaxy/pull/22386>`_
+* Fix dataset preview rendering to preserve newlines by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22397 <https://github.com/galaxyproject/galaxy/pull/22397>`_
+
+============
+Enhancements
+============
+
+* Refactor display application handling by `@guerler <https://github.com/guerler>`_ in `#15076 <https://github.com/galaxyproject/galaxy/pull/15076>`_
+* Tool Request API  by `@jmchilton <https://github.com/jmchilton>`_ in `#20935 <https://github.com/galaxyproject/galaxy/pull/20935>`_
+* Remove Trackster by `@guerler <https://github.com/guerler>`_ in `#20974 <https://github.com/galaxyproject/galaxy/pull/20974>`_
+* Move database revision tags to separate file by `@guerler <https://github.com/guerler>`_ in `#20998 <https://github.com/galaxyproject/galaxy/pull/20998>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21043 <https://github.com/galaxyproject/galaxy/pull/21043>`_
+* Remove Job.params by `@jdavcs <https://github.com/jdavcs>`_ in `#21075 <https://github.com/galaxyproject/galaxy/pull/21075>`_
+* Remove tabular chunked, binary and large file mako by `@guerler <https://github.com/guerler>`_ in `#21106 <https://github.com/galaxyproject/galaxy/pull/21106>`_
+* Add type annotations to job handling code by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21171 <https://github.com/galaxyproject/galaxy/pull/21171>`_
+* Reimplement keycloak/cilogon as PSA providers and remove custos by `@nuwang <https://github.com/nuwang>`_ in `#21234 <https://github.com/galaxyproject/galaxy/pull/21234>`_
+* Slight improvement of mztab2 datatype by `@nguilhot <https://github.com/nguilhot>`_ in `#21258 <https://github.com/galaxyproject/galaxy/pull/21258>`_
+* Move js-client bootstrapping to FastAPI by `@guerler <https://github.com/guerler>`_ in `#21264 <https://github.com/galaxyproject/galaxy/pull/21264>`_
+* Implement GA4GH WES API by `@jmchilton <https://github.com/jmchilton>`_ in `#21335 <https://github.com/galaxyproject/galaxy/pull/21335>`_
+* Fix: tool execution typing improvements/fixes by `@jmchilton <https://github.com/jmchilton>`_ in `#21374 <https://github.com/galaxyproject/galaxy/pull/21374>`_
+* Add initial support for the DICOM format by `@kostrykin <https://github.com/kostrykin>`_ in `#21385 <https://github.com/galaxyproject/galaxy/pull/21385>`_
+* Add AI Agent Framework and ChatGXY 2.0 by `@dannon <https://github.com/dannon>`_ in `#21434 <https://github.com/galaxyproject/galaxy/pull/21434>`_
+* Enable attaching sample sheet to landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21489 <https://github.com/galaxyproject/galaxy/pull/21489>`_
+* Discriminate decompression tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21510 <https://github.com/galaxyproject/galaxy/pull/21510>`_
+* Include subworkflow jobs in invocation metrics by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21511 <https://github.com/galaxyproject/galaxy/pull/21511>`_
+* Implement subworkflow invocation export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21512 <https://github.com/galaxyproject/galaxy/pull/21512>`_
+* Implement workflow completion monitoring with extensible hooks by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21532 <https://github.com/galaxyproject/galaxy/pull/21532>`_
+* Clean up code with pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21540 <https://github.com/galaxyproject/galaxy/pull/21540>`_
+* Drop support for Python 3.9 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21583 <https://github.com/galaxyproject/galaxy/pull/21583>`_
+* Apply 2026 black style by `@galaxybot <https://github.com/galaxybot>`_ in `#21618 <https://github.com/galaxyproject/galaxy/pull/21618>`_
+* Allow connecting sample sheet inputs to compatible collection inputs in editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21859 <https://github.com/galaxyproject/galaxy/pull/21859>`_
+* Add new datatypes: .taf and .taf.gz by `@Maed0x <https://github.com/Maed0x>`_ in `#22242 <https://github.com/galaxyproject/galaxy/pull/22242>`_
+* Add _F/_R auto-pairing filter for forward/reverse datasets by `@jmchilton <https://github.com/jmchilton>`_ in `#22267 <https://github.com/galaxyproject/galaxy/pull/22267>`_
+
+=============
+Other changes
+=============
+
+* Update revision tags for release 25.1 by `@arash77 <https://github.com/arash77>`_ in `#21022 <https://github.com/galaxyproject/galaxy/pull/21022>`_
+* Merge 25.1 into dev and create alembic merge revision by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21440 <https://github.com/galaxyproject/galaxy/pull/21440>`_
+* Add Database Revision for 26.0 by `@guerler <https://github.com/guerler>`_ in `#21675 <https://github.com/galaxyproject/galaxy/pull/21675>`_
+* Fix on_complete column type mismatch by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21765 <https://github.com/galaxyproject/galaxy/pull/21765>`_
+
+-------------------
+25.1.2 (2026-03-09)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix private dataset sharing error handling by `@davelopez <https://github.com/davelopez>`_ in `#21689 <https://github.com/galaxyproject/galaxy/pull/21689>`_
+* Fix database migration error from 25.0 > 25.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#21737 <https://github.com/galaxyproject/galaxy/pull/21737>`_
+* Make database heartbeat more robust (backport) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21812 <https://github.com/galaxyproject/galaxy/pull/21812>`_
+* Fix recording duplicate workflow_request_input_step_parameter rows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21980 <https://github.com/galaxyproject/galaxy/pull/21980>`_
+
+=============
+Other changes
+=============
+
+* Fix worker segfault in gunicorn preload mode on OSX by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21837 <https://github.com/galaxyproject/galaxy/pull/21837>`_
+
+-------------------
+25.1.1 (2026-02-03)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Sample sheet column fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21446 <https://github.com/galaxyproject/galaxy/pull/21446>`_
+* Maintain column definitions on map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21468 <https://github.com/galaxyproject/galaxy/pull/21468>`_
+* Add missing test file for sig datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21473 <https://github.com/galaxyproject/galaxy/pull/21473>`_
+* Do not update a user's update_time when an admin archives (and purges) a history by `@natefoo <https://github.com/natefoo>`_ in `#21484 <https://github.com/galaxyproject/galaxy/pull/21484>`_
+* Add missing ending newline to test.sig test data file by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21485 <https://github.com/galaxyproject/galaxy/pull/21485>`_
+* Usability fixes for sample sheet selection.  by `@jmchilton <https://github.com/jmchilton>`_ in `#21503 <https://github.com/galaxyproject/galaxy/pull/21503>`_
+* Fix exception message to enable debugging of missing dataset issue. by `@jmchilton <https://github.com/jmchilton>`_ in `#21504 <https://github.com/galaxyproject/galaxy/pull/21504>`_
+* Add missing dependencies to ``galaxy-files`` package by `@nsoranzo <https://github.com/nsoranzo>`_ in `#21518 <https://github.com/galaxyproject/galaxy/pull/21518>`_
+* Fix job cache collection copy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21558 <https://github.com/galaxyproject/galaxy/pull/21558>`_
+* Fix #21542 - allow workbook bootstrap generation for sample sheet collection types. by `@jmchilton <https://github.com/jmchilton>`_ in `#21584 <https://github.com/galaxyproject/galaxy/pull/21584>`_
+* Fix race condition in workflow collection populated state check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21613 <https://github.com/galaxyproject/galaxy/pull/21613>`_
+* Fix collection job state not preserved during history export/import by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21716 <https://github.com/galaxyproject/galaxy/pull/21716>`_
+
+============
+Enhancements
+============
+
+* Add Sourmash sig new datatype by `@SaimMomin12 <https://github.com/SaimMomin12>`_ in `#21469 <https://github.com/galaxyproject/galaxy/pull/21469>`_
+* Add database operation tool to convert sample sheets to list collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21625 <https://github.com/galaxyproject/galaxy/pull/21625>`_
+
+-------------------
+25.1.0 (2025-12-12)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix alembic down_revision for trigger replacement migration by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20501 <https://github.com/galaxyproject/galaxy/pull/20501>`_
+* Add a merge migration, revert previous edit by `@jdavcs <https://github.com/jdavcs>`_ in `#20507 <https://github.com/galaxyproject/galaxy/pull/20507>`_
+* Add missing cleanup table by `@jdavcs <https://github.com/jdavcs>`_ in `#20594 <https://github.com/galaxyproject/galaxy/pull/20594>`_
+* Fix anndata metadata by `@nilchia <https://github.com/nilchia>`_ in `#20778 <https://github.com/galaxyproject/galaxy/pull/20778>`_
+* Fix Ipynb datatype sniffer and add unit tests. by `@ksuderman <https://github.com/ksuderman>`_ in `#20811 <https://github.com/galaxyproject/galaxy/pull/20811>`_
+* Bump requirement of directory converters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20834 <https://github.com/galaxyproject/galaxy/pull/20834>`_
+* Extract: do not use common prefix dir by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20929 <https://github.com/galaxyproject/galaxy/pull/20929>`_
+* Ensure that conversion_key is defined by `@guerler <https://github.com/guerler>`_ in `#20984 <https://github.com/galaxyproject/galaxy/pull/20984>`_
+* Fix invocation export dataset exclusion by `@davelopez <https://github.com/davelopez>`_ in `#21091 <https://github.com/galaxyproject/galaxy/pull/21091>`_
+* Restore job.get_param_values by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21130 <https://github.com/galaxyproject/galaxy/pull/21130>`_
+* Improve _touch_collection_update_time_cte performance by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21134 <https://github.com/galaxyproject/galaxy/pull/21134>`_
+* Assorted workbook upload fixes.  by `@jmchilton <https://github.com/jmchilton>`_ in `#21203 <https://github.com/galaxyproject/galaxy/pull/21203>`_
+* Fix database revision tags by `@jdavcs <https://github.com/jdavcs>`_ in `#21377 <https://github.com/galaxyproject/galaxy/pull/21377>`_
+* Maintain columns on sample sheet map over by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21436 <https://github.com/galaxyproject/galaxy/pull/21436>`_
+
+============
+Enhancements
+============
+
+* Support credentials(secrets/variables) in tool requirements by `@arash77 <https://github.com/arash77>`_ in `#19084 <https://github.com/galaxyproject/galaxy/pull/19084>`_
+* Implement Sample Sheets  by `@jmchilton <https://github.com/jmchilton>`_ in `#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`_
+* 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>`_
+* Add short term storage expiration indicator to history items by `@davelopez <https://github.com/davelopez>`_ in `#20332 <https://github.com/galaxyproject/galaxy/pull/20332>`_
+* Type annotation fixes for mypy 1.16.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20424 <https://github.com/galaxyproject/galaxy/pull/20424>`_
+* Implement dataset source requested transformations. by `@jmchilton <https://github.com/jmchilton>`_ in `#20435 <https://github.com/galaxyproject/galaxy/pull/20435>`_
+* Remove deprecated tool document cache by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20510 <https://github.com/galaxyproject/galaxy/pull/20510>`_
+* 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>`_
