galaxy-test-api 26.0.1.dev0__tar.gz → 26.1.0__tar.gz

galaxy_test_api-26.0.1.dev0/galaxy_test_api.egg-info/PKG-INFO → galaxy_test_api-26.1.0/HISTORY.rst

@@ -1,50 +1,101 @@
-Metadata-Version: 2.4
-Name: galaxy-test-api
-Version: 26.0.1.dev0
-Summary: Galaxy API tests
-Home-page: https://github.com/galaxyproject/galaxy
-Author: Galaxy Project and Community
-Author-email: galaxy-committers@lists.galaxyproject.org
-License: MIT
-Requires-Python: >=3.10
-Description-Content-Type: text/x-rst
-License-File: LICENSE
-Requires-Dist: galaxy-test-base
-Requires-Dist: pytest
-Requires-Dist: python-dateutil
-Requires-Dist: requests
-Requires-Dist: tuspy
-Provides-Extra: driver
-Requires-Dist: galaxy-test-driver; extra == "driver"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Dynamic: license-file
-
+History
+-------
 
-.. image:: https://badge.fury.io/py/galaxy-test-api.svg
-   :target: https://pypi.org/project/galaxy-test-api/
+.. to_doc
 
+-------------------
+26.1.0 (2026-08-02)
+-------------------
 
 
-Overview
---------
+=========
+Bug fixes
+=========
 
-The Galaxy_ API tests.
+* Avoid missing field value failure in data tables by `@guerler <https://github.com/guerler>`_ in `#21008 <https://github.com/galaxyproject/galaxy/pull/21008>`_
+* Fix dbkey filter returning no options when dbkey unset by `@jmchilton <https://github.com/jmchilton>`_ in `#21916 <https://github.com/galaxyproject/galaxy/pull/21916>`_
+* Fix workflow implicit mapping of flat collections over paired_or_unpaired by `@jmchilton <https://github.com/jmchilton>`_ in `#21933 <https://github.com/galaxyproject/galaxy/pull/21933>`_
+* Fix test that transiently fails if GitHub rejects a request by `@jmchilton <https://github.com/jmchilton>`_ in `#22005 <https://github.com/galaxyproject/galaxy/pull/22005>`_
+* Skip X-Frame-Options header for published embed views by `@dannon <https://github.com/dannon>`_ in `#22107 <https://github.com/galaxyproject/galaxy/pull/22107>`_
+* 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 transient failure in test_workflow_with_deleted_dataset_step_parameter by `@jmchilton <https://github.com/jmchilton>`_ in `#22138 <https://github.com/galaxyproject/galaxy/pull/22138>`_
+* Fix more paired_or_unpaired collection issues by `@jmchilton <https://github.com/jmchilton>`_ in `#22170 <https://github.com/galaxyproject/galaxy/pull/22170>`_
+* Honor group-derived roles in unprivileged tool access check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22623 <https://github.com/galaxyproject/galaxy/pull/22623>`_
+* Update test workflows to respect gxformat2 0.26.0 syntax by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22642 <https://github.com/galaxyproject/galaxy/pull/22642>`_
+* Fix workflow extraction not including user-defined tool steps by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22694 <https://github.com/galaxyproject/galaxy/pull/22694>`_
+* Harden access control for user-defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22704 <https://github.com/galaxyproject/galaxy/pull/22704>`_
+* Fix WES workflow completion and add missing WES docs by `@jmchilton <https://github.com/jmchilton>`_ in `#22857 <https://github.com/galaxyproject/galaxy/pull/22857>`_
+* Create notebooks from invocation reports instead of a new page/report by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22872 <https://github.com/galaxyproject/galaxy/pull/22872>`_
+* Fix input mangling when conditional parameter name ends in \`_N\` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22891 <https://github.com/galaxyproject/galaxy/pull/22891>`_
+* 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>`_
+* Make unowned but accessible pages uneditable by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22911 <https://github.com/galaxyproject/galaxy/pull/22911>`_
+* Keep collection-operation outputs as workflow steps in extraction by `@jmchilton <https://github.com/jmchilton>`_ in `#22912 <https://github.com/galaxyproject/galaxy/pull/22912>`_
+* Accept dce collection references in the tool request model by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22926 <https://github.com/galaxyproject/galaxy/pull/22926>`_
+* Include hidden intermediates in workflow extraction summary (#22967) by `@jmchilton <https://github.com/jmchilton>`_ in `#22970 <https://github.com/galaxyproject/galaxy/pull/22970>`_
+* Resolve user-defined tools in by-ids workflow extraction by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22992 <https://github.com/galaxyproject/galaxy/pull/22992>`_
+* 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 \`set_history\` committing None \`galaxy_session\` by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#23156 <https://github.com/galaxyproject/galaxy/pull/23156>`_
+* 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>`_
+* Fix webhooks broken by the Backbone/underscore removal by `@itisAliRH <https://github.com/itisAliRH>`_ in `#23173 <https://github.com/galaxyproject/galaxy/pull/23173>`_
 
