
.. to_doc

20.09
===============================

.. announce_start

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

* Simplified Workflow Run Form
  `Pull Request 9151`_
* Allow uploading directly from the tool form
  `Pull Request 9809`_
* Pluggable URI handling across upload components.
  `Pull Request 9888`_
* API + UI for importing workflows from a GA4GH TRS server.
  `Pull Request 9999`_
* GTN in Galaxy
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 10024`_
* Revision of Workflow Reports
  `Pull Request 10121`_
* Markdown Editor Revision
  `Pull Request 10134`_
* GA4GH TRS Workflow Search
  `Pull Request 10158`_
* Vue rewrite of the data-library-folder
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9905`_
* Improve workflow layout algorithm
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 10045`_
* Added documentation for debugging Galaxy and unit/integration tests
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9664`_
* Feature/persist rule builder collection in web storage
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 9718`_
* Higlass InteractiveTool update
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 9805`_
* Add allowed_cilogon list functionality (idphint short list)
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 9862`_
* Add lastdb datatype for last tool
  (thanks to `@RomainDallet <https://github.com/RomainDallet>`__).
  `Pull Request 9872`_
* Adding user id to key so savedRules are specific for users
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 9882`_
* Add BLASTDBv5 datatype (for blast >=2.8.1)
  (thanks to `@abretaud <https://github.com/abretaud>`__).
  `Pull Request 9939`_
* Add galaxyp MVP visualization plugin
  (thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
  `Pull Request 10136`_
* Connect/disconnect multiple custos
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 10182`_
* Add missing database indexes
  `Pull Request 10385`_
* Add build artifact destination for plugins
  `Pull Request 9754`_
* Plugin watchBuilding, and fixes for several older visualization builds
  `Pull Request 10287`_
* Add VCF_BGZIP to VCF converter
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 7926`_
* Add NcbiTaxonomySQlite class to describe NCBI Taxonomy SQLite databases
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 9712`_
* Add Anndata peek capability
  (thanks to `@mtekman <https://github.com/mtekman>`__).
  `Pull Request 10013`_
* Add "tgz" datatype to config sample file for toolfactory and any other tools generating gzipped tar files
  (thanks to `@fubar2 <https://github.com/fubar2>`__).
  `Pull Request 10080`_
* Citations overhaul
  `Pull Request 9757`_
* Fix and simplify built-in trim tool
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 10145`_
* Allow unary plus and minus in filtering
  (thanks to `@wm75 <https://github.com/wm75>`__).
  `Pull Request 10154`_
* Toolbox refactoring, styling, and a couple bugfixes
  `Pull Request 10170`_
* Support for BioCompute Object Export
  (thanks to `@biocompute-objects <https://github.com/biocompute-objects>`__).
  `Pull Request 9077`_
* Workflow reports: multiple argument & add single job parameter
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9686`_
* Allow composite and extra file uploads via data fetch API.
  `Pull Request 9860`_
* Implement more Galaxy Markdown components.
  `Pull Request 9938`_
* Rework client datatype handling logic for reuse
  `Pull Request 9955`_
* Flush once for enqueue / workflow handler assignment
  `Pull Request 10019`_
* Workflow list: Add published column, add sort bookmarked
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10119`_
* Add workflow invocation grabbing with db-skipped-lock
  `Pull Request 10177`_
* Add user-is-owner context for display of published workflows.
  `Pull Request 10215`_
* Allow execution of workflows for certain tool updates
  `Pull Request 10569`_
* Early 20.09 full client dependency update.
  `Pull Request 9739`_
* Improve mocha test output for rule DSL specification tests.
  `Pull Request 9798`_
* Change usage of whitelist/blacklist terms to allowlist/blocklist
  `Pull Request 9864`_
* Allow option to remember the previously used IDP for login
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 10078`_
* Infrastructure for writing to pluggable Galaxy file sources.