+* Implement Data Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#20592 <https://github.com/galaxyproject/galaxy/pull/20592>`_
+* Clean up code from pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20642 <https://github.com/galaxyproject/galaxy/pull/20642>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20680 <https://github.com/galaxyproject/galaxy/pull/20680>`_
+* Attempt to reuse previously materialized datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20718 <https://github.com/galaxyproject/galaxy/pull/20718>`_
+* 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>`_
+* Hierarchical display collection dataset states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20731 <https://github.com/galaxyproject/galaxy/pull/20731>`_
+* 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>`_
+* Improve type annotation for job runners and ``InteractiveToolManager`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20871 <https://github.com/galaxyproject/galaxy/pull/20871>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#20905 <https://github.com/galaxyproject/galaxy/pull/20905>`_
+* Allow sending and tracking landing request origin by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20957 <https://github.com/galaxyproject/galaxy/pull/20957>`_
+* Track landing request with invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20960 <https://github.com/galaxyproject/galaxy/pull/20960>`_
+* Optimize /api/invocations/steps/{step_id} by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21249 <https://github.com/galaxyproject/galaxy/pull/21249>`_
+* A better way to designate config_watcher by `@jdavcs <https://github.com/jdavcs>`_ in `#21426 <https://github.com/galaxyproject/galaxy/pull/21426>`_
+
+=============
+Other changes
+=============
+
+* Small tweaks and cleanup from sample sheets branch by `@jmchilton <https://github.com/jmchilton>`_ in `#20229 <https://github.com/galaxyproject/galaxy/pull/20229>`_
+* Merge `release_25.0` into `dev` by `@davelopez <https://github.com/davelopez>`_ in `#20484 <https://github.com/galaxyproject/galaxy/pull/20484>`_
+* Merge release_25.0 into dev by `@davelopez <https://github.com/davelopez>`_ in `#20490 <https://github.com/galaxyproject/galaxy/pull/20490>`_
+* Sample Sheet Bug Fixes around Preserving Collection Metadata by `@jmchilton <https://github.com/jmchilton>`_ in `#20749 <https://github.com/galaxyproject/galaxy/pull/20749>`_
+* Add tool_id and tool_version column to tool_landing_request table by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20795 <https://github.com/galaxyproject/galaxy/pull/20795>`_
+* Add 25.1 migration tags by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21017 <https://github.com/galaxyproject/galaxy/pull/21017>`_
+* Restore .get_metadata function by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21045 <https://github.com/galaxyproject/galaxy/pull/21045>`_
+* Fix forward merge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21307 <https://github.com/galaxyproject/galaxy/pull/21307>`_
+* Fix db revision tags by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21442 <https://github.com/galaxyproject/galaxy/pull/21442>`_
+
+-------------------
+25.0.4 (2025-11-18)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Add safetensors datatype by `@nilchia <https://github.com/nilchia>`_ in `#20754 <https://github.com/galaxyproject/galaxy/pull/20754>`_
+* Skip sam metadata if we have too many references by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20820 <https://github.com/galaxyproject/galaxy/pull/20820>`_
+* Backport of #20984 by `@davelopez <https://github.com/davelopez>`_ in `#20994 <https://github.com/galaxyproject/galaxy/pull/20994>`_
+* Backport fix anndata datatype update by `@nilchia <https://github.com/nilchia>`_ in `#21111 <https://github.com/galaxyproject/galaxy/pull/21111>`_
+* Create new datasets when creating skipped database operation tool outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21142 <https://github.com/galaxyproject/galaxy/pull/21142>`_
+* Fix optional param unset in RO-Crate export by `@davelopez <https://github.com/davelopez>`_ in `#21192 <https://github.com/galaxyproject/galaxy/pull/21192>`_
+
+============
+Enhancements
+============
+
+* Add Auspice JSON datatype by `@pvanheus <https://github.com/pvanheus>`_ in `#20466 <https://github.com/galaxyproject/galaxy/pull/20466>`_
+* Add SpatialData datatype by `@nilchia <https://github.com/nilchia>`_ in `#21000 <https://github.com/galaxyproject/galaxy/pull/21000>`_
+* Use job cache also for implicit conversions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21021 <https://github.com/galaxyproject/galaxy/pull/21021>`_
+* support ZARR v3 for  Spatialdata dt by `@nilchia <https://github.com/nilchia>`_ in `#21265 <https://github.com/galaxyproject/galaxy/pull/21265>`_
+
+-------------------
+25.0.3 (2025-09-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Ensure that workflow invocations are persisted with state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20784 <https://github.com/galaxyproject/galaxy/pull/20784>`_
+* Fix password reset functionality for lowercase emails by `@jdavcs <https://github.com/jdavcs>`_ in `#20801 <https://github.com/galaxyproject/galaxy/pull/20801>`_
+* Drop eager argument from invocation related methods by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20863 <https://github.com/galaxyproject/galaxy/pull/20863>`_
+* Use ``populated_optimized`` when serializing collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20872 <https://github.com/galaxyproject/galaxy/pull/20872>`_
+* Speed up ``ImplicitCollectionJobs.job_list`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20887 <https://github.com/galaxyproject/galaxy/pull/20887>`_
+* Add LDDA purged property by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20895 <https://github.com/galaxyproject/galaxy/pull/20895>`_
+* Avoid potential race condition in replacement_for_connection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20909 <https://github.com/galaxyproject/galaxy/pull/20909>`_
+* Fix sessionless tag creation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20925 <https://github.com/galaxyproject/galaxy/pull/20925>`_
+
+============
+Enhancements
+============
+
+* Fix DOCX detection and add PPTX support by `@arash77 <https://github.com/arash77>`_ in `#20827 <https://github.com/galaxyproject/galaxy/pull/20827>`_
+* Add HiC datatype by `@abretaud <https://github.com/abretaud>`_ in `#20874 <https://github.com/galaxyproject/galaxy/pull/20874>`_
+
+=============
+Other changes
+=============
+
+* Undo accidental push by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#20854 <https://github.com/galaxyproject/galaxy/pull/20854>`_
+* Merge 25.0 into dev by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20911 <https://github.com/galaxyproject/galaxy/pull/20911>`_
+
+-------------------
+25.0.2 (2025-08-13)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Remove ``num_unique_values`` tiff metadata element by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20464 <https://github.com/galaxyproject/galaxy/pull/20464>`_
+* Propagate cached job output replacement to copies of outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20553 <https://github.com/galaxyproject/galaxy/pull/20553>`_
+* Fix deferred datasets in multiple dataset parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#20650 <https://github.com/galaxyproject/galaxy/pull/20650>`_
+* Add `num_unique_values` tiff metadata element, fixed by `@kostrykin <https://github.com/kostrykin>`_ in `#20669 <https://github.com/galaxyproject/galaxy/pull/20669>`_
+
+============
+Enhancements
+============
+
+* Improve workflow monitor loop times by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20522 <https://github.com/galaxyproject/galaxy/pull/20522>`_
+* Pairtool updated format and sniffers by `@Smeds <https://github.com/Smeds>`_ in `#20634 <https://github.com/galaxyproject/galaxy/pull/20634>`_
+* Add support for M4A audio files by `@arash77 <https://github.com/arash77>`_ in `#20667 <https://github.com/galaxyproject/galaxy/pull/20667>`_
+
+-------------------
+25.0.1 (2025-06-20)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Pin isa-rwval 0.10.11, drop conditional import handling by `@natefoo <https://github.com/natefoo>`_ in `#20527 <https://github.com/galaxyproject/galaxy/pull/20527>`_
+
+-------------------
+25.0.0 (2025-06-18)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Better handling of public pages and workflows authored by deleted users by `@jdavcs <https://github.com/jdavcs>`_ in `#19394 <https://github.com/galaxyproject/galaxy/pull/19394>`_
+* Alternative `format_source` fix by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19395 <https://github.com/galaxyproject/galaxy/pull/19395>`_
+* Use ``id`` entity attribute when setting ``exampleOfWork`` property by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19396 <https://github.com/galaxyproject/galaxy/pull/19396>`_
+* Fix package test errors: Ignore mypy errors caused by social-auth-core 4.5.5 by `@jdavcs <https://github.com/jdavcs>`_ in `#19620 <https://github.com/galaxyproject/galaxy/pull/19620>`_
+* Fix Galaxy ignoring job object_store_id for quota check by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19854 <https://github.com/galaxyproject/galaxy/pull/19854>`_
+* Fix various mypy issues around mapped attributes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19883 <https://github.com/galaxyproject/galaxy/pull/19883>`_
+* More fixes to `FormData` drag and drop and typing by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19900 <https://github.com/galaxyproject/galaxy/pull/19900>`_
+* Use lower case extension for setting datatype in data discovery by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#19954 <https://github.com/galaxyproject/galaxy/pull/19954>`_
+* Add new line to vtpascii test file by `@guerler <https://github.com/guerler>`_ in `#20051 <https://github.com/galaxyproject/galaxy/pull/20051>`_
+* Fix certain cases of collection parameter handling during workflow execution. by `@jmchilton <https://github.com/jmchilton>`_ in `#20152 <https://github.com/galaxyproject/galaxy/pull/20152>`_
+* Update tabular_csv.py to use less memory in tsv->csv conversion by `@cat-bro <https://github.com/cat-bro>`_ in `#20187 <https://github.com/galaxyproject/galaxy/pull/20187>`_
+* Fix tool-provided metadata for CONVERTER_tar_to_directory by `@mr-c <https://github.com/mr-c>`_ in `#20260 <https://github.com/galaxyproject/galaxy/pull/20260>`_
+* Log invalid vault paths by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20363 <https://github.com/galaxyproject/galaxy/pull/20363>`_
+* Update triggers by `@jdavcs <https://github.com/jdavcs>`_ in `#20425 <https://github.com/galaxyproject/galaxy/pull/20425>`_
+* Fix copying of job metrics for cached jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20436 <https://github.com/galaxyproject/galaxy/pull/20436>`_
+* Dataset Display and Preferred Viz fixes by `@dannon <https://github.com/dannon>`_ in `#20439 <https://github.com/galaxyproject/galaxy/pull/20439>`_
+* Recreate triggers by `@jdavcs <https://github.com/jdavcs>`_ in `#20491 <https://github.com/galaxyproject/galaxy/pull/20491>`_
+
+============
+Enhancements
+============
+
+* Workflow Editor Activity Bar by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#18729 <https://github.com/galaxyproject/galaxy/pull/18729>`_
+* Add author and tools details in RO-Crate by `@Marie59 <https://github.com/Marie59>`_ in `#18820 <https://github.com/galaxyproject/galaxy/pull/18820>`_
+* Extend image metadata by `@kostrykin <https://github.com/kostrykin>`_ in `#18951 <https://github.com/galaxyproject/galaxy/pull/18951>`_