-* Code: https://github.com/galaxyproject/galaxy
+============
+Enhancements
+============
 
-.. _Galaxy: http://galaxyproject.org/
+* Show persistent best practice results in workflow editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19546 <https://github.com/galaxyproject/galaxy/pull/19546>`_
+* Skip test_abort_fetch_job if httpstat.us is down by `@jmchilton <https://github.com/jmchilton>`_ in `#21718 <https://github.com/galaxyproject/galaxy/pull/21718>`_
+* Add Selenium tests for workflow extraction UI by `@jmchilton <https://github.com/jmchilton>`_ in `#21805 <https://github.com/galaxyproject/galaxy/pull/21805>`_
+* 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>`_
+* Migrate tool execution request from api/tools to api/jobs by `@guerler <https://github.com/guerler>`_ in `#21842 <https://github.com/galaxyproject/galaxy/pull/21842>`_
+* Support URL and TRS references for subworkflows in workflow import by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21887 <https://github.com/galaxyproject/galaxy/pull/21887>`_
+* Add the History Graph API by `@guerler <https://github.com/guerler>`_ in `#21932 <https://github.com/galaxyproject/galaxy/pull/21932>`_
+* Convert workflow extraction interface to Vue by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21935 <https://github.com/galaxyproject/galaxy/pull/21935>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21951 <https://github.com/galaxyproject/galaxy/pull/21951>`_
+* 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>`_
+* Model subcollection mapping (map_over_type) and DCE in tool parameter schema by `@jmchilton <https://github.com/jmchilton>`_ in `#21991 <https://github.com/galaxyproject/galaxy/pull/21991>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#22003 <https://github.com/galaxyproject/galaxy/pull/22003>`_
+* Enrich tool parameter JSON Schema with Galaxy metadata via model methods by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22020 <https://github.com/galaxyproject/galaxy/pull/22020>`_
+* Replace mocked agent tests with static YAML backend for deterministic API/E2E testing by `@jmchilton <https://github.com/jmchilton>`_ in `#22070 <https://github.com/galaxyproject/galaxy/pull/22070>`_
+* Add API tests proving __current_case__ is redundant at execution time by `@jmchilton <https://github.com/jmchilton>`_ in `#22134 <https://github.com/galaxyproject/galaxy/pull/22134>`_
+* Extend the favorite tool panel concept by `@bgruening <https://github.com/bgruening>`_ in `#22212 <https://github.com/galaxyproject/galaxy/pull/22212>`_
+* Add \`pick_value\` Workflow Module by `@jmchilton <https://github.com/jmchilton>`_ in `#22222 <https://github.com/galaxyproject/galaxy/pull/22222>`_
+* Simplify gxformat2 contract - drop ImporterGalaxyInterface, convert_and_import_workflow by `@jmchilton <https://github.com/jmchilton>`_ in `#22241 <https://github.com/galaxyproject/galaxy/pull/22241>`_
+* Search and paginate user and roles api by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22311 <https://github.com/galaxyproject/galaxy/pull/22311>`_
+* 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 various pytest warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22472 <https://github.com/galaxyproject/galaxy/pull/22472>`_
+* Narrow YAML schema by `@jmchilton <https://github.com/jmchilton>`_ in `#22507 <https://github.com/galaxyproject/galaxy/pull/22507>`_
+* Use now() wrapper instead of datetime.now() by `@bgruening <https://github.com/bgruening>`_ in `#22579 <https://github.com/galaxyproject/galaxy/pull/22579>`_
+* 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>`_
+* More structured HistoryGraph API references by `@jmchilton <https://github.com/jmchilton>`_ in `#22732 <https://github.com/galaxyproject/galaxy/pull/22732>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
 