  `Pull Request 10152`_
* Add support for cleaning up kubernetes jobs after a specified number of seconds since finish
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 8122`_
* Port and Vuefy AWS estimate from EU
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9621`_
* View support for galaxy model, hdca.job_state_summary option
  `Pull Request 9713`_
* Allow tool submission with DatasetCollectionElements / make build_for_rerun consumable by API
  `Pull Request 9802`_
* Allow setting metadata_strategy per destination
  `Pull Request 9956`_
* Flush once per mapped over execution
  `Pull Request 9985`_
* Job cache improvements
  `Pull Request 10020`_
* Edit post-job email to add history link and format text
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 10133`_
* Updated documentation to show how a job is de-queued and processed.
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 10185`_
* Allow CLI runner modules to be loaded from sys.path
  `Pull Request 10189`_
* Make cached container resolver pick newest build
  (thanks to `@torfinnnome <https://github.com/torfinnnome>`__).
  `Pull Request 10242`_
* Don't run local runner job processes in an unnecessary shell
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10257`_
* Improve kubernetes job selection
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 10407`_
* It docs additional info
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 9650`_
* GitLab error reporting - further features
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 9775`_
* Improve support for readonly tool caches
  `Pull Request 10411`_
* Dynamic options and metadata filter fixes
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 8599`_
* assign discovered extension, dbkey and designation for assign_primary=true
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9127`_
* Add dataset deserializer for 'datatype'
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 9374`_
* Add tests for admin interface jobs, dependencies, and containers sections
  `Pull Request 9618`_
* Remove DO_NOT_TEST from config unit tests
  `Pull Request 9644`_
* Framework for Browser Testing of Custom Configured Galaxy Instances
  `Pull Request 9652`_
* Clear error message for wrong authenticator type
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9670`_
* add doc for discover_datasets sort_by
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9674`_
* Collection pagination api resource route
  `Pull Request 9682`_
* xsd, docs, and test for sort_by (discover_datasets)
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9684`_
* Allow input element created by editable-text.js to change value on click/lose focus
  (thanks to `@lawrence14701 <https://github.com/lawrence14701>`__).
  `Pull Request 9703`_
* Allow oidc login icons to be specified through backend_config xml
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9704`_
* Display msg history no items
  (thanks to `@lawrence14701 <https://github.com/lawrence14701>`__).
  `Pull Request 9706`_
* Spinner in library folders
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9717`_
* Implement HDCA update_time
  `Pull Request 9722`_
* Skip check for branch protection
  `Pull Request 9723`_
* Upgrade to the newer nodejs lts (v10 -> v12; 12.16.3)
  `Pull Request 9725`_
* Move containers test from selenium to selenium integration.
  `Pull Request 9728`_
* Update to IT comment
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 9735`_
* Swap out node-sass for the new standard sass compiler
  `Pull Request 9737`_
* doc: dynamic destinations better set the id in JobDestination
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9742`_
* Allow tool search on tool id and wildcard before search string
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 9744`_
* linkify Data Libraries description and bugfix
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9746`_
* Improved dataset verification output
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9771`_
* Added config parameter for irods connection pool size.
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9774`_
* Add selenium test for user toolbox filters.
  `Pull Request 9782`_
* Minor improvements to API errors
  `Pull Request 9797`_
* switch branch of IUC CI earlier in release process
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9806`_
* Don't use Backbone to define masthead elements.
  `Pull Request 9811`_
* Add selenium test for user API keys
  `Pull Request 9820`_
* More reactive, tested Masthead.
  `Pull Request 9822`_
* i18n for tool page about email notification
  (thanks to `@shenweiyan <https://github.com/shenweiyan>`__).
  `Pull Request 9830`_
* Add option to text asserts to specify number of occurrences
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 9831`_
* History DBkey and refactor dataset state
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9841`_
* History Panel Tags&Annotation
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9846`_
* Add support for relative paths in dependency resolver mappings
  (thanks to `@rupertnash <https://github.com/rupertnash>`__).
  `Pull Request 9855`_
* History structure
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9858`_
* Improved UploadModal state handling during initialization.
  `Pull Request 9869`_
* Feature/9669 sort collection for paired collections
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 9874`_
* Full Python dependencies update
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9912`_
* Update AskOmics IT to askomics 4.0.0
  (thanks to `@xgaia <https://github.com/xgaia>`__).