+* Implement tool markdown reports. by `@jmchilton <https://github.com/jmchilton>`_ in `#19054 <https://github.com/galaxyproject/galaxy/pull/19054>`_
+* Let file sources choose a path for uploaded files by `@kysrpex <https://github.com/kysrpex>`_ in `#19154 <https://github.com/galaxyproject/galaxy/pull/19154>`_
+* Calculate hash for new non-deferred datasets when finishing a job by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19181 <https://github.com/galaxyproject/galaxy/pull/19181>`_
+* Fix UP031 errors - Part 1 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19194 <https://github.com/galaxyproject/galaxy/pull/19194>`_
+* Fix UP031 errors - Part 4 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19235 <https://github.com/galaxyproject/galaxy/pull/19235>`_
+* Fix UP031 errors - Part 5 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19282 <https://github.com/galaxyproject/galaxy/pull/19282>`_
+* Fix UP031 errors - Part 6 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19314 <https://github.com/galaxyproject/galaxy/pull/19314>`_
+* Misc fixes 202412 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19341 <https://github.com/galaxyproject/galaxy/pull/19341>`_
+* Type annotation fixes for mypy 1.14.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19372 <https://github.com/galaxyproject/galaxy/pull/19372>`_
+* Empower Users to Build More Kinds of Collections, More Intelligently by `@jmchilton <https://github.com/jmchilton>`_ in `#19377 <https://github.com/galaxyproject/galaxy/pull/19377>`_
+* SQLAlchemy 2.0 follow-up by `@jdavcs <https://github.com/jdavcs>`_ in `#19388 <https://github.com/galaxyproject/galaxy/pull/19388>`_
+* Set safe default extraction filter for tar archives by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19406 <https://github.com/galaxyproject/galaxy/pull/19406>`_
+* Remove transaction helper by `@jdavcs <https://github.com/jdavcs>`_ in `#19407 <https://github.com/galaxyproject/galaxy/pull/19407>`_
+* Prevent users from reusing a banned email after account is purged by `@jdavcs <https://github.com/jdavcs>`_ in `#19413 <https://github.com/galaxyproject/galaxy/pull/19413>`_
+* Add IGB display support for CRAM files by `@paige-kulzer <https://github.com/paige-kulzer>`_ in `#19428 <https://github.com/galaxyproject/galaxy/pull/19428>`_
+* Add User-Defined Tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19434 <https://github.com/galaxyproject/galaxy/pull/19434>`_
+* Type annotation improvements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19485 <https://github.com/galaxyproject/galaxy/pull/19485>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19567 <https://github.com/galaxyproject/galaxy/pull/19567>`_
+* Expand workflow metadata for readme.  by `@jmchilton <https://github.com/jmchilton>`_ in `#19591 <https://github.com/galaxyproject/galaxy/pull/19591>`_
+* Format code with black 25.1.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19625 <https://github.com/galaxyproject/galaxy/pull/19625>`_
+* Type annotation improvements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19642 <https://github.com/galaxyproject/galaxy/pull/19642>`_
+* Generate correct types for Dataset source transformations on backend. by `@jmchilton <https://github.com/jmchilton>`_ in `#19666 <https://github.com/galaxyproject/galaxy/pull/19666>`_
+* Drop support for Python 3.8 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19685 <https://github.com/galaxyproject/galaxy/pull/19685>`_
+* Define simple models for job messages. by `@jmchilton <https://github.com/jmchilton>`_ in `#19688 <https://github.com/galaxyproject/galaxy/pull/19688>`_
+* Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 1 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19706 <https://github.com/galaxyproject/galaxy/pull/19706>`_
+* Use model classes from ``galaxy.model`` instead of ``app.model`` object - Part 2 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19726 <https://github.com/galaxyproject/galaxy/pull/19726>`_
+* Add bigbed to bed converter and tests by `@d-callan <https://github.com/d-callan>`_ in `#19787 <https://github.com/galaxyproject/galaxy/pull/19787>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#19816 <https://github.com/galaxyproject/galaxy/pull/19816>`_
+* Populate image metadata without allocating memory for the entire image content by `@kostrykin <https://github.com/kostrykin>`_ in `#19830 <https://github.com/galaxyproject/galaxy/pull/19830>`_
+* Add mandatory RO-Crate metadata when exporting by `@elichad <https://github.com/elichad>`_ in `#19846 <https://github.com/galaxyproject/galaxy/pull/19846>`_
+* Improve type annotations of ``ModelPersistenceContext`` and derived classes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19852 <https://github.com/galaxyproject/galaxy/pull/19852>`_
+* Drop old galaxy_session records by `@jdavcs <https://github.com/jdavcs>`_ in `#19872 <https://github.com/galaxyproject/galaxy/pull/19872>`_
+* Clarify is_active method usage for Python Social Auth in Galaxy by `@dannon <https://github.com/dannon>`_ in `#19899 <https://github.com/galaxyproject/galaxy/pull/19899>`_
+* Drop old job metrics by `@jdavcs <https://github.com/jdavcs>`_ in `#19936 <https://github.com/galaxyproject/galaxy/pull/19936>`_
+* Allow PathLike parameters in ``make_fast_zipfile()`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19955 <https://github.com/galaxyproject/galaxy/pull/19955>`_
+* Add type hints around collection copying and job things by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19961 <https://github.com/galaxyproject/galaxy/pull/19961>`_
+* Job cache allow different names when possible by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19962 <https://github.com/galaxyproject/galaxy/pull/19962>`_
+* Improve type annotation of tool parameter wrapping by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19991 <https://github.com/galaxyproject/galaxy/pull/19991>`_
+* Implement dataset collection support in workflow landing requests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20004 <https://github.com/galaxyproject/galaxy/pull/20004>`_
+* Enable ``warn_redundant_casts`` mypy option and drop redundant casts by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20008 <https://github.com/galaxyproject/galaxy/pull/20008>`_
+* Add vitesscejson datatype by `@guerler <https://github.com/guerler>`_ in `#20027 <https://github.com/galaxyproject/galaxy/pull/20027>`_
+* Add VTK Visualization Toolkit Plugin by `@guerler <https://github.com/guerler>`_ in `#20028 <https://github.com/galaxyproject/galaxy/pull/20028>`_
+* Add DOI to workflow metadata by `@jdavcs <https://github.com/jdavcs>`_ in `#20033 <https://github.com/galaxyproject/galaxy/pull/20033>`_
+* Add sample datasets for visualizations by `@guerler <https://github.com/guerler>`_ in `#20046 <https://github.com/galaxyproject/galaxy/pull/20046>`_
+* Add docx datatype by `@bgruening <https://github.com/bgruening>`_ in `#20055 <https://github.com/galaxyproject/galaxy/pull/20055>`_
+* Add flac audio format by `@bgruening <https://github.com/bgruening>`_ in `#20057 <https://github.com/galaxyproject/galaxy/pull/20057>`_
+* Improve type annotation of `galaxy.util` submodules by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20104 <https://github.com/galaxyproject/galaxy/pull/20104>`_
+* Add specific datatypes for Cytoscape and Kepler.gl by `@guerler <https://github.com/guerler>`_ in `#20117 <https://github.com/galaxyproject/galaxy/pull/20117>`_
+* Visualization-First Display functionality by `@dannon <https://github.com/dannon>`_ in `#20190 <https://github.com/galaxyproject/galaxy/pull/20190>`_
+* Improve type annotation of ``galaxy.model.dataset_collections`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#20194 <https://github.com/galaxyproject/galaxy/pull/20194>`_
+* Improve performance of job cache query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20319 <https://github.com/galaxyproject/galaxy/pull/20319>`_
+* DatasetView and Card Polish by `@dannon <https://github.com/dannon>`_ in `#20342 <https://github.com/galaxyproject/galaxy/pull/20342>`_
+
+=============
+Other changes
+=============
+
+* Merge 24.2 into dev by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#19933 <https://github.com/galaxyproject/galaxy/pull/19933>`_
+* Fix copying job output from discovered outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19999 <https://github.com/galaxyproject/galaxy/pull/19999>`_
+* Add 25.0 migration tags by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#20265 <https://github.com/galaxyproject/galaxy/pull/20265>`_
+* Rename vitessce_json file_ext to vitessce.json by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20473 <https://github.com/galaxyproject/galaxy/pull/20473>`_
+
+-------------------
+24.2.4 (2025-06-17)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Reduce default framework tool test timeout to 60 seconds by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19819 <https://github.com/galaxyproject/galaxy/pull/19819>`_
+* Try to recover from recurring activation link error by `@jdavcs <https://github.com/jdavcs>`_ in `#19844 <https://github.com/galaxyproject/galaxy/pull/19844>`_
+* Check if index exists before creating by `@jdavcs <https://github.com/jdavcs>`_ in `#19873 <https://github.com/galaxyproject/galaxy/pull/19873>`_
+* Let pysam use extra threads available in job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19917 <https://github.com/galaxyproject/galaxy/pull/19917>`_
+* Handle special charater in raw SQL by `@jdavcs <https://github.com/jdavcs>`_ in `#19925 <https://github.com/galaxyproject/galaxy/pull/19925>`_
+* Use ``make_fast_zipfile`` directly by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19947 <https://github.com/galaxyproject/galaxy/pull/19947>`_
+* Job cache backports by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20078 <https://github.com/galaxyproject/galaxy/pull/20078>`_
+* Conditionally import from `galaxy.config` in `galaxy.model.mapping` if `TYPE_CHECKING` by `@natefoo <https://github.com/natefoo>`_ in `#20209 <https://github.com/galaxyproject/galaxy/pull/20209>`_
+* Refactor display_as URL generation for UCSC links and fix to remove double slashes in URL by `@natefoo <https://github.com/natefoo>`_ in `#20239 <https://github.com/galaxyproject/galaxy/pull/20239>`_
+* Make response header values strings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20475 <https://github.com/galaxyproject/galaxy/pull/20475>`_
+* Link workflow invocation outputs upon importing invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#20485 <https://github.com/galaxyproject/galaxy/pull/20485>`_
+* Make optional edam-ontology in datatypes registry optional by `@natefoo <https://github.com/natefoo>`_ in `#20492 <https://github.com/galaxyproject/galaxy/pull/20492>`_
+
+============
+Enhancements
+============
+
+* Bump up max_peek_size to 50MB by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19823 <https://github.com/galaxyproject/galaxy/pull/19823>`_
+
+-------------------
+24.2.3 (2025-03-16)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix private role name performance issue by `@jdavcs <https://github.com/jdavcs>`_ in `#19679 <https://github.com/galaxyproject/galaxy/pull/19679>`_
+* Fix anndata metadata setting for data with integer indexes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19774 <https://github.com/galaxyproject/galaxy/pull/19774>`_
+* Fix parameter model constructions with leading underscores, fixes converter linting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19790 <https://github.com/galaxyproject/galaxy/pull/19790>`_
+
+============
+Enhancements
+============
+
+* Add rDock prm datatype by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19783 <https://github.com/galaxyproject/galaxy/pull/19783>`_