-History
--------
 
-.. to_doc
+=========
+Bug fixes
+=========
 
------------
-26.0.1.dev0
------------
+* Hide hidden tools in the tool form by `@bgruening <https://github.com/bgruening>`_ in `#22215 <https://github.com/galaxyproject/galaxy/pull/22215>`_
+* Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements by `@ernestprovo23 <https://github.com/ernestprovo23>`_ in `#22282 <https://github.com/galaxyproject/galaxy/pull/22282>`_
+* 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>`_
+* Treat paused inputs as not-ready in DatabaseOperationTool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22529 <https://github.com/galaxyproject/galaxy/pull/22529>`_
+* Fix crash merging structurally invalid nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22546 <https://github.com/galaxyproject/galaxy/pull/22546>`_
+* Raise ToolInputsNotReady for unpopulated structured_like target by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22552 <https://github.com/galaxyproject/galaxy/pull/22552>`_
+* Raises error if decoding fails during relabeling from file by `@guerler <https://github.com/guerler>`_ in `#22595 <https://github.com/galaxyproject/galaxy/pull/22595>`_
+* Fix job access check for collection-only outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22603 <https://github.com/galaxyproject/galaxy/pull/22603>`_
+* Fix data source tool redirect back to Galaxy SPA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22720 <https://github.com/galaxyproject/galaxy/pull/22720>`_
+* Fix HDA leak in tool form for data managers (#22674) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22724 <https://github.com/galaxyproject/galaxy/pull/22724>`_
+* Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22778 <https://github.com/galaxyproject/galaxy/pull/22778>`_
 
+============
+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>`_
 
 -------------------
 26.0.0 (2026-04-08)

