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.. to_doc
20.01
===============================
.. announce_start
Enhancements
-------------------------------
* CLI tools for installing/testing Docker and Singularity containers
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 7936`_
* Markdown-based Galaxy Pages.
`Pull Request 8512`_
* Make Masthead and workflow page screenreader friendly
`Pull Request 8700`_
* Add data dialog input element to client form parameter list
`Pull Request 8774`_
* Add has_size option
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 8852`_
* Email notifications on job completion
`Pull Request 8948`_
* Make tours reloadable
`Pull Request 9032`_
* Add a config option to allow customizing the brand title
`Pull Request 9062`_
* IT fixes and 3 new ITs
`Pull Request 9141`_
* Remove GenomeSpace tools, OpenID, UI and requirements
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9363`_
* Hyphy-vision fixes and updates.
`Pull Request 9384`_
* Datatypes for MassSpec DIA dlib,elib
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
`Pull Request 8657`_
* Add bus as binary, remove extra datatype
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
`Pull Request 8705`_
* remove dada2_derep data type
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8902`_
* Add new GROMACS datatypes: ndx, xvg, edr
(thanks to `@simonbray <https://github.com/simonbray>`__).
`Pull Request 8964`_
* Add gff3.gz and gff3.bz2 datatypes
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
`Pull Request 8967`_
* Make mol2 visible
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 8995`_
* Add a datatype subclass for CAT (Contig Annotation Tool)
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
`Pull Request 9087`_
* Add tabular.gz datatype and add embl to uploadable formats
`Pull Request 9293`_
* Upgrade askomics interactive tool
(thanks to `@xgaia <https://github.com/xgaia>`__).
`Pull Request 8517`_
* Remove collection ID character restriction from 'Relabel collection from file' tool
(thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
`Pull Request 8571`_
* Allow space, dot and comma in relabel identifier tool
`Pull Request 8757`_
* Fix script shebangs
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8888`_
* Allow admins to import tools/workflows from paths.
`Pull Request 9003`_
* Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
`Pull Request 9320`_
* Interactive modification of invocation report.
`Pull Request 8691`_
* User-facing Workflow Invocation Grid
`Pull Request 8699`_
* PDF Export of Galaxy Markdown
`Pull Request 8893`_
* Refactor some workflow editor plumbing to VueJS
`Pull Request 8931`_
* Track non-history content outputs.
`Pull Request 9009`_
* Default format 2 workflows to be downloaded as YAML.
`Pull Request 9023`_
* Even Richer Workflow Inputs
`Pull Request 9086`_
* Separate Markdown Validation into its own module.
`Pull Request 9099`_
* add option select_type_workflow_threshold (rebase)
`Pull Request 9105`_
* Upgrade eslint (major version), fix compliance with new standard rules.
`Pull Request 8708`_
* JobMetrics.vue unit test.
`Pull Request 8732`_
* Fix the flexible Data Dialog to work independent of the page layout initialization hooks.
`Pull Request 8744`_
* axios-mock-adapter for cleaner, more expansive testing
`Pull Request 8749`_
* Added client-side application configs for each target environment
`Pull Request 8827`_
* Small cleanup for job runners kill
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8523`_
* Improvements to Galaxy and Pulsar job execution
`Pull Request 8625`_
* Allow assigning UUID job ids with Pulsar in MQ mode.
`Pull Request 8718`_
* Do not re-compute job input_ext/dbkey in job finish.
`Pull Request 8910`_
* Implement extended job metadata collection
`Pull Request 8930`_
* Move Jobs updated time display logic to client.
`Pull Request 8943`_
* Implement extended job metadata collection + fixes
`Pull Request 8984`_
* Place version output file in a writable directory for containerized jobs.
`Pull Request 8997`_
* Fix deletion of outputs and working before job
`Pull Request 9245`_
* Mount tool_data_path (ro) when running containerized tools
`Pull Request 9314`_
* Allow remote jobs to configure Interactive Tool entry points.