+
+-------------------
+24.2.2 (2025-03-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix recording transform action name. by `@jmchilton <https://github.com/jmchilton>`_ in `#19672 <https://github.com/galaxyproject/galaxy/pull/19672>`_
+
+============
+Enhancements
+============
+
+* Add bwa_mem2_index directory datatype, framework enhancements for testing directories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19694 <https://github.com/galaxyproject/galaxy/pull/19694>`_
+
+=============
+Other changes
+=============
+
+* Backport #19620 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19725 <https://github.com/galaxyproject/galaxy/pull/19725>`_
+
+-------------------
+24.2.1 (2025-02-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Set content-type to text/plain if dataset not safe by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19563 <https://github.com/galaxyproject/galaxy/pull/19563>`_
+* Fail request explicitly when sqlite provider used on non-sqlite file by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19630 <https://github.com/galaxyproject/galaxy/pull/19630>`_
+* Fix various bugs around tool data table bundles by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19659 <https://github.com/galaxyproject/galaxy/pull/19659>`_
+
+-------------------
+24.2.0 (2025-02-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Drop "Send to cloud" tool and associated cloudauthz code by `@jdavcs <https://github.com/jdavcs>`_ in `#18196 <https://github.com/galaxyproject/galaxy/pull/18196>`_
+* Raise Message Exception when displaying binary data by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18503 <https://github.com/galaxyproject/galaxy/pull/18503>`_
+* Fixes for errors reported by mypy 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18608 <https://github.com/galaxyproject/galaxy/pull/18608>`_
+* Fix new flake8-bugbear B039 and mypy type-var errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18755 <https://github.com/galaxyproject/galaxy/pull/18755>`_
+* Fix migration data fixes tests by `@jdavcs <https://github.com/jdavcs>`_ in `#18885 <https://github.com/galaxyproject/galaxy/pull/18885>`_
+* Fix backend role sharing bug by `@jdavcs <https://github.com/jdavcs>`_ in `#18942 <https://github.com/galaxyproject/galaxy/pull/18942>`_
+* Add merge migration to merge 2 heads by `@jdavcs <https://github.com/jdavcs>`_ in `#19163 <https://github.com/galaxyproject/galaxy/pull/19163>`_
+* Record implicitly converted dataset as input dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19301 <https://github.com/galaxyproject/galaxy/pull/19301>`_
+* Fix quota usage with user object stores by `@davelopez <https://github.com/davelopez>`_ in `#19323 <https://github.com/galaxyproject/galaxy/pull/19323>`_
+* Fix workflows with optional non-default parameter input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19332 <https://github.com/galaxyproject/galaxy/pull/19332>`_
+* Fix importing shared workflows with deeply nested subworkflows by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19335 <https://github.com/galaxyproject/galaxy/pull/19335>`_
+* Backport fix from #19396 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19399 <https://github.com/galaxyproject/galaxy/pull/19399>`_
+* Prevent cycling through failing conversion jobs in trackster by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19494 <https://github.com/galaxyproject/galaxy/pull/19494>`_
+* Fix extracting workflows from purged and deleted histories by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19525 <https://github.com/galaxyproject/galaxy/pull/19525>`_
+* Fix error message when subworkflow input connection missing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19526 <https://github.com/galaxyproject/galaxy/pull/19526>`_
+* Fix admin cancel job message not being displayed to the user by `@davelopez <https://github.com/davelopez>`_ in `#19537 <https://github.com/galaxyproject/galaxy/pull/19537>`_
+* Add tool_id index on job table by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19543 <https://github.com/galaxyproject/galaxy/pull/19543>`_
+* Update 24.2 db revision tags by `@jdavcs <https://github.com/jdavcs>`_ in `#19550 <https://github.com/galaxyproject/galaxy/pull/19550>`_
+* Provide guidance in case of deadlock during db migration by `@jdavcs <https://github.com/jdavcs>`_ in `#19551 <https://github.com/galaxyproject/galaxy/pull/19551>`_
+* Fix job paused on user defined object store by `@davelopez <https://github.com/davelopez>`_ in `#19578 <https://github.com/galaxyproject/galaxy/pull/19578>`_
+* Handle isatools dependency by `@jdavcs <https://github.com/jdavcs>`_ in `#19582 <https://github.com/galaxyproject/galaxy/pull/19582>`_
+
+============
+Enhancements
+============
+
+* Experimental galactic wizard by `@dannon <https://github.com/dannon>`_ in `#15860 <https://github.com/galaxyproject/galaxy/pull/15860>`_
+* Improve usability of Directory datatype by `@wm75 <https://github.com/wm75>`_ in `#17614 <https://github.com/galaxyproject/galaxy/pull/17614>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18226 <https://github.com/galaxyproject/galaxy/pull/18226>`_
+* Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by `@jmchilton <https://github.com/jmchilton>`_ in `#18272 <https://github.com/galaxyproject/galaxy/pull/18272>`_
+* More data access tests, some refactoring and cleanup by `@jdavcs <https://github.com/jdavcs>`_ in `#18312 <https://github.com/galaxyproject/galaxy/pull/18312>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18406 <https://github.com/galaxyproject/galaxy/pull/18406>`_
+* Add pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18419 <https://github.com/galaxyproject/galaxy/pull/18419>`_
+* Prepare for NumPy 2.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18422 <https://github.com/galaxyproject/galaxy/pull/18422>`_
+* Add unique constraints to the email and username fields in the galaxy_user table by `@jdavcs <https://github.com/jdavcs>`_ in `#18493 <https://github.com/galaxyproject/galaxy/pull/18493>`_
+* Improvements for K8S deployment (especially ITs) by `@almahmoud <https://github.com/almahmoud>`_ in `#18514 <https://github.com/galaxyproject/galaxy/pull/18514>`_
+* Refactor ``LibraryDatasetsManager`` and fix type annotation issue by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18773 <https://github.com/galaxyproject/galaxy/pull/18773>`_
+* Handle compressed content in dataset preview for all sequence classes by `@PlushZ <https://github.com/PlushZ>`_ in `#18776 <https://github.com/galaxyproject/galaxy/pull/18776>`_
+* Backend handling of setting user-role, user-group, and group-role associations by `@jdavcs <https://github.com/jdavcs>`_ in `#18777 <https://github.com/galaxyproject/galaxy/pull/18777>`_
+* Workflow Landing Requests by `@jmchilton <https://github.com/jmchilton>`_ in `#18807 <https://github.com/galaxyproject/galaxy/pull/18807>`_
+* Update Mypy to 1.11.2 and fix new signature override errors by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18811 <https://github.com/galaxyproject/galaxy/pull/18811>`_
+* Refactor migration testing setup code by `@jdavcs <https://github.com/jdavcs>`_ in `#18886 <https://github.com/galaxyproject/galaxy/pull/18886>`_
+* Allow setting a few global defaults for file source plugin types. by `@jmchilton <https://github.com/jmchilton>`_ in `#18909 <https://github.com/galaxyproject/galaxy/pull/18909>`_
+* Type annotations and fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18911 <https://github.com/galaxyproject/galaxy/pull/18911>`_
+* Add filter null collection operation tool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18928 <https://github.com/galaxyproject/galaxy/pull/18928>`_
+* Fix extra files path type hint by `@davelopez <https://github.com/davelopez>`_ in `#18958 <https://github.com/galaxyproject/galaxy/pull/18958>`_
+* Decouple user email from role name by `@jdavcs <https://github.com/jdavcs>`_ in `#18966 <https://github.com/galaxyproject/galaxy/pull/18966>`_
+* Optimize to_history_dataset_association in create_datasets_from_library_folder by `@arash77 <https://github.com/arash77>`_ in `#18970 <https://github.com/galaxyproject/galaxy/pull/18970>`_
+* Workflow landing improvements by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18979 <https://github.com/galaxyproject/galaxy/pull/18979>`_
+* Allow recovering a normalized version of workflow request state from API by `@jmchilton <https://github.com/jmchilton>`_ in `#18985 <https://github.com/galaxyproject/galaxy/pull/18985>`_
+* Add some Zarr-based datatypes by `@davelopez <https://github.com/davelopez>`_ in `#19040 <https://github.com/galaxyproject/galaxy/pull/19040>`_
+* Run installed Galaxy with no config and a simplified entry point by `@natefoo <https://github.com/natefoo>`_ in `#19050 <https://github.com/galaxyproject/galaxy/pull/19050>`_
+* Annotate ``DatasetAssociationManager`` as generic type by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19063 <https://github.com/galaxyproject/galaxy/pull/19063>`_
+* Move TRS import into WorkflowContentManager by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19070 <https://github.com/galaxyproject/galaxy/pull/19070>`_
+* Allow deferred datasets to behave as URIs by `@davelopez <https://github.com/davelopez>`_ in `#19077 <https://github.com/galaxyproject/galaxy/pull/19077>`_
+* Better cleanup of sharing roles on user purge by `@jdavcs <https://github.com/jdavcs>`_ in `#19096 <https://github.com/galaxyproject/galaxy/pull/19096>`_
+* Add XML based `vtk` datatype by `@tStehling <https://github.com/tStehling>`_ in `#19104 <https://github.com/galaxyproject/galaxy/pull/19104>`_
+* Access public history in job cache / job search by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19108 <https://github.com/galaxyproject/galaxy/pull/19108>`_
+* Always validate hashes when provided by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19110 <https://github.com/galaxyproject/galaxy/pull/19110>`_
+* Enable specifying dataset hash in test jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19113 <https://github.com/galaxyproject/galaxy/pull/19113>`_
+* Enhance UTF-8 support for filename handling in downloads by `@arash77 <https://github.com/arash77>`_ in `#19161 <https://github.com/galaxyproject/galaxy/pull/19161>`_
+* Backport of Workflow Editor Activity Bar by `@dannon <https://github.com/dannon>`_ in `#19212 <https://github.com/galaxyproject/galaxy/pull/19212>`_
+* Fix default value handling for parameters connected to required parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19219 <https://github.com/galaxyproject/galaxy/pull/19219>`_
+
+=============
+Other changes
+=============
+
+* Merge 24.1 by `@jdavcs <https://github.com/jdavcs>`_ in `#18386 <https://github.com/galaxyproject/galaxy/pull/18386>`_
+* Format dev to fix linting. by `@jmchilton <https://github.com/jmchilton>`_ in `#18860 <https://github.com/galaxyproject/galaxy/pull/18860>`_
+* Add 24.2 migration tags by `@jdavcs <https://github.com/jdavcs>`_ in `#19169 <https://github.com/galaxyproject/galaxy/pull/19169>`_
+* Fix type annotations for pysam 0.23.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19571 <https://github.com/galaxyproject/galaxy/pull/19571>`_
+
+-------------------
+24.1.4 (2024-12-11)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Allow cors in biom and q2view display applications by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18890 <https://github.com/galaxyproject/galaxy/pull/18890>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+* Optimize/fix sqlite hid update statement by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19106 <https://github.com/galaxyproject/galaxy/pull/19106>`_