galaxy_test_api-26.1.0/Makefile

@@ -0,0 +1,103 @@
+# Location of virtualenv used for development.
+VENV?=.venv
+# Open resource on Mac OS X or Linux
+OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
+# Source virtualenv to execute command (flake8, sphinx, twine, etc...)
+IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
+UPSTREAM?=galaxyproject
+SOURCE_DIR?=galaxy
+BUILD_SCRIPTS_DIR=scripts
+DEV_RELEASE?=0
+VERSION?=$(shell DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/print_version_for_release.py)
+PROJECT_NAME?=galaxy-$(shell basename $(CURDIR))
+PROJECT_NAME:=$(subst _,-,$(PROJECT_NAME))
+BRANCH?=$(shell git rev-parse --abbrev-ref HEAD)
+TEST_DIR?=tests
+DIST=dist
+TESTS?=$(SOURCE_DIR) $(TEST_DIR)
+
+.PHONY: clean-pyc clean-build docs clean
+
+help:
+	@echo "clean - remove all build, test, coverage and Python artifacts"
+	@echo "clean-build - remove build artifacts"
+	@echo "clean-pyc - remove Python file artifacts"
+	@echo "clean-test - remove test and coverage artifacts"
+	@echo "setup-venv - setup a development virtualenv in current directory."
+	@echo "lint-dist - twine check dist results, including validating README content"
+	@echo "dist - package project for PyPI distribution"
+
+clean: clean-build clean-pyc clean-tests
+
+clean-build:
+	rm -fr build/
+	rm -fr $(DIST)/
+	find . -name "*.egg-info" -type d -exec rm -rf {} +
+
+clean-pyc:
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-tests:
+	rm -fr .tox/
+
+setup-venv:
+	uv sync --inexact --all-extras
+
+_test:
+	uv run pytest $(TESTS)
+
+test: setup-venv _test
+
+_dist:
+	uv build -o $(DIST)
+	ls -l $(DIST)
+
+dist: clean _dist
+
+_setup-mypy-venv: setup-venv
+	uv pip install -r ../../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+
+_mypy:
+	uv run mypy .
+
+mypy: _setup-mypy-venv _mypy
+
+_setup-lint-venv: setup-venv
+	uv pip install -r ../../lib/galaxy/dependencies/pinned-lint-requirements.txt
+
+_lint:
+	uv run ruff check .
+
+lint: _setup-lint-venv _lint
+
+lint-dist:
+	uvx --with-requirements dev-requirements.txt --from twine twine check $(DIST)/*
+
+# black doesn't actually work on symlinked files because they are outside
+# the current directory
+
+#_setup-format-venv: setup-venv
+#	uv pip install isort black
+#_isort:
+#	uv run isort --sp ../../.isort.cfg . 
+#_black:
+#	uv run black --config ../pyproject.toml .
+#format: _setup-format-venv _isort _black
+
+commit-version:
+	$(IN_VENV) DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/commit_version.py $(VERSION)
+
+new-version:
+	$(IN_VENV) DEV_RELEASE=$(DEV_RELEASE) python $(BUILD_SCRIPTS_DIR)/new_version.py $(VERSION)
+
+release-local: commit-version release-artifacts new-version
+
+push-release:
+	# git push $(UPSTREAM) $(BRANCH)
+	# git push upstream $(PROJECT_NAME)-$(VERSION)
+	echo "Makefile doesn't manually push release."
+
+release: release-local push-release

{galaxy_test_api-26.0.1.dev0 → galaxy_test_api-26.1.0}/PKG-INFO

@@ -1,11 +1,26 @@
 Metadata-Version: 2.4
 Name: galaxy-test-api
-Version: 26.0.1.dev0
+Version: 26.1.0
 Summary: Galaxy API tests
 Home-page: https://github.com/galaxyproject/galaxy
 Author: Galaxy Project and Community
 Author-email: galaxy-committers@lists.galaxyproject.org
 License: MIT
+Keywords: Galaxy
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Testing
 Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
@@ -40,11 +55,99 @@ History
 