  `Pull Request 9915`_
* Documentation on Galaxy startup
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9918`_
* Speed up output discovery
  `Pull Request 9926`_
* Modify email address domain extraction
  `Pull Request 9949`_
* Refactor toward real cohesion toward testing packages. (1/n)
  `Pull Request 9951`_
* Stub unit tests for galaxy-web-stack.
  `Pull Request 9958`_
* Progress toward proper packaging of galaxy-web-framework package.
  `Pull Request 9959`_
* Decouple API and Selenium tests from galaxy-test-driver (and the whole app!)
  `Pull Request 9960`_
* Added doc explaining what happens when you upload a file to Galaxy.
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9963`_
* More packaging touches.
  `Pull Request 9964`_
* Refactor more unit tests into the galaxy-data package.
  `Pull Request 9966`_
* Revise workflow invocation status page
  `Pull Request 9978`_
* Simplify workflow invocations grid, remove drop down, add workflow execution option
  `Pull Request 9986`_
* Update Code of Conduct
  `Pull Request 9989`_
* Move unit tests to more appropriate packages.
  `Pull Request 9993`_
* Package rules DSL specification.
  `Pull Request 9995`_
* Optimize iRODS ``_exists()`` method
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9998`_
* Don't flush after each dataset creation in DistributedObjectStore
  `Pull Request 10008`_
* Touch up of toolbox search adjustments and messages
  `Pull Request 10036`_
* Rework galaxy.tool_util.verify.wait for reuse in Planemo.
  `Pull Request 10041`_
* Add GALAXY_ALLOW_FUTURE_DATABASE option in migration check
  `Pull Request 10044`_
* Upload tests to clarify behavior around handling files without trailing newlines.
  `Pull Request 10050`_
* Fix Galaxy tool/workflow staging and refactor for reuse in Planemo.
  `Pull Request 10052`_
* Update docs on from_work_dir and delta
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 10055`_
* Update environment_modules_mapping.yml.sample
  `Pull Request 10074`_
* Add generic CORS preflight options response
  `Pull Request 10077`_
* Progressively render conditional as they are being displayed
  `Pull Request 10083`_
* Selenium: Library Dataset Download Zip
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10084`_
* Selenium Delete Dataset from library folder
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10090`_
* Test import dataset from path
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10102`_
* Lib Folder pagination (backend)
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10104`_
* User self-delete
  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
  `Pull Request 10107`_
* Add subworkflow_invocation_id to invocation step
  `Pull Request 10109`_
* Selenium Library Subfolder
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10110`_
* expose dataset 'in use state' through api
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 10122`_
* Jest-based client testing
  `Pull Request 10123`_
* Copy to clipboard, instead of pop-up
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10124`_
* Open pages API a bit to allow anonymous users to view published pages
  `Pull Request 10129`_
* More structured errors for tool validation problems
  `Pull Request 10146`_
* Add hidden column, attach StoredWorkflow to subworkflows
  `Pull Request 10160`_
* Use tool_enable_ngram_search by default, whitespace search fix
  `Pull Request 10175`_
* Switch tool document cache to diskcache
  `Pull Request 10191`_
* Force pagination on Valid Galaxy Tools -> Tools page
  `Pull Request 10195`_
* Rebuild config for 20.09, including missing option in galaxy_options doc
  `Pull Request 10527`_
* Allow specyfying tool tests we expect to fail
  `Pull Request 10548`_
* Various fixes for conditional dependencies handling
  `Pull Request 10575`_
* Fixes/enhancements to use client tool test configs in Ephemeris
  `Pull Request 10578`_
* Mark test cases that use data tables or loc files
  `Pull Request 10602`_
* Fix saving rule builder rules when uploading in rule editing view
  (thanks to `@assuntad23 <https://github.com/assuntad23>`__).
  `Pull Request 10637`_
* Porting Masthead to Vue.js
  (thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
  `Pull Request 9071`_
* Remove unused and deprecated parameters from kubernetes runner
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9323`_
* Add Vue components for Workflow Inputs and Outputs, reduce Workflow loading time
  `Pull Request 9574`_
* Refactor helper functions
  (thanks to `@lawrence14701 <https://github.com/lawrence14701>`__).