+* Prefer auto-decompressed datatype when picking conversion target  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19162 <https://github.com/galaxyproject/galaxy/pull/19162>`_
+* Fix various invocation export issues by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19215 <https://github.com/galaxyproject/galaxy/pull/19215>`_
+* Fix bad merge conflict resolution by `@nsoranzo <https://github.com/nsoranzo>`_ in `#19297 <https://github.com/galaxyproject/galaxy/pull/19297>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+
+-------------------
+24.1.3 (2024-10-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+* Limit max number of items in dataproviders by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18881 <https://github.com/galaxyproject/galaxy/pull/18881>`_
+* Allow cors in biom and q2view display applications by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18890 <https://github.com/galaxyproject/galaxy/pull/18890>`_
+* Disable locking when opening h5 files, add missing ``with`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18976 <https://github.com/galaxyproject/galaxy/pull/18976>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+
+-------------------
+24.1.2 (2024-09-25)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18494 <https://github.com/galaxyproject/galaxy/pull/18494>`_
+* Prevent job submission if input collection element is deleted by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18517 <https://github.com/galaxyproject/galaxy/pull/18517>`_
+* Fix shared caches with extended metadata collection. by `@jmchilton <https://github.com/jmchilton>`_ in `#18520 <https://github.com/galaxyproject/galaxy/pull/18520>`_
+* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18547 <https://github.com/galaxyproject/galaxy/pull/18547>`_
+* Fix for not-null in 'column_list' object by `@hujambo-dunia <https://github.com/hujambo-dunia>`_ in `#18553 <https://github.com/galaxyproject/galaxy/pull/18553>`_
+* Fix h5ad metadata by `@nilchia <https://github.com/nilchia>`_ in `#18635 <https://github.com/galaxyproject/galaxy/pull/18635>`_
+* Don't set file size to zero by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18653 <https://github.com/galaxyproject/galaxy/pull/18653>`_
+* Make sure we set file size also for purged outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18681 <https://github.com/galaxyproject/galaxy/pull/18681>`_
+* Fix wrong extension on pick data output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18798 <https://github.com/galaxyproject/galaxy/pull/18798>`_
+* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18802 <https://github.com/galaxyproject/galaxy/pull/18802>`_
+* Make pylibmagic import optional by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18813 <https://github.com/galaxyproject/galaxy/pull/18813>`_
+* Ignore converted datasets in invalid input states by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18850 <https://github.com/galaxyproject/galaxy/pull/18850>`_
+* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18855 <https://github.com/galaxyproject/galaxy/pull/18855>`_
+* Raise MessageException instead of assertions on rerun problems by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18858 <https://github.com/galaxyproject/galaxy/pull/18858>`_
+* Fix wrong final state when init_from is used by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18871 <https://github.com/galaxyproject/galaxy/pull/18871>`_
+* Fix history import when parent_hda not serialized by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18873 <https://github.com/galaxyproject/galaxy/pull/18873>`_
+
+=============
+Other changes
+=============
+
+* Backport pod5 datatype by `@TomHarrop <https://github.com/TomHarrop>`_ in `#18507 <https://github.com/galaxyproject/galaxy/pull/18507>`_
+
+-------------------
+24.1.1 (2024-07-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix syntax for SA2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17663 <https://github.com/galaxyproject/galaxy/pull/17663>`_
+* Fix empty usernames in database + bug in username generation by `@jdavcs <https://github.com/jdavcs>`_ in `#18379 <https://github.com/galaxyproject/galaxy/pull/18379>`_
+* Fix `input_step_parameters` missing values that don't have a label by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#18405 <https://github.com/galaxyproject/galaxy/pull/18405>`_
+* Improve workflow-related exception reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18447 <https://github.com/galaxyproject/galaxy/pull/18447>`_
+
+============
+Enhancements
+============
+
+* Enable all-vs-all collection analysis patterns. by `@jmchilton <https://github.com/jmchilton>`_ in `#17366 <https://github.com/galaxyproject/galaxy/pull/17366>`_
+* Visualizing workflow runs with an invocation graph view by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#17413 <https://github.com/galaxyproject/galaxy/pull/17413>`_
+* Better display of estimated line numbers and add number of columns for tabular by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17492 <https://github.com/galaxyproject/galaxy/pull/17492>`_
+* Enable storage management by object store by `@jmchilton <https://github.com/jmchilton>`_ in `#17500 <https://github.com/galaxyproject/galaxy/pull/17500>`_
+* Set minimal metadata also for empty bed datasets by `@wm75 <https://github.com/wm75>`_ in `#17586 <https://github.com/galaxyproject/galaxy/pull/17586>`_
+* Type annotation improvements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17601 <https://github.com/galaxyproject/galaxy/pull/17601>`_
+* Type annotation and CWL-related improvements by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17630 <https://github.com/galaxyproject/galaxy/pull/17630>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17653 <https://github.com/galaxyproject/galaxy/pull/17653>`_
+* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17654 <https://github.com/galaxyproject/galaxy/pull/17654>`_
+* SQLAlchemy 2.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17778 <https://github.com/galaxyproject/galaxy/pull/17778>`_
+* Outline use of type_annotation_map to fix mypy issues by `@jmchilton <https://github.com/jmchilton>`_ in `#17902 <https://github.com/galaxyproject/galaxy/pull/17902>`_
+* Add `email` notifications channel by `@davelopez <https://github.com/davelopez>`_ in `#17914 <https://github.com/galaxyproject/galaxy/pull/17914>`_
+* Model edits and bug fixes by `@jdavcs <https://github.com/jdavcs>`_ in `#17922 <https://github.com/galaxyproject/galaxy/pull/17922>`_
+* Model typing and SA2.0 follow-up by `@jdavcs <https://github.com/jdavcs>`_ in `#17958 <https://github.com/galaxyproject/galaxy/pull/17958>`_
+* Enable ``warn_unused_ignores`` mypy option by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17991 <https://github.com/galaxyproject/galaxy/pull/17991>`_
+* Add galaxy to user agent by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18003 <https://github.com/galaxyproject/galaxy/pull/18003>`_
+* Refactor galaxy.files plugin loading + config handling. by `@jmchilton <https://github.com/jmchilton>`_ in `#18049 <https://github.com/galaxyproject/galaxy/pull/18049>`_
+* Add stronger type annotations in file sources + refactoring by `@davelopez <https://github.com/davelopez>`_ in `#18050 <https://github.com/galaxyproject/galaxy/pull/18050>`_
+* Add support for additional media types by `@arash77 <https://github.com/arash77>`_ in `#18054 <https://github.com/galaxyproject/galaxy/pull/18054>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#18063 <https://github.com/galaxyproject/galaxy/pull/18063>`_
+* Enable flake8-implicit-str-concat ruff rules by `@nsoranzo <https://github.com/nsoranzo>`_ in `#18067 <https://github.com/galaxyproject/galaxy/pull/18067>`_
+* Script for deleting userless histories from database + testing + drop unused model testing code by `@jdavcs <https://github.com/jdavcs>`_ in `#18079 <https://github.com/galaxyproject/galaxy/pull/18079>`_
+* Add Net datatype by `@martenson <https://github.com/martenson>`_ in `#18080 <https://github.com/galaxyproject/galaxy/pull/18080>`_
+* Empower users to bring their own storage and file sources by `@jmchilton <https://github.com/jmchilton>`_ in `#18127 <https://github.com/galaxyproject/galaxy/pull/18127>`_
+* Harden User Object Store and File Source Creation by `@jmchilton <https://github.com/jmchilton>`_ in `#18172 <https://github.com/galaxyproject/galaxy/pull/18172>`_
+* Update db revision 24.1 release tags by `@jdavcs <https://github.com/jdavcs>`_ in `#18183 <https://github.com/galaxyproject/galaxy/pull/18183>`_
+* Tighten axt sniffer by `@martenson <https://github.com/martenson>`_ in `#18204 <https://github.com/galaxyproject/galaxy/pull/18204>`_
+* More structured indexing for user data objects. by `@jmchilton <https://github.com/jmchilton>`_ in `#18291 <https://github.com/galaxyproject/galaxy/pull/18291>`_
+
+=============
+Other changes
+=============
+
+* Chore: remove repetitive words by `@tianzedavid <https://github.com/tianzedavid>`_ in `#18076 <https://github.com/galaxyproject/galaxy/pull/18076>`_
+* Fix import broken with forward merge by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18152 <https://github.com/galaxyproject/galaxy/pull/18152>`_
+
+-------------------
+24.0.3 (2024-06-28)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Downgrade count lines error to warning by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18175 <https://github.com/galaxyproject/galaxy/pull/18175>`_
+* Don't set dataset peek for errored jobs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18231 <https://github.com/galaxyproject/galaxy/pull/18231>`_
+* Transparently open compressed files in DatasetDataProvider by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18248 <https://github.com/galaxyproject/galaxy/pull/18248>`_
+* Raise exception when extracting dataset from collection without datasets by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18249 <https://github.com/galaxyproject/galaxy/pull/18249>`_
+* Set page importable to false when serializing by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18263 <https://github.com/galaxyproject/galaxy/pull/18263>`_
+* Fix first_dataset_element type hint by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18284 <https://github.com/galaxyproject/galaxy/pull/18284>`_
+* Do not copy purged outputs to object store by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18342 <https://github.com/galaxyproject/galaxy/pull/18342>`_
+* Fix user's private role can be missing by `@davelopez <https://github.com/davelopez>`_ in `#18381 <https://github.com/galaxyproject/galaxy/pull/18381>`_
+* Assign default ``data`` extension on discovered collection output  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18389 <https://github.com/galaxyproject/galaxy/pull/18389>`_
+
+=============
+Other changes
+=============
+
+* Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18428 <https://github.com/galaxyproject/galaxy/pull/18428>`_
+
+-------------------
+24.0.2 (2024-05-07)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+24.0.1 (2024-05-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Always serialize element_count and populated when listing contents by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17890 <https://github.com/galaxyproject/galaxy/pull/17890>`_
+* Fix deadlock that can occur when changing job state by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17896 <https://github.com/galaxyproject/galaxy/pull/17896>`_
+* Fix tool form building if select filters from unavailable dataset metadata by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17930 <https://github.com/galaxyproject/galaxy/pull/17930>`_
