
.. to_doc

20.05
===============================

.. announce_start

Enhancements
-------------------------------

.. major_feature

* New data types for OpenMS
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 8109`_
* Refactor Workflow Run Form Toward Vue (part 1)
  `Pull Request 9138`_
* Refactor Workflow Run Form Toward Vue (part 2)
  `Pull Request 9147`_
* Replace Workflow Editor Tool Panel with Vue component
  `Pull Request 9201`_
* Replace right panel in Workflow Editor with Vue component
  `Pull Request 9249`_
* Replacing Workflow Editor Node with Vue-component
  `Pull Request 9332`_
* Render workflow node connections using d3
  `Pull Request 9471`_
* Make Toolshed Python 3 compatible & tests
  `Pull Request 9528`_
* Migrate interactive tools from EU server
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 9559`_
* Allow Tool Data Tables to be backed by refgenie
  `Pull Request 9600`_
* Startup speedups (XML doc cache, delay non-essential tool param parsing & indexing)
  `Pull Request 9610`_

.. feature

* Enable admin to resend activation email
  `Pull Request 9154`_
* Create Python3 virtualenv by default
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9344`_
* iRODS object store rewrite
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9438`_
* Tool recommendation
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 9440`_
* Tool recommendations in workflow editor
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 9569`_
* Added whitelisting option for user registration
  (thanks to `@MiguelJulia <https://github.com/MiguelJulia>`__).
  `Pull Request 9501`_
* Editor as visualization
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9531`_
* Chira visualization for Chimeras
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9562`_
* Datasource tool for SRA manifest
  `Pull Request 9613`_, `Pull Request 9892`_

.. enhancement_tag_viz

* Skip visualization build, if no changes were registered
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9634`_

.. enhancement_tag_datatypes

* Add tpr datatype
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 9244`_
* Add datatypes for xcms and camera
  (thanks to `@computational-metabolomics <https://github.com/computational-metabolomics>`__).
  `Pull Request 9470`_
* index with -c flag for large bam (one region larger than 2**29 - 1)
  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
  `Pull Request 9570`_
* Sniffer for multi-member zip archives
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 9595`_

.. enhancement_tag_tools

* Followup to shed tool static fixes
  `Pull Request 9450`_
* Remove deprecated ``interpreter`` attribute from tools ``<command>``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9490`_
* Resize D3 tree and make it responsive
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 9547`_
* Fix ITs to work in remote Kubernetes
  `Pull Request 9614`_

.. enhancement_tag_workflows

* Fix galaxy_tool_util for composite file input testing in workflows.
  `Pull Request 9312`_
* Refactor toward testing workflow collection outputs.
  `Pull Request 9340`_
* Remove Backbone and Globals dependency from Workflow client code
  `Pull Request 9346`_
* Allow anonymous downloading of public workflows
  `Pull Request 9736`_

.. enhancement_tag_ui

* MS Edge Fixes
  `Pull Request 9289`_

.. enhancement_tag_jobs

* Refactor more of jobs admin component toward API.
  `Pull Request 9093`_
* make more tool parsing errors contain id
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9139`_
* "Normalize" more custom functions in admin jobs index.
  `Pull Request 9157`_
* Job Lock VueJS component.
  `Pull Request 9181`_
* add a new function to get the local ip address
  (thanks to `@gmauro <https://github.com/gmauro>`__).
  `Pull Request 9353`_
* Integration test for GxITs against remote proxies.
  `Pull Request 9504`_
* paramiko: load system host keys
  (thanks to `@eancelet <https://github.com/eancelet>`__).
  `Pull Request 9553`_
* Optimize setting external ID for jobs.
  `Pull Request 9691`_

.. enhancement_tag_admin

* Enable manual user activation
  `Pull Request 9143`_
* Skip migration if uninitialized database exists
  `Pull Request 9491`_

