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Update a couple PR titles, strip trailing . from PR titles

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mvdbeek
2022-08-19 12:29:25 +02:00
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doc/source/releases/22.05.rst
+87 -87
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@@ -17,10 +17,10 @@ Enhancements
* Add new molecule datatypes
(thanks to `@muon-spectroscopy-computational-project <https://github.com/muon-spectroscopy-computational-project>`__).
`Pull Request 12375`_
* Add DEFERRED datasets to Galaxy.
* Add DEFERRED datasets to Galaxy
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 12533`_
* Storage dashboard
* Add Storage dashboard
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13113`_
* Add built-in converters to tool panel
@@ -29,7 +29,7 @@ Enhancements
* Enable infinite scrolling / pagination for history and collection items
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 13477`_
* Reorganized alembic branch
* Replace SQLAlchemy Migrate with Alembic
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 13513`_
* Add filtering to new History
@@ -47,10 +47,10 @@ Enhancements
* Replace bootstrap-tour.js with popper.js
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 13778`_
* IT updates from EU
* Add and update various interactive tools
(thanks to `@gmauro <https://github.com/gmauro>`__).
`Pull Request 13811`_
* Beta History: add more bulk operations
* Add more bulk operations to Beta History
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13877`_
* Update color scheme collection progress bar
@@ -63,10 +63,10 @@ Enhancements
`Pull Request 13370`_
.. enhancement_tag_datatypes
* add mzqc datatype
* Add mzqc datatype
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 13564`_
* Update mypy to 0.942 . Fix new mypy errors.
* Update mypy to 0.942 and fix new mypy errors
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 13650`_
* Create data_fetch and set_metadata celery tasks
@@ -83,7 +83,7 @@ Enhancements
`Pull Request 13927`_
.. enhancement_tag_tools
* Add JupyTool, user-configurable interactive Jupyter-based tool.
* Add JupyTool, user-configurable interactive Jupyter-based tool
(thanks to `@blankenberg <https://github.com/blankenberg>`__).
`Pull Request 13606`_
.. enhancement_tag_workflows
@@ -91,25 +91,25 @@ Enhancements
* Simplified workflow form runtime options
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13613`_
* Selenium tests for much of `#13600 <https://github.com/galaxyproject/galaxy/issues/13600>`__.
* Selenium tests for much of `#13600 <https://github.com/galaxyproject/galaxy/issues/13600>`__
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13673`_
* Rework workflow index API for more consistency between deleted/hidden and showing shared workflows.
* Rework workflow index API for more consistency between deleted/hidden and showing shared workflows
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13699`_
* Implement API endpoints and tests for workflow sharing options.
* Implement API endpoints and tests for workflow sharing options
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13719`_
* Fix import workflow file and UX enhancements
* Fix workflow file import and enhance UX for workflow imports
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13754`_
* Implement more useful workflow tagging.
* Implement more useful workflow tagging
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13786`_
* Implement initial jest unit tests for WorkflowList.vue.
* Implement initial jest unit tests for WorkflowList.vue
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13856`_
* Use an Enum for invocations view.
* Use an Enum for invocations view
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13875`_
* Workflow List Vue Component Improvements
@@ -118,21 +118,21 @@ Enhancements
* More Workflow List Component Improvements
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13892`_
* API workflow index allow 'searching' by owner.
* API workflow index allow 'searching' by owner
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13934`_
* More Uniform URI Access and Validation
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13947`_
* Localize workflow deletion confirmation message...
* Localize workflow deletion confirmation message
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13987`_
* Workflow deletion selenium tests.
* Add workflow deletion selenium tests
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13994`_
.. enhancement_tag_ui
* Client dependency updates, swap to node 16.
* Update Client dependency, swap to node 16
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13282`_
* Run jest tests using node 16 in CI
@@ -144,7 +144,7 @@ Enhancements
* Add support for gulp build process to use a configurable directory
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13657`_
* Formalize supported browsers, drop transpilation, enforce with eslint.
* Formalize supported browsers, drop transpilation, enforce with eslint
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13709`_
* Swap to vue/recommended eslint
@@ -153,7 +153,7 @@ Enhancements
* Citation separation
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13847`_
* Add client build timestamp to application config.
* Add client build timestamp to application config
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13874`_
.. enhancement_tag_jobs
@@ -161,13 +161,13 @@ Enhancements
* Attach dataset source in model store imports
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13560`_
* Overhaul job metrics.