`Pull Request 9349`_
* Add Tool Manager Component for Admin Panel
`Pull Request 8601`_
* Add process ID to worker_process table
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8972`_
* Use official "login with" buttons for OIDC
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 8107`_, `Pull Request 9102`_
* Add data types to docs.galaxyproject.org
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8531`_
* python-ldap python3 update and documentation change
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8618`_
* GitLab error reporting
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8620`_
* Extend the list of attributes to be reported.
`Pull Request 8661`_
* Have CI ensure client PRs are formatted.
`Pull Request 8662`_
* Add area/configuration label
`Pull Request 8665`_
* Update BootstrapVue to 2.0.1
`Pull Request 8666`_
* add .gitattributes file and normalize line endings to use LF in…
`Pull Request 8677`_
* Improve CI reliability by annotating external resources.
`Pull Request 8678`_
* Restrict `/api/histories/shared_with_me` to logged-in users
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8685`_
* Automate path resolution for config options
`Pull Request 8689`_
* Remove unused Docker Swarm options
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8690`_
* LDAP search member of filter
(thanks to `@BioinformaticsPlatformWIV-ISP <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
`Pull Request 8697`_
* Rebuild and prettify config sample and doc
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8713`_
* Update zh/locale.js
(thanks to `@shenweiyan <https://github.com/shenweiyan>`__).
`Pull Request 8725`_
* Start using path_resolves_to; add integration tests
`Pull Request 8737`_
* Significant overhaul to container+dependency management
`Pull Request 8741`_
* Multi subdomains cookie support
(thanks to `@julozi <https://github.com/julozi>`__).
`Pull Request 8746`_
* One test case to rule them all
`Pull Request 8793`_
* Allow recording more performance statistics to statsd.
`Pull Request 8800`_
* Add installation monitor popup to toolshed client
`Pull Request 8810`_
* General server dependency updates (was/including catalina fix)
`Pull Request 8843`_
* Add badge to indicate availability of a newer toolshed repository version
`Pull Request 8860`_
* Add config options to integration test for abs path
`Pull Request 8862`_
* Make message_box style and visible options reloadable
`Pull Request 8863`_
* Remove 'area/cleanup', edit 'kind/refactoring'
`Pull Request 8874`_
* Unpin bdbag.
`Pull Request 8883`_
* Add separate knob for masthead colors
`Pull Request 8904`_
* Refactor galaxy_install and required dependencies into Galaxy's namespace.
`Pull Request 8905`_
* Enable interactivetools with other beta tools...
`Pull Request 8913`_
* Simplify logo replacement, fix height and alignment
`Pull Request 8914`_
* Simplify Python deps installation in `testing-base` Dockerfile
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8921`_
* Config: drop redundant `template_cache` attribute
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8924`_
* Enable secondary authorization
`Pull Request 8926`_
* Set up a cache dir for pip when running tests with Docker
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8929`_
* Add link for interactive tools
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
`Pull Request 8936`_
* Remove deprecated tool dependency scripts.
`Pull Request 8955`_
* Remove tool shed API examples.
`Pull Request 8956`_
* Remove script for migrating tools to the tool shed...
`Pull Request 8957`_
* Move galaxy testing utilities into cleaner package structure.
`Pull Request 8960`_
* Create packages for Galaxy tests and infrastructure.
`Pull Request 8962`_
* Remove workflow support from tool shed.
`Pull Request 8978`_
* Remove capsule feature from tool shed.
`Pull Request 8979`_
* trim long ldda messages; improve fluid media css
`Pull Request 9000`_
* Expose python version in api/config
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 9010`_
* Hot module reloading using webpack-dev-server for client dev
`Pull Request 9029`_
* when building ts index log parse errors at debug level
`Pull Request 9033`_
* Update quickstart.rst
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 9044`_
* Add Sergey Golitsynskiy to committers group
`Pull Request 9056`_
* Update Mercurial to Py3-compatible v5.2, and all other deps
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9065`_
* Automatically redirect to OIDC provider when only auth option
(thanks to `@machristie <https://github.com/machristie>`__).