.. enhancement

* Add Okta as OIDC authentication option
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 7497`_
* Added trigger to dataset table to update history.update_time
  `Pull Request 8187`_
* Notifications on job completion
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 8427`_
* Issue `#8445 <https://github.com/galaxyproject/galaxy/issues/8445>`__: Clicking on user/email in User menu triggers a page refresh - fix
  (thanks to `@janani-prasad <https://github.com/janani-prasad>`__).
  `Pull Request 8644`_
* Third Party Identity Management
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 9060`_
* Disable the admin_toolshed controller (except for tests).
  `Pull Request 9072`_
* Upgrade to Fontawesome 5
  `Pull Request 9101`_
* Add a test for a tool with `from_working_dir`, `outputs_to_working_directory` and `pulsar`
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 9108`_
* Client build work (HMR, build upgrades, refactoring asset placement)
  `Pull Request 9123`_
* Correct typos, update location of api tests
  `Pull Request 9158`_
* Add more repository installation test cases
  `Pull Request 9160`_
* Add support for logging out of OIDC Identity Provider
  (thanks to `@machristie <https://github.com/machristie>`__).
  `Pull Request 9162`_
* Vue-ify Upload Dialog w/small fixes
  `Pull Request 9167`_
* Update galaxy.tool_util.cwl for latest changes in CWL branch.
  `Pull Request 9175`_
* More progress on Tool shed cleanup
  `Pull Request 9186`_
* Full Python dependencies update
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9188`_, `Pull Request 9402`_, `Pull Request 9529`_, `Pull Request 9697`_
* Allow mixed store_by objectstore configurations.
  `Pull Request 9197`_
* implement workflow bookmark selenium test
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9208`_
* Use a Galaxy root path with a space for integration tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9223`_
* implementing a global tools-view component + schema.org support
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9261`_
* Add icons to dropdowns in dataset and workflow list
  `Pull Request 9273`_
* extend config file inputs tests
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9279`_
* Do not strip tab characters from data_column reference and clarify documentation for use_header_names
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9291`_
* Update CONTRIBUTING.md
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9299`_
* Add more info to debug logging for loading datatypes.
  `Pull Request 9301`_
* Add do_not_cache decorator, apply to codebase.
  `Pull Request 9311`_
* Use Bootstrap components to build the Workflow Editor Toolbar
  `Pull Request 9324`_
* implement selenium test User->Preferences->Manage information
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9355`_
* Fix success message in user preferences, add help text to toolbox filter page
  `Pull Request 9368`_
* CSS changes for a modern look and feel
  (thanks to `@bedroesb <https://github.com/bedroesb>`__).
  `Pull Request 9386`_
* Added conda python update
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 9390`_
* Replace editor grid image with css, add editor client unit tests
  `Pull Request 9392`_
* Vuefy interactive tools
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9409`_
* Add delta_frac for sim_size to specify relative file size differences
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9425`_
* Make mutable_config_dir configurable + rename
  `Pull Request 9444`_
* Remove `virtualenv<20` requirement for mulled tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9447`_
* Remove mapping related abstraction classes from workflow client, increase node header contrast
  `Pull Request 9474`_
* Add eslint rule to check for invalid slot specifications
  `Pull Request 9481`_
* Another undocumented option: job metrics path
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 9482`_
* Document maxpctfull objecto store option
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 9498`_
* Selenium Multi-History View
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9505`_
* Adjust dataset error reporting page, remove email option, remove long info text
  `Pull Request 9508`_
* Drop remaining Python 2.7 CircleCI tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9518`_
* Implementation selenium test for user change password
  (thanks to `@Realjuan <https://github.com/Realjuan>`__).
  `Pull Request 9521`_
* Rename and modify current_history_contents method
  `Pull Request 9526`_
* Improvement to the selenium test to change password from user preferences
  (thanks to `@Realjuan <https://github.com/Realjuan>`__).
  `Pull Request 9545`_
* Implementation of Selenium test for signout from user preferences
  (thanks to `@Realjuan <https://github.com/Realjuan>`__).
  `Pull Request 9546`_
* Move OSX startup tests to github CI, drop travis tests
  `Pull Request 9563`_
* Check if path is set before joining
  `Pull Request 9568`_
* Sort Tool Search Result by ranking
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 9579`_
* TS performance fixes
  `Pull Request 9580`_
* Vuefy Job Destination Parameters
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9583`_
* Fix kubernetes test failures again
  `Pull Request 9585`_
* Enabled various object store types to store data objects by uuid.
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9609`_
* Add IDs to admin links and selenium navigation.
  `Pull Request 9616`_
* Feature/refactor rule builder
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 9619`_
* Add selenium test for admin toolshed operations.
  `Pull Request 9628`_
* Add unit tests for all schema-defined config properties
  `Pull Request 9631`_
* Officially allow adding new datatypes to the latest tagged release
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9632`_
* Update the main readme with new Python version
  `Pull Request 9635`_
* Minor IT doc clarification
  `Pull Request 9668`_
* Enhance toolshed selenium test.
  `Pull Request 9678`_
* Optimize history_content union and filtering query
  `Pull Request 9680`_
* Add CSS class to messages in error report pages to make errors more visible
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 9690`_
* Feature/3937 advanced search tooltip
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 9696`_