* Overhaul job metrics
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13634`_
* More Python typing around job evaluation code
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13659`_
* Migrate jobs index to FastAPI controller.
* Migrate jobs index to FastAPI controller
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13767`_
* Port api/tools/fetch to FastAPI, add schema, and use `__FETCH_DATA__` in most tests
@@ -207,9 +207,6 @@ Enhancements
* Check prefix before complete loading when checking yaml and cwl tools
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 12604`_
* Support bulk dbkey and datatype collection changes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 14172`_
* Maintain redirect if login is necessary
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13274`_
@@ -237,7 +234,7 @@ Enhancements
* Add source_metadata attribute for workflows imported using TRS ID or via URL
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 13376`_
* Allow legacy EDAM mappings.
* Allow legacy EDAM mappings
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13413`_
* Add sorting function to Saved Rules Selector
@@ -252,7 +249,7 @@ Enhancements
* let linter check for duplicated names/labels
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 13459`_
* Small enhancements from the deferred data branch.
* Small enhancements from the deferred data branch
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13475`_
* Various Celery Framework Enhancements
@@ -264,7 +261,7 @@ Enhancements
* Run tests with ``metadata_strategy: extended`` on weekly schedule
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13503`_
* Integration end-to-end test for PDF export.
* Integration end-to-end test for PDF export
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13504`_
* Add API endpoint to recalculate user disk usage
@@ -273,10 +270,10 @@ Enhancements
* Add retries to `test_github_search`
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13509`_
* More small atomic enhancements from the deferred data branch.
* More small atomic enhancements from the deferred data branch
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13517`_
* Disable implicit optional types.
* Disable implicit optional types
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13519`_
* Update Python dependencies
@@ -339,7 +336,7 @@ Enhancements
* Update Python dependencies
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
`Pull Request 13661`_
* Disable implicitly attaching HDAs to histories.
* Disable implicitly attaching HDAs to histories
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13670`_
* Use authenticated git protocol in pre-commit repo
@@ -351,7 +348,7 @@ Enhancements
* Add OIDC PKCE parameter support
(thanks to `@gecage952 <https://github.com/gecage952>`__).
`Pull Request 13683`_
* Infrastructure for building dynamic files for download asynchronously.
* Infrastructure for building dynamic files for download asynchronously
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13691`_
* Update irods client
@@ -372,10 +369,10 @@ Enhancements
* Watch changes to history object instead of changed history items
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 13721`_
* Anonymous user history menu fixes.
* Anonymous user history menu fixes
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13724`_
* Implement pagination of workflows grid.
* Implement pagination of workflows grid
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13725`_
* Workflow index API fix and testing
@@ -405,7 +402,7 @@ Enhancements
* Adjust tours and tour tests to new history
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 13777`_
* Switch workflow sharing to common Vue component.
* Switch workflow sharing to common Vue component
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13780`_
* Replace 2 uses of deprecated ``imp`` module
@@ -417,7 +414,7 @@ Enhancements
* Update committers list
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 13791`_
* Allow users to view invocations only for a particular workflow.
* Allow users to view invocations only for a particular workflow
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13792`_
* Update Python dependencies
@@ -435,7 +432,7 @@ Enhancements
* Use ``load_app_properties()`` to load Galaxy config file
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 13809`_
* Improve assert error for transient citation rendering test issue.
* Improve assert error for transient citation rendering test issue
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13814`_
* Add allowance for members changing their own name…
@@ -453,7 +450,7 @@ Enhancements
* Beta History: display 'processing' message while running bulk operations
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13844`_
* Typing fixes from deferred data branch.
* Typing fixes from deferred data branch
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13845`_
* Beta History: display `global` history bulk operations only when necessary
@@ -462,7 +459,7 @@ Enhancements
* Beta History: notify query selection break
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13850`_
* Improved typing of Galaxy model store related stuff.
* Improved typing of Galaxy model store related stuff
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13861`_
* galaxy-tool-util: better link in the README
@@ -510,16 +507,16 @@ Enhancements
* Recommend rebasing PRs over merging the target branch
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 13961`_
* More remove legacy tool dependencies handling in tool shed.
* More remove legacy tool dependencies handling in tool shed
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13966`_
* Refactor authenticate controller into a services layer.
* Refactor authenticate controller into a services layer
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13967`_
* Use colon symbol instead of equal sign in history filters
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 13971`_
* Remove can_eliminate_tool_dependency from tool shed code.