 .. to_doc
 
------------
-26.0.1.dev0
------------
+-------------------
+26.1.0 (2026-08-02)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Avoid missing field value failure in data tables by `@guerler <https://github.com/guerler>`_ in `#21008 <https://github.com/galaxyproject/galaxy/pull/21008>`_
+* Fix dbkey filter returning no options when dbkey unset by `@jmchilton <https://github.com/jmchilton>`_ in `#21916 <https://github.com/galaxyproject/galaxy/pull/21916>`_
+* Fix workflow implicit mapping of flat collections over paired_or_unpaired by `@jmchilton <https://github.com/jmchilton>`_ in `#21933 <https://github.com/galaxyproject/galaxy/pull/21933>`_
+* Fix test that transiently fails if GitHub rejects a request by `@jmchilton <https://github.com/jmchilton>`_ in `#22005 <https://github.com/galaxyproject/galaxy/pull/22005>`_
+* Skip X-Frame-Options header for published embed views by `@dannon <https://github.com/dannon>`_ in `#22107 <https://github.com/galaxyproject/galaxy/pull/22107>`_
+* 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 transient failure in test_workflow_with_deleted_dataset_step_parameter by `@jmchilton <https://github.com/jmchilton>`_ in `#22138 <https://github.com/galaxyproject/galaxy/pull/22138>`_
+* Fix more paired_or_unpaired collection issues by `@jmchilton <https://github.com/jmchilton>`_ in `#22170 <https://github.com/galaxyproject/galaxy/pull/22170>`_
+* Honor group-derived roles in unprivileged tool access check by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22623 <https://github.com/galaxyproject/galaxy/pull/22623>`_
+* Update test workflows to respect gxformat2 0.26.0 syntax by `@nsoranzo <https://github.com/nsoranzo>`_ in `#22642 <https://github.com/galaxyproject/galaxy/pull/22642>`_
+* Fix workflow extraction not including user-defined tool steps by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22694 <https://github.com/galaxyproject/galaxy/pull/22694>`_
+* Harden access control for user-defined tools by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22704 <https://github.com/galaxyproject/galaxy/pull/22704>`_
+* Fix WES workflow completion and add missing WES docs by `@jmchilton <https://github.com/jmchilton>`_ in `#22857 <https://github.com/galaxyproject/galaxy/pull/22857>`_
+* Create notebooks from invocation reports instead of a new page/report by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22872 <https://github.com/galaxyproject/galaxy/pull/22872>`_
+* Fix input mangling when conditional parameter name ends in \`_N\` by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22891 <https://github.com/galaxyproject/galaxy/pull/22891>`_
+* 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>`_
+* Make unowned but accessible pages uneditable by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#22911 <https://github.com/galaxyproject/galaxy/pull/22911>`_
+* Keep collection-operation outputs as workflow steps in extraction by `@jmchilton <https://github.com/jmchilton>`_ in `#22912 <https://github.com/galaxyproject/galaxy/pull/22912>`_
+* Accept dce collection references in the tool request model by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22926 <https://github.com/galaxyproject/galaxy/pull/22926>`_
+* Include hidden intermediates in workflow extraction summary (#22967) by `@jmchilton <https://github.com/jmchilton>`_ in `#22970 <https://github.com/galaxyproject/galaxy/pull/22970>`_
+* Resolve user-defined tools in by-ids workflow extraction by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22992 <https://github.com/galaxyproject/galaxy/pull/22992>`_
+* 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 \`set_history\` committing None \`galaxy_session\` by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#23156 <https://github.com/galaxyproject/galaxy/pull/23156>`_
+* 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>`_
+* Fix webhooks broken by the Backbone/underscore removal by `@itisAliRH <https://github.com/itisAliRH>`_ in `#23173 <https://github.com/galaxyproject/galaxy/pull/23173>`_
+
+============
+Enhancements
+============
 