.. small_enhancement

* Rename function, params in ConfigSerializer
  `Pull Request 9247`_
* Make ``str.join()``\s more efficient
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9258`_
* Faster and cleaner set creation
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9300`_
* Remove broken script
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9302`_
* Clean up old 'blue' style path, update documentation and samples
  `Pull Request 9306`_
* Consistent "import" of maketrans
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9351`_
* Move schema loading/validating code out of config
  `Pull Request 9371`_
* Remove more duplication from TS, galaxy config
  `Pull Request 9379`_
* Unify default values used for delta (sim_size)
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9439`_
* Vue slot refactoring
  `Pull Request 9443`_
* Move sanitize_whitelist into mutable_config_dir
  `Pull Request 9455`_
* Use auto_create functionality of ``get_private_user_role()``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9509`_
* Combine selenium tests for creating and switching histories
  `Pull Request 9527`_
* Eslint one-var spec / airbnbstyle
  `Pull Request 9532`_
* unify usage of Popen
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9544`_
* Prettier 2.0
  `Pull Request 9552`_
* Abstract ObjectStore interface implementation
  `Pull Request 9554`_
* Misc. refactoring of galaxy+TS config
  `Pull Request 9582`_
* Use PyGithub for issue creation
  `Pull Request 9637`_
* clean up code to use helper function instead
  (thanks to `@lawrence14701 <https://github.com/lawrence14701>`__).
  `Pull Request 9643`_
* Respect retry-after header, raise on unexpected status codes
  `Pull Request 9659`_
* restore tool_util.deps.commands
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9707`_


Fixes
-------------------------------

.. major_bug


.. bug_tag_viz

* Update charts entrypoint inclusion of dist artifacts
  `Pull Request 9511`_

.. bug_tag_datatypes

* Python3 compatible SnpEff and SnpSift metadata detection
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 9282`_
* Add PAF, GFA1 and odgi datatypes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9592`_
* Add xg, vg and protobuf datatypes
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 9593`_
* Fix gff3.gz and gff3.bz2 datatypes
  `Pull Request 9731`_
* Use right extension in bz2_to_uncompressed.xml
  `Pull Request 9734`_
* Fix disappearing datatypes after restart
  `Pull Request 9835`_

.. bug_tag_tools

* fix error in bundled tool: shrimp_color_wrapper
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9665`_
* extract_genomic_dna.py: import Comment, Header from bx.tabular.io instead of bx.intervals.io
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 9748`_
* Move some tools that no longer need galaxy on the PATH
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9850`_

.. bug_tag_workflows

* Fix workflow list filtering dropdown
  `Pull Request 9468`_
* Fix workfow parameter connections and default values
  `Pull Request 9648`_
* Fix ChangeOutputDatatype being dropped on node update
  `Pull Request 9676`_
* Trigger onchange event, fixes tool version changes being lost
  `Pull Request 9695`_
* Input dataset module format filtering fix;
  `Pull Request 9884`_

.. bug_tag_ui

* fix for python3 and GEDA, was getting "Connection closed at byte 0"
  `Pull Request 9507`_
* Checkbox bugfix
  `Pull Request 9667`_