+* Fix ``InvalidRequestError: Can't operate on closed transaction inside context manager.  Please complete the context manager before emitting further commands.`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17932 <https://github.com/galaxyproject/galaxy/pull/17932>`_
+* Never fail dataset serialization if display_peek fails by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17937 <https://github.com/galaxyproject/galaxy/pull/17937>`_
+* Fix output datatype when uncompressing a dataset with incorrect datatype by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17944 <https://github.com/galaxyproject/galaxy/pull/17944>`_
+* Use or copy StoredWorkflow when copying step by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17988 <https://github.com/galaxyproject/galaxy/pull/17988>`_
+* Raise ``MessageException`` when report references invalid workflow output by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18009 <https://github.com/galaxyproject/galaxy/pull/18009>`_
+* Fix tag regex pattern by `@jdavcs <https://github.com/jdavcs>`_ in `#18025 <https://github.com/galaxyproject/galaxy/pull/18025>`_
+* Fix History Dataset Association creation so that hid is always set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#18036 <https://github.com/galaxyproject/galaxy/pull/18036>`_
+* Fix history export with missing dataset hids by `@davelopez <https://github.com/davelopez>`_ in `#18052 <https://github.com/galaxyproject/galaxy/pull/18052>`_
+* Fix comments lost on import by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#18060 <https://github.com/galaxyproject/galaxy/pull/18060>`_
+* Fix history update time after bulk operation by `@davelopez <https://github.com/davelopez>`_ in `#18068 <https://github.com/galaxyproject/galaxy/pull/18068>`_
+
+-------------------
+24.0.0 (2024-04-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix for converter tests by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17188 <https://github.com/galaxyproject/galaxy/pull/17188>`_
+* correct dbkey for minerva display app by `@hexylena <https://github.com/hexylena>`_ in `#17196 <https://github.com/galaxyproject/galaxy/pull/17196>`_
+* Fix invocation serialization if no state was set by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17278 <https://github.com/galaxyproject/galaxy/pull/17278>`_
+* Fix quotas ID encoding by `@davelopez <https://github.com/davelopez>`_ in `#17335 <https://github.com/galaxyproject/galaxy/pull/17335>`_
+* Fix model store exports that include implicit conversions.  by `@jmchilton <https://github.com/jmchilton>`_ in `#17346 <https://github.com/galaxyproject/galaxy/pull/17346>`_
+* Fix bug: create new PSAAssociation if not in database by `@jdavcs <https://github.com/jdavcs>`_ in `#17516 <https://github.com/galaxyproject/galaxy/pull/17516>`_
+* Fix social_core methods by `@jdavcs <https://github.com/jdavcs>`_ in `#17530 <https://github.com/galaxyproject/galaxy/pull/17530>`_
+* Fix ancient bug: incorrect usage of func.coalesce in User model by `@jdavcs <https://github.com/jdavcs>`_ in `#17577 <https://github.com/galaxyproject/galaxy/pull/17577>`_
+* Account for newlines in CIF Datatype sniffer by `@patrick-austin <https://github.com/patrick-austin>`_ in `#17582 <https://github.com/galaxyproject/galaxy/pull/17582>`_
+* Anticipate PendingRollbackError in ``check_database_connection`` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17598 <https://github.com/galaxyproject/galaxy/pull/17598>`_
+* Add basic model import attribute validation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17628 <https://github.com/galaxyproject/galaxy/pull/17628>`_
+* More efficient change_state queries, maybe fix deadlock by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17632 <https://github.com/galaxyproject/galaxy/pull/17632>`_
+* Npz sniffing: do not read the whole file by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17672 <https://github.com/galaxyproject/galaxy/pull/17672>`_
+* Assert that at least one file in npz zipfile ends with .npy by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17679 <https://github.com/galaxyproject/galaxy/pull/17679>`_
+* Workflow Comment Indexing by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#17700 <https://github.com/galaxyproject/galaxy/pull/17700>`_
+* Fix source history update_time being updated when importing a public history by `@jmchilton <https://github.com/jmchilton>`_ in `#17728 <https://github.com/galaxyproject/galaxy/pull/17728>`_
+* Also set extension and metadata on copies of job outputs when finishing job by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17777 <https://github.com/galaxyproject/galaxy/pull/17777>`_
+* Defer job attributes that are usually not needed by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17795 <https://github.com/galaxyproject/galaxy/pull/17795>`_
+* Fix change_datatype PJA for dynamic collections  by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17803 <https://github.com/galaxyproject/galaxy/pull/17803>`_
+* Simplify nested collection joins by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17817 <https://github.com/galaxyproject/galaxy/pull/17817>`_
+* Fix very slow user data table query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17830 <https://github.com/galaxyproject/galaxy/pull/17830>`_
+* Update db revision 24.0 release tags by `@jdavcs <https://github.com/jdavcs>`_ in `#17834 <https://github.com/galaxyproject/galaxy/pull/17834>`_
+* Minor refactor of query building logic for readability by `@jdavcs <https://github.com/jdavcs>`_ in `#17835 <https://github.com/galaxyproject/galaxy/pull/17835>`_
+* Fix user login when duplicate UserRoleAssociation exists by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17854 <https://github.com/galaxyproject/galaxy/pull/17854>`_
+
+============
+Enhancements
+============
+
+* Make columns types an empty list for empty tabular data  by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#13918 <https://github.com/galaxyproject/galaxy/pull/13918>`_
+* port invocation API to fastapi by `@martenson <https://github.com/martenson>`_ in `#16707 <https://github.com/galaxyproject/galaxy/pull/16707>`_
+* SQLAlchemy 2.0 upgrades (part 5) by `@jdavcs <https://github.com/jdavcs>`_ in `#16932 <https://github.com/galaxyproject/galaxy/pull/16932>`_
+* Python 3.8 as minimum by `@mr-c <https://github.com/mr-c>`_ in `#16954 <https://github.com/galaxyproject/galaxy/pull/16954>`_
+* Expose more tool information / navigability in UI. by `@jmchilton <https://github.com/jmchilton>`_ in `#17105 <https://github.com/galaxyproject/galaxy/pull/17105>`_
+* Add support for (fast5.tar).xz binary compressed files by `@tuncK <https://github.com/tuncK>`_ in `#17106 <https://github.com/galaxyproject/galaxy/pull/17106>`_
+* SA2.0 updates: handling "object is being merged into a Session along the backref cascade path" by `@jdavcs <https://github.com/jdavcs>`_ in `#17122 <https://github.com/galaxyproject/galaxy/pull/17122>`_
+* Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by `@jdavcs <https://github.com/jdavcs>`_ in `#17132 <https://github.com/galaxyproject/galaxy/pull/17132>`_
+* Create pydantic model for the return of show operation -  get: `/api/jobs/{job_id}`  by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#17153 <https://github.com/galaxyproject/galaxy/pull/17153>`_
+* Much simpler default dataset permissions for typical users. by `@jmchilton <https://github.com/jmchilton>`_ in `#17166 <https://github.com/galaxyproject/galaxy/pull/17166>`_
+* Add future=True flag to SA engine by `@jdavcs <https://github.com/jdavcs>`_ in `#17174 <https://github.com/galaxyproject/galaxy/pull/17174>`_
+* Add future=True flag to SA session by `@jdavcs <https://github.com/jdavcs>`_ in `#17179 <https://github.com/galaxyproject/galaxy/pull/17179>`_
+* Vueifiy History Grids by `@guerler <https://github.com/guerler>`_ in `#17219 <https://github.com/galaxyproject/galaxy/pull/17219>`_
+* Convert sample object store configuration to YAML and support configuring inline by `@natefoo <https://github.com/natefoo>`_ in `#17222 <https://github.com/galaxyproject/galaxy/pull/17222>`_
+* Migrate models to pydantic 2 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17262 <https://github.com/galaxyproject/galaxy/pull/17262>`_
+* API endpoint that allows "changing" the objectstore for "safe" scenarios.  by `@jmchilton <https://github.com/jmchilton>`_ in `#17329 <https://github.com/galaxyproject/galaxy/pull/17329>`_
+* Enable ``warn_unreachable`` mypy option by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17365 <https://github.com/galaxyproject/galaxy/pull/17365>`_
+* Fix type annotation of code using XML etree by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17367 <https://github.com/galaxyproject/galaxy/pull/17367>`_
+* Add explicit cache_ok attribute to JSONType subclass by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17376 <https://github.com/galaxyproject/galaxy/pull/17376>`_
+* More specific type annotation for ``BaseJobExec.parse_status()`` by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17381 <https://github.com/galaxyproject/galaxy/pull/17381>`_
+* Update to black 2024 stable style by `@nsoranzo <https://github.com/nsoranzo>`_ in `#17391 <https://github.com/galaxyproject/galaxy/pull/17391>`_
+* Allow using tool data bundles as inputs to reference data select parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17435 <https://github.com/galaxyproject/galaxy/pull/17435>`_
+* UI for "relocating" a dataset to a new object store (when safe) by `@jmchilton <https://github.com/jmchilton>`_ in `#17437 <https://github.com/galaxyproject/galaxy/pull/17437>`_
+* Allow filtering history datasets by object store ID and quota source. by `@jmchilton <https://github.com/jmchilton>`_ in `#17460 <https://github.com/galaxyproject/galaxy/pull/17460>`_
+* Faster FASTA and FASTQ metadata setting by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#17462 <https://github.com/galaxyproject/galaxy/pull/17462>`_
+* Feature SBOL datatypes by `@guillaume-gricourt <https://github.com/guillaume-gricourt>`_ in `#17482 <https://github.com/galaxyproject/galaxy/pull/17482>`_
+* Display workflow invocation counts. by `@jmchilton <https://github.com/jmchilton>`_ in `#17488 <https://github.com/galaxyproject/galaxy/pull/17488>`_
+* add npy datatype by `@astrovsky01 <https://github.com/astrovsky01>`_ in `#17517 <https://github.com/galaxyproject/galaxy/pull/17517>`_
+* Enhance Avivator display app to support regular Tiffs by `@davelopez <https://github.com/davelopez>`_ in `#17554 <https://github.com/galaxyproject/galaxy/pull/17554>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#17580 <https://github.com/galaxyproject/galaxy/pull/17580>`_
+* Add migrations revision identifier for 24.0 by `@jdavcs <https://github.com/jdavcs>`_ in `#17589 <https://github.com/galaxyproject/galaxy/pull/17589>`_
+
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Rename to_dict to populate in FormDefintion to fix bug by `@jdavcs <https://github.com/jdavcs>`_ in `#16553 <https://github.com/galaxyproject/galaxy/pull/16553>`_
+* MINERVA display application: enable cors, add for tabular by `@hexylena <https://github.com/hexylena>`_ in `#16737 <https://github.com/galaxyproject/galaxy/pull/16737>`_
+* Use AlignedSegment.to_string by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16803 <https://github.com/galaxyproject/galaxy/pull/16803>`_
+* Ruff and flake8 fixes by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16884 <https://github.com/galaxyproject/galaxy/pull/16884>`_
+* prep for updated h5py and typos by `@mr-c <https://github.com/mr-c>`_ in `#16963 <https://github.com/galaxyproject/galaxy/pull/16963>`_