* Remove can_eliminate_tool_dependency from tool shed code
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13975`_
* Update Python dependencies
@@ -531,25 +528,25 @@ Enhancements
* Add history update time to Beta History
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
`Pull Request 13989`_
* More workflow Jest tests.
* More workflow Jest tests
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13993`_
* Small tour tweaks.
* Small tour tweaks
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13996`_
* Add text to history import/switch buttons
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
`Pull Request 14001`_
* Script to validate tours structure.
* Script to validate tours structure
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14003`_
* Cleaner, More Robust Workflow Creation Form Testing Logic
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14004`_
* Add galaxy-test-driver to CI package tests.
* Add galaxy-test-driver to CI package tests
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14011`_
* Bring galaxy-test-api under CI also.
* Bring galaxy-test-api under CI also
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14012`_
* Update Python dependencies
@@ -558,10 +555,10 @@ Enhancements
* Use setuptools custom package discovery instead of explicit listing
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 14022`_
* Add a tour for deferred datasets.
* Add a tour for deferred datasets
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14036`_
* Add tour requirements.
* Add tour requirements
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14037`_
* Enable change datatype in bulk
@@ -588,9 +585,12 @@ Enhancements
* Rephrase 'updated' to 'refreshed' in history counter
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 14113`_
* Support bulk dbkey and datatype collection changes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 14172`_
.. small_enhancement
* Python code formatting standard, automatic.
* Python code formatting standard, automatic
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 11162`_
* Remove uWSGI / WSGI support
@@ -608,7 +608,7 @@ Enhancements
* Relax checks for `test_github_search`
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13410`_
* Disable implicit re-imports across the project.
* Disable implicit re-imports across the project
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13476`_
* Update logging configuration documentation
@@ -641,7 +641,7 @@ Enhancements
* Fix mypy error on bool expressions
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13712`_
* Rework admin job tables into reusable Galaxy job table component.
* Rework admin job tables into reusable Galaxy job table component
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13769`_
* Unused client dependency purge
@@ -662,10 +662,10 @@ Enhancements
* Duplicates removed from filtering.js
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
`Pull Request 13835`_
* ToolSourceDisplay dynamic import for shared libs bundle size improvement.
* ToolSourceDisplay dynamic import for shared libs bundle size improvement
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13837`_
* Refactor toward invocations service layer.
* Refactor toward invocations service layer
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13862`_
* Update committer login name
@@ -677,7 +677,7 @@ Enhancements
* Beta History Collections: set default visible and deleted state in ContentOptions
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13939`_
* Small code cleanup fixes to galaxy.model.store related code.
* Small code cleanup fixes to galaxy.model.store related code
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13944`_
* Drop update_time from JobStateHistory
@@ -714,7 +714,7 @@ Fixes
* Support phylocanvas autobuild
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 14023`_
* Fix a bug in PCA artifact staging that prevents a plugin rebuild.
* Fix a bug in PCA artifact staging that prevents a plugin rebuild
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 14148`_
.. bug_tag_datatypes
@@ -747,16 +747,16 @@ Fixes
`Pull Request 13853`_
.. bug_tag_workflows
* Fix workflow index API boolean parameters.
* Fix workflow index API boolean parameters
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13698`_
* More robust workflow grid selenium tests.
* More robust workflow grid selenium tests
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13855`_
* Fix workflow bookmarking API.
* Fix workflow bookmarking API
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13857`_
* Fix showing invocations for a particular workflow.
* Fix showing invocations for a particular workflow
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14102`_
.. bug_tag_ui
@@ -814,7 +814,7 @@ Fixes
* Only stream stdout/stderr on kubernetes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 13642`_
* Improve error handling for CLI job runner.
* Improve error handling for CLI job runner
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13759`_
* Fix error when getting destinations by tag
@@ -846,7 +846,7 @@ Fixes
* Fix persistent mulled cache unused for repo_has_name
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13718`_
* Fix up configuration for STS. Can't rebuild config without this.
* Fix up configuration for STS. Can't rebuild config without this
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13834`_
* Misc fixes 2022-05
@@ -855,7 +855,7 @@ Fixes
* Fix a small error in job doc
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 14013`_
* Interactivetool doc/sample tweaks.
* Interactivetool doc/sample tweaks
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 14025`_
.. bug
@@ -866,12 +866,6 @@ Fixes
* Trim spaces from around email addresses and usernames when registering
(thanks to `@natefoo <https://github.com/natefoo>`__).