  `Pull Request 9700`_
* Modify loading of email white/blacklists
  `Pull Request 9793`_
* Cleanup and refactoring client code around upload/data dialog
  `Pull Request 9827`_
* Mount workflow nodes in v-for loop
  `Pull Request 9883`_
* Fix DeprecationWarning: Flags not at the start of the expression
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9899`_
* Trim the inflector
  `Pull Request 9902`_
* Fix name of container resolver method name.
  `Pull Request 9914`_
* Python3 cleanup
  `Pull Request 9923`_
* Small tweaks to packaging of unit test utilities.
  `Pull Request 9953`_
* Small refactoring for plugin_config.
  `Pull Request 9982`_
* Cleanup WorkflowRun.test.js with flush promises.
  `Pull Request 9984`_
* Fix copy/paste in workflow editor
  `Pull Request 10056`_
* Client error handling fixes, updates.
  `Pull Request 10082`_
* Client structure refactoring for packaging
  `Pull Request 10086`_
* Uniformly process config files
  `Pull Request 10172`_
* javascript es6 arrow functions
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 10181`_
* Abstraction for purging the dataset quota usage from a user.
  `Pull Request 10208`_
* Improve job error logging
  `Pull Request 10226`_
* Pass user to the ObjectStorePopulator
  `Pull Request 10231`_
* mvpapp visualization fixes and refinement
  `Pull Request 10355`_
* Move linting to GitHub action, fix linting
  `Pull Request 10615`_


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

* Hyphyvision visualization dependency fix
  `Pull Request 10011`_
* Bugfix: include an index link in visualization base
  `Pull Request 10391`_
* Use compression_utils to safely peek in compressed datasets
  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
  `Pull Request 9990`_
* fix OSError in fastq_to_fqtoc converter
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 10042`_
* Don't display download link for optional, non-existant metadata files
  `Pull Request 10068`_
* Fix determining 'int', 'float' column type in Tabular and BaseCSV
  (thanks to `@selten <https://github.com/selten>`__).
  `Pull Request 10155`_
* Decrease pysam verbosity
  `Pull Request 10225`_
* Remove references to missing types from sample config file
  `Pull Request 10269`_
* Fix ``Wav`` datatype to inherit from ``Audio``
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10312`_
* Fix wiggle estimated_display_viewport
  `Pull Request 10333`_
* AnnData Peek Fix
  (thanks to `@mtekman <https://github.com/mtekman>`__).
  `Pull Request 10555`_
* Fix Anndata index access, use numpy-safe JSON encoder
  (thanks to `@mtekman <https://github.com/mtekman>`__).
  `Pull Request 10640`_
* Allow submission of tools with unset hidden parameters
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9656`_
* Fix error in get_open_tempfile()
  `Pull Request 10060`_
* Backport bugfix in `#10060 <https://github.com/galaxyproject/galaxy/issues/10060>`__ to 20.05
  `Pull Request 10138`_
* Fix filtering.py failing all expressions
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 10266`_
* Rev gxformat2 for a bunch of bug fixes.
  `Pull Request 10028`_
* Fix running workflows with parameters restricted on connections
  `Pull Request 10048`_
* Count all terminal jobs when rendering job complete string
  `Pull Request 10089`_
* Remove duplicates from tool recommendations
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 10094`_
* Tensorflow update to support python 3.8
  `Pull Request 10096`_
* Fix tool recommendation node injection
  `Pull Request 10097`_
* Fix Workflow node insertion via recommendations
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 10103`_
* Fix change datatype PJA not applied when loaded from server
  `Pull Request 10237`_
* Fix db-skip-locked invocation grabbing for pool members
  `Pull Request 10371`_
* Fix TRS search when Galaxy deployed behind a proxy.
  `Pull Request 10406`_
* Fix wf step annotations dropped after rename.