`Pull Request 9115`_
* Automatically use extended-base-image if necessary
`Pull Request 9116`_
* Add HMR to client readme.
`Pull Request 9121`_
* Add admin functionality to histories API
(thanks to `@thomcuddihy <https://github.com/thomcuddihy>`__).
`Pull Request 9124`_
* Don't break generated reStructuredText and YAML on hyphens
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9128`_
* mulled: use threading.Event in PrintProgress to avoid unnecessary wai…
`Pull Request 9163`_
* Set Conda environment variables when running biocontainers
`Pull Request 9170`_
* Update my username
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 9195`_
* Add base_image column to mulled-build-files
`Pull Request 9199`_
* Allow passing conda_context to any_target_requires_extended_base
`Pull Request 9202`_
* Backport 9175: Update galaxy.tool_util.cwl for latest changes in CWL branch.
`Pull Request 9210`_
* Extended base annotation fixes
`Pull Request 9224`_
* External auth login refinement
`Pull Request 9233`_
* Fixes for IGV GEDA handling of genomes
`Pull Request 9413`_
* Factor out yaml read/write from config_manage.py
`Pull Request 8509`_
* Implementation of the workflow list as vue component
`Pull Request 8551`_
* Refactor config loading
`Pull Request 8573`_
* Change reloadable config + misc cleanup
`Pull Request 8600`_
* Case-insensitive match user-supplied email when logging in
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8631`_
* Modify schema defaults and their loading
`Pull Request 8639`_
* Replace resolve_path() with os.path.join()
`Pull Request 8646`_
* Simplify config code (minor edits)
`Pull Request 8648`_
* Refactor/cleanup config loading (misc edits)
`Pull Request 8651`_
* Remove unused Tags file since it was converted to a Vue component
`Pull Request 8722`_
* Update slot syntax to v-slot across the board.
`Pull Request 8730`_
* Remove deprecated Toolshed API endpoints
`Pull Request 8734`_
* Client build process refinement
`Pull Request 8742`_
* Add vue component and endpoint to reset repository metadata
`Pull Request 8754`_
* Cleanup SQL query in ``_calculate_or_set_disk_usage()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8776`_
* Drop DetachedInstanceError workaround
`Pull Request 8785`_
* Simplify code for expand_meta_parameters
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 8794`_
* Convert User Preferences page to Vue Component
`Pull Request 8803`_
* client-side current user store module
`Pull Request 8813`_
* Refactor database_connection config loading
`Pull Request 8855`_
* Refactor default_locale config option; test
`Pull Request 8856`_
* Refactor infrastructure_url/port values; fix tests
`Pull Request 8857`_
* Refactor pretty-datatime_format config loading
`Pull Request 8858`_
* Fix misc. integration tests for config values
`Pull Request 8859`_
* Do not specify None as default in dict.get()
`Pull Request 8865`_
* Delete 'resolve path' integration tests
`Pull Request 8870`_
* Do not raise Exception to manage control flow
`Pull Request 8876`_
* Eliminate interactive debugging middleware
`Pull Request 8877`_
* Normalize myexperiment_target_url / myexperiment_url
`Pull Request 8882`_
* Do not override schema defaults if they exist
`Pull Request 8884`_
* Use schema defaults in galaxy masthead
`Pull Request 8885`_
* Cleanup config loading (minor fixes)
`Pull Request 8890`_
* Refactor _set_config_base; fix config_dir value
`Pull Request 8915`_
* Library tags tweaks and tests
`Pull Request 8947`_
* Refactor Toolshed webapp into tool_shed package.
`Pull Request 8949`_
* Separate Shed and Galaxy makos, package shed makos.
`Pull Request 8958`_
* Remove admin tool shed controller code (Part 1)
`Pull Request 8988`_
* Remove unused helper code from twilltestcase.