`Pull Request 12482`_
* Fix logic around tool favorites for anonymous users.
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14189`_
* Support stop_job param in query string
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 14194`_
* Fix a bug in username minimum length transformation and set minimum length to 1
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 13195`_
@@ -908,7 +902,7 @@ Fixes
* Fix copy tool id
(thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
`Pull Request 13463`_
* Make test_user_library_permissions.py more robust.
* Make test_user_library_permissions.py more robust
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13487`_
* Expand input parameter workflow steps in workflow run form
@@ -965,7 +959,7 @@ Fixes
* Minor tweak to language in history dropdown in beta history
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 13631`_
* Potentially fix flakey rename test with beta history.
* Potentially fix flakey rename test with beta history
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13633`_
* Limit tool parameter value to show only 20 lines with overflow scrolling
@@ -974,13 +968,13 @@ Fixes
* Forward type annotation of depends
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13643`_
* Fix package CI for pysam errors.
* Fix package CI for pysam errors
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13644`_
* Fix unselect file in FTP uploader popup
(thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
`Pull Request 13652`_
* Correct data fetch API call in the client.
* Correct data fetch API call in the client
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13669`_
* Update supervisor config when starting galaxy via run.sh
@@ -1001,10 +995,10 @@ Fixes
* Fix sorting of recursively discovered datasets
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 13688`_
* Fix download collection button in history panel.
* Fix download collection button in history panel
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13690`_
* Two small fixes to testing infrastructure.
* Two small fixes to testing infrastructure
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13693`_
* Raise a more appropriate error when there's no version table
@@ -1025,25 +1019,25 @@ Fixes
* Miscellaneous Histories API fixes
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 13717`_
* Simplify some selenium upload tests to respect either history properly.
* Simplify some selenium upload tests to respect either history properly
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13726`_
* Converge testing and classes for history options across new and old history panel.
* Converge testing and classes for history options across new and old history panel
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13727`_
* Eliminate dependency of legacy history for history sharing tests.
* Eliminate dependency of legacy history for history sharing tests
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13729`_
* Unquote url before using it
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 13730`_
* Fix test_navigates_galaxy.py for beta history panel.
* Fix test_navigates_galaxy.py for beta history panel
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13732`_
* Fix tests for simple_constructs.yml.
* Fix tests for simple_constructs.yml
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13758`_
* More robust is_beta_history() testing check.
* More robust is_beta_history() testing check
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13762`_
* Add an option to disable searching for distributed object store datasets that don't have an object_store_id
@@ -1058,7 +1052,7 @@ Fixes
* Do not store toolbox on ToolPanelViewSearch
(thanks to `@cat-bro <https://github.com/cat-bro>`__).
`Pull Request 13776`_
* Fixes for sharing component error handling.
* Fixes for sharing component error handling
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13779`_
* Beta History: fix history query counts synchronization
@@ -1070,7 +1064,7 @@ Fixes
* Fix thread accumulation in testing
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13788`_
* Potential fix for certain kind of transient Selenium library errors.
* Potential fix for certain kind of transient Selenium library errors
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13794`_
* Pulsar fix for tools that use chromosome len files
@@ -1115,7 +1109,7 @@ Fixes
* Backport: Respect GRAVITY_STATE_DIR when activating venv
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 13897`_
* Fix typing for unpinned request dependency.
* Fix typing for unpinned request dependency
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 13898`_
* Expand/collapse history dataset display content
@@ -1193,7 +1187,7 @@ Fixes
* Fix missing biotools package
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 14020`_
* Remove fabric as a dependency for Galaxy.
* Remove fabric as a dependency for Galaxy
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14030`_
* Add sessioncookie with ``SameSite=None; secure`` for tool_runner path
@@ -1223,7 +1217,7 @@ Fixes
* Clear history refresh timeout for snappier operations in new history
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 14088`_
* Storage Dashboard: fix unlimited quota display
* Fix unlimited quota display in Storage Dashboard
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 14090`_
* Update window manager margin
@@ -1307,9 +1301,15 @@ Fixes
* Fix histories API URL building
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 14186`_
* Fix logic around tool favorites for anonymous users
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 14189`_
* Fix `FilesDialog` navigation back when a file source shows an error
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 14190`_
* Support stop_job param in query string
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 14194`_
* Replace release note videos with youtube links
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 14201`_
doc/source/releases/22.05_announce_user.rst
+7 -7
View File
@@ -37,7 +37,7 @@ New Visualizations
* Support phylocanvas autobuild
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 14023`_
* Fix a bug in PCA artifact staging that prevents a plugin rebuild.