.. bug_tag_jobs

* Fix none type exception in provided metadata handling.
  `Pull Request 9173`_
* Handles floats correctly in ByteSize
  (thanks to `@pcm32 <https://github.com/pcm32>`__).
  `Pull Request 9418`_
* unicodify message
  (thanks to `@ieguinoa <https://github.com/ieguinoa>`__).
  `Pull Request 9494`_
* Fixes for embedded Pulsar with MQ (with tests)
  `Pull Request 9519`_
* Fix outputs written to storage despite outputs_to_working_directory
  `Pull Request 9683`_
* Fix collection mapping in extended metadata mode.
  `Pull Request 9709`_
* Force container image names to lower case to satisfy Docker
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9733`_
* Make watcher more resilient to missing files
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9738`_
* Improved exception handling for kubernetes runner
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9751`_
* Check dataset is accessible and use payload in job error API
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9753`_
* Fix the cleanup condition when job state is OK and cleanup_job is set as "onsuccess'
  (thanks to `@gmauro <https://github.com/gmauro>`__).
  `Pull Request 9761`_
* Migrate condor runner to jwd for job-files
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 9833`_
* Fix incorrect variable assignment
  `Pull Request 9907`_

.. bug_tag_admin

* Fix vue helper in admin router, fixes toolshed installation, avoids console errors
  `Pull Request 9220`_
* Fix default quota creation message.
  `Pull Request 9479`_
* Fix data manager table headers
  `Pull Request 9480`_
* Save integrated tool panel once on toolbox reload
  `Pull Request 9487`_
* Cannot find migrate directory for tools database
  (thanks to `@phac-nml <https://github.com/phac-nml>`__).
  `Pull Request 9699`_