`Pull Request 8989`_
* Fix tool image loading (was broken due to failing repo dir resolution)
`Pull Request 9006`_
* Convert Custom builds vue
`Pull Request 9016`_
* Implement datasets grid as vue component
`Pull Request 9018`_
* remove unused toolshed template code
`Pull Request 9084`_
* Default the authnz_manager to None
`Pull Request 9117`_
* Update github username @erasche to @hexylena and correct inconsistencies
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 9194`_
* Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
`Pull Request 9336`_
* Add requirements to (almost) all converters, profile and minor fixes
`Pull Request 9345`_
Fixes
-------------------------------
* Wrap SQL statement in a text() function as required by sqlalchemy
(thanks to `@kaukrise <https://github.com/kaukrise>`__).
`Pull Request 9216`_
* Ensure visible overflow on navbar container
(thanks to `@kaukrise <https://github.com/kaukrise>`__).
`Pull Request 9217`_
* Various python 3 fixes from sentry
`Pull Request 9337`_
* Fix cool sniffing on python3
`Pull Request 9153`_
* Fix `SearchGuiArchive.set_meta()`
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 9437`_
* grouping: strip newlines
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8953`_
* Add requirements to interval_to_bed_converter.xml
`Pull Request 9041`_
* Fix version in which ``sam_pileup`` was fixed
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9350`_
* Expunge tool shed repository objects, prevents ParentInstanceDetachedError
`Pull Request 9354`_
* Fix maf tools
`Pull Request 9393`_
* Exports reports with workflows (if configured).
`Pull Request 9055`_
* Rev gxformat2 dependency to fix various export issues.
`Pull Request 9075`_
* Fix workflow editor save as functionality
`Pull Request 9315`_
* Various fixes and enhancements to reports
`Pull Request 9316`_
* Small fixes for k8s.
`Pull Request 8759`_
* Fix output.file_path writing to read-only path on Docker
`Pull Request 9048`_
* Add job home to writable paths
`Pull Request 9051`_
* Fix LocalShell returncode
`Pull Request 9171`_
* Fix: Added support for specifying k8s job pod priority class
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 9219`_
* Fix: Added support for specifying k8s job affinity and tolerations
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 9225`_
* Mount job_working_directory/configs rw
`Pull Request 9234`_
* Limit async hack to async tools
`Pull Request 9242`_
* Fix moving of data manager output for entries
`Pull Request 9243`_
* python3 fixes for setups using drmaa and realuser setups
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 9246`_, `Pull Request 9253`_
* Email notifications aren't used from just workflow steps anymore.
`Pull Request 9276`_
* Use requests for slots instead of limit
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 9322`_
* Make set metadata exec after process more robust
`Pull Request 9395`_
* Make dataset discovery respect final_job_state
`Pull Request 9406`_
* Strip unicode null characters from traceback and job_messages
`Pull Request 9430`_
* Encode lines in filter_file_fields
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8652`_
* Git error reporting - bug fixes and better error handling
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8900`_
* Assorted admin panel fixes
`Pull Request 9097`_
* Run integration tests on github, fix various bugs (interactive tools, kubernetes, test framework)
`Pull Request 9193`_
* Always add shed_tool_config file to tool_configs
`Pull Request 9364`_
* Documentation update
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8508`_
* Asynchronous data source: unable to create the file
(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
`Pull Request 8515`_
* OIDC config patch
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 8572`_
* set uwsgi umask default
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8581`_
* Fix `test_validate_simple_config` unit test
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8632`_
* Fix a bug that occurs while installing a data manager.
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8634`_
* Fix bug in build_dependency_manager()
`Pull Request 8660`_
* Get rid of fix timeout in admin app Selenium test.
`Pull Request 8667`_
* More robust login/logout with Selenium.
`Pull Request 8676`_
* Fixes for BootstrapVue Tables
`Pull Request 8684`_
* More bootstrap vue upgrade fixes.