  `Pull Request 10464`_
* Fix workflow extraction if nested collection in input step
  `Pull Request 10560`_
* Mark workflow as changed if tools were upgraded
  `Pull Request 10570`_
* Fix workflow editor version switching
  `Pull Request 10597`_
* Fix trs_id and trs_server query strings
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10616`_
* Fix Workflow node input terminal not updating
  `Pull Request 10626`_
* Rework pollUntil* to avoid building up queries
  `Pull Request 10710`_
* Speed up invocation serialization
  `Pull Request 10711`_
* Tool recommendation node bug
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 9836`_
* Fix history sharing link (ref. `#10040 <https://github.com/galaxyproject/galaxy/issues/10040>`__)
  `Pull Request 10112`_
* fix history import and export for real user setups
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9001`_
* Rev pulsar-galaxy-lib for latest fixes.
  `Pull Request 9910`_
* Fix MetadataFile handing with metadata_strategy: extended
  `Pull Request 9974`_
* Fix metadata_source handling when dataset does not exist in object store
  `Pull Request 10059`_
* Fix change_datatype PJA when dataset is not yet in object store
  `Pull Request 10087`_
* Fix outputs_to_working_directory with extended metadata
  `Pull Request 10100`_
* Don't fail to complete the job fail method if job outputs cannot be updated
  `Pull Request 10111`_
* Fix for the hour value depicted as a float value in CPU and Job Runtime
  (thanks to `@npinter <https://github.com/npinter>`__).
  `Pull Request 10159`_
* Restore the use of set_job_destination() in the Pulsar runner's queue_job() method
  `Pull Request 10255`_
* Fix webless handler --attach-to-pool
  `Pull Request 10294`_
* Ensure that kubernetes job ids are unique
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 10307`_
* Prevent endless cleanup loops when duplicate job or kubernetes job not found
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 10308`_
* enable validation of ITs
  `Pull Request 10341`_
* Defer metadata strategy resolution in job wrapper
  `Pull Request 10367`_
* Restrict kubernetes max job name length to 63 and shorten prefix
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 10416`_
* Fixing bug in kubernetes runner's k8s_pod_retrials
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 10444`_
* Move more non-dns compliant labels to annotations
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 10470`_
* Fix ``maximum_workflow_jobs_per_scheduling_iteration`` and set 1000 as default value
  `Pull Request 10490`_
* Fix get_output_path when HDA identity changes
  `Pull Request 10552`_
* Don't pass resources as job params when reading job config as a dict
  `Pull Request 10561`_
* Stop monitoring terminal Pulsar Kubernetes jobs
  `Pull Request 10572`_
* Fix IntegrityError when flushing DC/DCE relationship
  `Pull Request 10606`_
* Fix admin data_types_list bug
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 10148`_
* Restore welcome html link for non-uwsgi setups
  `Pull Request 10623`_
* Python37 lock fix
  `Pull Request 9642`_
* Fix history panel collapse
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 9688`_
* Improve tool recommendations
  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
  `Pull Request 9708`_
* Various spelling and log message error fixes.
  `Pull Request 9721`_
* Minor fixes to docs on how to build a job runner
  (thanks to `@nuwang <https://github.com/nuwang>`__).
  `Pull Request 9749`_
* Client watch fix -- force everything to use modern chokidar
  `Pull Request 9755`_
* Handled unexpected exceptions in iRods objectstore
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9765`_
* Remove unused code and other fixes
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9766`_
* Added the missing return value. Added try/catch for another irods call.
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9768`_
* Hide masthead dropdown on iframe click
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9789`_
* Fix refactoring in linkifing libraries description
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9790`_
* Babel peer dependency fix,
  `Pull Request 9795`_
* InteractiveTool unit test fix
  `Pull Request 9800`_
* Make AuthN attribute optional for Azure and GCP.
  `Pull Request 9801`_
* Fix bug: add self arg to method
  `Pull Request 9808`_
* Fix conditional conda activate syntax in job script
  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
  `Pull Request 9832`_
* Fix line-height property for upload button in tool panel
  `Pull Request 9845`_
* hide expression tools
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 9859`_
* Added missing dev flag to hot module reload script, sourcemaps work now
  `Pull Request 9891`_
* Typo in the uWSGI default umask description
  (thanks to `@gmauro <https://github.com/gmauro>`__).