+* Fix cardinality violation error: subquery returns multiple results by `@jdavcs <https://github.com/jdavcs>`_ in `#17224 <https://github.com/galaxyproject/galaxy/pull/17224>`_
+* Fix Display Application link generation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17227 <https://github.com/galaxyproject/galaxy/pull/17227>`_
+* Display application fixes and tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17233 <https://github.com/galaxyproject/galaxy/pull/17233>`_
+* Rollback invalidated transaction by `@jdavcs <https://github.com/jdavcs>`_ in `#17280 <https://github.com/galaxyproject/galaxy/pull/17280>`_
+* Set metadata states on dataset association, not dataset by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17474 <https://github.com/galaxyproject/galaxy/pull/17474>`_
+* Provide working routes.url_for every ASGI request by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17497 <https://github.com/galaxyproject/galaxy/pull/17497>`_
+
+============
+Enhancements
+============
+
+* Implement default locations for data and collection parameters. by `@jmchilton <https://github.com/jmchilton>`_ in `#14955 <https://github.com/galaxyproject/galaxy/pull/14955>`_
+* Display beginning of non-text files as text instead of triggering a download by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#15447 <https://github.com/galaxyproject/galaxy/pull/15447>`_
+* Tool Shed 2.0 by `@jmchilton <https://github.com/jmchilton>`_ in `#15639 <https://github.com/galaxyproject/galaxy/pull/15639>`_
+* Limit number of celery task executions per second per user by `@claudiofr <https://github.com/claudiofr>`_ in `#16232 <https://github.com/galaxyproject/galaxy/pull/16232>`_
+* Delete non-terminal jobs and subworkflow invocations when cancelling invocation by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16252 <https://github.com/galaxyproject/galaxy/pull/16252>`_
+* Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by `@jdavcs <https://github.com/jdavcs>`_ in `#16264 <https://github.com/galaxyproject/galaxy/pull/16264>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16409 <https://github.com/galaxyproject/galaxy/pull/16409>`_
+* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by `@jdavcs <https://github.com/jdavcs>`_ in `#16431 <https://github.com/galaxyproject/galaxy/pull/16431>`_
+* SQLAlchemy 2.0 upgrades to ORM usage in /lib by `@jdavcs <https://github.com/jdavcs>`_ in `#16434 <https://github.com/galaxyproject/galaxy/pull/16434>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#16436 <https://github.com/galaxyproject/galaxy/pull/16436>`_
+* Implement datatype upload warnings by `@jmchilton <https://github.com/jmchilton>`_ in `#16564 <https://github.com/galaxyproject/galaxy/pull/16564>`_
+* Support new genome browser chain file format by `@claudiofr <https://github.com/claudiofr>`_ in `#16576 <https://github.com/galaxyproject/galaxy/pull/16576>`_
+* Workflow Comments 💬 by `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`_ in `#16612 <https://github.com/galaxyproject/galaxy/pull/16612>`_
+* Bump samtools converters by `@bernt-matthias <https://github.com/bernt-matthias>`_ in `#16668 <https://github.com/galaxyproject/galaxy/pull/16668>`_
+* Misc. edits/refactorings to session handling  by `@jdavcs <https://github.com/jdavcs>`_ in `#16712 <https://github.com/galaxyproject/galaxy/pull/16712>`_
+* SQLAlchemy 2.0 upgrades (part 2) by `@jdavcs <https://github.com/jdavcs>`_ in `#16724 <https://github.com/galaxyproject/galaxy/pull/16724>`_
+* Migrate `collection elements` store to Pinia by `@davelopez <https://github.com/davelopez>`_ in `#16725 <https://github.com/galaxyproject/galaxy/pull/16725>`_
+* Reset autocommit to False by `@jdavcs <https://github.com/jdavcs>`_ in `#16745 <https://github.com/galaxyproject/galaxy/pull/16745>`_
+* Drop legacy server-side search by `@jdavcs <https://github.com/jdavcs>`_ in `#16755 <https://github.com/galaxyproject/galaxy/pull/16755>`_
+* Optimize iteration in DatasetInstance model + SA2.0 fix by `@jdavcs <https://github.com/jdavcs>`_ in `#16776 <https://github.com/galaxyproject/galaxy/pull/16776>`_
+* Migrate a part of the jobs API to Fast API by `@heisner-tillman <https://github.com/heisner-tillman>`_ in `#16778 <https://github.com/galaxyproject/galaxy/pull/16778>`_
+* Replace file_name property with get_file_name function by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#16783 <https://github.com/galaxyproject/galaxy/pull/16783>`_
+* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by `@sveinugu <https://github.com/sveinugu>`_ in `#16795 <https://github.com/galaxyproject/galaxy/pull/16795>`_
+* Allow partial matches in workflow name tag search and search all tags for unquoted query by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#16860 <https://github.com/galaxyproject/galaxy/pull/16860>`_
+* Vueify Visualizations Grid by `@guerler <https://github.com/guerler>`_ in `#16892 <https://github.com/galaxyproject/galaxy/pull/16892>`_
+* Standardize to W3C naming for color. by `@dannon <https://github.com/dannon>`_ in `#16949 <https://github.com/galaxyproject/galaxy/pull/16949>`_
+* Move and re-use persist_extra_files by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16955 <https://github.com/galaxyproject/galaxy/pull/16955>`_
+* Fix invocation report to target correct workflow version. by `@jmchilton <https://github.com/jmchilton>`_ in `#17008 <https://github.com/galaxyproject/galaxy/pull/17008>`_
+* optimize object store cache operations by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#17025 <https://github.com/galaxyproject/galaxy/pull/17025>`_
+* Use python-isal for fast zip deflate compression in rocrate export by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17342 <https://github.com/galaxyproject/galaxy/pull/17342>`_
+* Add magres datatype by `@martenson <https://github.com/martenson>`_ in `#17499 <https://github.com/galaxyproject/galaxy/pull/17499>`_
+
+=============
+Other changes
+=============
+
+* Merge 23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16534 <https://github.com/galaxyproject/galaxy/pull/16534>`_
+* Merge release_23.1 into dev by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16768 <https://github.com/galaxyproject/galaxy/pull/16768>`_
+* Create db head merge revision. by `@dannon <https://github.com/dannon>`_ in `#16838 <https://github.com/galaxyproject/galaxy/pull/16838>`_
+* merge release_23.1 into dev by `@martenson <https://github.com/martenson>`_ in `#16933 <https://github.com/galaxyproject/galaxy/pull/16933>`_
+* Minor clarification/typo fix in datatypes.data by `@dannon <https://github.com/dannon>`_ in `#16993 <https://github.com/galaxyproject/galaxy/pull/16993>`_
+* Fix `.file_name` access in merge forward by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17097 <https://github.com/galaxyproject/galaxy/pull/17097>`_
+* Backport model store fixes by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17439 <https://github.com/galaxyproject/galaxy/pull/17439>`_
+* Fix succces typo by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17481 <https://github.com/galaxyproject/galaxy/pull/17481>`_
+
+-------------------
+23.1.4 (2024-01-04)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix User.current_galaxy_session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17232 <https://github.com/galaxyproject/galaxy/pull/17232>`_
+
+=============
+Other changes
+=============
+
+* Backport #17188: Fix for converter tests by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17231 <https://github.com/galaxyproject/galaxy/pull/17231>`_
+
+-------------------
+23.1.3 (2023-12-01)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Add missing optional description field, fixes ephemeris data library example by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17116 <https://github.com/galaxyproject/galaxy/pull/17116>`_
+
+-------------------
+23.1.2 (2023-11-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Skip change_datatype things if we're not actually changing the extension by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16931 <https://github.com/galaxyproject/galaxy/pull/16931>`_
+* Fix copying metadata to copied job outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17007 <https://github.com/galaxyproject/galaxy/pull/17007>`_
+* Update tar_to_directory dependency by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17009 <https://github.com/galaxyproject/galaxy/pull/17009>`_
+* Assert that ``DatasetCollectioElement`` has an associated object by `@mvdbeek <https://github.com/mvdbeek>`_ in `#17071 <https://github.com/galaxyproject/galaxy/pull/17071>`_
+* Fix input dates in notifications: consider timezone offset by `@davelopez <https://github.com/davelopez>`_ in `#17088 <https://github.com/galaxyproject/galaxy/pull/17088>`_
+* Allow relative URLs in broadcasts action links by `@davelopez <https://github.com/davelopez>`_ in `#17093 <https://github.com/galaxyproject/galaxy/pull/17093>`_
+
+============
+Enhancements
+============
+
+* Improve invocation error reporting by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16917 <https://github.com/galaxyproject/galaxy/pull/16917>`_
+* Add support for larch datatypes by `@patrick-austin <https://github.com/patrick-austin>`_ in `#17080 <https://github.com/galaxyproject/galaxy/pull/17080>`_
+
+-------------------
+23.1.1 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix bad auto-merge of dev. by `@jmchilton <https://github.com/jmchilton>`_ in `#15386 <https://github.com/galaxyproject/galaxy/pull/15386>`_
+* Merge conflicting db migration branches into one by `@jdavcs <https://github.com/jdavcs>`_ in `#15771 <https://github.com/galaxyproject/galaxy/pull/15771>`_
+* Enable ``strict_equality`` mypy option by `@nsoranzo <https://github.com/nsoranzo>`_ in `#15808 <https://github.com/galaxyproject/galaxy/pull/15808>`_
+* Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by `@jdavcs <https://github.com/jdavcs>`_ in `#15811 <https://github.com/galaxyproject/galaxy/pull/15811>`_
+* Fix anonymous user uploads when vault is configured by `@tchaussepiedifb <https://github.com/tchaussepiedifb>`_ in `#15858 <https://github.com/galaxyproject/galaxy/pull/15858>`_
+* Fix nullable deleted column in API Keys table by `@davelopez <https://github.com/davelopez>`_ in `#15956 <https://github.com/galaxyproject/galaxy/pull/15956>`_
+* Attempt to fix mypy check by `@davelopez <https://github.com/davelopez>`_ in `#16103 <https://github.com/galaxyproject/galaxy/pull/16103>`_
+* Ensure session is request-scoped for legacy endpoints by `@jdavcs <https://github.com/jdavcs>`_ in `#16207 <https://github.com/galaxyproject/galaxy/pull/16207>`_
+* Reset autocommit to True (temporarily) by `@jdavcs <https://github.com/jdavcs>`_ in `#16283 <https://github.com/galaxyproject/galaxy/pull/16283>`_
+* Update 23.1 release tags for migration scripts by `@jdavcs <https://github.com/jdavcs>`_ in `#16294 <https://github.com/galaxyproject/galaxy/pull/16294>`_
+* Fix form builder value handling by `@guerler <https://github.com/guerler>`_ in `#16304 <https://github.com/galaxyproject/galaxy/pull/16304>`_
+* Fix tags ownership by `@davelopez <https://github.com/davelopez>`_ in `#16339 <https://github.com/galaxyproject/galaxy/pull/16339>`_
+* Fix disk usage recalculation for distributed object stores by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16380 <https://github.com/galaxyproject/galaxy/pull/16380>`_
+* Job cache fixes for DCEs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16384 <https://github.com/galaxyproject/galaxy/pull/16384>`_
+* Fix histories count by `@davelopez <https://github.com/davelopez>`_ in `#16400 <https://github.com/galaxyproject/galaxy/pull/16400>`_
+* Fix double-encoding notification content by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16530 <https://github.com/galaxyproject/galaxy/pull/16530>`_