`Pull Request 8692`_
* GRT: Ensure correct encoding, no partial lines
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 8712`_
* Revise toolshed config dependency check error message in repository install manager
`Pull Request 8720`_
* Fix data dialog height, modal test case and table slots
`Pull Request 8724`_
* Do not overwrite existing attributes
`Pull Request 8728`_
* Replace hardcoded configuration
`Pull Request 8731`_
* Fix `new_secure_hash()` when passed an empty string
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8739`_
* data_manager_conf.xml.sample is missing
(thanks to `@lecorguille <https://github.com/lecorguille>`__).
`Pull Request 8784`_
* Revert "[19.09] Fix detached parent instance error in 8769"
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 8791`_
* Handles k8s job recently created with no status set yet
(thanks to `@pcm32 <https://github.com/pcm32>`__).
`Pull Request 8799`_
* Add postcss-loader and autoprefixer dependencies
`Pull Request 8821`_
* LDAP fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8823`_
* Ensure app.config.config_file is an absolute path
`Pull Request 8836`_
* Fix rare bug in config loading + add unit test
`Pull Request 8837`_
* fix plugin name
(thanks to `@gmauro <https://github.com/gmauro>`__).
`Pull Request 8840`_
* Restore portlet section style for repeat blocks
`Pull Request 8864`_
* Prevent potential bug in config loading; test
`Pull Request 8866`_
* Fix authnz manager's oidc config parsing for python3
`Pull Request 8871`_
* Update check_py3_compatibility script for new ack versions.
`Pull Request 8872`_
* If config_file is None, use cwd, not its parent
`Pull Request 8894`_
* Log LDAP authenticate exceptions at the right level
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8907`_
* make pgcleanup also delete HDAs
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8908`_
* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}` exception handling
`Pull Request 8935`_
* Set `deleted` attribute of history datasets when purging histories from grid
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8940`_
* Fix default logo path in configuration manager
`Pull Request 8941`_
* Fix API decorator order
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9015`_
* do not use var from inner scope
`Pull Request 9026`_
* escape double hyphen in IT sample config, making it valid XML
`Pull Request 9034`_
* Fix input parameter comparisons
`Pull Request 9047`_
* Restore casting a boolean param to str when comparing with one
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9052`_
* Fix comparison if parameter is optional and value is not provided
`Pull Request 9054`_
* Small refactor of ``InputValueWrapper`` comparison methods
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9059`_
* Add create_time to the signature of Repository constructor.
`Pull Request 9063`_
* Listify value for multiple SelectToolParameterWrapper
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9067`_
* Use newer psycopg2 conditional requirement for wheels on 3.7
`Pull Request 9068`_
* Fix mulled version comparison
`Pull Request 9078`_
* linter: accept outputs with auto_format only
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 9081`_
* Create temporary files for cgi.FieldsStorage with delete=False
`Pull Request 9082`_
* Fix importing a directory from user_library_import_dir
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9090`_
* Make callbacks for tour and config watchers a control task
`Pull Request 9092`_
* Don't watch tool files through watchdog
`Pull Request 9094`_
* Allow html in registration warning message.
`Pull Request 9098`_
* Admin job info display fix
`Pull Request 9120`_
* Client build readme followup
`Pull Request 9122`_
* Fix mulled cache/data locations, rebuild schema
`Pull Request 9125`_
* More fixes for publishing decomposed packages.
`Pull Request 9126`_
* fix url for workflow sharing
`Pull Request 9132`_
* Add click prevent to workflow list dropdowns
`Pull Request 9133`_
* Remove legacy admin panel entry for installation monitor, fix typo
`Pull Request 9134`_
* Parse brand label option in legacy mako
`Pull Request 9136`_
* Restore returning "None" when casting unselected multiselect param to str
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9144`_
* Misc fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9145`_
* Add implementation of `parse_interactivetool` to `CwlToolSource` class
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9146`_
* Fix optional unset integer and float params
`Pull Request 9149`_
* Assorted OIDC fixes
`Pull Request 9150`_
* Cast to None for optional params if not comparing strings
`Pull Request 9156`_
* Ensure that users have a private role before login
`Pull Request 9168`_
* Add static-safe mapping to config management
`Pull Request 9179`_
* Fix tool shed tests for `#9168 <https://github.com/galaxyproject/galaxy/issues/9168>`__.