  `Pull Request 9909`_
* Do not automatically overwrite the output labels for subworkflows
  `Pull Request 9917`_
* Fix issues reported by flake8-bugbear and W504 errors 1/N
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 9943`_
* Using context manager for irods session object
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9944`_
* Strip leading whitespace before calling urlparse
  `Pull Request 9947`_
* Fixes to package dependency declarations.
  `Pull Request 9950`_
* Various small fixes for galaxy packages.
  `Pull Request 9952`_
* actually `set -e` for non-legacy tools
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 9962`_
* Fix workflow run default icon
  `Pull Request 9971`_
* Remove unnecessary log statements for number of connections
  (thanks to `@kxk302 <https://github.com/kxk302>`__).
  `Pull Request 9975`_
* Use optimized path of setting dataset size during output discovery
  `Pull Request 9980`_
* Cookie names to work with PR `#9921 <https://github.com/galaxyproject/galaxy/issues/9921>`__ and py3 Exception printing
  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
  `Pull Request 9991`_
* Tweak requirements for recent changes to package structure.
  `Pull Request 9992`_
* Properly update active version in workflow attribute form
  `Pull Request 10009`_
* Fix pip error around markdown tables.
  `Pull Request 10014`_
* Pass stdin to hg clone to fix planemo tests
  `Pull Request 10018`_
* Mulled packaging dependency fixes
  `Pull Request 10025`_
* Fix reports webapp template resolution
  `Pull Request 10037`_
* Encoding issue fix for hmac_new
  `Pull Request 10047`_
* add missing $ in docs
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 10057`_
* Fix non-unique entries in tool search index
  `Pull Request 10061`_
* Restore preview rendering of bam files
  `Pull Request 10067`_
* Allow numbers as filenames while adding datasets to library folder
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10070`_
* Fix library zip download
  `Pull Request 10072`_
* fix masthead dropdown
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10098`_
* Handle python2-related syntax errors in Cheetah code
  `Pull Request 10099`_
* Filter pages of deleted users from the published list.
  `Pull Request 10106`_
* Update toolshed/ie js dist locations
  `Pull Request 10143`_
* Pin latex-to-unicode js module
  `Pull Request 10157`_
* Make visualization unit tests independent
  `Pull Request 10162`_
* Keycloak/custos tweaks and cleanup
  `Pull Request 10168`_
* Don't include hidden tools in tool search index
  `Pull Request 10173`_
* Send activation email upon custos account creation
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 10174`_
* Fix ToolValidator get_list_of_copied_sample_files
  `Pull Request 10183`_
* Bump http-proxy from 1.17.0 to 1.18.1 in /lib/galaxy/web/proxy/js
  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
  `Pull Request 10190`_
* Unicodify binary strings in Tool Shed alert emails
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10196`_
* use GalaxyTagHandlerSession for data library uploads
  (thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
  `Pull Request 10197`_
* Display proper clientside error
  (thanks to `@juleengraham <https://github.com/juleengraham>`__).
  `Pull Request 10199`_
* Add pwd when overriding tool_config_file in run.sh
  `Pull Request 10200`_
* If a config file is not found, try resolving w.r.t. root
  `Pull Request 10201`_
* Use pagination on most tool shed pages
  `Pull Request 10207`_
* Remove exec permissions from tools/__init__.py
  `Pull Request 10213`_
* Strip deprecated dir from all paths in comma-separated option values
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10220`_
* Fix flake8 issues in dev
  `Pull Request 10234`_
* Logout fix and refactoring
  `Pull Request 10248`_
* Catch all possible repo install errors
  `Pull Request 10250`_
* Include an upgrade warning for 20.05 regarding the drop of the blue symlink in static
  `Pull Request 10256`_
* Persist tool_cache_data_dir tag if specified
  `Pull Request 10281`_
* Bump tensorflow from 2.3.0 to 2.3.1 in /lib/galaxy/dependencies
  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
  `Pull Request 10300`_
* Fix container resolution when requirement version is not specified
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10305`_
* Fix tool search to not display 'no results' prior to result return
  `Pull Request 10317`_
* Respect ``use_shared_home="false"`` when running tools in container
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10321`_
* Fix double masthead in some spaces
  `Pull Request 10329`_
* Fix composite data download from collection
  `Pull Request 10330`_
* Handle resend_activation_email gracefully without session
  `Pull Request 10331`_
* Strip trailing ``/`` from tool_id for data source redirects
  `Pull Request 10332`_
* Allow 'planemo run' to stage in existing datasets without reuploading
  (thanks to `@simonbray <https://github.com/simonbray>`__).