+* Optimize getting current user session by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16604 <https://github.com/galaxyproject/galaxy/pull/16604>`_
+* Fixes for conditional subworkflow steps by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16632 <https://github.com/galaxyproject/galaxy/pull/16632>`_
+* Copy the collection contents by default when copying a collection by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16717 <https://github.com/galaxyproject/galaxy/pull/16717>`_
+* Fix allowlist deserialization in file sources by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16729 <https://github.com/galaxyproject/galaxy/pull/16729>`_
+* Fix workflow output display without label by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16749 <https://github.com/galaxyproject/galaxy/pull/16749>`_
+* Fix and prevent persisting null file_size by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16855 <https://github.com/galaxyproject/galaxy/pull/16855>`_
+* Fix workflow import losing tool_version by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16869 <https://github.com/galaxyproject/galaxy/pull/16869>`_
+* Remove more flushes in database operation tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16875 <https://github.com/galaxyproject/galaxy/pull/16875>`_
+* Fix join condition for nested collection query by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16880 <https://github.com/galaxyproject/galaxy/pull/16880>`_
+
+============
+Enhancements
+============
+
+* Empower Users to Select Storage Destination by `@jmchilton <https://github.com/jmchilton>`_ in `#14073 <https://github.com/galaxyproject/galaxy/pull/14073>`_
+* Add Storage Dashboard visualizations for histories by `@davelopez <https://github.com/davelopez>`_ in `#14820 <https://github.com/galaxyproject/galaxy/pull/14820>`_
+* Towards decoupling datatypes and model by `@jdavcs <https://github.com/jdavcs>`_ in `#15186 <https://github.com/galaxyproject/galaxy/pull/15186>`_
+* Add Storage Management API by `@davelopez <https://github.com/davelopez>`_ in `#15295 <https://github.com/galaxyproject/galaxy/pull/15295>`_
+* OIDC tokens by `@SergeyYakubov <https://github.com/SergeyYakubov>`_ in `#15300 <https://github.com/galaxyproject/galaxy/pull/15300>`_
+* Expose additional beaker caching backends  by `@claudiofr <https://github.com/claudiofr>`_ in `#15349 <https://github.com/galaxyproject/galaxy/pull/15349>`_
+* Follow up to #15186 by `@jdavcs <https://github.com/jdavcs>`_ in `#15388 <https://github.com/galaxyproject/galaxy/pull/15388>`_
+* Add support for visualizing HDF5 datasets. by `@jarrah42 <https://github.com/jarrah42>`_ in `#15394 <https://github.com/galaxyproject/galaxy/pull/15394>`_
+* Towards SQLAlchemy 2.0: drop session autocommit setting by `@jdavcs <https://github.com/jdavcs>`_ in `#15421 <https://github.com/galaxyproject/galaxy/pull/15421>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15435 <https://github.com/galaxyproject/galaxy/pull/15435>`_
+* Unify url handling with filesources by `@nuwang <https://github.com/nuwang>`_ in `#15497 <https://github.com/galaxyproject/galaxy/pull/15497>`_
+* Move TS to Alembic by `@jdavcs <https://github.com/jdavcs>`_ in `#15509 <https://github.com/galaxyproject/galaxy/pull/15509>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15564 <https://github.com/galaxyproject/galaxy/pull/15564>`_
+* Update database_heartbeat for SA 2.0 compatibility by `@jdavcs <https://github.com/jdavcs>`_ in `#15611 <https://github.com/galaxyproject/galaxy/pull/15611>`_
+* Update supports_skip_locked, supports_returning for SA 2.0 compatibility by `@jdavcs <https://github.com/jdavcs>`_ in `#15633 <https://github.com/galaxyproject/galaxy/pull/15633>`_
+* Add Galaxy Notification System by `@davelopez <https://github.com/davelopez>`_ in `#15663 <https://github.com/galaxyproject/galaxy/pull/15663>`_
+* Drop model mapping unit tests by `@jdavcs <https://github.com/jdavcs>`_ in `#15669 <https://github.com/galaxyproject/galaxy/pull/15669>`_
+* Add transactional state to workflow scheduling manager by `@jdavcs <https://github.com/jdavcs>`_ in `#15683 <https://github.com/galaxyproject/galaxy/pull/15683>`_
+* Remove DELETED_NEW job state from code base by `@jdavcs <https://github.com/jdavcs>`_ in `#15690 <https://github.com/galaxyproject/galaxy/pull/15690>`_
+* Fix/Enhance recalculate disk usage API endpoint by `@davelopez <https://github.com/davelopez>`_ in `#15739 <https://github.com/galaxyproject/galaxy/pull/15739>`_
+* Drop database views by `@jdavcs <https://github.com/jdavcs>`_ in `#15876 <https://github.com/galaxyproject/galaxy/pull/15876>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#15890 <https://github.com/galaxyproject/galaxy/pull/15890>`_
+* FITS data format by `@volodymyrss <https://github.com/volodymyrss>`_ in `#15905 <https://github.com/galaxyproject/galaxy/pull/15905>`_
+* Improve display chunk generation for BAMs by `@wm75 <https://github.com/wm75>`_ in `#15972 <https://github.com/galaxyproject/galaxy/pull/15972>`_
+* Add History Archival feature by `@davelopez <https://github.com/davelopez>`_ in `#16003 <https://github.com/galaxyproject/galaxy/pull/16003>`_
+* Add alter_column migration utility by `@jdavcs <https://github.com/jdavcs>`_ in `#16009 <https://github.com/galaxyproject/galaxy/pull/16009>`_
+* Code cleanups from ruff and pyupgrade by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16035 <https://github.com/galaxyproject/galaxy/pull/16035>`_
+* Add missing fields to HistorySummary schema model by `@davelopez <https://github.com/davelopez>`_ in `#16041 <https://github.com/galaxyproject/galaxy/pull/16041>`_
+* Dataset chunking tests (and small fixes) by `@jmchilton <https://github.com/jmchilton>`_ in `#16069 <https://github.com/galaxyproject/galaxy/pull/16069>`_
+* Add create_foreign_key migration utility by `@jdavcs <https://github.com/jdavcs>`_ in `#16077 <https://github.com/galaxyproject/galaxy/pull/16077>`_
+* Refactor models enums to eliminate schema dependency on model layer. by `@jmchilton <https://github.com/jmchilton>`_ in `#16080 <https://github.com/galaxyproject/galaxy/pull/16080>`_
+* Use automated naming convention to generate indexes and constraints in database by `@jdavcs <https://github.com/jdavcs>`_ in `#16089 <https://github.com/galaxyproject/galaxy/pull/16089>`_
+* Add zipped mongodb and genenotebook datatypes by `@abretaud <https://github.com/abretaud>`_ in `#16173 <https://github.com/galaxyproject/galaxy/pull/16173>`_
+* Drop workarounds for old ro-crate-py and docutils versions by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16198 <https://github.com/galaxyproject/galaxy/pull/16198>`_
+* bring grids for (published) pages on par with workflows by `@martenson <https://github.com/martenson>`_ in `#16209 <https://github.com/galaxyproject/galaxy/pull/16209>`_
+* Add Visium datatype for squidpy and spatialomics tools by `@astrovsky01 <https://github.com/astrovsky01>`_ in `#16255 <https://github.com/galaxyproject/galaxy/pull/16255>`_
+* Filter deleted keys from api_keys relationship by `@dannon <https://github.com/dannon>`_ in `#16321 <https://github.com/galaxyproject/galaxy/pull/16321>`_
+* Increase `CustosAuthnzToken.external_user_id` column size by `@davelopez <https://github.com/davelopez>`_ in `#16818 <https://github.com/galaxyproject/galaxy/pull/16818>`_
+
+=============
+Other changes
+=============
+
+* Follow up on object store selection PR. by `@jmchilton <https://github.com/jmchilton>`_ in `#15654 <https://github.com/galaxyproject/galaxy/pull/15654>`_
+* Fix Enums in API docs by `@davelopez <https://github.com/davelopez>`_ in `#15740 <https://github.com/galaxyproject/galaxy/pull/15740>`_
+* merge release_23.0 into dev by `@martenson <https://github.com/martenson>`_ in `#15830 <https://github.com/galaxyproject/galaxy/pull/15830>`_
+* Fix linting of FITS datatype code by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16169 <https://github.com/galaxyproject/galaxy/pull/16169>`_
+* backport of pysam tostring by `@martenson <https://github.com/martenson>`_ in `#16822 <https://github.com/galaxyproject/galaxy/pull/16822>`_
+
+-------------------
+23.0.6 (2023-10-23)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Fix extra files path handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16541 <https://github.com/galaxyproject/galaxy/pull/16541>`_
+* Don't fail invocation message without dependent_workflow_step_id by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16628 <https://github.com/galaxyproject/galaxy/pull/16628>`_
+
+-------------------
+23.0.5 (2023-07-29)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Copy when_expression when copying workflow step by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16377 <https://github.com/galaxyproject/galaxy/pull/16377>`_
+
+-------------------
+23.0.4 (2023-06-30)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+23.0.3 (2023-06-26)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+23.0.2 (2023-06-13)
+-------------------
+
+No recorded changes since last release
+
+-------------------
+23.0.1 (2023-06-08)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Display DCE in job parameter component, allow rerunning with DCE input by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15744 <https://github.com/galaxyproject/galaxy/pull/15744>`_
+* Fix folder listing via file browser by `@mvdbeek <https://github.com/mvdbeek>`_ in `#15950 <https://github.com/galaxyproject/galaxy/pull/15950>`_
+* Fix RO-crate invocation export with complex collections by `@davelopez <https://github.com/davelopez>`_ in `#15971 <https://github.com/galaxyproject/galaxy/pull/15971>`_
+* Backport Improve display chunk generation for BAMs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16007 <https://github.com/galaxyproject/galaxy/pull/16007>`_
+* Ensure history export contains all expected datasets by `@davelopez <https://github.com/davelopez>`_ in `#16013 <https://github.com/galaxyproject/galaxy/pull/16013>`_
+* Various fixes to path prefix handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16033 <https://github.com/galaxyproject/galaxy/pull/16033>`_
+* Fix dataype_change not updating HDCA update_time by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16099 <https://github.com/galaxyproject/galaxy/pull/16099>`_
+* Fix mypy error due to alembic 1.11.0 by `@nsoranzo <https://github.com/nsoranzo>`_ in `#16104 <https://github.com/galaxyproject/galaxy/pull/16104>`_
+* Fix extended metadata file size handling by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16109 <https://github.com/galaxyproject/galaxy/pull/16109>`_
+* Fix implicit converters with optional parameters by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16133 <https://github.com/galaxyproject/galaxy/pull/16133>`_
+* Make ``ctx_rev`` optional in InstalledToolShedRepository response model by `@dannon <https://github.com/dannon>`_ in `#16139 <https://github.com/galaxyproject/galaxy/pull/16139>`_
+* Fix optional fields being validated as missing in ts api by `@jmchilton <https://github.com/jmchilton>`_ in `#16141 <https://github.com/galaxyproject/galaxy/pull/16141>`_
+* Support ro crate 0.8.0 and 0.7.0 by `@mvdbeek <https://github.com/mvdbeek>`_ in `#16193 <https://github.com/galaxyproject/galaxy/pull/16193>`_
+* Verify existence of default value attribute for user forms fields by `@guerler <https://github.com/guerler>`_ in `#16205 <https://github.com/galaxyproject/galaxy/pull/16205>`_
+
+-------------------
+20.9.0 (2020-10-15)
+-------------------
+
+* First release from the 20.09 branch of Galaxy.
+
+-------------------
+20.5.0 (2020-07-04)
+-------------------
+
+* First release from the 20.05 branch of Galaxy.