`Pull Request 9182`_
* Add require_login bypass for entire authnz controller.
`Pull Request 9192`_
* Fix runtime error in ToolConfWatcher
`Pull Request 9212`_
* Fix extended base for singularity and add base_image_for_targets
`Pull Request 9215`_
* More mulled-build-files fixes
`Pull Request 9228`_
* Fix mailto hrefs in menus
`Pull Request 9232`_
* Move meme_fimo out of unversioned lib tools
`Pull Request 9237`_
* Fallback to binary download if header lies about content encoding
`Pull Request 9239`_
* Fix lint warning string formatting
`Pull Request 9240`_
* Fix unselected select parameter comparison to empty string
`Pull Request 9260`_
* Fix iteritems use in build_from_current_history.mako
`Pull Request 9266`_
* Fix suffix for single target mulled builds
`Pull Request 9267`_
* backport 9268: Fix target_str_to_targets
`Pull Request 9269`_
* Backwards compatible build number parsing
`Pull Request 9278`_
* Tag display fixes for ui-select.
`Pull Request 9281`_
* Python3: don't check for has_key attribute
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9290`_
* Prevent caching of bootstrapped client data
`Pull Request 9294`_
* Add build_sites_config_file option to config_schema
`Pull Request 9297`_
* Backport reports config/py3 fix
`Pull Request 9309`_
* Python3: unicodify the output of ``subprocess.check_output()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9319`_
* Fix reports disk usage query for python 3
`Pull Request 9321`_
* Fix string module use
`Pull Request 9327`_
* Fix Python 3 error in containers lib
`Pull Request 9329`_
* Fix use of next() as a meethod instead of a function
`Pull Request 9330`_
* Automatically resolve and add static-safe mappings for client-based images
`Pull Request 9331`_
* Various doc fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9334`_
* Fix app reference in guess_shed_config
`Pull Request 9339`_
* Make linters more robust on python 3
`Pull Request 9348`_
* Use RenamedTemporaryFile for safer integrated_tool_panel_file writing
`Pull Request 9359`_
* Only get non-deleted datasets when listing custom dbkeys
`Pull Request 9360`_
* Prevent duplicate listing of doi link and link (text, with href doi link)
`Pull Request 9366`_
* Styleguide fixes
`Pull Request 9367`_
* Prevent tool execution getting stuck in history when a chromInfo data…
`Pull Request 9385`_
* Move migrated_tools_conf > mutable_config_dir (`#9376 <https://github.com/galaxyproject/galaxy/issues/9376>`__)
`Pull Request 9388`_
* Fix dependency for CONVERTER_tar_to_directory
`Pull Request 9389`_
* Fix for qp method used in GEDAs.
`Pull Request 9391`_
* Fix hid comparison failing with hdas without hid
`Pull Request 9398`_
* Don't raise exception if anon goes to <galaxy_url>/user/resend_verification
`Pull Request 9404`_
* Update bleach to 3.1.1
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9408`_
* Fix shed image resolution
`Pull Request 9411`_
* Fixes for get_estimated_display_viewport
`Pull Request 9415`_
* Fix wrong map use in many places
`Pull Request 9416`_
* Conda startup fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9421`_
* fix two cases of opening a file binary
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 9424`_
* Remove '.sample' from default value; rebuild schema
`Pull Request 9427`_
* Fix login to accounts using different email capitalization
`Pull Request 9432`_
* Fix TwoBitFile handle not opened in binary mode
`Pull Request 9433`_
* Fix uploading workflow archives
`Pull Request 9434`_
* Fix to_dict for upload1 tool
`Pull Request 9441`_
* Fix data tables vue display
`Pull Request 9442`_
* Fix `UserManager.get_reset_token()` after `#9432 <https://github.com/galaxyproject/galaxy/issues/9432>`__
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 9446`_
.. include:: 20.01_prs.rst
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