  `Pull Request 10335`_
* Pin pytest < 6.1
  `Pull Request 10337`_
* Fix 'Newer Version Available' tag in admin tool management section
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 10339`_
* Use block elements for labels to handle wrapping indentation
  `Pull Request 10342`_
* Add missing index migrations
  `Pull Request 10344`_
* Bugfix: chrome forgets scroll offset upon show/hide cycle of GTN in Galaxy webhook
  (thanks to `@hexylena <https://github.com/hexylena>`__).
  `Pull Request 10362`_
* Allow GEDAs to respond to Access-Control-Request-*
  `Pull Request 10384`_
* Fix regex replacement wrongly appearing in rule builder
  `Pull Request 10390`_
* add recurse attribute for discover_datasets
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 10394`_
* Try case-insensitive match on email also when it's lowercase
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10401`_
* Python 3 fix and client build fix for the proxy
  (thanks to `@bgruening <https://github.com/bgruening>`__).
  `Pull Request 10403`_
* Rework new collection order testing in 20.09.
  `Pull Request 10434`_
* backport `#10365 <https://github.com/galaxyproject/galaxy/issues/10365>`__: add test for data_column parameter referring to non-tabular data (bed) and fix bug
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 10438`_
* Change response body from str to bytes
  (thanks to `@qiagu <https://github.com/qiagu>`__).
  `Pull Request 10441`_
* Add ``*requirements.txt`` files to source packages
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10447`_
* Fix mulled-search to not assume conda APIs from vanilla environments
  `Pull Request 10465`_
* Fix trailing commas in history dataset search
  (thanks to `@cat-bro <https://github.com/cat-bro>`__).
  `Pull Request 10518`_
* Allow username or email for authenticate API identity
  `Pull Request 10521`_
* Improved error handling for data_fetch API.
  `Pull Request 10543`_
* Fix composite dataset listing in upload modal
  `Pull Request 10551`_
* allow adding dataset to library from history by default
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10556`_
* Make package names lowercase for mulled dependency resolving
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10559`_
* Fix listing idps
  `Pull Request 10567`_
* Fix progress bar floating text
  `Pull Request 10579`_
* bugfix: external login component fetching idps when it should not
  `Pull Request 10581`_
* Resolve LDDA <-> Library Dataset circular dependency
  `Pull Request 10582`_
* Fix file_path bug; change default assignment of file_path and id/uuid
  `Pull Request 10617`_
* Fix masthead items disappearing on small screens
  `Pull Request 10641`_
* Fix hide history panel glitch
  `Pull Request 10644`_
* Fix cache key for lint CI workflow
  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
  `Pull Request 10649`_
* Fix creating hdas without history when creating collection from library
  `Pull Request 10654`_
* Backport: Fix saving rule builder rules when uploading in rule editing view
  `Pull Request 10661`_
* Fix border between list items
  `Pull Request 10675`_
* Fix UTC Date date change
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10678`_
* Several fixes for multipanel interface
  `Pull Request 10680`_
* Fix element_is_set for MetadataWrapper
  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
  `Pull Request 10691`_
* Bugfix for tool search filtering for tools outside sections.
  `Pull Request 10693`_
* Bump cryptography dependency to 3.2.1
  `Pull Request 10704`_
* Add 'Constant' to allowed node types.
  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
  `Pull Request 10709`_
* Pathbar race bugfix
  (thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
  `Pull Request 10724`_
* Use newer setup-miniconda action
  `Pull Request 10731`_

.. include:: 20.09_prs.rst