.. bug

* Fix S3 issue discovered during admin training
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 7294`_
* Make failing to load tools from a tool_dir non-fatal.
  `Pull Request 9106`_
* Fix incorrect reference to app
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9159`_
* Missing env in AskOmics IT
  (thanks to `@xgaia <https://github.com/xgaia>`__).
  `Pull Request 9177`_
* Check return value of quick_load
  `Pull Request 9185`_
* Fix sending email error on python-3.7
  (thanks to `@shenweiyan <https://github.com/shenweiyan>`__).
  `Pull Request 9204`_
* Properly quote paths in upload tool
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9222`_
* Fix reference in workflows API docs
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9259`_
* Fix target_str_to_targets
  `Pull Request 9268`_
* Do not test config_dir default value
  `Pull Request 9288`_
* Remove a dead symlink
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 9292`_
* Fixes reports app under py3
  `Pull Request 9305`_
* Allow setting container path for docker_volumes
  (thanks to `@AndreasSko <https://github.com/AndreasSko>`__).
  `Pull Request 9310`_
* Skip ``test_config_option[build_sites_config_file]``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9357`_
* fix special characters in citation field
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9373`_
* Use ES6 function declaration to handle error response in workflow form
  `Pull Request 9412`_
* Fix first_startup Travis tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9423`_
* Use a Galaxy root path with a space for converters and mulled tests
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9429`_
* Fix ``test_run_simple()`` test broken on Python 2 by virtualenv 20.0.5
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9458`_
* Use browser locale over global default
  `Pull Request 9460`_
* Fix login handling w/ redirects and user creation disabled.
  `Pull Request 9462`_
* Add missing `pygithub` dev-requirement
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9463`_
* Drop manage_dependency_relationships option
  `Pull Request 9465`_
* fix options_filter_attribute: needs to be str
  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
  `Pull Request 9466`_
* History Dropdown Fix
  `Pull Request 9469`_
* Print error message if no action is selected in pgcleanup script
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9489`_
* Drop custom json encoding for tool test API endpoint
  (thanks to `@nvk747 <https://github.com/nvk747>`__).
  `Pull Request 9496`_
* Keep status code on message exception and history import/export fixes
  `Pull Request 9500`_
* Fixed tool locations
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 9512`_
* Update the current_history method in navigates_galaxy.py
  `Pull Request 9514`_
* Free space before running tests
  `Pull Request 9533`_
* History import/export fixes
  `Pull Request 9535`_
* Retry reading tool conf on IOError
  `Pull Request 9537`_
* Fix citation ids and vue unit test in ToolsView
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9538`_
* Bump tensorflow from 1.12.2 to 1.15.2 in /lib/galaxy/dependencies
  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
  `Pull Request 9540`_
* Incremental indexing for tool shed whoosh indexes
  `Pull Request 9541`_
* fix documentation for data checksum attribute
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9543`_
* Prevent exception in toolshed if userid is 'current'
  `Pull Request 9548`_
* Fix setting annotation that contains only integers
  `Pull Request 9549`_
* Fix docs to update conda from conda-forge
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9550`_
* Disable workflow parameter switch for data inputs, augment form handling
  `Pull Request 9551`_
* Hide LDDA when creating collection in library interface
  `Pull Request 9561`_
* Fix indexing script
  `Pull Request 9565`_
* Assign random password in user manager if none specified
  (thanks to `@nuwang <https://github.com/nuwang>`__, `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9587`_, `Pull Request 9851`_
* Fix removal of workflow outputs from workflow nodes in editor
  `Pull Request 9606`_
* Fix ELIXIR AAI
  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
  `Pull Request 9620`_
* Fix tensorflow bug
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 9622`_
* Change session timeout redirect URL to login entrypoint.
  `Pull Request 9626`_
* Changed CSS overflow property from scroll to hidden to make table scrollable
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 9627`_
* fix links in Galaxy xsd docs
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9633`_
* Fix `TypeError: OSError object is not subscriptable` under Python 3
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9640`_
* Fix vcf_bgzip mimetype, allow cors, tbi from metadata element
  `Pull Request 9653`_
* Hide "python: not found" error when Python 2 is not installed
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9657`_
* Fix for ``time.clock()`` removal in Python 3.8
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9666`_
* Fixed an issue in object store integration tests
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9677`_
* Plugin build hash bugfix
  `Pull Request 9679`_
* Backport auth process lock fix
  `Pull Request 9681`_
* Update documentation
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9693`_
* Rename galaxy.util.logging to galaxy.util.custom_logging
  `Pull Request 9705`_
* Make collection import from library import into correct history
  `Pull Request 9715`_
* Fix workflow steps import feature in workflow editor
  `Pull Request 9724`_
* Fix custos credential fetching in python3
  `Pull Request 9726`_
* oidc-based authnz provider overhaul; breaking changes for keycloak
  `Pull Request 9730`_
* Sort Workflow list by last updated time instead of created time
  `Pull Request 9740`_
* Remove dummy tool sequence
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 9752`_
* Switch to lxml for xml parsing
  `Pull Request 9759`_
* Set UTF-8 for parsing tool xml
  (thanks to `@AndreasSko <https://github.com/AndreasSko>`__).
  `Pull Request 9760`_
* inputs config file generation depend on profile
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9776`_
* Pass through IOError/OSError in tool_shed parse_xml
  `Pull Request 9781`_
* Maintain whitespace when parsing token from xml
  `Pull Request 9815`_
* Log exception if reading tool file failed unexpectedly
  `Pull Request 9816`_
* Drop custom in-process lock class
  `Pull Request 9817`_
* Update NoseHTML to 0.4.6 for Python 3.8 compatibility
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9821`_
* Tolerate exception in container resolution
  `Pull Request 9824`_
* Invalidate tool cache when tool modified outside of Galaxy
  `Pull Request 9866`_
* Custos spec fixes
  `Pull Request 9889`_
* Fixes for flake8 3.8 and bugbear
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9896`_
* Fix webpack import proxy prefix
  `Pull Request 9898`_
* Fix extra preference values leaking between requests
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9913`_
* Rewrite ``check_html()`` and ``Text.count_data_lines()`` to read a chunk of each line
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9920`_
* Make cookie handling more robust
  `Pull Request 9921`_
* Enable regex validator to validate lists of values.
  `Pull Request 9925`_
* oidc: fix dict_keys does not support indexing
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 9931`_
* Move the ``--debug`` flag after the conda subcommand
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9932`_

.. include:: 20.05_prs.rst