+* Show persistent best practice results in workflow editor by `@mvdbeek <https://github.com/mvdbeek>`_ in `#19546 <https://github.com/galaxyproject/galaxy/pull/19546>`_
+* Skip test_abort_fetch_job if httpstat.us is down by `@jmchilton <https://github.com/jmchilton>`_ in `#21718 <https://github.com/galaxyproject/galaxy/pull/21718>`_
+* Add Selenium tests for workflow extraction UI by `@jmchilton <https://github.com/jmchilton>`_ in `#21805 <https://github.com/galaxyproject/galaxy/pull/21805>`_
+* 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>`_
+* Migrate tool execution request from api/tools to api/jobs by `@guerler <https://github.com/guerler>`_ in `#21842 <https://github.com/galaxyproject/galaxy/pull/21842>`_
+* Support URL and TRS references for subworkflows in workflow import by `@mvdbeek <https://github.com/mvdbeek>`_ in `#21887 <https://github.com/galaxyproject/galaxy/pull/21887>`_
+* Add the History Graph API by `@guerler <https://github.com/guerler>`_ in `#21932 <https://github.com/galaxyproject/galaxy/pull/21932>`_
+* Convert workflow extraction interface to Vue by `@ahmedhamidawan <https://github.com/ahmedhamidawan>`_ in `#21935 <https://github.com/galaxyproject/galaxy/pull/21935>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#21951 <https://github.com/galaxyproject/galaxy/pull/21951>`_
+* 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>`_
+* Model subcollection mapping (map_over_type) and DCE in tool parameter schema by `@jmchilton <https://github.com/jmchilton>`_ in `#21991 <https://github.com/galaxyproject/galaxy/pull/21991>`_
+* Update Python dependencies by `@galaxybot <https://github.com/galaxybot>`_ in `#22003 <https://github.com/galaxyproject/galaxy/pull/22003>`_
+* Enrich tool parameter JSON Schema with Galaxy metadata via model methods by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22020 <https://github.com/galaxyproject/galaxy/pull/22020>`_
+* Replace mocked agent tests with static YAML backend for deterministic API/E2E testing by `@jmchilton <https://github.com/jmchilton>`_ in `#22070 <https://github.com/galaxyproject/galaxy/pull/22070>`_
+* Add API tests proving __current_case__ is redundant at execution time by `@jmchilton <https://github.com/jmchilton>`_ in `#22134 <https://github.com/galaxyproject/galaxy/pull/22134>`_
+* Extend the favorite tool panel concept by `@bgruening <https://github.com/bgruening>`_ in `#22212 <https://github.com/galaxyproject/galaxy/pull/22212>`_
+* Add \`pick_value\` Workflow Module by `@jmchilton <https://github.com/jmchilton>`_ in `#22222 <https://github.com/galaxyproject/galaxy/pull/22222>`_
+* Simplify gxformat2 contract - drop ImporterGalaxyInterface, convert_and_import_workflow by `@jmchilton <https://github.com/jmchilton>`_ in `#22241 <https://github.com/galaxyproject/galaxy/pull/22241>`_
+* Search and paginate user and roles api by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22311 <https://github.com/galaxyproject/galaxy/pull/22311>`_
+* 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 various pytest warnings by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22472 <https://github.com/galaxyproject/galaxy/pull/22472>`_
+* Narrow YAML schema by `@jmchilton <https://github.com/jmchilton>`_ in `#22507 <https://github.com/galaxyproject/galaxy/pull/22507>`_
+* Use now() wrapper instead of datetime.now() by `@bgruening <https://github.com/bgruening>`_ in `#22579 <https://github.com/galaxyproject/galaxy/pull/22579>`_
+* 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>`_
+* More structured HistoryGraph API references by `@jmchilton <https://github.com/jmchilton>`_ in `#22732 <https://github.com/galaxyproject/galaxy/pull/22732>`_
+
+-------------------
+26.0.1 (2026-06-04)
+-------------------
+
+
+=========
+Bug fixes
+=========
+
+* Hide hidden tools in the tool form by `@bgruening <https://github.com/bgruening>`_ in `#22215 <https://github.com/galaxyproject/galaxy/pull/22215>`_
+* Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements by `@ernestprovo23 <https://github.com/ernestprovo23>`_ in `#22282 <https://github.com/galaxyproject/galaxy/pull/22282>`_
+* 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>`_
+* Treat paused inputs as not-ready in DatabaseOperationTool by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22529 <https://github.com/galaxyproject/galaxy/pull/22529>`_
+* Fix crash merging structurally invalid nested collections by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22546 <https://github.com/galaxyproject/galaxy/pull/22546>`_
+* Raise ToolInputsNotReady for unpopulated structured_like target by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22552 <https://github.com/galaxyproject/galaxy/pull/22552>`_
+* Raises error if decoding fails during relabeling from file by `@guerler <https://github.com/guerler>`_ in `#22595 <https://github.com/galaxyproject/galaxy/pull/22595>`_
+* Fix job access check for collection-only outputs by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22603 <https://github.com/galaxyproject/galaxy/pull/22603>`_
+* Fix data source tool redirect back to Galaxy SPA by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22720 <https://github.com/galaxyproject/galaxy/pull/22720>`_
+* Fix HDA leak in tool form for data managers (#22674) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22724 <https://github.com/galaxyproject/galaxy/pull/22724>`_
+* Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by `@mvdbeek <https://github.com/mvdbeek>`_ in `#22778 <https://github.com/galaxyproject/galaxy/pull/22778>`_
+
+============
+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>`_
 
 -------------------
 26.0.0 (2026-04-08)