* Fix a bug in PCA artifact staging that prevents a plugin rebuild
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 14148`_
@@ -45,7 +45,7 @@ New Datatypes
===========================================================
.. datatypes
* Python code formatting standard, automatic.
* Python code formatting standard, automatic
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 11162`_
* Add new molecule datatypes
@@ -54,10 +54,10 @@ New Datatypes
* Upgrade syntax to Python 3.7
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 13500`_
* add mzqc datatype
* Add mzqc datatype
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 13564`_
* Update mypy to 0.942 . Fix new mypy errors.
* Update mypy to 0.942 and fix new mypy errors
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 13650`_
* Create data_fetch and set_metadata celery tasks
@@ -95,19 +95,19 @@ Builtin Tool Updates
===========================================================
.. tools
* Python code formatting standard, automatic.
* Python code formatting standard, automatic
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 11162`_
* Add built-in converters to tool panel
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 13447`_
* Add JupyTool, user-configurable interactive Jupyter-based tool.
* Add JupyTool, user-configurable interactive Jupyter-based tool
(thanks to `@blankenberg <https://github.com/blankenberg>`__).
`Pull Request 13606`_
* Fix David URL
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 13666`_
* IT updates from EU
* Add and update various interactive tools
(thanks to `@gmauro <https://github.com/gmauro>`__).
`Pull Request 13811`_
* Bump ncb-datasets-cli dependency to 13.14.0
doc/source/releases/22.05_prs.rst
+3 -3
View File
@@ -7,9 +7,6 @@
.. _Pull Request 12482: https://github.com/galaxyproject/galaxy/pull/12482
.. _Pull Request 12533: https://github.com/galaxyproject/galaxy/pull/12533
.. _Pull Request 12604: https://github.com/galaxyproject/galaxy/pull/12604
.. _Pull Request 14172: https://github.com/galaxyproject/galaxy/pull/14172
.. _Pull Request 14189: https://github.com/galaxyproject/galaxy/pull/14189
.. _Pull Request 14194: https://github.com/galaxyproject/galaxy/pull/14194
.. _Pull Request 13071: https://github.com/galaxyproject/galaxy/pull/13071
.. _Pull Request 13113: https://github.com/galaxyproject/galaxy/pull/13113
.. _Pull Request 13177: https://github.com/galaxyproject/galaxy/pull/13177
@@ -429,12 +426,15 @@
.. _Pull Request 14167: https://github.com/galaxyproject/galaxy/pull/14167
.. _Pull Request 14170: https://github.com/galaxyproject/galaxy/pull/14170
.. _Pull Request 14171: https://github.com/galaxyproject/galaxy/pull/14171
.. _Pull Request 14172: https://github.com/galaxyproject/galaxy/pull/14172
.. _Pull Request 14176: https://github.com/galaxyproject/galaxy/pull/14176
.. _Pull Request 14179: https://github.com/galaxyproject/galaxy/pull/14179
.. _Pull Request 14181: https://github.com/galaxyproject/galaxy/pull/14181
.. _Pull Request 14183: https://github.com/galaxyproject/galaxy/pull/14183
.. _Pull Request 14186: https://github.com/galaxyproject/galaxy/pull/14186
.. _Pull Request 14189: https://github.com/galaxyproject/galaxy/pull/14189
.. _Pull Request 14190: https://github.com/galaxyproject/galaxy/pull/14190
.. _Pull Request 14194: https://github.com/galaxyproject/galaxy/pull/14194
.. _Pull Request 14196: https://github.com/galaxyproject/galaxy/pull/14196
.. _Pull Request 14198: https://github.com/galaxyproject/galaxy/pull/14198
.. _Pull Request 14201: https://github.com/galaxyproject/galaxy/pull/14201
scripts/bootstrap_history.py
+1 -1
View File
@@ -378,7 +378,7 @@ def do_release(argv):
for pr in _get_prs(release_name):
# 2015-06-29 18:32:13 2015-04-22 19:11:53 2015-08-12 21:15:45
as_dict = {
"title": pr.title,
"title": pr.title.rstrip("."),
"number": pr.number,
"head": pr.head,
"labels": _pr_to_labels(pr),